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Pathogenomics analysis of high-risk clone ST147 multidrug-resistant Klebsiella pneumoniae isolated from a patient in Egypt

The emergence of multi-drug-resistant Klebsiella pneumoniae (MDR-KP) represents a serious clinical health concern. Antibiotic resistance and virulence interactions play a significant role in the pathogenesis of K...

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Biocontrol potential and growth-promoting effect of endophytic fungus Talaromyces muroii SD1-4 against potato leaf spot disease caused by Alternaria alternata

Alternaria alternata is the primary pathogen of potato leaf spot disease, resulting in significant potato yield losses globally. Endophytic microorganism-based biological control, especially using microorganisms ...

Green synthesis of zinc oxide nanoparticles (ZnO-NPs) by Streptomyces baarnensis and its active metabolite (Ka): a promising combination against multidrug-resistant ESKAPE pathogens and cytotoxicity

Various eco-friendly techniques are being researched for synthesizing ZnO-NPs, known for their bioactivity. This study aimed at biosynthesizing ZnO-NPs using Streptomyces baarnensis MH-133, characterizing their p...

Evaluating the probiotic effects of spraying lactiplantibacillus plantarum P-8 in neonatal piglets

Gut microbes play an important role in the growth and health of neonatal piglets. Probiotics can promote the healthy growth of neonatal piglets by regulating their gut microbes. The study investigated the effe...

Design of a two functional permeable reactive barrier for synergistic enzymatic and microbial bioremediation of phenol-contaminated waters: laboratory column evaluation

The present study aimed to develop a system using a combination of enzymatic and microbial degradation techniques for removing phenol from contaminated water. In our prior research, the HRP enzyme extracted fr...

Evaluating the effects of temperature and agitation on biofilm formation of bacterial pathogens isolated from raw cow milk

To study the effect of agitation and temperature on biofilm formation (cell aggregates embedded within a self-produced matrix) by pathogenic bacteria isolated from Raw cow milk (RCM).

Genomic characterization of multi drug resistant ESBL-producing Escherichia coli isolates from patients and patient environments in a teaching hospital in Ghana

ESBL-producing Escherichia coli pose a growing health risk in community and healthcare settings. We investigated the resistome, virulome, mobilome, and genetic relatedness of multidrug-resistant (MDR) E. coli iso...

Evaluation of vaccine candidates against Rhodococcus equi in BALB/c mice infection model: cellular and humoral immune responses

Rhodococcus equi ( R. equi ) is a zoonotic opportunistic pathogen that mainly causes fatal lung and extrapulmonary abscesses in foals and immunocompromised individuals. To date, no commercial vaccine against R. equ...

Comparative genomics of quinolone-resistant Escherichia coli from broilers and humans in Norway

The usage of fluoroquinolones in Norwegian livestock production is very low, including in broiler production. Historically, quinolone-resistant Escherichia coli (QREC) isolated from Norwegian production animals r...

Horizontal gene transfer of the Mer operon is associated with large effects on the transcriptome and increased tolerance to mercury in nitrogen-fixing bacteria

Mercury (Hg) is highly toxic and has the potential to cause severe health problems for humans and foraging animals when transported into edible plant parts. Soil rhizobia that form symbiosis with legumes may p...

Rose Bengal diacetate-mediated antimicrobial photodynamic inactivation: potentiation by potassium iodide and acceleration of wound healing in MRSA-infected diabetic mice

Previous studies have shown that antimicrobial photodynamic inactivation (aPDI) can be strongly potentiated by the addition of the non-toxic inorganic salt, potassium iodide (KI). This approach was shown to ap...

Comparative genome analysis of the genus Marivirga and proposal of two novel marine species: Marivirga arenosa sp. nov., and Marivirga salinae sp. nov.

The phylum Bacteroidota represents a significant proportion of heterotrophic bacteria found in marine ecosystems. Members of the phylum Bacteroidota are actively involved in the degradation of biopolymers such as...

Correction: Vibrio cholerae O1 and Escherichia coli O157:H7 from drinking water and wastewater in Addis Ababa, Ethiopia

The original article was published in BMC Microbiology 2024 24 :219

Continental scale comparison of mycobiomes in Parmelia and Peltigera lichens from Turkey and South Korea

Lichens, traditionally considered as a simple partnership primarily between mycobiont and photobiont, are, in reality, complex holobionts comprised of a multitude of microorganisms. Lichen mycobiome represents...

Tumour-associated and non-tumour-associated bacteria co-abundance groups in colorectal cancer

Gut microbiota is closely related to the occurrence and development of colorectal cancer (CRC). However, the differences in bacterial co-abundance groups (CAGs) between tumor tissue (TT) and normal tissue (NT)...

Biofilm-producing ability of methicillin-resistant Staphylococcus aureus clinically isolated in China

Staphylococcus aureus , a commensal bacterium, colonizes the skin and mucous membranes of approximately 30% of the human population. Apart from conventional resistance mechanisms, one of the pathogenic features of...

CRISPR-Cas3 and type I restriction-modification team up against bla KPC -IncF plasmid transfer in Klebsiella pneumoniae

We explored whether the Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas and restriction-modification (R-M) systems are compatible and act together to resist plasmid attacks.

Impact of captivity and natural habitats on gut microbiome in Epinephelus akaara across seasons

The gut microbiota significantly influences the health and growth of red-spotted grouper ( Epinephelus akaara ), a well-known commercial marine fish from Fujian Province in southern China. However, variations in su...

Formic acid sandwich method is well-suited for filamentous fungi identification and improves turn around time using Zybio EXS2600 mass spectrometry

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is extensively employed for the identification of filamentous fungi on MALDI Biotyper (Bruker Daltonics) and Vitek MS...

Gut microbiota Parabacteroides distasonis enchances the efficacy of immunotherapy for bladder cancer by activating anti-tumor immune responses

Bladder cancer(BCa) was a disease that seriously affects patients’ quality of life and prognosis. To address this issue, many researches suggested that the gut microbiota modulated tumor response to treatment;...

Correction: Study of the gut microbiome in Egyptian patients with Parkinson’s Disease

The original article was published in BMC Microbiology 2023 23 :196

Alterations of the bile microbiome is associated with progression-free survival in pancreatic ductal adenocarcinoma patients

Patients with pancreatic ductal adenocarcinoma (PDAC) display an altered oral, gastrointestinal, and intra-pancreatic microbiome compared to healthy individuals. However, knowledge regarding the bile microbiom...

fENko-Kae01 is a flagellum-specific jumbo phage infecting Klebsiella aerogenes

Klebsiella aerogenes is an opportunistic pathogen that causes a wide variety of infections. Due to the rising problem of antibiotic resistance, novel antibiotics and strategies to combat bacterial infections are ...

Taxonomic and phenotypic analysis of bifidobacteria isolated from IBD patients as potential probiotic strains

Inflammatory Bowel Diseases (IBD) are a major public health issue with unclear aetiology. Changes in the composition and functionality of the intestinal microbiota are associated with these pathologies, includ...

Gut fungi of black-necked cranes ( Grus nigricollis ) respond to dietary changes during wintering

Migratory birds exhibit heterogeneity in foraging strategies during wintering to cope with environmental and migratory pressures, and gut bacteria respond to changes in host diet. However, less is known about ...

Lipopeptides from Bacillus velezensis ZLP-101 and their mode of action against bean aphids Acyrthosiphon pisum Harris

Natural products are important sources for the discovery of new biopesticides to control the worldwide destructive pests Acyrthosiphon pisum Harris . Here, insecticidal substances were discovered and characterized...

Molecular characterization and epidemiological investigation of colistin resistance in carbapenem-resistant Klebsiella pneumoniae in a tertiary care hospital in Tehran, Iran

Carbapenemase-producing Klebsiella pneumoniae (CRKP) presents a significant challenge to antimicrobial therapy, especially when compounded by resistance to colistin. The objective of this study was to explore mol...

Metabolomics analysis of the lactobacillus plantarum ATCC 14917 response to antibiotic stress

Lactobacillus plantarum has been found to play a significant role in maintaining the balance of intestinal flora in the human gut. However, it is sensitive to commonly used antibiotics and is often incidentally k...

Living in mangroves: a syntrophic scenario unveiling a resourceful microbiome

Mangroves are complex and dynamic coastal ecosystems under frequent fluctuations in physicochemical conditions related to the tidal regime. The frequent variation in organic matter concentration, nutrients, an...

Inhibitory activity of bacterial lipopeptides against Fusarium oxysporum f.sp. Strigae

This study investigated the influence of bacterial cyclic lipopeptides (LP; surfactins, iturins, fengycins) on microbial interactions. The objective was to investigate whether the presence of bacteria inhibits...

Mining biosynthetic gene clusters in Paenibacillus genomes to discover novel antibiotics

Bacterial antimicrobial resistance poses a severe threat to humanity, necessitating the urgent development of new antibiotics. Recent advances in genome sequencing offer new avenues for antibiotic discovery. Paen...

Characterization and genetic analysis of extensively drug-resistant hospital acquired Pseudomonas aeruginosa isolates

The incidence of hospital-acquired infections in extensively drug-resistant Pseudomonas aeruginosa (XDR-PA) has been increasing worldwide and is frequently associated with an increase in mortality and morbidity r...

Antibacterial activity and mechanisms of D-3263 against Staphylococcus aureus

Multi-drug-resistant Staphylococcus aureus infections necessitate novel antibiotic development. D-3263, a transient receptor potential melastatin member 8 (TRPM8) agonist, has potential antineoplastic properties....

Molecular prevalence and genotypes of Enterocytozoon bieneusi in cancer patients under chemotherapy in Aegean region of Türkiye

Enterocytozoon bieneusi is the most common species found in humans. Although E. bieneusi has been investigated in humans, genotype profile of E. bieneusi is not known in Türkiye.

Prebiotic fibre mixtures counteract the manifestation of gut microbial dysbiosis induced by the chemotherapeutic 5-Fluorouracil (5-FU) in a validated in vitro model of the colon

5-Fluorouracil (5-FU) is used as an antineoplastic agent in distinct cancer types. Increasing evidence suggests that the gut microbiota might modulate 5-FU efficacy and toxicity, potentially affecting the pati...

The serine-rich repeat glycoprotein Srr2 mediates Streptococcus agalactiae interaction with host fibronectin

Group B Streptococcus (GBS) is a commensal of healthy adults and an important pathogen in newborns, the elderly and immunocompromised individuals. GBS displays several virulence factors that promote colonisati...

Correction: A culture‑independent approach, supervised machine learning, and the characterization of the microbial community composition of coastal areas across the Bay of Bengal and the Arabian Sea

The original article was published in BMC Microbiology 2024 24 :162

Vibrio cholerae O1 and Escherichia coli O157:H7 from drinking water and wastewater in Addis Ababa, Ethiopia

In Addis Ababa, Ethiopia, open ditches along innner roads in residential areas serve to convey domestic wastewater and rainwater away from residences. Contamination of drinking water by wastewater through faul...

The Correction to this article has been published in BMC Microbiology 2024 24 :244

Exploring endophytic bacteria communities of Vanilla planifolia

Rhizosphere bacterial community and endophytes are now known to influence plant health and response to environmental stress. Very few studies have reported the diversity of endophytic bacterial communities of Van...

Biological characteristics and metabolic phenotypes of different anastomosis groups of Rhizoctonia solani strains

Rhizoctonia solani is an important plant pathogen worldwide, and causes serious tobacco target spot in tobacco in the last five years. This research studied the biological characteristics of four different anasto...

Genetic characteristics of chromosomally integrated carbapenemase gene ( bla NDM−1 ) in isolates of Proteus mirabilis

This study aims to conduct an in-depth genomic analysis of a carbapenem-resistant Proteus mirabilis strain to uncover the distribution and mechanisms of its resistance genes.

Completed genome and emergence scenario of the multidrug-resistant nosocomial pathogen Staphylococcus epidermidis ST215

A multidrug-resistant lineage of Staphylococcus epidermidis named ST215 is a common cause of prosthetic joint infections and other deep surgical site infections in Northern Europe, but is not present elsewhere. T...

Characterization and the first complete genome sequence of a novel strain of Bergeyella porcorum isolated from pigs in China

Bergeyella porcorum is a newly identified bacterium that has an ambiguous relationship with pneumonia in pigs. However, few studies have adequately characterized this species.

In Vivo and in Vitro activity of colistin-conjugated bimetallic silver-copper oxide nanoparticles against Pandrug-resistant Pseudomonas aeruginosa

Addressing microbial resistance urgently calls for alternative treatment options. This study investigates the impact of a bimetallic formulation containing colistin, silver, and copper oxide on a pandrug-resis...

Integrative omics analysis reveals insights into small colony variants of Staphylococcus aureus induced by sulfamethoxazole-trimethoprim

Long-term treatment with trimethoprim-sulfamethoxazole (SXT) can lead to the formation of small-colony variants (SCVs) of Staphylococcus aureus . However, the mechanism behind SCVs formation remains poorly underst...

Analysis of a new phage, KZag1, infecting biofilm of Klebsiella pneumoniae : genome sequence and characterization

This study investigates the effectiveness of the bacteriophage KZag1 against drug-resistant Klebsiella pneumoniae , aiming to assess its potential as a therapeutic agent. The novelty lies in the characterization o...

Exploring the decolorization efficiency and biodegradation mechanisms of different functional textile azo dyes by Streptomyces albidoflavus 3MGH

Efficiently mitigating and managing environmental pollution caused by the improper disposal of dyes and effluents from the textile industry is of great importance. This study evaluated the effectiveness of Strept...

Mycobiota contaminating some market cake samples with reference to their toxin and enzyme

Fungi can spoil the majority of baked products. Spoilage of cake during storage is commonly associated with fungi. Therefore, this study aimed to assess the quality of different types of cakes sold in the mark...

Probiotic potential of Streptomyces levis strain HFM-2 isolated from human gut and its antibiofilm properties against pathogenic bacteria

Antimicrobial resistance (AMR) is a serious worldwide public health concern that needs immediate action. Probiotics could be a promising alternative for fighting antibiotic resistance, displaying beneficial ef...

Quorum sensing gene lasR promotes phage vB_Pae_PLY infection in Pseudomonas aeruginosa

Quorum sensing (QS) is a cell density-based intercellular communication system that controls virulence gene expression and biofilm formation. In Pseudomonas aeruginosa ( P. aeruginosa ), the LasR system sits at the...

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Citation Impact 2023 Journal Impact Factor: 4.0 5-year Journal Impact Factor: 4.6 Source Normalized Impact per Paper (SNIP): 1.081 SCImago Journal Rank (SJR): 0.999 Speed 2023 Submission to first editorial decision (median days): 15 Submission to acceptance (median days): 135 Usage 2023 Downloads: 2,970,572 Altmetric mentions: 1,619

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Top 10 most downloaded papers: Access Microbiology

Posted on June 1, 2023   by Microbiology Society

Publishing in Access Microbiology – our sound science open research platform – is free until the end of June 2023 . Submit your manuscript before the end of the month to make the most of free Open Access publication.

Access Microbiology publishes a range of sound science research , including replication studies, negative or null results, research proposals, case reports and more. We welcome work from all branches of microbiology and virology, offering fully transparent peer review.

See the top 10 most downloaded papers from 2019 to May 2023 below:

When good bacteria behave badly: a case report of Bacillus clausii sepsis in an immunocompetant adult

Isabella Princess, T. Natarajan, Siddhartha Ghosh​

Case Report

9350 full text downloads

A case report: insights into reducing plastic waste in a microbiology laboratory     

Joana Alves, Fiona A. Sargison, Hanne Stawarz, Willow B. Fox, Samuel G. Huete, Amany Hassan,​ Brian McTeir, Amy C. Pickering

Short Communication

9017 full text downloads

High SARS-CoV-2 viral load is associated with a worse clinical outcome of COVID-19 disease

María Eugenia Soria, Marta Cortón, Brenda Martínez-González, Rebeca Lobo-Vega, Lucía Vázquez-Sirvent, Rosario López-Rodríguez​, Berta Almoguera​, Ignacio Mahillo​, Pablo Mínguez, Antonio Herrero, Juan Carlos Taracido​, Alicia Macías-Valcayo, Jaime Esteban, Ricardo Fernandez-Roblas​, Ignacio Gadea, Javier Ruíz-Hornillos​, Carmen Ayuso, Celia Perales

8714 full text downloads

Disseminated sporotrichosis in a person with human immunodeficiency virus disease

Vhudzani Tshisevhe, Lebogang Skosana, Kagiso Motse, Tinashe Maphosa, Barend Mitton​

8225 full text downloads

Phylogenetic diversity and activity screening of cultivable Actinobacteria isolated from marine sponges and associated environments from the western coast of India

Ulfat Baig​, Neelesh Dahanukar, Neha Shintre, Ketki Holkar​, Anagha Pund​, Uttara Lele​, Tejal Gujarathi​, Kajal Patel​, Avantika Jakati​, Ruby Singh​, Harshada Vidwans​, Vaijayanti Tamhane, Neelima Deshpande​, Milind Watve

Research Article

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Not all wavelengths are created equal: disinfection of SARS-CoV-2 using UVC radiation is wavelength-dependent

Richard M. Mariita, James W. Peterson

8214 full text downloads

Streptococcus lutetiensis neonatal meningitis with empyema

Allen T. Yu, Kate Shapiro​, Christy A. Beneri, Lisa S. Wilks-Gallo

8173 full text downloads

Disinfection of methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus faecium and Acinetobacter baumannii using Klaran WD array system

Richard M. Mariita, Rajul V. Randive

8106 full text downloads

Distribution of cycle threshold values in RT-qPCR tests during the autumn 2020 peak of the COVID-19 pandemic in the Czech Republic

Michal Koblížek, Daniela Hávová​, Karel Kopejtka, Jürgen Tomasch, Kateřina Bišová

8000 full text downloads

Rapid growth atypical mycobacteria infection associated with growth hormone injections: a case report

Christian David Cardozo Lomaquiz, Tamara Frontanilla, Natalia Scavone, Alba Fretes​, Nathalia Torales, María Elena Pereira​, Herminia Mino de Kaspar, Xavier Ortiz​, Renate Henning

7992 full text downloads

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Home > Biological Sciences > Papers in the Biological Sciences > Microbiology

Papers in the Biological Sciences

Papers in microbiology.

Thoughts on Quorum Sensing and Fungal Dimorphism , Kenneth W. Nickerson, Audrey L. Atkin, Jessica C. Hargarten, Ruvini U. Pathirana, and Sahar Hasim

In Vivo and In Vitro Anaerobic Mating in Candida albicans , Raluca Dumitru, Dhammika H.M.L.P. Navarathna, Camile P. Semighini, Christian G. Elowsky, Razvan Dumitru, Daniel Dignard, Malcom Whiteway, Audrey L. Atkin, and Kenneth W. Nickerson

Effect of Farnesol on a Mouse Model of Systemic Candidiasis, Determined by Use of a DPP3 Knockout Mutant of Candida albicans , Dhammika H.M.L.P. Navarathna, Jacob M. Hornby, Navasona Krishnan, Anne M. Parkhurst, Gerald E. Duhamel, and Kenneth W. Nickerson

Exogenous Farnesol Interferes with the Normal Progression of Cytokine Expression during Candidiasis in a Mouse Model , Dhammika H. M. L. P. Navarathna, Kenneth W. Nickerson, Gerald E. Duhamel, Thomas R. Jerrels, and Thomas M. Petro

Quorum Sensing in Dimorphic Fungi: Farnesol and Beyond , Kenneth W. Nickerson, Audrey L. Atkin, and Jacob M. Hornby

Pichia pastoris fermentation optimization: energy state and testing a growth-associated model , Bradley A. Plantz, Jayanta Sinha, Lorelie Villarete, Kenneth W. Nickerson, and Vicki Schlegel

Surface Display of Recombinant Proteins on Bacillus thuringiensis Spores , Cheng Du, Wing C. Chan, Timothy W. McKeithan, and Kenneth W. Nickerson

Farnesol Concentrations Required To Block Germ Tube Formation in Candida albicans in the Presence and Absence of Serum , Daniel D. Mosel, Raluca Dumitru, Jacob M. Hornby, Audrey L. Atkin, and Kenneth W. Nickerson

Survey of Extreme Solvent Tolerance in Gram-Positive Cocci: Membrane Fatty Acid Changes in Staphylococcus haemolyticus Grown in Toluene , Lindsey E. Nielsen, Dana R. Kadavy, Soumitra Rajagopal, Rhae A. Drijber, and Kenneth W. Nickerson

Biologically Active Fluorescent Farnesol Analogs , Roman Shchepin, Razvan Dumitru, Kenneth W. Nickerson, Miranda Lund, and Patrick Dussault

Defined Anaerobic Growth Medium for Studying Candida albicans Basic Biology and Resistance to Eight Antifungal Drugs , Raluca Dumitru, Jacob M. Hornby, and Kenneth W. Nickerson

Inoculum Size Effect in Dimorphic Fungi: Extracellular Control of Yeast-Mycelium Dimorphism in Ceratocystis ulmi , Jacob M. Hornby, Sarah M. Jacobitz-Kizzier, Donna J. McNeel, Ellen C. Jensen, David S. Treves, and Kenneth W. Nickerson

Enhanced Production of Farnesol by Candida albicans Treated with Four Azoles , Jacob M. Hornby and Kenneth Nickerson

Farnesol Biosynthesis in Candida albicans : Cellular Response to Sterol Inhibition by Zaragozic Acid B , Jacob M. Hornby, Bessie W. Kebaara, and Kenneth W. Nickerson

Phenotype of the Triplo-lethal locus of Drosophila melanogaster and its suppression by hyperoxia , Laura K. Smoyer, Douglas R. Dorer, Kenneth W. Nickerson, and Alan C. Christensen

Sodium Dodecyl Sulfate Hypersensitivity of clpP and clpB Mutants of Escherichia coli , Soumitra Rajagopal, Narasimhan Sudarsan, and Kenneth W. Nickerson

Membrane glycoprotein gp130 of Dictyostelium discoideum is lipid-linked and its fate altered in the presence of tunicamycin , Betsy L. Barent and Catherine P. Chia

Quorum Sensing in the Dimorphic Fungus Candida albicans Is Mediated by Farnesol , Jacob M. Hornby, Ellen C. Jensen, Amber C. Lisec, Joseph J. Tasto, Brandon Jahnke, Richard Shoemaker, Patrick Dussault, and Kenneth W. Nickerson

Giant Vacuoles Observed in Dictyostelium discoideum , Aidong Yuan and Catherine P. Chia

Natural Antibiotic Resistance of Bacteria Isolated from Larvae of the Oil Fly, Helaeomyia petrolei , Dana R. Kadavy, Jacob M. Hornby, Terry Haverkost, and Kenneth W. Nickerson

Influence of Infected Cell Growth State on Bacteriophage Reactivation Levels , Dana R. Kadavy, Julie J. Shaffer, Susan E. Lott, Thomas A. Wolf, Cathy E. Bolton, William H. Gallimore, Eugene L. Martin, Kenneth W. Nickerson, and Tyler A. Kokjohn

A Receptor-Like Glycoprotein from Dictyostelium discoideum : Functions in Phagocytosis and Cell Adhesion? , P. Christopher LaRosa, Melissa B. Meirer, and Catherine P. Chia

A role for calcineurin in Dictyostelium discoideum phagocytosis , Aidong Yuan and Catherine P. Chia

Integrity of the actin cytoskeleton required for both phagocytosis and macropinocytosis in Dictyostelium discoideum , Aidong Yuan and Catherine P. Chia

Role of Esterase gp70 and Its Influence on Growth and Development of Dictyostelium discoideum , Aidong Yuan and Catherine P. Chia

Tubulin and Neurofilament Proteins Are Transported Differently in Axons of Chicken Motoneurons , Aidong Yuan, Roland G. Mills, Catherine P. Chia, and John J. Bray

Microbiology of the Oil Fly, Helaeomyia petrolei , Dana R. Kadavy, Bradley A. Plantz, Christopher A. Shaw, Jill Myatt, Tyler A. Kokjohn, and Kenneth Nickerson

Nonspecific interactions alter lipopolysaccharide patterns and protein mobility on sodium dodecyl sulfate polyacrylamide gels , Aidong Yuan, R L. Pardy, and Catherine P. Chia

Cytoskeletal Association of an Esterase in Dictyostelium discoideum , Catherine P. Chia, Lothar Bomblies, and Kristy K. Taylor

Prevalence of Broad-Host-Range Lytic Bacteriophages of Sphaerotilus natans , Escherichia coli , and Pseudomonas aeruginosa , Ellen C. Jensen, Holly S. Schrader, Brenda Rieland, Thomas L. Thompson, Kit W. Lee, Kenneth W. Nickerson, and Tyler A. Kokjohn

Phagosomal Proteins of Dictyostelium discoideum , Betsy L. Rezabek, Juan M. Rodriguez-Paris, James A. Cardelli, and Catherine P. Chia

Bacillus thuringiensis HD-73 Spores Have Surface-Localized Cry1Ac Toxin: Physiological and Pathogenic Consequences , Cheng Du and Kenneth Nickerson

The Bacillus thuringiensis Insecticidal Toxin Binds Biotin-Containing Proteins , Cheng Du and Kenneth Nickerson

CRYSTAL PROTEIN EXPRESSION DURING VEGETATIVE GROWTH OF DICTYOSTELIUM , Kristy K. Taylor and Catherine P. Chia

Comparison of Disulfide Contents and Solubility at Alkaline pH of Insecticidal and Noninsecticidal Bacillus thuringiensis Protein Crystals , Cheng Du, Phyllis A.W. Martin, and Kenneth W. Nickerson

Nonenzymatic Glycosylation of Lepidopteran-Active Bacillus thuringiensis Protein Crystals , Meenakshi Bhattacharyi, Bradley A. Plantz, Jane D. Swanson-Kobler, and Kenneth W. Nickerson

The Entner-Doudoroff Pathway in Escherichia coli Is Induced for Oxidative Glucose Metabolism via Pyrroloquinoline Quinone-Dependent Glucose Dehydrogenase , Ronda Fliege, Suxiang Tong, Annemarie Shibata, Kenneth W. Nickerson, and Tyrrell Conway

Lipoxygenase Inhibitors Shift the Yeast/Mycelium Dimorphism in Ceratocystis ulmi , Ellen C. Jensen, Clyde Ogg, and Kenneth W. Nickerson

Nutritional Complementation of Oxidative Glucose Metabolism in Escherichia coli via Pyrroloquinoline Quinone-Dependent Glucose Dehydrogenase and the Entner-Doudoroff Pathway , Michael Adamowicz, Tyrrell Conway, and Kenneth W. Nickerson

Detergent (Sodium Dodecyl Sulfate) Shock Proteins in Escherichia coli , Michael Adamowicz, Philip M. Kelley, and Kenneth W. Nickerson

Toxicity of Protease-Resistant Domains from the Delta-Endotoxin of Bacillus thuringiensis subsp. israelensis in Culex quinquefasciatus and Aedes aegypti Bioassays , Mary Ann Pfannenstiel, William C. Cray Jr., Graham Couche, and Kenneth W. Nickerson

Isolation and Characterization of Monoclonal Antibodies Directed Against Plant Plasma Membrane and Cell Wall Epitopes: Identification of a Monoclonal Antibody that Recognizes Extensin and Analysis of the Process of Epitope Biosynthesis in Plant Tissues and Cell Cultures , David J. Meyer, Claudio L. Alfonso, and David W. Galbraith

Structural Disulfide Bonds in the Bacillus thuringiensis subsp. israelensis Protein Crystal , Graham A. Couche, Mary A. Pfannenstiel, and Kenneth W. Nickerson

The Glycoprotein Toxin of Bacillus thuringiensis subsp. israelensis Indicates a Lectinlike Receptor in the Larval Mosquito Gut , Ganapathy Muthukumar and Kenneth Nickerson

Amino Sugars in the Glycoprotein Toxin from Bacillus thuringiensis subsp. israelensis , Mary Ann Pfannenstiel, Ganapathy Muthukumar, Graham A. Couche, and Kenneth W. Nickerson

Immunological Relationships among Proteins Making Up the Bacillus thuringiensis subsp. israelensis Crystalline Toxin , Mary Ann Pfannenstiel, Graham A. Couche, Elise J. Ross, and Kenneth W. Nickerson

Analysis of Mosquito Larvicidal Potential Exhibited by Vegetative Cells of Bacillus thuringiensis subsp. israelensis , Corey J. Walther, Graham A. Couche, Mary Ann Pfannenstiel, Sara E. Egan, Lisa A. Bivin, and Kenneth W. Nickerson

Calmodulin Levels in the Yeast and Mycelial Phases of Ceratocystis ulmi , Ganapathy Muthukumar, Rajiv K. Kulkarni, and Kenneth W. Nickerson

Stability of the Larvicidal Activity of Bacillus thuringiensis subsp. israelensis : Amino Acid Modification and Denaturants , Mary Ann Pfannenstiel, Graham A. Couche, Ganapathy Muthukumar, and Kenneth Nickerson

Ca(II)-Calmodulin Regulation of Fungal Dimorphism in Ceratocystis ulmi , Ganapathy Muthukumar and Kenneth W. Nickerson

Bioassay of Solubilized Bacillus thuringiensis var. israelensis Crystals by Attachment to Latex Beads , Danny J. Schnell, Mary Ann Pfannenstiel, and Kenneth W. Nickerson

Toxicity of Bacillus thuringiensis var. israelensis Crystals to Aedes aegypti Larvae: Carbonate Reversal , Danny J. Schnell and Kenneth Nickerson

Purification of Poly-3-Hydroxybutyrate by Density Gradient Centrifugation in Sodium Bromide , Kenneth W. Nickerson

Growth of Enterobacter cloacae in the Presence of 25% Sodium Dodecyl Sulfate , Vance C. Kramer, Diane M. Calabrese, and Kenneth W. Nickerson

Incorporation of Specific Fatty Acid Precursors During Spore Germination and Outgrowth in Bacillus thuringiensis , Kenneth W. Nickerson and Lee A. Bulla Jr.

Purification of the Protein Crystal from Bacillus thuringiensis by Zonal Gradient Centrifugation , Kenneth W. Nickerson and Barabara J. Ang

Absence of Spermine in Filamentous Fungi , Kenneth W. Nickerson, Larry D. Dunkle, and James L. Van Etten

Lipid Metabolism During Bacterial Growth, Sporulation, and Germination: an Obligate Nutritional Requirement in Bacillus thuringiensis for Compounds That Stimulate Fatty Acid Synthesis , Kenneth W. Nickerson and Lee A. Bulla Jr.

Lipid Metabolism During Bacterial Growth, Sporulation, and Germination: Differential Synthesis of Individual Branched and Normal-Chain Fatty Acids During Spore Germination and Outgrowth of Bacillus thuringiensis , Kenneth W. Nickerson, Lee A. Bulla Jr., and Timothy L. Mounts

Lipid Metabolism During Bacterial Growth, Sporulation, and Germination: Kinetics of Fatty Acid and Macromolecular Synthesis During Spore Germination and Outgrowth of Bacillus thuringiensis , Kenneth W. Nickerson, John De Pinto, and Lee A. Bulla Jr.

Separation of Spores and Parasporal Crystals of Bacillus thuringiensis in Gradients of Certain X-Ray Contrasting AgentsSeparation of Spores and Parasporal Crystals of Bacillus thuringiensis in Gradients of Certain X-Ray Contrasting Agents , Eugene S. Sharpe, Kenneth W. Nickerson, Lee A. Bulla Jr., and John N. Aronson

Physiology of Sporeforming Bacteria Associated with Insects: Minimal Nutritional Requirements for Growth, Sporulation, and Parasporal Crystal Formation of Bacillus thuringiensis . , Kenneth W. Nickerson and Lee A. Bulla Jr.

Sporulation of Bacillus thuringiensis Without Concurrent Derepression of the Tricarboxylic Acid Cycle , Kenneth W. Nickerson, John De Pinto, and Lee A. Bulla Jr.

Physiology of Sporeforming Bacteria Associated with Insects: Radiorespirometric Survey of Carbohydrate Metabolism In the 12 Serotypes of Bacillus thuringiensis , Kenneth W. Nickerson, Grant St. Julian, and Lee A. Bulla Jr.

Control of Pantothenate Accumulation in Agrobacterium tumefaciens , Tsuneo Kaneshiro, Larry O. Arthur, and Kenneth W. Nickerson

A Circular Dichroic Study of Cu (II) -Ribonuclease Complexes , Kenneth W. Nickerson and Kensal E. Van Holde

Antigenic Relationships in Seven Strains of Tetrahymena , W.E. Engelhard and B.W. McCashland

Peptidoglycan Differences in Strains of Bacillus cereus Constitutive and Inducible for Penicillinase Production , Kenneth W. Nickerson and Richard A. Day

Transferable Drug Resistance Among Enterobacteriaceae Isolated from Human Urinary Tract Infections , Donna G. Sieckmann, Norman D. Reed, and Carl E. Georgi

Relationship Between Protein and Ribonucleic Acid Synthesis During Outgrowth of Spores of Bacillus cereus , S. Rodenberg, W. Steinberg, J. Piper, Kenneth W. Nickerson, J. Vary, R. Epstein, and H.O. Halvorson

Lethal Action of Ribonuclease for Thermophilic Bacilli , T.L. Thompson and J.M. Shively

CALCIUM ION REQUIREMENT FOR PROLIFERATION OF BACTERIOPHAGE Φμ-4 , Fred Shafia and T.L. Thompson

ISOLATION AND PRELIMINARY CHARACTERIZATION OF BACTERIOPHAGE Φμ-4 , Fred Shafia and T.L. Thompson

INTERACTION BETWEEN THE PARAMETERS OF HYDROSTATIC PRESSURE AND TEMPERATURE ON ASPARTASE OF Escherichia coli , Roger D. Haight and Richard Y. Morita

MALIC DEHYDROGENASE ACTIVITY AT 101 C UNDER HYDROSTATIC PRESSURE , Richard Y. Morita and Roger D. Haight

SOME CHARACTERISTICS OF A PURIFIED HEAT-STABLE ALDOLASE , P.J. Thompson and T.L. Thompson

The Coexistence of Pathogens and Pseudomonads in Soluble Oil Emulsions , R. Samuel-Maharajah, Hilliard Pivnik, W.E. Engelhard, and Sheila Templeton

Pustule Formation by Lactobacilli on Fermented Vegetables , T.L. Thompson, W.E. Engelhard, and Hilliard Pivnik

The Production of 2, 3-Butanediol by Fermentation of Sugar Beet Molasses , Keith B. McCall and Carl E. Georgi

The Growth of Pathogenic Bacteria in Soluble Oil Emulsions , Hilliard Pivnik, W.E. Engelhard, and T.L. Thompson

RIBOFLAVIN PRODUCTION BY MOLDS , George L. Peltier and Raymond Borchers

THE EFFECTS OF OXYGEN, CARBON DIOXIDE, AND PRESSURE ON GROWTH IN CHILOMONAS PARAMECIUM AND TETRAHYMENA GELEII FURGASON , D.M. Pace and R.L. Ireland

SOURCES OF AMYLASE-PRODUCING BACTERIA , George L. Peltier and L.D. Beckord

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A Guide to Writing Research Papers for Introductory Microbiology

A research paper is a report of original research and is, without doubt, one of the most important documents written by scientists. Research papers communicate important findings and ideas to other scientists, especially those working in the same or similar fields. In turn, they are given the opportunity to evaluate, revise and extend the research you have communicated. One of the important components of this course is to train you on how to conduct research and communicate your findings in the form of a professionally produced research paper. You will be carrying two research projects during the semester. One will involve the isolation and characterization of a particular microbe or microbes, the other focuses on various aspects of antibiotic drug resistance. The research papers you will be required to write follow a format common to most journals dedicated to the biological sciences. The format given below conforms to that stipulated by many biological journals. The format is broadly based upon that required for full research papers in  The Journal of Bacteriology , published by the American Society of Microbiology.

Manuscripts should be written in concise and grammatically correct American-English, and must be submitted according to the format specified below. The manuscript should be typed, the lines double-spaced, and one inch margins reserved on either side of the page. All titles should be bold and centered. Each section should begin on a new page. Typically, the paper will consist of seven sections: The  Title page : a descriptive title of the article, the name of the author, and her/his departmental and university affiliation, and e-mail address for correspondence. The  Abstract : a short narrative that summarizes the major accomplishments of the work being described . An   Introduction : a statement placing the work to follow in historical perspective and explaining its intent and significance.  Materials and Methods  that describes how the research was conducted so that it can be repeated by other investigators. The  Results  section describes and analyzes the experimental data. The  Discussion  explains the interpretation of the results and their significance.  References  documents all the sources consulted in carrying out the research and writing the paper, and  Figures and Tables  which illustrate the major data as photographs, graphs and tables.

Writing research papers is a very difficult enterprise, so do not expect to become an expert straight away. Familiarize yourself with the style of research papers by carefully studying published material: you will be given ample opportunity to do this during the course. You do not have to aspire to the professional level of these papers. However, you must pay careful attention to the content and style of the papers. Bear in mind that the papers you consult reflect many weeks, or months of intensive research, and your research projects will only last a few weeks. Therefore, the audience for your papers will be your peers and instructors. You will, in fact, be given the opportunity to review and evaluate papers submitted by your peers during the semester. The guide below is based upon these premises while at the same time reflecting the requirements for professional journals. Excerpts (edited for anonymity) included here are from previous student papers and sample papers prepared by students in previous years will be posted on Blackboard.  

The title identifies the work accomplished and should be descriptive rather than vague and immediately inform the reader about the work you are about to describe. Also include on the title page your full name, your affiliation (in most cases, this will be the Department of Biological Sciences, the George Washington University), a contact address (which nowadays is an email address) and the date of submission on the manuscript. The title should be informative and specific and accurately indicate the major focus of your work. For example, a title:  “The Isolation of Bacteria from Raw and Cooked Food Samples”  is too general and unfocused. A more descriptive title is:  “A Quantitative Study of Fecal Coliforms Found in Cooked and Raw Samples of Minced Beef.”

Similarly, a paper that is titled:  “Isolation of Staphylococcus aureus From Swimming Pools”  is best replaced by a title that reflects the research more specifically:  “Isolation and Characterization of Chlorine-Resistant Staphylococcus aureus from the Recreational Indoor Swimming Pool in the Lerner Health Center of the George Washington University.”

The title may also reflect the major finding of the research:  “Halobacterium Species Isolated from Salt Water Marshes near the Patapsco River Estuary of the Chesapeake Bay.”

Bear in mind that with the large number of research papers published each month, indexing services rely heavily on the titles of papers, as do scientists scanning the literature for papers pertinent to their own fields of research.  

The Abstract is a summary of the major points of the paper, including the purpose of the research, the methods used, the results obtained, and the conclusions drawn from them. The Abstract typically consists of a single paragraph of about three hundred words. It should be borne in minds that, together with the Title, the Abstract will be read by many people who may not necessarily read the rest of the paper. Therefore, this section of the paper must stand on its own. It is also the most difficult part of the paper to write because you must summarize, in a short space, the entire scope of your project. The excerpt below reflects a typical first draft, followed by an acceptable revision.

Example 1: First Draft

“Cell phones may harbor all kinds of bacteria and the purpose of this study was to isolate  Staphylococcus aureus , a potentially pathogenic microbe. Several cell phones were employed in this study. The phones were swabbed and S, aureus isolated by growth on mannitol salts agar plates. A number of techniques were used to test the colonies. The resultant colonies were tested by gram-staining, for mannitol fermentation, and oxidase and catalase activity to confirm the isolation of S. aureus. Several isolates were then tested for antibiotic resistance using methicillin, ampicillin and penicillin. About 40% of the isolates tested positive for methicillin resistance and 20% were found to be resistant to ampicillin and penicillin. These results indicate that cell phones may be a source of potentially pathogenic, and antibiotic-resistance bacteria, and may well pose a significant public health threat.”

This example presents an interesting study but the Abstract is unfocused and vague. Why were cell phones chosen in particular for this study? How many cell phones were tested and how many were found to be contaminated with  S. aureus ? Why was mannitol salts agar used as the selective medium? The sentence, “A number of techniques were used to test the colonies” is superfluous and should have been removed. Although the analytical tests are indicated, the results are not. The author should have stated these precisely in order to convince the reader that  S. aureus  strains were, in fact, isolated. The studies on the antibiotic resistances of the isolates unnecessarily are presented in a vague manner. Again, the author should have briefly justified why these particular antibiotics were chosen and given the actual numbers of isolates that were tested and found to be resistant to different antibiotics as well as the percentages. Finally, the last sentence is too dramatic and not warranted based upon this present study. A more conservative conclusion is called for. All these points are reflected in the revision:

Example 2: Revised Abstract

“Over the past decade, advances in cellular technology have contributed to increases in cell phone usage. Cellular devices have become an integral form of communication and are used by over 23 million people worldwide. Phone conversations, text messaging, and emailing, are all behaviors associated with cell phone use, and require the skin to be in contact with these devices. We hypothesized that cell phones may harbor  Staphylococcus aureus. S. aureus  is a bacterium that inhabits human skin. Certain strains of  S. aureus  are capable of causing disease and some are antibiotic-resistant. In an effort to determine if  S. aureus  was associated with cell phones, sterile swab samples were collected from twelve different phones (flip and non-flip styles) and plated onto mannitol salts agar medium which is recommended for the isolation and identification of  S. aureus . Putative  S. aureus  colonies were obtained from all the phones tested. 192 out of 200 colonies tested positive for mannitol fermentation and were characterized further. All bacteria were gram positive, aggregated cocci and tested positive for oxidase and negative for catalase, confirming the isolation of  S.aureus  by Bergey’s criteria. Previous studies have shown that many S. aureus strains have developed resistance to the β-lactam class of antibiotics. Therefore, 40 randomly selected isolates were tested for resistance to three β-lactam antibiotics, methicillin, ampicillin and penicillin, widely used in medicine. Results from the Kirby Bauer procedure suggested that 16 (40%) of the isolates were methicillin-resistant and 8 (20%) were additionally resistant to both ampicillin and penicillin. The results of this investigation suggest that cell phones may pose public health concerns.

This version of the Abstract is much better. It begins by stating the problem and justifying the research. Results rather than procedures are emphasized. The hypothesis is clearly stated and the major data clearly presented, substantiating the isolation of antibiotic-resistant  S. aureus  and lending credence to the author’s hypothesis. Note, too, that the Abstract is written in the past tense, and abbreviations, literature citations and figures are not present.  

INTRODUCTION

The Introduction provides a framework for the paper including a background (which is often in the form of a literature review) of the topic, and the purpose of the work. This section should be neither too broad nor too narrow. There is no specific length requirement but generally this section can be written in two main paragraphs. The first paragraph should summarize prior research in the area that you have studied. Do not provide a detailed and extensive literature review but instead confine the background information to what is strictly relevant to the work you’ve undertaken. Be sure to indicate references in the text (this will be discussed later). This paragraph must be written in the past tense. In the next paragraph, describe the unique aspects of your work (written in the present or, as appropriate, the future tense); that is to say, provide a justification (and a hypothesis) for the work you’ve carried out. For example, how does your research contribute to the studies undertaken by previous authors? What new information is your research attempting to discover and clarify? You may also briefly preview some of the results in order to lend credence to the importance of your study. Since your paper will be evaluated by your peers and the instructors, the scope of the introduction should be aimed at this audience.

You must follow the conventions of the International Union of Microbiological Societies ( http://www.iums.org ) in naming bacterial species. The convention specifies that binomial names of species must be used and underlined or italicized in the text. When a microbe is first named, its full genus and species name must be written; thereafter, the genus name can be abbreviated. Thus, the species  Pseudomonas fluorescens  must be stated in full when first introduced, but afterwards shortened to  P. flourescens . Do not confuse proper nouns with common nouns.  P. fluorescens  is a particular species, but the term pseudomonads (which is not italicized) refers to many of these species. Similarly, staphylococci are a wide range of bacteria that exhibit a similar shape and aggregation, whereas  Staphylococcus  is a particular genus that exhibits these properties.  

MATERIALS AND METHODS

This section provides the information which will enable other researchers to reproduce the experiments you have carried out. It describes the procedures you used to conduct your research, the controls you incorporated and the means by which you evaluated your data. It is important to be precise. The materials and procedures you carried out lend credibility to your scientific arguments presented later. Similar experiments carried out by others may not always yield the same conclusions, reflecting, perhaps, different interpretations of the data. In addition, this section will provide critical information to others who may be working on similar research and may need to use experimental approaches and techniques similar to the one you employed. Throughout, use the past tense.

Make sure that you organize the description of experiments logically and methodically, in the order that they were performed. It is helpful to organize this section into subheadings, beginning with a description of the materials used in the project. This makes the text easier to write and makes it more understandable, and easier to follow, for the reader. You do not need to provide an extensive list of all the materials you used, such as Petri dishes, gram stain reagent kits, and other common purpose items. You simply state that all chemicals and apparatuses “were provided by the Department of Biological Sciences, the George Washington University”. However, you must relate carefully the sources of your specimens, how they were collected and under what conditions. In addition, if you used standard bacterial strains in your study, these must be described and their sources noted. When describing the methods you used, again be precise, but not over-descriptive. Common microbiological techniques, such as Gram staining, oxidase testing, etc., do not need to be described but simply referenced in the text (usually, you will cite the laboratory manuals). It is necessary, however, to emphasize the purpose for using particular procedures, but be careful not to describe any results until the next section.

Avoid common grammatical errors which often pop up in this section. Media (not mediums) is the plural of medium; datum (singular) should not be confused with data (plural). Never use phrases such as, “The  S. epidermidis -containing cultures were…” when you mean “The samples containing  S. epidermidis  were…” Surely, you would never write, “The coffee-containing cup was…”?  

This section presents the data you accumulated in the course of the study. Once more, the narrative must be in the past tense. Before writing this section, it is advisable that you first construct the tables and figures you will be presenting in the text (see later). Be sure to reference each table and figure in the text (as Table 1, Figure 2, etc.) In the text, it is best to summarize the data and point out important facts and trends; the details can be included in the tables and figures. In order to present the data effectively, this section must be well-organized, preferably in the sequence in which you described your methods. Since many projects will involve the isolation of novel microorganisms, you should carefully designate each isolate, preferably using letters and/or numbers, as follows: “Two isolates, chosen for further characterization, were designated GH104 and KJ106. The characteristics of both strains are summarized in Table 3. After describing the characteristics of a particular isolate, you can then propose a putative identification. Thus,  “Isolate HG411 was found to be a large Gram-positive motile bacillus, often occurring in short chains. It was non-fermentative and tested negative for nitrate reductase. It did not grow in anaerobic medium leading us to hypothesize that it was an obligate aerobe. This was substantiated by positive results for both oxidase and catalase activities. In addition, the presence of clearly defined endospores, shown by malachite green staining, led to the tentative identification of HG411 as  Bacillus cereus .”  Note that the author is careful to point out that this is only a tentative identification. It would take many more weeks of experimentation, probably using determinative tests unavailable to us, to confirm this deduction. Of course, these further tests can, and should, be described in the Discussion

When writing the Results (and Discussion), do so in a direct, straightforward manner. Use the past tense. The use of simple and effective prose is more likely to convey your ideas to the reader (the excerpt above is an excellent example of this kind of writing). Use short sentences. One of the most common errors in writing papers is a tendency to wordiness and the use of jargon. Most jargon is long-winded and confusing, employing words that are unfamiliar to a general reader and this can change what should be an interesting paper into one that is tedious and even boring to read. In fact, it often has the effect of alienating rather than engaging the reader. In addition, you are encouraged to avoid wordiness and the use of redundant phrases. Common modifiers such as “very, “rather” and “quite” are unnecessary and should not be used. Other common examples of wordiness, and how they might be corrected, are given below. Note that simple direct phrases and sentences have a clear and confident tone.

The results would seem to indicate…. The results indicated….

Due to the fact that…. Because….

It may be that…. Perhaps….

A further piece of evidence that pointed…. Further evidence was….

The following day, after 24 hours of incubation, Colonial growth was observed after 24 the plates were removed from the incubator hours of incubation. and observed.

The data indicated that strain AB14 was a Gram- Strain AB14 was a Gram-negative bacillus. bacillus.

Many writers are torn between whether they should write the paper in the active or passive voice. In the former, the subject performs the action; in the latter, the subject receives the action. Too much use of the active voice has the tendency to make the text monotonous because of too many first-person references. On the other hand, overuse of the passive voice can cause the tone of the paper to be dry, boring and even pompous. To ensure that the text is more lively and readable, it is best to try and strike a balance. Consider the following example:

“We used eosin-methylene blue agar plates for the preliminary isolation  of P. aeruginosa . The bacteria were Gram-negative bacilli, and motile. The results for oxidase and catalase activities were negative. Additional experiments showed that the bacteria did not ferment glucose, galactose, maltose or lactose (Table 2). Based on these results, we concluded that the organism had an oxidative metabolism.

Try translating this in to an entirely passive or active tone. You’ll notice that the creative mix of both voices makes this narrative not only lively and engaging but also states the results in a clear, confident and unambiguous manner.  

In this section, you will interpret the results in the context of the questions and hypothesis you explicated in the Introduction, as well as addressing broader issues that were raised by your research. Before you begin, consider the issues raised by your results. Were they the results you expected? Did they support your hypothesis or not? If they did, your Discussion will be brief: if they did not, then you must consider alternative explanations. How might you address any unexpected results in future research? What future directions might this research follow? Finally, what are the scientific and/or public health implications of your research? It is important that you draw your conclusions from the data you obtained and relate them to previously published work (which, of course, must be cited). Your results may be open to many interpretations, but only you can decide which one(s) are the most significant.

It is essential that the text convey confidence in your results and conclusions. Avoid ambiguity and uncertainty. For example, consider the extract below:

“ Our analysis of Georgetown Canal water samples showed that  E. coli  was present in excess of 10 3  cfu/ml; however, quantitative data on other coliform bacteria were not completed. This study must, therefore, be considered only as a preliminary study.”

The statement, although strong to begin with, ends on an evasive and inconclusive note that leads the reader to doubt the author’s belief in her own research. An acceptable revision would read as follows:

Our analysis of the Georgetown canal water samples showed that  E. coli  was greater than 10 3  cfu/ml. The presence of other coliform bacteria was not investigated but our results clearly indicate that the fecal contamination of the canal is in excess of city standards for public health (reference). In view of these results, we propose that further investigation on the canal be carried out.

This narrative is much more confident. It emphasizes the results and points to their significance, and the reader, in return, is assured of the author’s credibility. Furthermore, the author’s proposal for future research, asserted by these bold statements, appears authoritative, logical and fully justified.  

Documenting your paper thoroughly is a hallmark of good scientific writing. Any ideas or results which are not your own must be cited at the appropriate places. Cite sources in the text using the format recommended by the Council of Science Editors (CSE:  www.councilscienceeditors.org ), often referred to as the name-year system (this is different from the format specified by the Journal of Bacteriology). For example,  “ Staphyococcus aureus  is a Gram-positive coccus, widespread in nature, which has been implicated in a number of human and animal diseases (Tolura, 2008)”  or  “Shimkets and Dworkin (1998) point out that many  Myxococcus  species…”  or  “Water samples were evaluated for  E. coli  contamination following the procedure described by Nathan (2002). ” You do not need to repeat the citation for every sentence attributable to a particular source. However, if you are discussing the work at some length it is advisable to cite the reference at the beginning and the end of the paragraph to indicate that you are still referring to the same source. Do not reference general material that is widely known. For your major sources, you may include your textbook, laboratory manuals, published research and review papers and class handouts. If one or more of your sources is attributable to word of mouth (a discussion with the instructor, for example) then indicate this in the text as “(Morris, DW, personal communication).” This is not repeated in the References section. Use quotations from other authors only sparingly in the text when you need to emphasize a particularly significant aspect that has drawn wide attention.

Sources in the References section can be ordered as they appear in the text or alphabetically. Common examples are given below.

Tolura, GM. 2006. Microbiology. 4 th  ed. San Francisco: WH Freeman. 670 p.

Article or Chapter in an Edited Book

Shimkets, LM, Dworkin, M. 1998. The Myxobacteria. In: Shapiro, JM, Dworkin, M. editors. Bacteria as Multicellular Organisms. Oxford: Blackwell Scientific. p. 121-145.

Journal Article with a Single Author

Neu, H. 1992.. The Crisis in antibiotic resistance. Science. 306: 1064-1073.

Journal Article with Two or More Authors

Chanishvili, N, Chanishvili, T, Tediashvili, NM, Barrow , PA. 2001. Phages and their application against drug-resistant bacteria”.  J. Chem. Technol .  36: 192-198.

District of Columbia Water and Sewer Authority (2000).  Facilities: Water Treatment . Retrieved October 29, 2008, from DC Water and Sewer Authority Web site:  https://www.dcwater.com/

Course Handouts or Laboratory Manuals

Morris, DW. 2008. Biological Sciences 137 Laboratory Manual: The George Washington University. 112 p.  

TABLES AND FIGURES

Most scientific papers are supplemented with tables and figures that summarize and present essential data that convey information more effectively than the text. All must be of high quality. When you begin to construct your tables and figures, you must decide how you are going to depict your data most effectively. Is a graph more effective than a table? Do you need both? You must ultimately decide how best to display your data so that it is a convincing argument for your hypothesis and emphasizes the major findings of you research. When you have made your tables and figures, number them consecutively in the order they are referred to in the text. Each should have a title and a brief descriptive legend. It is important that each table and figure stand on its own and still be understandable to the reader.

A common fault beginners make is to include all their data in the form of tables and figures. However, this is unnecessary and in some instances, data can be more easily and more effectively summarized in the text. Tables and figures must include only selective and important data. For example, the table below reflects uniform data and is unnecessary. The data may be explained more concisely in the text as,  “All three strains (NM 102 – 104), originally isolated on mannitol salts agar, were found to be non-motile gram-positive staphylococci and tested positive for catalase and negative for oxidase.”  Tables must display more variable data. The examples in your laboratory manuals contain many good examples.

Table 2 : Morphological and Physiological Characteristics of Thee Independent Clones Isolated on Mannitol Salts Agar.

Key:  1  + indicates a gram positive reaction; – indicates a gram negative reaction.  2 + indicates a positive reaction; – indicates no reaction.

Similarly, photographs or drawings of microbial cells can be omitted and described in the text, unless you are pointing out important features on the illustration. If you present graphs, clearly label each axis. Do not be tempted to provide a graph and a table of the same data: one or the other is sufficient.  

DRAFTING AND REVISING

You can expect to produce several drafts of your paper before it is ready for submission. Before you begin, study the instructions for the paper format carefully so that your paper is organized properly from the beginning. In fact, for the first draft, you should concentrate on the content and organization of the paper, and write down all of the information that you wish to include in the paper. Later, you can focus on style, grammar and punctuation. Start with the easiest writing rather than at the beginning. I find that writing the Materials and Methods first is best and it can usually be commenced before the project is finished. Alternatively, you may want to start with the Introduction since much of this can be adapted from your proposal. Be sure to prepare the Tables and Figures before you start writing the Results and Discussion sections. Generally, it is best to write the Abstract last of all, once all of the other sections of the paper have been completed. Be sure the follow the guidelines outline above.

I have found that there is a marked tendency for many beginning writers, lacking confidence in the power of their own prose, to rely on the quotations of other authors when wishing to make important points. This does not necessarily enhance the text and can, in fact, cause the reader to doubt the originality of the paper. It is perfectly permissible to paraphrase carefully material from other authors’ papers as long as the sources are cited. However, if you determine that a quotation will emphasize a particular point you are making, keep it short. A representative example is:  “Baker (2007) describes  Campylobacter jejunii  as the ‘major causative agent of food poisoning deaths among children under five years of age in the U.S.’ His experimental data indicated that at least 67% of reported food poisoning cases were due to this organism.”  The carefully selected quotation, enclosed within the author’s own text, emphasizes, and adds veracity to, the point the author wants to make.

Once you have written the first draft, go through the paper and check that is correctly formatted before you begin revising the text. Pay careful attention to grammar and punctuation. If you have a spell checker on your word processing program, by all means use it, but do not rely on it to detect all errors: these can only be spotted by carefully reading the draft. Proofreading can be tedious, especially if you have spent many hours writing the drafts. However, it is a task that must be performed with the utmost care. I have found that the best way to spot mistakes is to read the paper aloud, either to yourself or someone else. This practice will also enable to revise sentences that are unduly long or drawn out.  

Research Proposal

The research proposal has much in common with the research paper. The proposal asks a question or poses a hypothesis that can be tested experimentally. There is no standard format for proposals, but it is important to conform to the guidelines laid down by the funding agency or organization. Your proposal must adhere to the format given below. The text must be double-spaced and include one-inch margins either side. Refer to Blackboard for sample proposals. The proposal must consist of five sections, beginning with a descriptive  Title . The  Introduction  presents a review of the literature pertinent to the proposed research and leads to  Research Aims  which explicitly states the research question being asked and outlines its significance. The  Methods  section outlines your experimental strategy and, finally, the  References  section records your sources for the proposal.  

A full title of the project, your departmental affiliation and the due date for submission of the proposal should be presented on a single page. You will be working in groups of two or three but each individual must submit her/his proposal independently. The title, as with the research paper, must be specific and informative. The author’s name, affiliation and the submission date must also appear on this page.  

Background information (that is, a brief review of the literature concerning the topic of your proposal) should be presented in this section. To do a good job, you must read the literature carefully and selectively. Be aware of who you are writing for: in this case it will be your instructor and must, therefore, be scientifically accurate. This section should conclude with a short paragraph that states the research problem to be addressed by your proposal.  

RESEARCH AIMS

The next two sections must be written in the future tense. In this section, clearly state the research objectives of your proposal. It is essential that you justify the aims of the proposal. How will it enlarge, clarify or disprove existing knowledge. What makes your proposal unique? Make your arguments convincing, citing references if appropriate. Try to predict the outcome(s) of your research. Finally, is the proposal adequate to address the research problem you have posed, or is it a preliminary investigation? Remember, you only have three weeks in which to carry out the research so you must be realistic about what you can accomplish in this short time.  

Describe the experiments to be conducted and the order in which they will be carried out. If you expect problems or ambiguities to arise, how would you explain or solve them? A detailed description of each experimental step need not be given (procedures for common microbiological techniques, such as Gram staining for example, should not be detailed at all) as long as the procedures are referenced and you explain why you are using this strategy. Point out the kinds of data you expect to generate and how you would evaluate and interpret it. Finally, be careful to explain how the data would support your hypothesis.  

References should be indicated in the text and cited in this section in the name-year manner as in the research paper.  

The WID Studio is a primary source of help and students are encouraged to use this facility. Two recent and helpful books on writing in the biological sciences are also available:

McMillan, VE. 2006. Writing Papers in the Biological Sciences. 4 th  ed. Boston: Bedford/St.Martins. 269 p.

Pechenik, JA. 2007 A Short Guide to Writing about Biology. 6 th  ed. New York: Pearson Longman. 281 p.

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Microbiological Research on Fermented Dairy Products

Fermented dairy products are widely consumed worldwide due to the nutritional and health benefits. Microorganisms play an extremely important role in fermented dairy products, which are essential for obtaining final products with well-defined organoleptic and physico-chemical properties. Microbial ecology of dairy products is composed of complex microbiota, including bacteria, yeasts and filamentous fungi. Recently, particular attention has been given to the extracellular biopolymers called exopolysaccharides (EPS) isolated from lactic acid bacteria (LAB) owing to their prebiotic properties and applicability in the food industry. Furthermore, gastro-intestinal digestion of dairy proteins is an important step to supply the organism of essential and non-essential amino acids, and thus peptidomics approach has proven to be a suitable method to monitor hydrolysis during digestion of diary proteins.

This Special Issue belongs to the section “Food Microbiology” and focuses on the microbiota diversity, carbohydrate metabolism, peptidomic pattern and quality improvement of fermented dairy products. This Special Issue includes six research papers related to microbiological research on fermented dairy products, all of which are valuable contributions to this issue made by distinguished experts and researchers in this area.

Wang et al. (2021) [ 1 ] analyzed bacterial diversity of traditional Tibetan kefir grains. Kefir grains are made up of complex microbiota including LAB, yeast and acetic acid bacteria (AAB). Lactobacillus kefiranofaciens , L. kefiri and Kluyveromyces marxianus were identified as the main dominant strains in the kefir grains. The authors investigated the chemical structure of EPS and biofilm formation to clarify the internal relationship between biofilm and the formation process of kefir grains.

The dominant microbiota of four Traditional Agri-food Products (TAP) cheeses as well as their peptidase activities were studied by Celano et al. (2022) [ 2 ]. The authors concluded that L. helveticus dominated both Caprino and Vaccino cheeses, while Staphylococcus equorum and Streptococcus thermophilus dominated Cacioricotta and Pecorino cheeses, respectively. Potential relationship between the microbiological and their biochemical characteristics were predicted for valorizing and safeguarding these TAP cheeses.

An EPS was extracted from soybean whey fermented by Lactiplantibacillus plantarum 70810. The preliminary structural characteristics and antioxidant activity of the EPS, that could be used as a promising ingredient for health-beneficial function foods, were examined by Tian et al. (2021) [ 3 ]. Soybean whey is a by-product of the soybean production and could be transformed into bioactive ingredients by microbial fermentation. The authors suggested that EPS from soybean whey fermented by L. plantarum 70810 exhibited great scavenging bioactivities against the DPPH radical and superoxide anion radical.

Ye et al. (2021) [ 4 ] reported the peptidomics of milk fermented by Lactobacillus delbrueckii both before and after the simulated gastrointestinal digestion. The peptides derived from β-casein were abundant in the samples of L. delbreuckii ssp. bulgaricus , while the peptides originating from αs1-casein and αs2-casein were more likely to dominate in those of L. delbrueckeii ssp. lactis . The research provided a reference approach for evaluating the peptide profile of the Lactobacillus delbrueckii during fermentation and digestion.

The physicochemical, rheological and microstructural properties of non-fat yogurt fortified with whey protein isolate was examined by Hashim et al. (2021) [ 5 ] to explore the potential of whey protein isolate (WPI) in improving the yogurt quality compared with skim milk powder (SMP). The authors concluded that the incorporation of WPI improved the water holding capacity, rheological properties, compared sensory and textural characteristics, and could be further exploited for producing low- and non-fat fermented dairy food products.

A unique gene (the glycosyltransferase family 8) was identified to differentiate Lacticaseibacillus zeae from other Lacticaseibacillus species by pan-genome analysis, and a real-time PCR method was developed and applied to accurately detect the unique gene by Kim et al. (2021) [ 6 ]. The traditional method for differentiation of lactic acid bacteria is based on the highly conservative 16S rRNA gene. The development of this technology could facilitate the identification of specific strains among its closely related species.

The manuscripts in this Special Issue deal with the undeniable importance of microbiota for the fermented fairy products. Further studies are required to obtain a better understanding of how fermented dairy products provide health benefits, and more attention should be paid to the mechanisms by which organisms, cellular fractions or the byproducts are responsible for each benefit.

Acknowledgments

The authors gratefully acknowledge laboratory colleagues for their help.

Funding Statement

This work was co-financed by National Natural Science Foundation of China (No. 31871771 and U1903108), Natural Science Foundation of Jiangsu Province (No. BK20201320), Jiangsu Agriculture Science and Technology Innovation Fund (No. CX(20)3043), Jiangsu Provincial Key Research and Development Program (No. BK2020305 and BK2022325), Qing Lan Project of Jiangsu Province and Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).

Author Contributions

Conceptualization, L.X.; software, L.X.; validation, L.X.; writing—original draft preparation, L.X. and W.L.; writing—review and editing, W.L.; supervision, W.L.; project administration, W.L.; funding acquisition, W.L. All authors have read and agreed to the published version of the manuscript.

Conflicts of Interest

The authors declare no conflict of interest.

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Get science-backed answers as you write with Paperpal's Research feature

How to Write an Abstract in Research Papers (with Examples)

An abstract in research papers is a keyword-rich summary usually not exceeding 200-350 words. It can be considered the “face” of research papers because it creates an initial impression on the readers. While searching databases (such as PubMed) for research papers, a title is usually the first selection criterion for readers. If the title matches their search criteria, then the readers read the abstract, which sets the tone of the paper. Titles and abstracts are often the only freely available parts of research papers on journal websites. The pdf versions of full articles need to be purchased. Journal reviewers are often provided with only the title and abstract before they agree to review the complete paper. [ 1]  

Abstracts in research papers provide readers with a quick insight into what the paper is about to help them decide whether they want to read it further or not. Abstracts are the main selling points of articles and therefore should be carefully drafted, accurately highlighting the important aspects. [ 2]  

This article will help you identify the important components and provide tips on how to write an abstract in research papers effectively

What is an Abstract?  

An abstract in research papers can be defined as a synopsis of the paper. It should be clear, direct, self-contained, specific, unbiased, and concise. These summaries are published along with the complete research paper and are also submitted to conferences for consideration for presentation.  

Abstracts are of four types and journals can follow any of these formats: [ 2]  

• Structured  
• Unstructured  
• Descriptive  
• Informative  

Structured abstracts are used by most journals because they are more organized and have clear sections, usually including introduction/background; objective; design, settings, and participants (or materials and methods); outcomes and measures; results; and conclusion. These headings may differ based on the journal or the type of paper. Clinical trial abstracts should include the essential items mentioned in the CONSORT (Consolidated Standards Of Reporting Trials) guidelines.  

Figure 1. Structured abstract example [3] 

Unstructured abstracts are common in social science, humanities, and physical science journals. They usually have one paragraph and no specific structure or subheadings. These abstracts are commonly used for research papers that don’t report original work and therefore have a more flexible and narrative style.  

Figure 2. Unstructured abstract example [3] 

Descriptive abstracts are short (75–150 words) and provide an outline with only the most important points of research papers. They are used for shorter articles such as case reports, reviews, and opinions where space is at a premium, and rarely for original investigations. These abstracts don’t present the results but mainly list the topics covered.  

Here’s a sample abstract . [ 4]  

“Design of a Radio-Based System for Distribution Automation”  

A new survey by the Maryland Public Utilities Commission suggests that utilities have not effectively explained to consumers the benefits of smart meters. The two-year study of 86,000 consumers concludes that the long-term benefits of smart meters will not be realized until consumers understand the benefits of shifting some of their power usage to off-peak hours in response to the data they receive from their meters. The study presents recommendations for utilities and municipal governments to improve customer understanding of how to use the smart meters effectively.  

Keywords: smart meters, distribution systems, load, customer attitudes, power consumption, utilities  

Informative abstracts (structured or unstructured) give a complete detailed summary, including the main results, of the research paper and may or may not have subsections.   

Figure 3. Informative abstract example [5] 

Purpose of Abstracts in Research    

Abstracts in research have two main purposes—selection and indexing. [ 6,7]  

• Selection : Abstracts allow interested readers to quickly decide the relevance of a paper to gauge if they should read it completely.   
• Indexing : Most academic journal databases accessed through libraries enable you to search abstracts, allowing for quick retrieval of relevant articles and avoiding unnecessary search results. Therefore, abstracts must necessarily include the keywords that researchers may use to search for articles.  

Thus, a well-written, keyword-rich abstract can p ique readers’ interest and curiosity and help them decide whether they want to read the complete paper. It can also direct readers to articles of potential clinical and research interest during an online search.  

Contents of Abstracts in Research  

Abstracts in research papers summarize the main points of an article and are broadly categorized into four or five sections. Here are some details on how to write an abstract .   

Introduction/Background and/or Objectives  

This section should provide the following information:  

• What is already known about the subject?  
• What is not known about the subject or what does the study aim to investigate?  

The hypothesis or research question and objectives should be mentioned here. The Background sets the context for the rest of the paper and its length should be short so that the word count could be saved for the Results or other information directly pertaining to the study. The objective should be written in present or past simple tense.  

Examples:  

The antidepressant efficacy of desvenlafaxine (DV) has been established in 8-week, randomized controlled trials. The present study examined the continued efficacy of DV across 6 months of maintenance treatment . [ 1]  

Objective: To describe gastric and breast cancer risk estimates for individuals with CDH1 variants.  

Design, Setting, and Participants (or Materials and Methods)  

This section should provide information on the processes used and should be written in past simple tense because the process is already completed.  

A few important questions to be answered include:  

• What was the research design and setting?  
• What was the sample size and how were the participants sampled?  
• What treatments did the participants receive?  
• What were the data collection and data analysis dates?  
• What was the primary outcome measure?  

Hazard ratios (HRs) were estimated for each cancer type and used to calculate cumulative risks and risks per decade of life up to age 80 years.  

This section, written in either present or past simple tense, should be the longest and should describe the main findings of the study. Here’s an example of how descriptive the sentences should be:  

Avoid: Response rates differed significantly between diabetic and nondiabetic patients.  

Better: The response rate was higher in nondiabetic than in diabetic patients (49% vs 30%, respectively; P<0.01).  

This section should include the following information:  

• Total number of patients (included, excluded [exclusion criteria])  
• Primary and secondary outcomes, expressed in words, and supported by numerical data  
• Data on adverse outcomes  

Example: [ 8]  

In total, 10.9% of students were reported to have favorable study skills. The minimum score was found for preparation for examination domain. Also, a significantly positive correlation was observed between students’ study skills and their Grade Point Average (GPA) of previous term (P=0.001, r=0.269) and satisfaction with study skills (P=0.001, r=0.493).  

Conclusions  

Here, authors should mention the importance of their findings and also the practical and theoretical implications, which would benefit readers referring to this paper for their own research. Present simple tense should be used here.  

Examples: [ 1,8]  

The 9.3% prevalence of bipolar spectrum disorders in students at an arts university is substantially higher than general population estimates. These findings strengthen the oft-expressed hypothesis linking creativity with affective psychopathology.  

The findings indicated that students’ study skills need to be improved. Given the significant relationship between study skills and GPA, as an index of academic achievement, and satisfaction, it is necessary to promote the students’ study skills. These skills are suggested to be reinforced, with more emphasis on weaker domains.  

When to Write an Abstract  

In addition to knowing how to write an abstract , you should also know when to write an abstract . It’s best to write abstracts once the paper is completed because this would make it easier for authors to extract relevant parts from every section.  

Abstracts are usually required for: [ 7]    

• submitting articles to journals  
• applying for research grants   
• writing book proposals  
• completing and submitting dissertations  
• submitting proposals for conference papers  

Mostly, the author of the entire work writes the abstract (the first author, in works with multiple authors). However, there are professional abstracting services that hire writers to draft abstracts of other people’s work.   

How to Write an Abstract (Step-by-Step Process)  

Here are some key steps on how to write an abstract in research papers: [ 9]  

• Write the abstract after you’ve finished writing your paper.  
• Select the major objectives/hypotheses and conclusions from your Introduction and Conclusion sections.  
• Select key sentences from your Methods section.  
• Identify the major results from the Results section.  
• Paraphrase or re-write the sentences selected in steps 2, 3, and 4 in your own words into one or two paragraphs in the following sequence: Introduction/Objective, Methods, Results, and Conclusions. The headings may differ among journals, but the content remains the same.  
• Ensure that this draft does not contain: a.   new information that is not present in the paper b.   undefined abbreviations c.   a discussion of previous literature or reference citations d.   unnecessary details about the methods used  
• Remove all extra information and connect your sentences to ensure that the information flows well, preferably in the following order: purpose; basic study design, methodology and techniques used; major findings; summary of your interpretations, conclusions, and implications. Use section headings for structured abstracts.  
• Ensure consistency between the information presented in the abstract and the paper.  
• Check to see if the final abstract meets the guidelines of the target journal (word limit, type of abstract, recommended subheadings, etc.) and if all the required information has been included.  

Choosing Keywords for Abstracts  

Keywords [ 2] are the important and repeatedly used words and phrases in research papers and can help indexers and search engines find papers relevant to your requirements. Easy retrieval would help in reaching a wider audience and eventually gain more citations. In the fields of medicine and health, keywords should preferably be chosen from the Medical Subject Headings (MeSH) list of the US National Library of Medicine because they are used for indexing. These keywords need to be different from the words in the main title (automatically used for indexing) but can be variants of the terms/phrases used in the title, abstract, and the main text. Keywords should represent the content of your manuscript and be specific to your subject area.  

Basic tips for authors [ 10,11]  

• Read through your paper and highlight key terms or phrases that are most relevant and frequently used in your field, to ensure familiarity.  
• Several journals provide instructions about the length (eg, 3 words in a keyword) and maximum number of keywords allowed and other related rules. Create a list of keywords based on these instructions and include specific phrases containing 2 to 4 words. A longer string of words would yield generic results irrelevant to your field.  
• Use abbreviations, acronyms, and initializations if these would be more familiar.  
• Search with your keywords to ensure the results fit with your article and assess how helpful they would be to readers.  
• Narrow down your keywords to about five to ten, to ensure accuracy.  
• Finalize your list based on the maximum number allowed.  

  Few examples: [ 12]  

Important Tips for Writing an Abstract  

Here are a few tips on how to write an abstract to ensure that your abstract is complete, concise, and accurate. [ 1,2]  

• Write the abstract last.  
• Follow journal-specific formatting guidelines or Instructions to Authors strictly to ensure acceptance for publication.  
• Proofread the final draft meticulously to avoid grammatical or typographical errors.  
• Ensure that the terms or data mentioned in the abstract are consistent with the main text.  
• Include appropriate keywords at the end.

Do not include:  

• New information  
• Text citations to references  
• Citations to tables and figures  
• Generic statements  
• Abbreviations unless necessary, like a trial or study name  

Key Takeaways    

Here’s a quick snapshot of all the important aspects of how to write an abstract . [2]

• An abstract in research is a summary of the paper and describes only the main aspects. Typically, abstracts are about 200-350 words long.  
• Abstracts are of four types—structured, unstructured, descriptive, and informative.  
• Abstracts should be simple, clear, concise, independent, and unbiased (present both favorable and adverse outcomes).  
• They should adhere to the prescribed journal format, including word limits, section headings, number of keywords, fonts used, etc.  
• The terminology should be consistent with the main text.   
• Although the section heading names may differ for journals, every abstract should include a background and objective, analysis methods, primary results, and conclusions.  
• Nonstandard abbreviations, references, and URLs shouldn’t be included.  
• Only relevant and specific keywords should be used to ensure focused searches and higher citation frequency.  
• Abstracts should be written last after completing the main paper.  

Frequently Asked Questions   

Q1. Do all journals have different guidelines for abstracts?  

A1. Yes, all journals have their own specific guidelines for writing abstracts; a few examples are given in the following table. [ 6,13,14,15]  

Q2. What are the common mistakes to avoid when writing an abstract?  

A2. Listed below are a few mistakes that authors may make inadvertently while writing abstracts.  

• Copying sentences from the paper verbatim  

An abstract is a summary, which should be created by paraphrasing your own work or writing in your own words. Extracting sentences from every section and combining them into one paragraph cannot be considered summarizing.  

• Not adhering to the formatting guidelines  

Journals have special instructions for writing abstracts, such as word limits and section headings. These should be followed strictly to avoid rejections.  

• Not including the right amount of details in every section  

Both too little and too much information could discourage readers. For instance, if the Background has very little information, the readers may not get sufficient context to appreciate your research. Similarly, incomplete information in the Methods and a text-heavy Results section without supporting numerical data may affect the credibility of your research.  

• Including citations, standard abbreviations, and detailed measurements  

Typically, abstracts shouldn’t include these elements—citations, URLs, and abbreviations. Only nonstandard abbreviations are allowed or those that would be more familiar to readers than the expansions.  

• Including new information  

Abstracts should strictly include only the same information mentioned in the main text. Any new information should first be added to the text and then to the abstract only if necessary or if permitted by the word limit.  

• Not including keywords  

Keywords are essential for indexing and searching and should be included to increase the frequency of retrieval and citation.  

Q3. What is the difference between abstracts in research papers and conference abstracts? [16]  

A3. The table summarizes the main differences between research and conference abstracts.  

  Thus, abstracts are essential “trailers” that can market your research to a wide audience. The better and more complete the abstract the more are the chances of your paper being read and cited. By following our checklist and ensuring that all key elements are included, you can create a well-structured abstract that summarizes your paper accurately.  

References  

• Andrade C. How to write a good abstract for a scientific paper or conference presentation. Indian J Psychiatry . 2011; 53(2):172-175. Accessed June 14, 2024. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3136027/  
• Tullu MS. Writing the title and abstract for a research paper: Being concise, precise, and meticulous is the key. 2019; 13(Suppl 1): S12-S17. Accessed June 14, 2024. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6398294/  
• Zawia J. Writing an Academic Paper? Get to know Abstracts vs. Structured Abstracts. Medium. Published October 16, 2023. Accessed June 16, 2024. https://medium.com/@jamala.zawia/writing-an-academic-paper-get-to-know-abstracts-vs-structured-abstracts-11ed86888367  
• Markel M and Selber S. Technical Communication, 12 th edition. 2018; pp. 482. Bedford/St Martin’s.  
• Abstracts. Arkansas State University. Accessed June 17, 2024. https://www.astate.edu/a/global-initiatives/online/a-state-online-services/online-writing-center/resources/How%20to%20Write%20an%20Abstract1.pdf  
• AMA Manual of Style. 11 th edition. Oxford University Press.  
• Writing an Abstract. The University of Melbourne. Accessed June 16, 2024. https://services.unimelb.edu.au/__data/assets/pdf_file/0007/471274/Writing_an_Abstract_Update_051112.pdf  
• 10 Good Abstract Examples that will Kickstart Your Brain. Kibin Essay Writing Blog. Published April 5, 2017. Accessed June 17, 2024. https://www.kibin.com/essay-writing-blog/10-good-abstract-examples/  
• A 10-step guide to make your research paper abstract more effective. Editage Insights. Published October 16, 2013. Accessed June 17, 2024. https://www.editage.com/insights/a-10-step-guide-to-make-your-research-paper-abstract-more-effective  
• Using keywords to write your title and abstract. Taylor & Francis Author Services. Accessed June 15, 2024. https://authorservices.taylorandfrancis.com/publishing-your-research/writing-your-paper/using-keywords-to-write-title-and-abstract/  
• How to choose and use keywords in research papers. Paperpal by Editage blog. Published March 10, 2023. Accessed June 17, 2024. https://paperpal.com/blog/researcher-resources/phd-pointers/how-to-choose-and-use-keywords-in-research-papers  
• Title, abstract and keywords. Springer. Accessed June 16, 2024. https://www.springer.com/it/authors-editors/authorandreviewertutorials/writing-a-journal-manuscript/title-abstract-and-keywords/10285522  
• Abstract and keywords guide. APA Style, 7 th edition. Accessed June 18, 2024. https://apastyle.apa.org/instructional-aids/abstract-keywords-guide.pdf  
• Abstract guidelines. American Society for Microbiology. Accessed June 18, 2024. https://asm.org/events/asm-microbe/present/abstract-guidelines  
• Guidelines for conference abstracts. The Lancet. Accessed June 16, 2024. https://www.thelancet.com/pb/assets/raw/Lancet/pdfs/Abstract_Guidelines_2013.pdf  
• Is a conference abstract the same as a paper abstract? Global Conference Alliance, Inc. Accessed June 18, 2024. https://globalconference.ca/is-a-conference-abstract-the-same-as-a-paper-abstract/  

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MINI REVIEW article

Microplastics and viruses in the aquatic environment: a mini review.

• 1 School of Environmental Science and Engineering, Tianjin University, Tianjin, China
• 2 The Eighth Geological Brigade, Hebei Geological Prospecting Bureau, Qinhuangdao, China
• 3 Marine Ecological Restoration and Smart Ocean Engineering Research Center of Hebei Province, Qinhuangdao, China
• 4 College of Environment and Safety Engineering, Fuzhou University, Fuzhou, China

Microplastics (MPs) have been widely found in the environment and have exerted non-negligible impacts on the environment and human health. Extensive research has shown that MPs can act as carriers for viruses and interacts with them in various ways. Whether MPs influence the persistence, transmission and infectivity of virus has attracted global concern in the context of increasing MPs contamination. This review paper provides an overview of the current state of knowledge regarding the interactions between MPs and viruses in aquatic environments. Latest progress and research trends in this field are summarized based on literature analysis. Additionally, we discuss the potential risks posed by microplastic-associated viruses to human health and the environmental safety, highlighting that MPs can affect viral transmission and infectivity through various pathways. Finally, we underscores the need for further research to address key knowledge gaps, such as elucidating synergistic effects between MPs and viruses, understanding interactions under real environmental conditions, and exploring the role of biofilms in virus–MPs interactions. This review aims to contribute to a deeper understanding on the transmission of viruses in the context of increasing MPs pollution in water, and promote actions to reduce the potential risks.

1 Introduction

Microplastics (MPs), as an emerging pollutants, has garnered significant global attention due to their ubiquitous presence and uni-negligible risks. MPs are defined as plastic fibers, fragments, and films with a diameter of less than 5 mm ( Thompson et al., 2004 ; Hartmann et al., 2019 ). MPs can be categorized into primary MPs, directly manufactured by industries, and secondary MPs, which are derived from the degradation of larger plastic fragments ( Cole et al., 2011 ; Wang et al., 2021a ). They are capable of long-distance migration aided by hydrodynamic forces and atmospheric transport, leading to widespread distribution and contamination in remote regions. MPs have been detected in various water bodies, including oceans ( Cole et al., 2011 ), freshwater systems ( Li et al., 2018 ), and domestic wastewater ( Zhang et al., 2022a ). The distinctive properties of MPs, including large specific surface area, pronounced hydrophobicity, and robust adsorption capacity, render them ideal ecological niches for a diverse range of microorganisms ( Zettler et al., 2013 ). Upon adherence to MPs surfaces, microorganisms secrete a wide variety of extracellular polymeric substances (EPS) ( Webb et al., 2009 ). EPS serves as a protective shield against physical and chemical stresses, such as sand abrasion and photodegradation ( Wang et al., 2021b ). This protective mechanism promotes microbial colonization and facilitates the formation of biofilms on the MPs surfaces. These biofilms situate at the interface between the plastic surface and the surrounding environment, being commonly referred to as the “plastisphere” ( Zettler et al., 2013 ).

Viruses are widely present on Earth and are critical components of ecosystems and human health. Aquatic environments harbor highly abundant and diverse viruses that outnumber the total number of cellular organisms. The transmission of viruses has led to the emergence of numerous epidemic diseases, such as influenza A (H1N1), SARS, Middle East respiratory syndrome, COVID-19 ( Sabar et al., 2022 ; Yang et al., 2022 ; Zamhuri et al., 2022 ). Viral transmission occurs through diverse mechanisms, including direct contact and indirect transmission by environmental substrates (water, air, and food) and various other vectors ( Armanious et al., 2016 ; Yamada et al., 2020 ; Wang et al., 2023a ). Consequently, investigations on the viral transmission mechanisms and factors influencing their virulence have garnered significant concerns.

The adsorption characteristics of MPs and the formation of plastisphere indicate that MPs can serve as artificial “microbial reefs” in aquatic habitats ( Bayo et al., 2020 ). Li et al. (2018) conducted an assessment of virus diversity and potential risks associated with MPs collected from the Beilun River, identifying a total of 1719 different viruses present in the MPs. Additionally, the interaction between MPs and viruses can increase virus virulence through various mechanisms, leading to increased mortality rate of virus-infected organisms ( Deng et al., 2021 ; Seeley et al., 2023 ). Studies also revealed that co-exposure to SARS-CoV-2 and MPs enhances SARS-CoV-2 infection ( Zhang et al., 2022b ). However, the precise mechanisms and influencing factors for the microplastic-mediated viral infection remain unclear and warrant further investigation.

In a word, interactions between MPs and viruses in the aquatic environment are an area of emerging research, and there is a considerable lack of knowledge on them. Therefore, this review aims to address the following aspects: (1) conducting a quantitative analysis of the existing literature in this field to summarize the latest progress and research trends; (2) examining the interaction mechanism between MPs and viruses and influencing factors in aquatic environments; (3) suggesting future research directions in this field.

2 Literature analysis

Bibliometric analysis was conducted to gain a comprehensive understanding of research trends and hotspots in this field. A detailed literature search was performed in the Web of Science core collection database by using the search formula TS = (microplastic* OR nanoplastic*) AND TS = (*virus*) for the period between January 1, 2014, and January 1, 2024. A total of 170 articles were retrieved. After careful screening, 52 articles were identified as relevant to the research field. These screened articles were used as the input dataset for the subsequent quantitative analysis by using CiteSpace. Before 2020, this research field caught fewer concern and there are only 2 publications during 2019–2020. From 2021, the number of publications kept increasing, reaching 28 in 2023. The increased concern may be attributed to the sudden outbreak of COVID-19 pandemic and the wide use of face masks. The global concern on public health prompted researchers to investigate the interaction between viruses and MPs. Figure 1A shows the keyword co-occurrence network, where the size of the nodes corresponds to the frequency of the respective keyword. Keywords such as particles, marine environment, adsorption, and COVID-19 show high frequencies. This phenomenon suggests that the COVID-19 outbreak has raised concerns about the interaction between MPs and viruses, and the marine environment is a current focus. Figure 1B shows the 20 emergent keywords generated by using Citespace. The red line in the figure represents the time interval during which these emergent keywords garnered significant attention from researchers. For instance, the sudden appearance of “human health” in 2021 indicates that human health issues emerged after the outbreak of the COVID-19 pandemic in 2020. The emergence of keywords such as “trout,” “Atlantic salmon,” “ Daphnia magna ,” and “European sea bass” suggests that these animals serve as important models for studying the mechanisms of MPs-mediated viral toxicity. Furthermore, the emergence of “inactivation” indicates the growing concern on the public health, which facilitates the development of efficient remediation techniques.

Figure 1 . (A) Keyword co-occurrence network diagram. (B) Keyword burst analysis. 1. Keywords refer to emergent keywords. 2. Year indicates the year when the keyword emerged. 3. Strength represents the prominence intensity of the keyword, with higher values indicating greater influence. 4. Begin and End denote the start and end time of the keyword’s prominence.

3 Adsorption of viruses by MPs

3.1 adsorption mechanism.

Several studies have demonstrated the robust adsorption properties of MPs towards viruses. For example, Lu et al. (2022) reported a high adsorption rate of 98.6% of the T4 bacteriophages by polystyrene (PS). There are generally two mechanisms: electrostatics and hydrophobic effect governed interactions, and plastisphere-mediated interactions. Viruses can be adsorbed onto the abiotic surface of MPs through non-specific electrostatic interactions ( Lu et al., 2022 ) and hydrophobic forces ( Dika et al., 2015 ). Polyethylene terephthalate (PET) and polypropylene (PP) have been observed to adsorb viruses predominantly through non-ionic forces ( Gassilloud et al., 2007 ), which are directly influenced by the medium pH and the isoelectric point of the virus. Plastisphere plays an important role in the process of virus adsorption onto MPs. Bacteria in plastisphere can produce a diverse array of EPS, enhancing the adhesion and the aggregation of viruses and MPs ( Rummel et al., 2017 ; Moresco et al., 2021 ). Niu et al. (2023) found that microplastic biofilms selectively enrich certain phages, and Reeves et al. (2023) supposed the association between SARS-CoV-2 transmission and the formation of viral plastisphere in sewage. Moreover, viruses attached to biofilms on microplastic surfaces exhibit increased virulence ( Moresco et al., 2021 ). However, the current understanding on the interaction mechanisms remains limited, necessitating further study.

3.2 Influencing factors

The adsorption of viruses by MPs is influenced by various factors. These factors can be classified into three main categories: the aquatic environment, the physicochemical properties of MPs, and the properties of the viruses themselves.

3.2.1 Aquatic environment

Various factors within the aquatic environment can influence the adsorption of viruses on MPs. Water flow rate can directly impact the adhesion of viruses to solid surfaces. Solution pH and ionic strength can affect electrostatic interactions between viruses and MPs. Salinity can affect the ability of bacterial cells to aggregate or form biofilms ( De Tender et al., 2015 ; Oberbeckmann et al., 2018 ). Dissolved organic matter (DOM) can hinder the interaction between non-enveloped viruses (e.g., MS2 phages) and sorbent surfaces ( Armanious et al., 2016 ). Factors such as water temperature and oxygen content can indirectly affect the bacterial colonization on MPs, thereby impacting the adsorption of MPs to viruses ( De Tender et al., 2015 ).

3.2.2 Physical and chemical properties of MPs

The adsorption of viruses by MPs is directly influenced by the physical and chemical properties of the MPs. Different types of MPs exhibit significant variations in their ability to adsorb viruses, including variations in size, functional group type, surface roughness, zeta potential and aging degree, etc. Lu et al. (2022) found that the adsorption rate of E. coli bacteriophage T4 on MPs rose with higher microplastic concentrations but declined with larger MPs sizes. Moreover, MPs functional groups exhibit varying affinities, leading to differences in their adsorption capacities for different viruses. For instance, the presence of a benzene ring in PS enables it to interact with SARS-CoV-2 RNA fragments, forming π–π bonds that potentially modulate the interaction affinity ( Zhang et al., 2022a ). Zeta potential plays a crucial role in the adsorption of particles by affecting the electrostatic adsorption of viruses onto the MPs surfaces ( Savaji et al., 2014 ). The ultraviolet (UV) aging of MPs was found to enhance the adsorption of viruses due to changed surface zeta potential, increased surface roughness ( Dika et al., 2015 ), and increased hydrophilicity ( Wang et al., 2020 ).

3.2.3 Viral characteristics

Both the surface composition (e.g., proteins, lipids, and polysaccharides) and structure (e.g., viral capsid, tail, and envelope) of the virus can influence its affinity and binding capacity to the surface of MPs ( Nobrega et al., 2018 ; Yamada et al., 2020 ). Moresco et al. (2022) conducted a study where the non-enveloped SA11virus and the enveloped Phi6 virus were cultured together with PE. They found that the SA11 remained more stable than the Phi6 due to the lack of capsule structure of SA11 promote its binding to the biofilm colonizing MPs. In contrast, the enveloped Phi6 phages experienced rapid envelope dissolution, leading to virus inactivation. Consequently, viral characteristics can determine different virus–plastisphere interactions, which in turn affect the stability and dissemination of viruses themselves.

4 MPs affect the transport, survival, and virulence of the viruses

Several studies have demonstrated that MPs can facilitate the dissemination of viruses and exacerbate their biological toxicity. Figure 2 show the proposed mechanisms through which MPs affect the transport, survival and virulence of the viruses.

Figure 2 . Schematic of the mechanism of microplastics affecting viral biotoxicity in the aquatic environment.

4.1 Act as vectors to facilitate viral transport

MPs can adsorb viruses through electrostatic interactions and formation of surface biofilms, thereby creating a favorable habitat for viruses and serving as efficient carriers for their migration. The formation of surface biofilms alters the buoyancy and viscosity of MPs in water, promoting the long distance transport of viruses via MPs ( Bhagat et al., 2021 ; Li et al., 2022 ). Besides, the small size of MPs makes them highly prone to ingestion by organisms ( Prata et al., 2020 ). The viruses attached to these MPs can thus easily enter the animal bodies, increasing the infection rate of the virus. This, in turn, can contribute to the emergence of infectious diseases and an escalation in pathogen prevalence ( Seeley et al., 2023 ). For instance, during the COVID-19 pandemic, MPs generated from the decomposed human-used masks may harbor the SARS-CoV-2 virus, prolonging the human exposure to SARS-CoV-2 ( Shukla et al., 2022 ).

4.2 Prolong the survival rate and time of the viruses

Several studies ( Lu et al., 2022 ; Moresco et al., 2022 ) have shown that compared to viruses present in water, viruses harbored in MPs biofilms exhibit longer survival time. Furthermore, these biofilm-associated viruses demonstrate increased stability and a greater capacity to induce biotoxic effects. For instance, more than half of the viruses harbored on the surface of PS MPs remain being detectable even after 10 days, significantly longer than those of free virus particles suspended in water ( Lu et al., 2022 ). Microorganisms attached on MPs may have a higher activity stimulated by dissolved organic carbon leached from plastics ( Romera-Castillo et al., 2018 ). Additionally, microplastic biofilms can offer protection against environmental stressors ( Rummel et al., 2017 ). These “shelters” enable an extended survival time and an increased survival rate of viruses. Furthermore, MPs can form stable complexes with viral genetic fragments, extending the persistence of DNA or RNA fragments within the virus ( Zhang et al., 2022b ). Zhang et al. (2022a) employed molecular dynamics simulation to investigate the interaction between MPs and viral RNA fragments from SARS-CoV-2, SARS-CoV-1, and HBV. They revealed that MPs can effectively bind to SARS-CoV-2 RNA fragments, leading to the prolonged existence of viral RNA in environment. It is important to note that the type of MPs and viruses, as well as environmental factors can influence the mechanism and intensity of these interactions.

4.3 Alter the expression of immune-relevant genes

MPs have been shown to impact immune-related enzyme activity and alter the expression levels of immune-related genes ( Liu et al., 2019 ). This, in turn, compromises the immunity of organisms and leads to increased mortality and infection rates ( Liu et al., 2023 ). Brandts et al. (2021) discovered that MPs have immuno-modulatory effects on juvenile European sea bass ( Dicentrarchus labrax ). Similarly, Limonta et al. (2019) found that after exposure with high-density PE and PS MPs, adult zebrafish showed altered expression of immune-related genes, resulting in a weakened defense ability against pathogens. Liu et al. (2019) also reported a significant decrease in the expression of immune-related genes in blood cells with increasing exposure to MPs. Furthermore, viruses bound to MPs can increase expression of inflammation-related genes and increase viral infectivity ( Zhang et al., 2022b ).

4.4 Damage to biological tissues

MPs ingested by aquatic animals can accumulate in their gastrointestinal tracts, leading to blockages and injuries ( Lusher et al., 2013 ; Bhuyan, 2022 ). These physical damages can also happened in other biological tissues ( Abarghouei et al., 2021 ). Hamed et al. (2021) found exposure to MPs led to histopathological damage in the kidneys, liver, pancreas, and gills of Oreochromis niloticus . Tissue damage can compromise the organism’s immune barrier, heightening susceptibility to viral infections ( Zhang et al., 2018 ). Seeley et al. (2023) demonstrated that simultaneous exposure of fish to viruses and MPs significantly escalates mortality rates compared to exposure to viruses alone. In addition to leading to causing direct physical damage, MPs can also provoke inflammation in biological tissues ( Zhang et al., 2023 ). Various mechanisms have been proposed for this inflammatory response. For instance, once MPs enter into cells, they can induce oxidative stress by generating reactive oxygen species (ROS), consequently triggering inflammation ( Cao, 2023 ). Alternatively, inflammation may be indirectly induced by microbial dysbiosis provoked by MPs ( Jin et al., 2018 ; Wang et al., 2023b ). However, further investigations are needed to more comprehensively elucidate these mechanisms.

4.5 Inactivation of the viruses

Most studies reported that MPs enhanced the virulence and infectivity of viruses in the aquatic environment. However, there are also studies reporting that MPs exposure can lead to virus inactivation under specific conditions. For instance, Gassilloud and Gantzer (2005) observed the inactivation of poliovirus type 1 through surface adhesion to hydrophobic PP containers. Moresco et al. (2022) investigated PE MPs particles bound to viruses and found that enveloped viruses may undergo solubilization by the biofilm on the MP surface. Furthermore, the elevated concentration of copper ions within the MP surface may increase ROS production ( Borkow and Gabbay, 2005 ). These ROS can impact viral stability, degrade the viral genome and alter the morphology of viral particles ( Warnes et al., 2015 ). These studies is important for developing efficient virus inactivation treatments to control transmission of viruses. Further investigation is needed to find efficient inactivation methods and to understand involved mechanisms.

5 Conclusions and prospects

This paper presents a comprehensive overview of the complex interactions between MPs and viruses in the aquatic environment. Electrostatic forces and the hydrophobic effect dominated the interactions. However, these effects are modulated by various factors, including the aquatic environment, the physicochemical properties of the MPs and the characteristics of the viruses. Viruses can adhere to the surface of microplastic particles, potentially altering their transport, fate, and persistence in the environment. Viruses are protected against inactivation factors when bound with the MPs biofilm, and the stability provided by the microplastic environment can potentially enhance the persistence and transmission of viruses in aquatic ecosystems. Once viruses are adsorbed onto MPs, their virulence and transmissibility can be altered through diverse mechanisms. Most of studies reported that MPs tend to enhance the virulence of viruses in the aquatic environment, however, some studies have found MPs can deactivate viruses under some specific conditions, suggesting interaction mechanisms warrants further investigation.

Although researchers have conducted extensive research in this field, there is still a significant gap in our understanding of them. To address these knowledge gaps, it is imperative to prioritize the following issues for further investigation:

1. There is a noticeable dearth of research on the synergistic effects of MPs with viruses. A substantial efforts are needed to unveil how viruses adhere to the surface of microplastic particles, and how these attachments can alter their transport, fate, and persistence in the aquatic environment.

2. The existing research findings primarily concentrate on specific viruses present on plastic objects under laboratory conditions. It is worth noting that the real environmental conditions are more complicated and the interactions between virus and MPs are influenced by various other factors.

3. Biofilms can offer more surfaces for viruses to stick and multiply, but there aren’t many thorough studies in scientific literature about how viruses interact with microplastic biofilm, especially EPS.

4. Many involved mechanisms need to be further elucidated, such as the detail relationships among viruses, water, MPs, and biofilm under different environmental conditions, and how nutrients and energy flow within the microplastic ecosystem? Answering all of these questions requires sophisticated testing methods and the participation of researchers from multiple disciplines.

5. MPs serve as reservoirs for viruses could pose risks to human health if they enter the food chain. Consumption of contaminated seafood or water could potentially expose individuals to viral pathogens associated with MPs. Therefore, the public and policymakers need to be aware of these risks, and develop preventive measures.

Author contributions

XW: Data curation, Investigation, Writing – original draft, Formal analysis, Methodology. KZ: Investigation, Writing – original draft, Methodology. YW: Investigation, Writing – original draft, Methodology. XH: Investigation, Writing – original draft, Methodology. YH: Investigation, Writing – original draft, Methodology. ZW: Resources, Writing – review & editing. JZ: Resources, Writing – review & editing. XC: Resources, Writing – review & editing. XL: Conceptualization, Funding acquisition, Supervision, Writing – review & editing.

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This work was partially supported by the National Natural Science Foundation of China (#42377380 and #41807116) and the Key R&D Projects of Tianjin City (#21YFSNSN00180).

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.

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Yang, M., Zhao, F., Tong, L., Wang, S., and Zhou, D. (2022). Contamination, bioaccumulation mechanism, detection, and control of human norovirus in bivalve shellfish: a review. Crit. Rev. Food Sci. Nutr. 62, 8972–8985. doi: 10.1080/10408398.2021.1937510

Zamhuri, S. A., Soon, C. F., Nordin, A. N., Ab Rahim, R., Sultana, N., Khan, M. A., et al. (2022). A review on the contamination of SARS-CoV-2 in water bodies: transmission route, virus recovery and recent biosensor detection techniques. Sens. Bio-Sens. Res. 36:100482. doi: 10.1016/j.sbsr.2022.100482

Zettler, E. R., Mincer, T. J., and Amaral-Zettler, L. A. (2013). Life in the “plastisphere”: microbial communities on plastic marine debris. Environ. Sci. Technol. 47, 7137–7146. doi: 10.1021/es401288x

Zhang, G., Cao, G., Luo, R.-H., Song, Q., Zeng, Y., Liu, K., et al. (2022a). Microplastics interact with SARS-CoV-2 and facilitate host cell infection. Environ. Sci. Nano 9, 2653–2664. doi: 10.1039/D2EN00019A

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Keywords: microplastics, viruses, adsorption, mechanism, impact

Citation: Wang X, Zheng K, Wang Y, Hou X, He Y, Wang Z, Zhang J, Chen X and Liu X (2024) Microplastics and viruses in the aquatic environment: a mini review. Front. Microbiol . 15:1433724. doi: 10.3389/fmicb.2024.1433724

Received: 16 May 2024; Accepted: 17 June 2024; Published: 03 July 2024.

Reviewed by:

Copyright © 2024 Wang, Zheng, Wang, Hou, He, Wang, Zhang, Chen and Liu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) . The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: Xianhua Liu, [email protected] ; Jiabo Zhang, [email protected]

Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

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Collection  31 March 2021

Top 100 in Microbiology

This collection highlights our most downloaded* microbiology papers published in 2020. Featuring authors from around the world, these papers showcase valuable research from an international community.

*Data obtained from SN Inights which is based on Digital Science's Dimensions.

Effect of restricted dissolved oxygen on expression of Clostridium difficile toxin A subunit from E. coli

• Ashish K. Sharma
• Joseph Shiloach

Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention

• Jessica A. Grembi
• Lan H. Nguyen
• Julie Parsonnet

Azlocillin can be the potential drug candidate against drug-tolerant Borrelia burgdorferi sensu stricto JLB31

• Venkata Raveendra Pothineni
• Hari-Hara S. K. Potula
• Jayakumar Rajadas

Station and train surface microbiomes of Mexico City’s metro (subway/underground)

• Apolinar Misael Hernández
• Daniela Vargas-Robles
• Mariana Peimbert

Alcohol pretreatment of stools effect on culturomics

• Pamela Afouda
• Marie Hocquart
• Didier Raoult

Cannabidiol is an effective helper compound in combination with bacitracin to kill Gram-positive bacteria

• Claes Søndergaard Wassmann
• Peter Højrup
• Janne Kudsk Klitgaard

A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes

• Anders B. Nygaard
• Hege S. Tunsjø
• Colin Charnock

Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study

• Zachary M. Burcham
• Nicole L. Garneau
• Genetics of Taste Lab Citizen Scientists

Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing

• Arne M. Taxt
• Ekaterina Avershina

Surveillance of Enterococcus spp . reveals distinct species and antimicrobial resistance diversity across a One-Health continuum

• Rahat Zaheer
• Shaun R. Cook
• Tim A. McAllister

Intermittent Lactobacilli-containing Vaginal Probiotic or Metronidazole Use to Prevent Bacterial Vaginosis Recurrence: A Pilot Study Incorporating Microscopy and Sequencing

• Janneke H. H. M. van de Wijgert
• Marijn C. Verwijs
• Alistair C. Darby

Implication of the gut microbiome composition of type 2 diabetic patients from northern China

• Chang Yujun

DNA extraction approaches substantially influence the assessment of the human breast milk microbiome

• Chloe A. Douglas
• Kerry L. Ivey
• Geraint B. Rogers

Triterpenoid acids isolated from Schinus terebinthifolia fruits reduce Staphylococcus aureus virulence and abate dermonecrosis

• Huaqiao Tang
• Gina Porras
• Cassandra L. Quave

Resistance to change: AMR gene dynamics on a commercial pig farm with high antimicrobial usage

• Jolinda Pollock
• Adrian Muwonge
• Alexander Corbishley

Proton pump inhibitors act synergistically with fluconazole against resistant Candida albicans

• Mengjiao Lu
• Haiying Yan
• Shujuan Sun

Diversity, compositional and functional differences between gut microbiota of children and adults

• Djawad Radjabzadeh
• Cindy G. Boer
• Robert Kraaij

Genome mining of biosynthetic and chemotherapeutic gene clusters in Streptomyces bacteria

• Kaitlyn C. Belknap
• Cooper J. Park
• Cheryl P. Andam

PARGT: a software tool for predicting antimicrobial resistance in bacteria

• Abu Sayed Chowdhury
• Douglas R. Call
• Shira L. Broschat

Gut, oral and skin microbiome of Indian patrilineal families reveal perceptible association with age

• Diptaraj S. Chaudhari
• Dhiraj P. Dhotre
• Yogesh S. Shouche

Beneficial bile acid metabolism from Lactobacillus plantarum of food origin

• Roberta Prete
• Sarah Louise Long
• Susan A. Joyce

Changes in microbiome and metabolomic profiles of fecal samples stored with stabilizing solution at room temperature: a pilot study

• Mi Young Lim
• Seungpyo Hong
• Young-Do Nam

Scanning electron microscopy and machine learning reveal heterogeneity in capsular morphotypes of the human pathogen Cryptococcus spp.

• William Lopes
• Giuliano N. F. Cruz
• Augusto Schrank

Nitrate as a potential prebiotic for the oral microbiome

• B. T. Rosier

Insect pollination: an ecological process involved in the assembly of the seed microbiota

• Alberto Prado
• Brice Marolleau
• Gloria Torres-Cortes

Setting a baseline for global urban virome surveillance in sewage

• David F. Nieuwenhuijse
• Bas B. Oude Munnink
• Marion P. G. Koopmans

Microbial lag phase can be indicative of, or independent from, cellular stress

• Philip G. Hamill
• Andrew Stevenson
• John E. Hallsworth

Plantaricin NC8 αβ exerts potent antimicrobial activity against Staphylococcus spp. and enhances the effects of antibiotics

• Torbjörn Bengtsson
• Robert Selegård
• Hazem Khalaf

A novel vibriophage exhibits inhibitory activity against host protein synthesis machinery

• Khrongkhwan Thammatinna
• MacKennon E. Egan
• Vorrapon Chaikeeratisak

Isolation and characterization of nutrient dependent pyocyanin from Pseudomonas aeruginosa and its dye and agrochemical properties

• Savitha DeBritto
• Tanzeembanu D. Gajbar
• Shin-ichi Ito

The association of Chlamydia trachomatis and Mycoplasma genitalium infection with the vaginal metabolome

• Joanna-Lynn C. Borgogna
• Michelle D. Shardell
• Susan Tuddenham

Antibacterial effects of low-temperature plasma generated by atmospheric-pressure plasma jet are mediated by reactive oxygen species

• McKayla J. Nicol
• Timothy R. Brubaker
• Girish S. Kirimanjeswara

Exploiting phage receptor binding proteins to enable endolysins to kill Gram-negative bacteria

• Athina Zampara
• Martine C. Holst Sørensen
• Lone Brøndsted

Optimizing bacteriophage engineering through an accelerated evolution platform

• Andrew H. Favor
• Carlos D. Llanos
• Jorge A. Bardales

Microbial community profiling of ammonia and nitrite oxidizing bacterial enrichments from brackishwater ecosystems for mitigating nitrogen species

• Viswanathan Baskaran
• Prasanna K. Patil
• Kizhakedath K. Vijayan

Study on antibiotic susceptibility of Salmonella typhimurium L forms to the third and forth generation cephalosporins

• Cuiping Yang
• Dengyu Chen

Lavender essential oil induces oxidative stress which modifies the bacterial membrane permeability of carbapenemase producing Klebsiella pneumoniae

• Shun-Kai Yang
• Khatijah Yusoff
• Kok-Song Lai

Characterization of a bacteriophage, vB_Eco4M-7, that effectively infects many Escherichia coli O157 strains

• Agnieszka Necel
• Sylwia Bloch
• Alicja Węgrzyn

Antimicrobial biosynthetic potential and diversity of culturable soil actinobacteria from forest ecosystems of Northeast India

• Priyanka Sharma
• Debajit Thakur

A novel silkworm infection model with fluorescence imaging using transgenic Trichosporon asahii expressing eGFP

• Yasuhiko Matsumoto
• Hideki Yamazaki
• Takashi Sugita

Bifidobacterium adolescentis as a key member of the human gut microbiota in the production of GABA

• Sabrina Duranti
• Lorena Ruiz
• Francesca Turroni

Manuka honey microneedles for enhanced wound healing and the prevention and/or treatment of Methicillin-resistant Staphylococcus aureus (MRSA) surgical site infection

• Galit H. Frydman
• David Olaleye
• James G. Fox

Colorectal cancer-associated anaerobic bacteria proliferate in tumor spheroids and alter the microenvironment

• Stephen H. Kasper
• Carolina Morell-Perez
• Erik C. Hett

Pathogenomics and Evolutionary Epidemiology of Multi-Drug Resistant Clinical Klebsiella pneumoniae Isolated from Pretoria, South Africa

• Nontombi Marylucy Mbelle
• Charles Feldman
• Sabiha Yusuf Essack

Increasing relevance of Gram-positive cocci in urinary tract infections: a 10-year analysis of their prevalence and resistance trends

• Márió Gajdács
• Marianna Ábrók
• Katalin Burián

The antibiotic vancomycin induces complexation and aggregation of gastrointestinal and submaxillary mucins

• Stephen E. Harding

A continuous evolution system for contracting the host range of bacteriophage T7

• Tzvi Holtzman

Characterizing the microbiomes of Antarctic sponges: a functional metagenomic approach

• Mario Moreno-Pino
• Antonia Cristi
• Nicole Trefault

Molecular characterization of Extended-spectrum β lactamase- producing E. coli recovered from community-acquired urinary tract infections in Upper Egypt

• Noha A. Hassuna
• Ahmed S. Khairalla
• Medhat Abdel-Fattah

Soil bacterial diversity correlates with precipitation and soil pH in long-term maize cropping systems

• Junman Wang
• Weimin Chen

Metagenomic views of microbial dynamics influenced by hydrocarbon seepage in sediments of the Gulf of Mexico

• Zarath M. Summers
• Jennifer F. Biddle

Akkermansia muciniphila uses human milk oligosaccharides to thrive in the early life conditions in vitro

• Ioannis Kostopoulos
• Janneke Elzinga
• Clara Belzer

Rapid antibiotic susceptibility testing of bacteria from patients’ blood via assaying bacterial metabolic response with surface-enhanced Raman spectroscopy

• Yi-Chun Lin
• Yuh-Lin Wang

Plant growth-promoting activity and quorum quenching-mediated biocontrol of bacterial phytopathogens by Pseudomonas segetis strain P6

• Miguel Rodríguez
• Marta Torres
• Inmaculada Llamas

Rapid colorimetric loop-mediated isothermal amplification for hypersensitive point-of-care Staphylococcus aureus enterotoxin A gene detection in milk and pork products

• Grittaya Srimongkol
• Boonsong Ditmangklo
• Naraporn Somboonna

DNA extraction of microbial DNA directly from infected tissue: an optimized protocol for use in nanopore sequencing

• Karin Helmersen
• Hege Vangstein Aamot

Bacterial associated urinary tract infection, risk factors, and drug susceptibility profile among adult people living with HIV at Haswassa University Comprehensive Specialized Hospital, Hawassa, Southern Esthiopia

• Netsanet Nigusse Tessema
• Musa Mohammed Ali
• Mengistu Hyilemeriam Zenebe

Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals

• Stefania Vaga
• Saeed Shoaie

Improved efficacy of antifungal drugs in combination with monoterpene phenols against Candida auris

• Siham Shaban
• Mrudula Patel
• Aijaz Ahmad

Wheat dwarfing influences selection of the rhizosphere microbiome

• Vanessa N. Kavamura
• Rebekah J. Robinson
• Tim H. Mauchline

Longitudinal Study of Oral Microbiome Variation in Twins

• Marcelo Freire
• Ahmed Moustafa
• Karen E. Nelson

The wasted chewing gum bacteriome

• Leila Satari
• Alba Guillén
• Manuel Porcar

Inulin with different degrees of polymerization protects against diet-induced endotoxemia and inflammation in association with gut microbiota regulation in mice

• Yu-Ting Wang

Effects of enrofloxacin treatment on the bacterial microbiota of milk from goats with persistent mastitis

• Richard Costa Polveiro
• Pedro Marcus Pereira Vidigal
• Maria Aparecida Scatamburlo Moreira

Shotgun sequencing of honey DNA can describe honey bee derived environmental signatures and the honey bee hologenome complexity

• Samuele Bovo
• Valerio Joe Utzeri
• Luca Fontanesi

Genome-wide screens reveal Escherichia coli genes required for growth of T1-like phage LL5 and V5-like phage LL12

• Denish Piya
• Lauren Lessor
• Jason J. Gill

Evolution of Mycobacterium tuberculosis complex lineages and their role in an emerging threat of multidrug resistant tuberculosis in Bamako, Mali

• Madikay Senghore
• Bassirou Diarra
• Martin Antonio

Tendentious effects of automated and manual metagenomic DNA purification protocols on broiler gut microbiome taxonomic profiling

• Gabor Fidler
• Emese Tolnai
• Melinda Paholcsek

Reduced microbial diversity induces larger volatile organic compound emissions from soils

• Letizia Abis
• Benjamin Loubet
• Sophie Sadet-Bourgeteau

Evaluation of PCR conditions for characterizing bacterial communities with full-length 16S rRNA genes using a portable nanopore sequencer

• So Fujiyoshi
• Ai Muto-Fujita
• Fumito Maruyama

Effects of two probiotic spores of Bacillus species on hematological, biochemical, and inflammatory parameters in Salmonella Typhimurium infected rats

• Somaye Mazkour
• Seyed Shahram Shekarforoush
• Masoumeh Honarmand

Essential oils against bacterial isolates from cystic fibrosis patients by means of antimicrobial and unsupervised machine learning approaches

• Rosanna Papa
• Marco Artini

Contamination of wounds with fecal bacteria in immuno-suppressed mice

• Lisa Karner
• Susanne Drechsler
• Peter Dungel

Fluconazole resistance in Candida albicans is induced by Pseudomonas aeruginosa quorum sensing

• H. M. H. N. Bandara
• D. L. A. Wood
• L. P. Samaranayake

The Antioxidants Glutathione, Ascorbic Acid and Uric Acid Maintain Butyrate Production by Human Gut Clostridia in The Presence of Oxygen In Vitro

• Matthieu Million
• Nicholas Armstrong

Apoptosis of vaginal epithelial cells in clinical samples from women with diagnosed bacterial vaginosis

• Elena Roselletti
• Samuele Sabbatini
• Claudia Monari

Microbial modulation of host body composition and plasma metabolic profile

• M. Nazmul Huda
• Jason H. Winnike
• Brian J. Bennett

Unravelling the antimicrobial action of antidepressants on gut commensal microbes

• Yasmina Ait Chait
• Walid Mottawea
• Riadh Hammami

An intra-bacterial activity for a T3SS effector

• Samir El Qaidi
• Nichollas E. Scott
• Philip R. Hardwidge

Trichoderma virens Gl006 and Bacillus velezensis Bs006: a compatible interaction controlling Fusarium wilt of cape gooseberry

• L. F. Izquierdo-García
• A. González-Almario
• C. A. Moreno-Velandia

Droplet-based digital antibiotic susceptibility screen reveals single-cell clonal heteroresistance in an isogenic bacterial population

• Ott Scheler
• Karol Makuch
• Piotr Garstecki

Actinobacteria from Antarctica as a source for anticancer discovery

• Leonardo Jose Silva
• Eduardo José Crevelin
• Itamar Soares Melo

In vitro dual (anticancer and antiviral) activity of the carotenoids produced by haloalkaliphilic archaeon Natrialba sp. M6

• Ghada E. Hegazy
• Marwa M. Abu-Serie
• Yasser R. Abdel-Fattah

Exploring yeast interactions through metabolic profiling

• C. Roullier-Gall
• H. Alexandre

Evaluation of plant growth promotion properties and induction of antioxidative defense mechanism by tea rhizobacteria of Darjeeling, India

• Chandrima Bhattacharyya
• Srimoyee Banerjee
• Abhrajyoti Ghosh

High resolution metagenomic characterization of complex infectomes in paediatric acute respiratory infection

Genotype–phenotype correlation of β-lactamase-producing uropathogenic Escherichia coli (UPEC) strains from Bangladesh

• Maqsud Hossain
• Tahmina Tabassum
• Rita R. Colwell

Safety and functional enrichment of gut microbiome in healthy subjects consuming a multi-strain fermented milk product: a randomised controlled trial

• Anne-Sophie Alvarez
• Muriel Derrien

Isolation, Characterization and Genomic Analysis of a Novel Bacteriophage VB_EcoS-Golestan Infecting Multidrug-Resistant Escherichia coli Isolated from Urinary Tract Infection

• Mahsa Yazdi
• Majid Bouzari
• Khashayar Shahin

Antibiotic resistance in bacterial isolates from freshwater samples in Fildes Peninsula, King George Island, Antarctica

• Daniela Jara
• Helia Bello-Toledo
• Gerardo González-Rocha

Protective action of Bacillus clausii probiotic strains in an in vitro model of Rotavirus infection

• Lorella Paparo
• Lorella Tripodi
• Roberto Berni Canani

Pseudomonas aeruginosa core metabolism exerts a widespread growth-independent control on virulence

• Stavria Panayidou
• Kaliopi Georgiades
• Yiorgos Apidianakis

Metagenomic analysis of an urban resistome before and after wastewater treatment

• Felipe Lira
• Ivone Vaz-Moreira
• José Luis Martínez

Structural and functional differentiation of bacterial communities in post-coal mining reclamation soils of South Africa: bioindicators of soil ecosystem restoration

• Obinna T. Ezeokoli
• Cornelius C. Bezuidenhout
• Rasheed A. Adeleke

Site-specific molecular analysis of the bacteriota on worn spectacles

• Birgit Fritz
• Melanie März
• Markus Egert

Evaluation of antibiotic resistance dissemination by wastewater treatment plant effluents with different catchment areas in Germany

• Johannes Alexander
• Norman Hembach
• Thomas Schwartz

A Cyclic-di-GMP signalling network regulates biofilm formation and surface associated motility of Acinetobacter baumannii 17978

• Irfan Ahmad
• Evelina Nygren
• Bernt Eric Uhlin

Structure and membership of gut microbial communities in multiple fish cryptic species under potential migratory effects

Genomic Epidemiology of Vancomycin-Resistant Enterococcus faecium (VR Efm ) in Latin America: Revisiting The Global VRE Population Structure

• Rafael Rios
• Jinnethe Reyes
• Lorena Diaz

Identification of a newly isolated lytic bacteriophage against K24 capsular type, carbapenem resistant Klebsiella pneumoniae isolates

• Marianna Horváth
• Tamás Kovács
• György Schneider

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