recent research topics in microbiology 2020

• Search by keyword
• Search by citation

Page 1 of 113

Structural and functional bacterial biodiversity in a copper, zinc and nickel amended bioreactor:  shotgun metagenomic study

At lower concentrations copper (Cu), zinc (Zn) and nickel (Ni) are trace metals essential for some bacterial enzymes. At higher concentrations they might alter and inhibit microbial functioning in a bioreactor...

• View Full Text

Downregulation of Klebsiella pneumoniae RND efflux pump genes following indole signal produced by Escherichia coli

More than a century has passed since it was discovered that many bacteria produce indole, but research into the actual biological roles of this molecule is just now beginning. The influence of indole on bacter...

Alterations in the gut microbiota community are associated with childhood obesity and precocious puberty

To explore the distribution and differences in the intestinal microbiota in girls with obesity-related precocious puberty and the relationship between intestinal microbiota and obesity-related precocious puberty.

In vitro characterization of probiotic potential of Lactobacillus plantarum CM49 against selected cattle mastitogens

Bovine mastitis results in significant economic losses for the dairy industry globally due to milk production losses and decreased herd efficiency. This research aimed to isolate, select, and characterize indi...

Retrospective analysis of molecular characteristics, risk factors, and outcomes in carbapenem-resistant Klebsiella pneumoniae bloodstream infections

Klebsiella pneumoniae (KP) is the second most prevalent Gram-negative bacterium causing bloodstream infections (BSIs). In recent years, the management of BSIs caused by KP has become increasingly complex due to t...

Solid waste dumpsite leachate and contiguous surface water contain multidrug-resistant ESBL-producing Escherichia coli carrying Extended Spectrum β-Lactamase (ESBL) genes

Dumpsites generate leachates containing bacteria that may carry antibiotic resistance genes, such as extended spectrum β-lactamase (ESBL). However, the contribution of dumpsite leachates in the environmental s...

Vaginal colonization with virulent and methicillin resistant Staphylococcus aureus among Ugandan women in Labour

Staphylococcus aureus ( S. aureus ) often colonizes the human skin, upper respiratory and genital tracts. In the female genital tract, it can be passed on to the newborn during vaginal delivery leading to either or...

Diametral influence of deoxynivalenol (DON) and deepoxy-deoxynivalenol (DOM-1) on the growth of Campylobacter jejuni with consequences on the bacterial transcriptome

Deoxynivalenol (DON) is a type B trichothecene mycotoxin that is commonly found in cereals and grains worldwide. The presence of this fungal secondary-metabolite raises public-health concerns at both the agric...

Linking watershed formation with the phylogenetic distribution of a soil microscopic fungus in Yunnan Province, China

Phylogeographic studies have gained prominence in linking past geological events to the distribution patterns of biodiversity, primarily in mountainous regions. However, such studies often focus on plant taxa,...

Role of ectomycorrhizal colonization in enhancement of nutrients for survival of plants collected from mountainous cold stress areas

Ectomycorrhizal (ECM and ECM-like) structures associated with plant root systems are a challenge for scientists. The dispersion pattern of roots within the soil profile and the nutritional conditions are both ...

Antibiotic-resistant bacteria contaminating leafy vegetables in Saudi Arabia’s eastern region

Food-associated antibiotic-resistant bacteria can cause infections that may critically impact human health. The objectives of this study were to determine the microbial contamination level of green leafy veget...

Effective microorganism combinations improve the quality of compost-bedded pack products in heifer barns: exploring pack bacteria-fungi interaction mechanisms

Compost-bedded pack barns (CBP) are getting huge attention as an alternative housing system for dairy cows due to their beneficial impact on animal welfare. Effective microorganisms (EM) inoculums are believed...

Dynamic changes in and correlations between microbial communities and physicochemical properties during the composting of cattle manure with Penicillium oxalicum

Penicillium oxalicum is an important fungal agent in the composting of cattle manure, but the changes that occur in the microbial community, physicochemical factors, and potential functions of microorganisms at d...

Variations of soil metal content, soil enzyme activity and soil bacterial community in Rhododendron delavayi natural shrub forest at different elevations

Rhododendron delavayi is a natural shrub that is distributed at different elevations in the karst region of Bijie, China, and that has an important role in preventing land degradation in this region. In this stud...

The Velvet transcription factor PnVeA regulates necrotrophic effectors and secondary metabolism in the wheat pathogen Parastagonospora nodorum

The fungus Parastagonospora nodorum causes septoria nodorum blotch on wheat. The role of the fungal Velvet-family transcription factor VeA in P. nodorum development and virulence was investigated here. Deletion o...

Integrating multi-wet laboratory diagnostics to study staphylococci in animals in Uganda

Several diagnostic environments in Uganda lack real-time, robust and high-throughput technologies for comprehensive typing of microbes, which is a setback to infectious disease surveillance. This study combine...

Multi-omics analysis reveals genes and metabolites involved in Streptococcus suis biofilm formation

Streptococcus suis is an important zoonotic pathogen. Biofilm formation largely explains the difficulty in preventing and controlling S. suis . However, little is known about the molecular mechanism of S. suis bio...

Microbial life in preferential flow paths in subsurface clayey till revealed by metataxonomy and metagenomics

Subsurface microorganisms contribute to important ecosystem services, yet little is known about how the composition of these communities is affected by small scale heterogeneity such as in preferential flow pa...

Potential antivirulence and antibiofilm activities of sub-MIC of oxacillin against MDR S. aureus isolates: an in-vitro and in-vivo study

Multi-drug resistant Staphylococcus aureus is one of the most common causes of nosocomial and community-acquired infections, with high morbidity and mortality. Treatment of such infections is particularly problem...

Rhizosphere microbial community construction during the latitudinal spread of the invader Chromolaena odorata

The colonization of alien plants in new habitats is typically facilitated by microorganisms present in the soil environment. However, the diversity and structure of the archaeal, bacterial, and fungal communit...

Distribution and functional perspective analysis of epiphytic and endophytic bacterial communities associated with marine seaweeds, Alexandria shores, Egypt

There is an enormous diversity of life forms present in the extremely intricate marine environment. The growth and development of seaweeds in this particular environment are controlled by the bacteria that set...

Large-scale genetic correlation studies explore the causal relationship and potential mechanism between gut microbiota and COVID-19-associated risks

Recent observational studies suggest that gut microorganisms are involved in the onset and development of coronavirus disease 2019 (COVID-19), but the potential causal relationship behind them remains unclear....

Fungal endophytes of Taxus species and regulatory effect of two strains on taxol synthesis

Taxol, derived from Taxus trees, is a valuable natural resource for the development of anticancer drugs. Endophytic fungi from Taxus trees are a promising alternative source of Taxol. However, the impact of plant...

Low-dose zinc oxide nanoparticles trigger the growth and biofilm formation of Pseudomonas aeruginosa : a hormetic response

Hormesis describes an inverse dose-response relationship, whereby a high dose of a toxic compound is inhibitory, and a low dose is stimulatory. This study explores the hormetic response of low concentrations o...

The role of gut microbiota in chronic restraint stress-induced cognitive deficits in mice

Chronic stress induces cognitive deficits. There is a well-established connection between the enteric and central nervous systems through the microbiota-gut-brain (MGB) axis. However, the effects of the gut mi...

Microbial and transcriptional response of Acropora valida and Turbinaria peltata to Vibrio coralliilyticus challenge: insights into corals disease resistance

Coral diseases are significant drivers of global coral reef degradation, with pathogens dominated by Vibrio coralliilyticus playing a prominent role in the development of coral diseases. Coral phenotype, symbioti...

Effects of berberine hydrochloride on antioxidant response and gut microflora in the Charybdis japonica infected with Aeromonas hydrophila

This study used berberine hydrochloride to treat the Asian paddle crab, Charybdis japonica infected with the Gram-negative bacterium Aeromonas hydrophila at concentrations of 0, 100, 200 and 300 mg/L. The effect ...

Strain-dependent induction of primary bile acid 7-dehydroxylation by cholic acid

Bile acids (BAs) are steroid-derived molecules with important roles in digestion, the maintenance of host metabolism, and immunomodulation. Primary BAs are synthesized by the host, while secondary BAs are prod...

Microbial carbohydrate active enzyme (CAZyme) genes and diversity from Menagesha Suba natural forest soils of Ethiopia as revealed by shotgun metagenomic sequencing

The global over-reliance on non-renewable fossil fuels has led to the emission of greenhouse gases, creating a critical global environmental challenge. There is an urgent need for alternative solutions like bi...

Identification and antimicrobial susceptibility profiles of Staphylococcus species isolated from raw cow milk, and swabs in smallholder dairy farms in Meta district, Eastern Ethiopia

The safety of milk production in terms of foodborne infections is a worldwide issue, particularly in developing countries where production is often unhygienic. A cross-sectional study was conducted from Decemb...

Effects of antibiotic cocktail on the fecal microbiota and their potential correlation of local immune response

The guts of mammals are home to trillions of microbes, forming a complex and dynamic ecosystem. Gut microbiota is an important biological barrier for maintaining immune homeostasis. Recently, the use of antibi...

Unearthing Lactococcus lactis and Scheffersomyeces symbionts from edible wood-boring beetle larvae as a bio-resource for industrial applications

Gut microbiota have several advantages in influencing the host nutrition, metabolism, immunity and growth. However, the understanding of the gut microbiota in key edible wood-boring beetle larvae remain largel...

Vaginal microbiome differences between patients with adenomyosis with different menstrual cycles and healthy controls

Adenomyosis is a commonly observed benign gynecological disease that affects the quality of life and social psychology of women of childbearing age. However, because of the unknown etiology and incidence of ad...

Investigation of cross-opsonic effect leads to the discovery of PPIase-domain containing protein vaccine candidate to prevent infections by Gram-positive ESKAPE pathogens

Enterococcus faecium and Staphylococcus aureus are the Gram-positive pathogens of the ESKAPE group, known to represent a great threat to human health due to their high virulence and multiple resistances to antibi...

The transcriptional regulator Fur modulates the expression of uge , a gene essential for the core lipopolysaccharide biosynthesis in Klebsiella pneumoniae

Klebsiella pneumoniae is a Gram-negative pathogen that has become a threat to public health worldwide due to the emergence of hypervirulent and multidrug-resistant strains. Cell-surface components, such as polysa...

Emergence of heteroresistance to carbapenems in Gram-negative clinical isolates from two Egyptian hospitals

Antimicrobial resistance is a global concern, linking bacterial genotype and phenotype. However, variability in antibiotic susceptibility within bacterial populations can lead to misclassification. Heteroresis...

Silver nanoparticle with potential antimicrobial and antibiofilm efficiency against multiple drug resistant, extensive drug resistant Pseudomonas aeruginosa clinical isolates

The study aims to investigate the effect of combining silver nanoparticles (AGNPs) with different antibiotics on multi-drug resistant (MDR) and extensively drug resistant (XDR) isolates of Pseudomonas aeruginosa ...

Potentially pathogenic culturable bacteria in hemodialysis waters

Hemodialysis patients are at risk of acquiring healthcare-related infections due to using non-sterile water to prepare hemodialysis fluid. Therefore, microbiological control and monitoring of used water are of...

Low salinity stress increases the risk of Vibrio parahaemolyticus infection and gut microbiota dysbiosis in Pacific white shrimp

Extreme precipitation events often cause sudden drops in salinity, leading to disease outbreaks in shrimp aquaculture. Evidence suggests that environmental stress increases animal host susceptibility to pathog...

Sustained gut dysbiosis and intestinal inflammation show correlation with weight gain in person with chronic HIV infection on antiretroviral therapy

Person with human immunodeficiency virus type-1 (PWH) are prone to chronic inflammation due to residual viral production, even with antiretroviral therapy (ART), which increases the risk of age-related disease...

Antibiotic feeding changes the bacterial community of Chilo suppressalis and thereby affects its pesticide tolerance

Owing to the widespread use of chemical pesticides to control agricultural pests, pesticide tolerance has become a serious problem. In recent years, it has been found that symbiotic bacteria are related to pes...

Gut microbiota in preterm infants with late-onset sepsis and pneumonia: a pilot case-control study

Late-onset sepsis (LOS) and pneumonia are common infectious diseases, with high morbidity and mortality in neonates. This study aimed to investigate the differences in the gut microbiota among preterm infants ...

Optimization of fermentation parameters to improve the biosynthesis of selenium nanoparticles by Bacillus licheniformis F1 and its comprehensive application

Selenium nanoparticles (SeNPs) are increasingly gaining attention due to its characteristics of low toxicity, high activity, and stability. Additionally, Bacillus licheniformis , as a probiotic, has achieved remar...

Cutibacterium acnes biofilm formation is influenced by bone microenvironment, implant surfaces and bacterial internalization

The bacterial persistence, responsible for therapeutic failures, can arise from the biofilm formation, which possesses a high tolerance to antibiotics. This threat often occurs when a bone and joint infection ...

Chitinase-functionalized UiO-66 framework nanoparticles active against multidrug-resistant Candida Auris

Candida auris ( C. auris ) is a yeast that has caused several outbreaks in the last decade. Cell wall chitin plays a primary role in the antifungal resistance of C. auris . Herein, we investigated the potential of c...

Adolescent gut microbiome imbalance and its association with immune response in inflammatory bowel diseases and obesity

Recently, there has been an increase in the number of studies focusing on the association between the gut microbiome and obesity or inflammatory diseases, especially in adults. However, there is a lack of stud...

A single viral amino acid shapes the root system architecture of a plant host upon virus infection

Grapevine fanleaf virus (GFLV) is one of the most detrimental viral pathogens of grapevines worldwide but no information is available on its effect on the root system architecture (RSA) of plant hosts. We used...

Legionella pneumophila cell surface RtxA release by LapD/LapG and its role in virulence

Legionella pneumophila is a Gram-negative intracellular bacillus and is the causative agent of a severe form of pneumonia called Legionnaires’ disease which accounts for 2-9% of cases of community acquired pneumo...

Investigation of gyrA and parC mutations and the prevalence of plasmid-mediated quinolone resistance genes in Klebsiella pneumoniae clinical isolates

The emergence of fluoroquinolone resistance in clinical isolates of Klebsiella pneumoniae is a growing concern. To investigate the mechanisms behind this resistance, we studied a total of 215 K. pneumoniae isolat...

Coagulase-negative staphylococci from bovine milk: Antibiogram profiles and virulent gene detection

Coagulase-negative Staphylococcus species are an emerging cause of intramammary infection, posing a significant economic and public health threat. The aim of this study was to assess the occurrence of coagulase-n...

Important information

Editorial board

For authors

For editorial board members

For reviewers

• Manuscript editing services

Annual Journal Metrics

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

• More about our metrics
• Follow us on Twitter

BMC Microbiology

ISSN: 1471-2180

• General enquiries: [email protected]

You are using an outdated browser. Please upgrade your browser or activate Google Chrome Frame to improve your experience.

Our most downloaded articles from 2020

Posted on December 4, 2020   by Laura Cox

In this blog, we will look back at the some of the most popular research published in the Microbiology Society’s journals this year.

In our flagship journal Microbiology, popular articles included an interesting pedagogic project and a review of the 2019 advances in actinomycete research. Jeffery Errington and Lizah T van der Aart reflect on the history and applications of the bacterium Bacillus subtilis . An undergraduate biology class published a research article exploring the gut microbiome and its role in health. The class of 94 students examined the reciprocal relationships between the host and microbiome . ActinoBase is a community resource developed by actinomycete researchers to share knowledge, research findings and techniques. In June, a research group reviewed the most discussed topics on ActinoBase in 2019 and discussed the value of this resource.

As expected, much of the most popular research published in the Journal of General Virology this year focused on SARS-CoV-2. The most downloaded article in any of the Microbiology Society’s journals this year was a review into the human immune response to coronaviruses by Professor Wendy Barclay and Professor Paul Kellam. Another article on SARS-CoV-2, published in June, discussed how the virus behaved when cultured in Vero E6 cells – an important cell culture model used to study viruses. Researchers also reported their finding that curcumin, a compound found in the spice turmeric, has antiviral properties .

Microbial Genomics included articles on a variety of topics ranging from new software to predicting antimicrobial resistance.  An international collaboration explored using bioinformatics to predict whether bacterial isolates are resistant to antibiotics . Researchers in the UK developed a software named Coinfinder . This computer programme allows researchers to identify gene patterns to understand which genes associate with or avoid one another. A popular review article discussed the different ways whole genome sequencing is used to study microbial diversity and evolution. The authors compare different approaches and applications of metagenomics and the current challenges in the field.

Our newest journal, Access Microbiology , has continued to be a great success in 2020. A popular case report in the journal reported a case of sepsis caused by probiotics ; a scenario which the authors described as good bacteria behaving badly. In February, an article comparing the methods used to identify the deadly bacterium Klebsiella pneumoniae in Sudan was published. The article assessed the accuracy of conventional, biochemical and genotypic tests, and what this could mean for disease reporting in the country. Meanwhile, another article also involved the comparison of different scientific methods to avoid the use of a cancer-causing chemical. Researchers from the University of Hertfordshire assessed a new, safer technique to stain arbuscular mycorrhizal fungi, which are common symbionts of crop plants.

Like JGV, the Journal of Medical Microbiology had a lot of popular articles discussing SARS-CoV-2 this year. Dr Tim Inglis’ editorial Logic in the time of coronavirus – which launched the popular Coronastream blog series – provided an overview of how scientists can help navigate a way out of the pandemic. In May, a research group based at Florida International University used computer modelling to identify target sites for antiviral drugs against SARS-CoV-2 . They then compared the shape and structure of these target sites with current medicines, to see whether any known drugs might be effective in treating COVID-19. Another article in the journal discussed a 20-minute test for COVID-19 diagnosis . The findings showed the rapid molecular test called N1-STOP-LAMP, was able to diagnose samples containing SARS-CoV-2 at high loads.

The International Journal of Systematic and Evolutionary Microbiology (IJSEM) published a list of prokaryotic Candidatus taxa , which are the bacteria which have been characterised but not yet cultured; a resource that proved extremely popular amongst the taxonomy community. In another article in IJSEM, researchers re-classified many probiotic bacteria from the genus formerly known as Lactobacillus into 23 new genera. And, in February, Sudip Patel and Radhey Gupta published an article discussing the evolutionary development of the bacterial genus Bacillus . Their investigation into Bacillus’ history led to them proposing six new genera of bacteria.

Thank you to everyone that has contributed to our journals in 2020, whether by submitting their research, being on an Editorial Board or peer reviewing articles.

Remember, all journals income is invested back into the society be it through funding grants, scientific meetings or helping to fund our policy activities. learn more about our journals or submit a paper on  the website . , categories:.

Publishing and Journals Microbiology News

Share this page:

• Search Menu
• Sign in through your institution
• FEMS Microbiology Ecology
• FEMS Microbiology Letters
• FEMS Microbiology Reviews
• FEMS Yeast Research
• Pathogens and Disease
• FEMS Microbes
• Awards & Prizes
• Editor's Choice Articles
• Thematic Issues
• Virtual Special Issues
• Call for Papers
• Journal Policies
• Open Access Options
• Submit to the FEMS Journals
• Why Publish with the FEMS Journals
• About the Federation of European Microbiological Societies
• About the FEMS Journals
• Advertising and Corporate Services
• Conference Reports
• Editorial Boards
• Investing in Science
• Journals Career Network
• Journals on Oxford Academic
• Books on Oxford Academic

Six Key Topics in Microbiology: 2024

This collection from the FEMS journals presents the latest high-quality research in six key topic areas of microbiology that have an impact across the world. All of the FEMS journals aim to serve the microbiology community with timely and authoritative research and reviews, and by investing back into the science community . 

Interested in publishing your research relevant to the six key microbiology topics?

Learn more about why the FEMS journals are the perfect home for your microbiology research.  

Browse the collection categories: 

Antimicrobial resistance, environmental microbiology, pathogenicity and virulence, biotechnology and synthetic biology, microbiomes, food microbiology.

FEMS and Open Access: Embracing an Open Future

As of January 2024, FEMS has flipped four of its journals to fully open access (OA), making six out of its seven journals OA. FEMS Microbiology Letters remains a subscription journal and free to publish in. 

We are excited to be making high quality science freely available to anyone to read anywhere in the world and further supporting the advancement of our discipline. 

View our FAQs page

Never miss the latest research from the FEMS Journals

Stay up to date on the latest microbiology research with content alerts delivered directly to your inbox. This free service  from OUP allows you to create custom email alerts to make sure you never miss our on the latest research from your favorite FEMS journals. 

Learn more & sign up

Affiliations

• Copyright © 2024
• About Oxford Academic
• Publish journals with us
• University press partners
• What we publish
• New features  
• Open access
• Institutional account management
• Rights and permissions
• Get help with access
• Accessibility
• Advertising
• Media enquiries
• Oxford University Press
• Oxford Languages
• University of Oxford

Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide

• Copyright © 2024 Oxford University Press
• Cookie settings
• Cookie policy
• Privacy policy
• Legal notice

This Feature Is Available To Subscribers Only

Sign In or Create an Account

This PDF is available to Subscribers Only

For full access to this pdf, sign in to an existing account, or purchase an annual subscription.

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

• View all journals
• Explore content
• About the journal
• Publish with us
• Sign up for alerts

Collection  10 March 2022

Top 100 in Microbiology

This collection highlights our most downloaded* microbiology papers published in 2021. 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.

The in-vitro effect of famotidine on SARS-CoV-2 proteases and virus replication

• Madeline Loffredo
• Hector Lucero
• Ali H. Munawar

In vitro efficacy of artemisinin-based treatments against SARS-CoV-2

• Yuyong Zhou
• Kerry Gilmore
• Peter H. Seeberger

Identification of CRF89_BF, a new member of an HIV-1 circulating BF intersubtype recombinant form family widely spread in South America

• Elena Delgado
• Aurora Fernández-García
• Michael M. Thomson

The effectiveness of various gargle formulations and salt water against SARS-CoV-2

• Vunjia Tiong
• Pouya Hassandarvish
• Ilina Isahak

The serotonin reuptake inhibitor Fluoxetine inhibits SARS-CoV-2 in human lung tissue

• Melissa Zimniak
• Luisa Kirschner
• Jochen Bodem

Probenecid inhibits SARS-CoV-2 replication in vivo and in vitro

• Jackelyn Murray
• Robert J. Hogan
• Ralph A. Tripp

UV-C irradiation is highly effective in inactivating SARS-CoV-2 replication

• Mara Biasin
• Andrea Bianco
• Mario Clerici

Diagnostic performance of rapid antigen tests (RATs) for SARS-CoV-2 and their efficacy in monitoring the infectiousness of COVID-19 patients

• John G. Routsias
• Maria Mavrouli
• Athanasios Tsakris

Epidemiology and outcomes of COVID-19 in HIV-infected individuals: a systematic review and meta-analysis

• Paddy Ssentongo
• Emily S. Heilbrunn

Temporal dynamics of viral load and false negative rate influence the levels of testing necessary to combat COVID-19 spread

• Katherine F. Jarvis
• Joshua B. Kelley

Nasopharyngeal SARS-CoV-2 viral loads in young children do not differ significantly from those in older children and adults

• Sharline Madera
• Emily Crawford
• Joseph L. DeRisi

Morphometry of SARS-CoV and SARS-CoV-2 particles in ultrathin plastic sections of infected Vero cell cultures

• Michael Laue
• Anne Kauter
• Andreas Nitsche

Glycan reactive anti-HIV-1 antibodies bind the SARS-CoV-2 spike protein but do not block viral entry

• Dhiraj Mannar
• Karoline Leopold
• Sriram Subramaniam

The Spanish gut microbiome reveals links between microorganisms and Mediterranean diet

• Adriel Latorre-Pérez
• Marta Hernández
• Luis Collado

In vitro inactivation of SARS-CoV-2 by commonly used disinfection products and methods

Methylene Blue has a potent antiviral activity against SARS-CoV-2 and H1N1 influenza virus in the absence of UV-activation in vitro

• Valeria Cagno
• Chiara Medaglia
• Caroline Tapparel

A novel highly quantitative and reproducible assay for the detection of anti-SARS-CoV-2 IgG and IgM antibodies

• Kouki Matsuda
• Akinobu Hamada

Colorimetric RT-LAMP SARS-CoV-2 diagnostic sensitivity relies on color interpretation and viral load

• Mateus Nóbrega Aoki
• Bruna de Oliveira Coelho
• Lucas Blanes

Field-deployable, rapid diagnostic testing of saliva for SARS-CoV-2

• Hemant Suryawanshi
• Zev Williams

No evidence for basigin/CD147 as a direct SARS-CoV-2 spike binding receptor

• Jarrod Shilts
• Thomas W. M. Crozier
• Gavin J. Wright

Carvacrol exhibits rapid bactericidal activity against Streptococcus pyogenes through cell membrane damage

• Niluni M. Wijesundara
• Song F. Lee
• H. P. Vasantha Rupasinghe

In silico analysis of epitope-based vaccine candidate against tuberculosis using reverse vaccinology

• Shaheen Bibi
• Inayat Ullah
• Shiquan Niu

Antiviral activity of lambda-carrageenan against influenza viruses and severe acute respiratory syndrome coronavirus 2

• Heegwon Shin
• Meehyein Kim

Nicotinamide mononucleotide production by fructophilic lactic acid bacteria

• Kazane Sugiyama
• Kana Iijima
• Nobuyuki Yoshida

Molecular features similarities between SARS-CoV-2, SARS, MERS and key human genes could favour the viral infections and trigger collateral effects

• Lucas L. Maldonado
• Andrea Mendoza Bertelli
• Laura Kamenetzky

Silicon nitride: a potent solid-state bioceramic inactivator of ssRNA viruses

• Giuseppe Pezzotti
• Francesco Boschetto

The meta-gut: community coalescence of animal gut and environmental microbiomes

• Christopher L. Dutton
• Amanda L. Subalusky
• David M. Post

Ingestion of probiotic ( Lactobacillus helveticus and Bifidobacterium longum ) alters intestinal microbial structure and behavioral expression following social defeat stress

• Katherine A. Partrick
• Anna M. Rosenhauer
• Kim L. Huhman

Direct diagnostic testing of SARS-CoV-2 without the need for prior RNA extraction

• Esther Kohl

Solar UV-B/A radiation is highly effective in inactivating SARS-CoV-2

• Fabrizio Nicastro
• Giorgia Sironi

High prevalence of antibiotic resistance in commensal Escherichia coli from healthy human sources in community settings

• Emmanuel Nji
• Joseph Kazibwe
• La Thi Quynh Lien

Pupal cannibalism by worker honey bees contributes to the spread of deformed wing virus

• Francisco Posada-Florez
• Zachary S. Lamas
• Eugene V. Ryabov

Network analysis of Down syndrome and SARS-CoV-2 identifies risk and protective factors for COVID-19

• Ilario De Toma
• Mara Dierssen

MRC5 cells engineered to express ACE2 serve as a model system for the discovery of antivirals targeting SARS-CoV-2

• Kentaro Uemura
• Michihito Sasaki
• Akihiko Sato

A descriptive analysis of antimicrobial resistance patterns of WHO priority pathogens isolated in children from a tertiary care hospital in India

• Vijayalaxmi V. Mogasale
• Prakash Saldanha
• Vittal Mogasale

Metagenomic identification of a new sarbecovirus from horseshoe bats in Europe

• Jack M. Crook
• Ivana Murphy

Comprehensive study of antimicrobial susceptibility pattern and extended spectrum beta-lactamase (ESBL) prevalence in bacteria isolated from urine samples

• Mohammad Javad Gharavi
• Javad Zarei
• Niloufar Rashidi

A PCR amplicon-based SARS-CoV-2 replicon for antiviral evaluation

• Tomohiro Kotaki
• Masanori Kameoka

An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities

• Denise M. O’Sullivan
• Ronan M. Doyle
• Jim F. Huggett

Microplastics accumulate fungal pathogens in terrestrial ecosystems

• Gerasimos Gkoutselis
• Stephan Rohrbach
• Gerhard Rambold

The lower respiratory tract microbiome of critically ill patients with COVID-19

• Paolo Gaibani
• Elisa Viciani
• Simone Ambretti

Functional profiling of COVID-19 respiratory tract microbiomes

• Niina Haiminen
• Filippo Utro
• Laxmi Parida

The rhizosphere microbiome plays a role in the resistance to soil-borne pathogens and nutrient uptake of strawberry cultivars under field conditions

• Cristina Lazcano
• Kelly Ivors

Comparative evaluation of 19 reverse transcription loop-mediated isothermal amplification assays for detection of SARS-CoV-2

• Yajuan Dong
• Chiyu Zhang

Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing

• Ki Wook Kim
• Ira W. Deveson
• William D. Rawlinson

UVC disinfects SARS-CoV-2 by induction of viral genome damage without apparent effects on viral morphology and proteins

• Chieh-Wen Lo
• Ryosuke Matsuura

Co-infection of SARS-CoV-2 and influenza virus causes more severe and prolonged pneumonia in hamsters

• Takaaki Kinoshita
• Kenichi Watanabe
• Jiro Yasuda

Identification of ebselen and its analogues as potent covalent inhibitors of papain-like protease from SARS-CoV-2

• Ewelina Weglarz-Tomczak
• Jakub M. Tomczak
• Stanley Brul

Neurotropic influenza A virus infection causes prion protein misfolding into infectious prions in neuroblastoma cells

• Hideyuki Hara
• Junji Chida
• Suehiro Sakaguchi

The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host

• Maria J. Soto-Giron
• Gerardo Toledo

Blockade of SARS-CoV-2 spike protein-mediated cell–cell fusion using COVID-19 convalescent plasma

Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures

• Santiago Justo Arevalo
• Daniela Zapata Sifuentes
• Roberto Pineda Chavarría

Lactobacillus reuteri AN417 cell-free culture supernatant as a novel antibacterial agent targeting oral pathogenic bacteria

• Kyung Mi Yang
• Kwang-Hak Bae

CRISPR-based transcriptional activation tool for silent genes in filamentous fungi

• László Mózsik
• Mirthe Hoekzema
• Arnold J. M. Driessen

An immortalized porcine macrophage cell line competent for the isolation of African swine fever virus

• Kentaro Masujin
• Tomoya Kitamura
• Takehiro Kokuho

The potential of COVID-19 patients’ sera to cause antibody-dependent enhancement of infection and IL-6 production

• Jun Shimizu
• Tadahiro Sasaki
• Tatsuo Shioda

Digital PCR for high sensitivity viral detection in false-negative SARS-CoV-2 patients

• Paolo Poggio
• Paola Songia
• Maurizio Pesce

Natural variants in SARS-CoV-2 Spike protein pinpoint structural and functional hotspots with implications for prophylaxis and therapeutic strategies

• Suman Pokhrel
• Benjamin R. Kraemer
• Daria Mochly-Rosen

Asymptomatic COVID-19 Adult Outpatients identified as Significant Viable SARS-CoV-2 Shedders

• Marie Glenet
• Anne-Laure Lebreil
• Laurent Andreoletti

Bacterial associations in the healthy human gut microbiome across populations

• Mark Loftus
• Sayf Al-Deen Hassouneh
• Shibu Yooseph

Analysis and forecasting of global real time RT-PCR primers and probes for SARS-CoV-2

• Gowri Nayar
• Edward E. Seabolt
• James H. Kaufman

Antibiotic-resistant bacteria and gut microbiome communities associated with wild-caught shrimp from the United States versus imported farm-raised retail shrimp

• Laxmi Sharma
• Ravinder Nagpal
• Prashant Singh

Emergence of novel SARS-CoV-2 variants in the Netherlands

• Aysun Urhan
• Thomas Abeel

Induction of interferon response by high viral loads at early stage infection may protect against severe outcomes in COVID-19 patients

• Eric C. Rouchka
• Julia H. Chariker
• Donghoon Chung

Early life dietary intervention in dairy calves results in a long-term reduction in methane emissions

• S. J. Meale
• D. P. Morgavi

The relationships between microbiota and the amino acids and organic acids in commercial vegetable pickle fermented in rice-bran beds

• Kazunori Sawada
• Hitoshi Koyano
• Takuji Yamada

Response of bacterial and fungal communities to high petroleum pollution in different soils

• Polina Galitskaya
• Liliya Biktasheva
• Svetlana Selivanovskaya

A streamlined clinical metagenomic sequencing protocol for rapid pathogen identification

• Xiaofang Jia
• Xiaonan Zhang

Sensitive detection and quantification of SARS-CoV-2 in saliva

• Mustafa Fatih Abasiyanik
• Blake Flood
• Evgeny Izumchenko

Whole genome sequencing of clinical samples reveals extensively drug resistant tuberculosis (XDR TB) strains from the Beijing lineage in Nigeria, West Africa

• Idowu B. Olawoye
• Jessica N. Uwanibe
• Christian T. Happi

The SARS-CoV-2 viral load in COVID-19 patients is lower on face mask filters than on nasopharyngeal swabs

• Agnieszka Smolinska
• David S. Jessop
• Marc P. van der Schee

Metagenomics analysis of bacteriophages and antimicrobial resistance from global urban sewage

• Josephine E. S. Strange
• Pimlapas Leekitcharoenphon
• Frank M. Aarestrup

Limited intestinal inflammation despite diarrhea, fecal viral RNA and SARS-CoV-2-specific IgA in patients with acute COVID-19

• Graham J. Britton
• Alice Chen-Liaw
• Jeremiah J. Faith

Genomic evolution of antimicrobial resistance in Escherichia coli

• Markus Hans Kristofer Johansson

Outer membrane vesicles containing OmpA induce mitochondrial fragmentation to promote pathogenesis of Acinetobacter baumannii

• Varnesh Tiku
• Eric M. Kofoed
• Man-Wah Tan

Meta-analysis of host transcriptional responses to SARS-CoV-2 infection reveals their manifestation in human tumors

• Fengju Chen
• Yiqun Zhang
• Chad J. Creighton

Detection of extended spectrum beta-lactamase genes in Pseudomonas aeruginosa isolated from patients in rural Eastern Cape Province, South Africa

• Mojisola C. Hosu
• Sandeep D. Vasaikar
• Teke Apalata

Production of bacterial cellulose using Gluconacetobacter kombuchae immobilized on Luffa aegyptiaca support

• Sameeha Syed Abdul Rahman
• T. Vaishnavi
• Sugumaran Karuppiah

An efficient direct screening system for microorganisms that activate plant immune responses based on plant–microbe interactions using cultured plant cells

• Mari Kurokawa
• Masataka Nakano
• Toshiki Furuya

Glucose confers protection to Escherichia coli against contact killing by Vibrio cholerae

• Cristian V. Crisan
• Holly L. Nichols
• Brian K. Hammer

Neutral evolution test of the spike protein of SARS-CoV-2 and its implications in the binding to ACE2

• Georgina I. López-Cortés
• Miryam Palacios-Pérez
• Marco V. José

Bispecific repurposed medicines targeting the viral and immunological arms of COVID-19

• Martin A. Redhead
• C. David Owen
• Martin A. Walsh

Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems

• Zachary S. Ladin
• Barbra Ferrell
• K. Eric Wommack

Comparative analysis of the diagnostic performance of five commercial COVID-19 qRT PCR kits used in India

• A. K. Yadav

Dissecting industrial fermentations of fine flavour cocoa through metagenomic analysis

• Miguel Fernández-Niño
• María Juliana Rodríguez-Cubillos
• Andrés Fernando González Barrios

Isolation of viable Babesia bovis merozoites to study parasite invasion

• Hassan Hakimi
• Masahito Asada
• Shinichiro Kawazu

Incorporating human mobility data improves forecasts of Dengue fever in Thailand

• Mathew V. Kiang
• Mauricio Santillana
• Caroline O. Buckee

A rapid near-patient detection system for SARS-CoV-2 using saliva

• Noah B. Toppings
• Abu Naser Mohon
• Dylan R. Pillai

In vitro and in vivo inhibition of malaria parasite infection by monoclonal antibodies against Plasmodium falciparum circumsporozoite protein (CSP)

• Merricka C. Livingstone
• Alexis A. Bitzer
• Sheetij Dutta

Covid-19 diagnosis by combining RT-PCR and pseudo-convolutional machines to characterize virus sequences

• Juliana Carneiro Gomes
• Aras Ismael Masood
• Wellington Pinheiro dos Santos

Dysbiosis of gut microbiota in Polish patients with ulcerative colitis: a pilot study

• Oliwia Zakerska-Banaszak
• Hanna Tomczak
• Marzena Skrzypczak-Zielinska

Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations

• Jacquelyn Jones
• Stacey N Reinke
• Claus T. Christophersen

An ultra-portable, self-contained point-of-care nucleic acid amplification test for diagnosis of active COVID-19 infection

• Asanka Jayawardena
• Patrick Kwan

Oral hygiene and oral microbiota in children and young people with neurological impairment and oropharyngeal dysphagia

• Luiz Fernando Fregatto
• Isabela Bazzo Costa
• Paula Cristina Cola

Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19

• Brian L. Le
• Gaia Andreoletti
• Marina Sirota

Importance of crop phenological stages for the efficient use of PGPR inoculants

• Alexandra Stoll
• Ricardo Salvatierra-Martínez
• Jaime Bravo

Isolation and screening of multifunctional phosphate solubilizing bacteria and its growth-promoting effect on Chinese fir seedlings

• Guangyu Zhao
• Ruzhen Jiao

Persimmon-derived tannin has antiviral effects and reduces the severity of infection and transmission of SARS-CoV-2 in a Syrian hamster model

• Ryutaro Furukawa
• Masahiro Kitabatake
• Toshihiro Ito

Bacterial resistance to CRISPR-Cas antimicrobials

• Ruben V. Uribe
• Christin Rathmer
• Morten Otto Alexander Sommer

First report on antibiotic resistance and antimicrobial activity of bacterial isolates from 13,000-year old cave ice core

• Victoria I. Paun
• Paris Lavin
• Cristina Purcarea

Quick links

• Explore articles by subject
• Guide to authors
• Editorial policies

Current Research in Microbiology

Aims and scope.

Current Research in Microbiology is a peer reviewed international journal aimed to publish current research and review articles on microorganisms, which are unicellular or cell-cluster microscopic organisms, includes eukaryotes such as fungi and protists, and prokaryotes, which are bacteria and archaea. CRM is a broad based journal which also includes articles on virology, mycology, parasitology, bacteriology and other branches. Current Research in Microbiology is a specialist journal in microbiology.

It is with great pleasure that we announce the SGAMR Annual Awards 2020. This award is given annually to Researchers and Reviewers of International Journal of Structural Glass and Advanced Materials Research (SGAMR) who have shown innovative contributions and promising research as well as others who have excelled in their Editorial duties.

This special issue "Neuroinflammation and COVID-19" aims to provide a space for debate in the face of the growing evidence on the affectation of the nervous system by COVID-19, supported by original studies and case series.

The SGAMR Editorial Board is pleased to announce the inauguration of the yearly “SGAMR Young Researcher Award” (SGAMR-YRA). The best paper published by a young researcher will be selected by a journal committee, from the Editorial Board.

• Recently Published
• Most Viewed
• Most Downloaded

An official website of the United States government

The .gov means it’s official. Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

The site is secure. The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

• Publications
• Account settings

Preview improvements coming to the PMC website in October 2024. Learn More or Try it out now .

• Advanced Search
• Journal List
• J Transl Med

Emerging trends and focus of human gastrointestinal microbiome research from 2010–2021: a visualized study

Xingzhu yuan.

West China School of Nursing/ West China  Hospital, Sichuan University, No.8 Teaching Building, Chengdu City, 610041 Sichuan province China

Chengting Chang

Xinrong chen, associated data.

Not applicable.

The gastrointestinal microbiome is an important component of the human body and is closely related to human health and disease. This study describes the hotspots of the human gastrointestinal microbiome research and its evolution in the past decade, evaluates the scientific cooperation network, and finally predicts the field’s future development trend using bibliometric analysis and a visualized study.

We searched the original articles from January 2010 to February 2021 in the Scopus database using the term “gastrointestinal microbiome” and its synonyms. CiteSpace was used to construct country and author co-occurrence map; conduct journal, citation cocitation analysis, and reference co-citation knowledge map; and form a keywords co-occurrence map, a clustering knowledge map, timeline view of keywords, and burst term map.

A total of 4444 documents published from January 2010 to February 2021 were analysed. In approximately the past decade, the number of articles on the human gastrointestinal microbiome has increased rapidly, and the research topics focus on different populations, research methods, and detection methods. All countries and regions in the world, led by the US, are studying the human gastrointestinal microbiome, and many research teams with close cooperation have been formed. The research has been published extensively in microbiology journals and clinical medicine journals, and the highly cited articles mainly describe the relationship between gastrointestinal microorganisms and human health and disease. Regarding the research emphasis, researchers' exploration of the human gastrointestinal microbiome (2011–2013) was at a relatively macro and superficial stage and sought to determine how the gastrointestinal microbiome relates to humans. From 2014 to 2017, increasingly more studies were conducted to determine the interaction between human gastrointestinal flora and various organs and systems. In addition, researchers (2018–2021) focused on the gastrointestinal microbial community and the diversity of certain types of microbes.

Over time, the scope of the research on the clinical uses of the gastrointestinal microbiome gradually increased, and the contents were gradually deepened and developed towards a more precise level. The study of the human gastrointestinal microbiome is an ongoing research hotspot and contributes to human health.

Background/introduction

It is currently well appreciated that diverse microbial communities reside within the intestinal tract, on the skin, and on nearly all of the exposed surfaces of the human body [ 1 ]. The human gastrointestinal (GI) tract harbours the highest density and complexity of microbial organisms in the body [ 2 ], and the gastrointestinal microbiota has a level of complexity comparable to that of an organ system [ 3 ]. A key role of the gastrointestinal microbiome in the establishment and maintenance of health, as well as in the pathogenesis of diseases, has been identified over the past two decades [ 4 ]. In addition, the relationship between the gastrointestinal microbiome and populations with different ages and genders has been gradually revealed [ 5 , 6 ]. An increasing number of gastrointestinal microbiome detection methods, such as Polymerase Chain Reaction (PCR) or Fluorescence in situ hybridization (FISH), have also emerged [ 7 , 8 ]. Importantly, the microbiome (including bacteria, viruses, fungi, etc.) regulates health, and its alterations can contribute to disease [ 9 ]. A large number of systematic reviews and meta-analyses have shown that gastrointestinal microorganisms are interrelated with inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), diabetes, hepatitis, and autism in humans [ 10 – 14 ]. For example, IBS can disturb the intestinal microecology, which may continue to aggravate IBS. Conversely, the improvement of the intestinal microecology using probiotics and other means may be conducive to the alleviation of the symptoms of IBS [ 15 – 17 ]. However, most research on the gastrointestinal microbiome is still in the stage of animal experiments, and the results of animal studies cannot be directly applied to humans. For instance, bidirectional microbiota-gut-brain communication has mostly been explored in animal models with human research lagging [ 18 ].

Characterizing the structure of knowledge, the evolution of research topics, and the emergence of topics have always been an important part of information science (IS) [ 19 ]. Bibliometric analysis is an important tool in assessing the research activity and research trends on a particular topic, as well as the most prominent research trends, for future research. A knowledge map, visualizing the connections between complex silos of information, is one way to accurately capture and display disparate pieces of information [ 20 ]. Moreover, key researchers, countries, and collaboration networks between leading research groups can be identified [ 21 , 22 ]. However, previous bibliometric analysis or visualized study of the gastrointestinal microbiome did not exclude animal experiments, and the articles related to the human gastrointestinal microbiome were not analyzed separately. Such research could not describe how well the gastrointestinal microbiome works in humans. Therefore, it is necessary to conduct systematic, intuitive, and scientific bibliometric analysis and visualized study of the growing number of original research articles on the human gastrointestinal microbiome.

This study aims to visualize articles on the human gastrointestinal microbiome in the last ten years by using knowledge maps. We described the research hotspots of the human gastrointestinal microbiome and its evolution in the past decade, evaluated the scientific cooperation network, discussed the relationship between humans and gastrointestinal microbiomes, and predicted the field’s future development trend.

The literature data used in this study were downloaded from the Scopus database, which is widely accepted among researchers conducting high-quality bibliometric analyses [ 23 – 26 ]. We used “gastrointestinal microbiome” for topical retrieval and the following search queries in titles, abstracts, and keywords: (gastrointestinal AND microbiome), (gut AND microbiota), (gut AND flora), (intestinal AND microbial AND population), (intestinal AND microecology), (enteric AND microorganism), (gut AND microecology), and (intestinal AND microorganism). In addition, the time was defined as “2010–2021” without any language limitation. The above keywords were chosen from a list of Medical Subject Headings (MeSHs) provided by the National Library of Medicine (NLM)/PubMed. The literature type was defined as “articles”. Studies in the subject areas of veterinary, poultry science, soil biology, dentistry, engineering, material science, animal experiments, in vitro cell culture experiments, and secondary studies were excluded.

CiteSpace (Chaomei Chen, China), a freely available software tool for analysis, was used to make visualization maps in this study. Developed by Chaomei Chen in 2004 at Drexel University (USA), CiteSpace is usually used to analyze, detect and visualize trends and patterns in scientific literature [ 27 ]. The principle of the software includes coword analysis used to measure the number of occurrences of a group of words (keywords, authors, regions, and citations) in the same group of literature and to perform matrix analysis [ 28 ]. In this paper, we use CiteSpace 5.5.R2 to construct country and author co-occurrence map; conduct journal, citation cocitation analysis, and reference co-citation knowledge map; and form a keywords co-occurrence map, a clustering knowledge map, timeline view of keywords, and burst term map.

Distribution of articles by publication years

Overall, 4444 documents published from January 2010 to February 2021 were analysed. The number of annual documents during this period showed an exponential growth trend (y = 83.518e0.172x, R2 = 0.4625). The specific numbers of annual documents are shown in Fig.  1 .

Time-trend distribution of articles in the field of human gastrointestinal microbiome

Scientific cooperation network analysis

In the country co-occurrence knowledge map (Fig.  2 ), 4444 articles about the human gastrointestinal microbiome were published by research groups in 104 countries or regions. There are 105 nodes and 128 lines, and the centrality is 0.02. The landmark node includes the United States with a count of 1387, China with a count of 756, the United Kingdom with a count of 344, Italy with a count of 311, and Germany (263 texts). The turning points with more connections include Hong Kong, South Africa, the United Kingdom, Switzerland, and Germany. The annual distribution trends in the top five most published countries was shown in Fig. ​ Fig.3. 3 . The United States has been leading the way in annual publication.

The country co-occurrence knowledge map of the human gastrointestinal microbiome during 2010–2021. Nodes show in the form of annual rings that the annual ring width represents how many papers the country/region publishes in a given year. The more papers are published, the wider the annual ring is in that year [ 28 ]

Annual distribution trends in the top five most published countries in the field of human gastrointestinal microbiome

In the author’s co-occurrence knowledge map (Fig.  4 ), there are 588 nodes and 1233 lines, and the centrality is 0.007. The landmark nodes include Y Zhang, Y Wang, J Li, J Zhang, and Y Chen. The turning points with more connections include L Wang, L Li, X Yang, Y Chen, and J Wang.

The author co-occurrence knowledge map of the human gastrointestinal microbiome during 2010–2021. The connection between nodes represents the cooperation between authors, and the width of the connection represents the strength of cooperation. The color of the connection represents the author’s first cooperation time. After the network is generated, the author’s cooperation will form several natural clusters. The author cooperation within the cluster is close, and the author cooperation between each class is less [ 28 ]

Journal and citation analysis

A total of 1255 journals published the 4444 articles on the human gastrointestinal microbiome. We analyzed the top ten journals that published articles on the human gastrointestinal microbiome (Table ​ (Table1), 1 ), reference co-citation knowledge map (Fig.  5 ) and the details of the top ten articles with the most citations on the human gastrointestinal microbiome in the last ten years (Table ​ (Table2 2 ).

Top 10 journals that published articles on human gastrointestinal microbiome during 2010–2021

The co-citation knowledge map of the human gastrointestinal microbiome during 2010–2021

The top 10 co-cited articles of the human gastrointestinal microbiome during 2010–2021

16S rRNA 16S ribosomal RNA, MGWAS analysis metabolome-based genome-wide association studies

Six of the top 10 journals specialize in microbiology: two are general medicine journals, and the rest are gut and nutrition journals. Most of these journals are of good quality and are European and American journals.

An overview of the 427 top-cited articles among the 1,13,598 articles in the human gastrointestinal microbiome literature and the details of the ten most cited articles on the human gastrointestinal microbiome are summarized in Table ​ Table2. 2 . The size of a node represents the number of times the corresponding article has been cited in the dataset.

The highly cited articles on the human gastrointestinal microbiome have been published in top journals such as Nature and Science. The topics of these literatures include the relationship between the human gastrointestinal microbiome and diet, diabetes, human health and metabolism, and microbiome analysis methods.

Emerging trends and research focus based on keywords analysis

The articles were imported into CiteSpace, and the keywords were set as nodes. Through a series of software operations, the keyword co-occurrence knowledge map (Fig.  6 ), clustering knowledge map (Fig.  7 ), timeline view of keywords (Fig.  8 ), and keyword burst term map (Fig.  9 ) were obtained.

The Keyword co-occurrence knowledge map of the human gastrointestinal microbiome during 2010–2021. Each node represents a keyword, and the size of the node represents the frequency of their occurrence, and the line between nodes represents the intensity of co-occurrence, and the color of the line corresponds to the time range at the top of the picture. The frequency of keywords and centrality were listed is in the lower-left corner of the graph [ 28 ]

The Keyword clustering knowledge map of the human gastrointestinal microbiome during 2010–2021. CiteSpace uses Log-likelihood rate (LLR) to cluster closely related keywords. Different patterns represent a cluster. Tag # was assigned to the cluster, and the smaller the number is, the more keywords are in the cluster. The size of each cluster, the Silhouette value, and the mean publication year of articles in that cluster are shown in the upper right corner [ 28 ]

The timeline view of the human gastrointestinal microbiome during 2010–2021. In the timeline view, the keywords on the same horizontal line belong to the right cluster. The colors of lines and keywords in the view correspond to the colors of the time slice at the top [ 28 ]

Top 20 Keywords with the Strongest Citation Bursts of the human gastrointestinal microbiome during 2010–2021. *1 The year in which this keyword first appeared. 2 the bursts’ strength of the keyword. 3 The year in which this keyword begins and ends the burst. 4 Red represents the period during which the keyword is burst

The keyword co-occurrence knowledge map (Fig.  6 ) contains 165 nodes and 270 lines, and the centrality is 0.02. The landmark nodes that are larger include human, intestinal flora, female, male, adult, and controlled study. They represent the most critical components of the human gastrointestinal microbiome field. The turning points with more connections include adults, microbiology, middle-aged, faecal, RNA 16, child, infant, and Bifidobacterium, indicating that they had higher centrality in the domain and were associated with more keywords.

There were 11 clustering patterns in the research field of the human gastrointestinal microbiome, which are shown in the keyword clustering knowledge map (Fig.  7 ). In addition, the top 20 most typical labels in each cluster are shown in Table ​ Table3 3 .

The most typical label in each cluster

By combining the keyword clustering knowledge map (Fig.  7 ), timeline view (Fig.  8 ), and keyword burst map (Fig.  9 ), we found the evolutionary path of research hotspots. Amoxicillin treatment, vocabulary related to RCTs, the intestines, the gastrointestinal tract, lactobacillus, Escherichia coli, DNA, probiotics host gene regulation, and the metagenome began to attract attention in the early years (2010–2013). The middle stage (2014–2017) focused on microflora, complications, chemistry, newborns, normal humans, on-chronic liver failure, Japanese female patients, autism spectrum disorder, gastric cancer, and HIV-infected patients. In addition, in recent years (2018–2021), researchers have been interested in metagenomics, microbial communities, microbial diversity, inflammation, and other aspects.

The annual number of articles on the human gastrointestinal microbiome shows exponential growth (Fig.  1 ), indicating that this field is a research hotspot, and its popularity will continue to increase. This is consistent with previous studies [ 23 , 39 ]. Researchers should give continuous attention to trends in related fields to uncover more connections between humans and the gastrointestinal microbiome. All countries and regions in the world have studied the human gastrointestinal microbiome (Fig.  2 ). The United States has the most publications, which may be related to the Human Microbiome Project (HMP) programme launched by the NIH in 2007 and the Gut Microbiota Brain AXIS programme in 2013 [ 40 , 41 ]. The second most published country is China, which may be related to the importance attached to the study of the human microbiome mentioned by the National Natural Science Foundation of China, the 14th Five-Year National Key Research and Development Plan of the Ministry of Science and Technology and the Outline of the 2035 Vision Goals [ 42 – 44 ]. Although China is the second largest publishing country, there are no Chinese journals in the top 10 journals, which indicates that China can strengthen its construction of periodicals in this field. The largest collaborator is J Zhang's team from Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol in China, which focuses on probiotics and intestinal microorganisms. It is suggested that researchers from all countries continue to maintain close cooperation and share the latest research results on the human gastrointestinal microbiome.

The top 10 journals (Table ​ (Table1) 1 ) may be given priority when researchers publish and read articles on the human gastrointestinal microbiome because they have published a large number of studies on the human gastrointestinal flora. The reference co-citation knowledge map (Fig.  5 ) is clearly divided into three clusters according to time (from 2010 to 2013, from 2014 to 2018 and from 2019 to 2021), which indicates that the themes of each research stage are different. Researchers can read highly cited papers (those with large circle areas in Fig.  5 ) to find research hotspots at that stage. Moreover, beginning researchers can read the highly cited literature (Table ​ (Table2) 2 ) to help them understand the important findings in the field.

Compared with previous bibliometrics and visualized studies on the gastrointestinal microbiome that did not exclude animal studies, these studies on the human gastrointestinal microbiome mainly focus on the following aspects [ 23 , 39 ]. As shown in the keyword co-occurrence knowledge map (Fig.  6 ), the larger landmark nodes can be divided into three categories: population, research methods, and detection methods. A large number of studies have been conducted on the relationship between age (newborn [ 45 ], infant [ 46 ], child [ 47 ], teenager [ 48 ], adult [ 49 ], middle aged [ 50 ] and aged [ 51 ]), gender (male [ 52 ] and female [ 53 ]) and population groups and gastrointestinal microorganisms. This may be related to researchers finding that the gastrointestinal floras of different populations are significantly different, which requires classification to further study the topic. Additionally, various research methods have been used to study this field. Experimental studies often include the effects of probiotics [ 54 ], faecal microbiota transplantation [ 55 ], Chinese medicine [ 56 ], and antibiotic therapy [ 57 , 58 ] on the human gastrointestinal microbiome. Observational studies often include interactions between the gastrointestinal microbiome and various human diseases such as obesity [ 59 ], diabetes [ 60 ], and irritable bowel syndrome [ 61 ]. In addition, there are a variety of molecular biology technologies that have been used for gastrointestinal microbiome research. These technologies mainly include the following methods: bacterial culture technology based on molecular biotechnology, polymerase chain reaction (PCR), fluorescent in situ hybridization (FISH) [ 8 ], gene chips [ 62 ], and metagenome sequencing [ 63 ], and it is more popular to establish a gene bank of the gastrointestinal microbiome [ 64 ]. Each technology has advantages and disadvantages, and researchers can select the technologies suitable for their purposes.

As for research emphases, researchers’ exploration of the human gastrointestinal microbiome from 2010 to 2013 was at a relatively macro and superficial stage. Researchers have sought to determine how the gastrointestinal microbiome relates to humans. In 2011, one study combined 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets to identify three robust clusters (referred to as enterotypes), which attracted intense attention at the time [ 32 ]. But since then, the discussion of enterotype has become less and less popular. Every year, a small number of studies look at the relationship between human enterotype and diet [ 33 , 65 ], feces [ 66 ], human population [ 67 ], obesity [ 68 ], etc. Some researchers have suggested that grouping the microbiota of individual subjects into enterotypes, based on the dominance of certain genera may have oversimplified a complex situation [ 69 ]. Researchers have also explored the link between human gastrointestinal flora and certain diseases (such as type 2 diabetes, autism, obesity, irritable bowel syndrome, etc.) at this stage [ 70 – 72 ] and the relationship between Lactobacillus and human gastrointestinal flora [ 73 – 75 ]. In addition, a series of randomized controlled trials on the human gastrointestinal flora began to emerge at this stage [ 76 – 80 ]. The effect of antibiotics on human gastrointestinal flora was also a research hotspot during this period [ 81 , 82 ].

From 2014 to 2017, increasingly more studies were conducted to determine the interaction between human gastrointestinal flora and various organs and systems (such as liver cirrhosis, Parkinson’s disease, rheumatoid arthritis, etc.) [ 83 – 85 ]. For instance, Francesco’s research suggested that the gut mycobiota contributed to the alteration of the intestinal microbial community structure in ASDs, which made it possible to develop new potential intervention strategies aimed at the relief of gastrointestinal symptoms in ASDs [ 86 ]. Dillon’s study suggested that an important relationship existed between altered mucosal bacterial communities and intestinal inflammation during chronic HIV-1 infection [ 87 ]. Moreover, the relationship between diet and human gastrointestinal flora is a research hotspot during this period [ 30 , 88 , 89 ].

From 2018 to 2021, researchers shifted their focus from certain types of gastrointestinal bacteria to the gastrointestinal microbial community [ 90 ] and microbial diversity [ 90 ]. Studies [ 91 , 92 ] on the effects of the gastrointestinal microbiome and its metabolites on inflammation [ 93 ] and immunology [ 94 ] and their application as biomarkers [ 95 ] at the molecular level have also gradually become hotspots.

It is worth noting that researchers are often inspired by animal experiments to explore the mechanisms of diseases caused by the gastrointestinal microbiome and modify the gastrointestinal microbiome to treat disease; then, they judge the feasibility and safety of treatment methods [ 96 ]. However, human research has lagged behind animal models, and applying the results of animal experiments to humans requires more rigorous experiments and theories [ 18 , 97 ]. At present, theories such as microbiota-gut-brain communication [ 98 ], gut-lung axis [ 99 , 100 ], and enterohepatic circulation [ 101 ] can explain parts of the relationship between the gastrointestinal microbiome and various human organs and systems, but it is not yet completely clear. With the development of new technologies, such as omics and sequencing, the detection of the gastrointestinal microbiome has become more accurate. Big data also makes it possible to conduct comprehensive artificial intelligence research on multicentre, multidisease, and human gastrointestinal microbiome databases. Future research needs to be based on previous research results, combined with emerging technologies, and explore the relationship between gastrointestinal flora and humans at the molecular mechanism level to improve health.

There are some limitations to this study. In this study, only articles in the Scopus database were retrieved. Although using the Scopus database to conduct high-quality bibliometric analyses is widely accepted by researchers, it is still possible that some studies related to the human gastrointestinal microbiome have not been included, which may change the results of the study. This study examined only the last ten years of research on the human gastrointestinal microbiome, which may miss the development process of the human gastrointestinal microbiome from the start.

In this study, 4444 original studies from January 2010 to February 2021 related to the human gastrointestinal microbiome were downloaded from the Scopus database and analyzed using CiteSpace to generate knowledge maps. The number of articles on the human gastrointestinal microbiome has increased rapidly in the past decade, and the scientific cooperation network showed that cooperation between different countries and institutions has been sufficient. The research topics focus on different populations, research methods, and detection methods. In addition, the research scope has gradually increased over time, and the research content has been gradually deeper and moving towards precision medicine. In short, the study of the human gastrointestinal microbiome is an ongoing research hotspot and contributes to human health.

Acknowledgements

Authors would like to thank West China School of Nursing, Sichuan University/West China Hospital, Sichuan University and Sichuan University Library for supporting the work.

Authors' contributions

Guarantor of the article: LK. LK conceived the study and performed critical revision of manuscript. YX designed the study, performed statistical analyses and drafted the manuscript. CC designed the study and wrote the manuscript. CX performed the article retrieval, data interpretation and provided supervision. All authors read and approved the final manuscript.

This work was supported by the Key research and development project of Science & Technology Department of Sichuan Province (No. 2021YFS0022). The funder had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Availability of data and materials

Declarations.

All authors agree publication.

We declare that all authors have no competing interests.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.