Tag Archives: gut microbiome

July 31, 2026

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Diet, Gut Health & Microbiome

Dietitian-led intervention to manage constipation in Parkinson’s disease: Study protocol for a parallel-group randomized controlled trial (NUTRI-GUT-PD) – Juliana Heitich Brendler – PLOS ONE

Efficacy and safety of prebiotics, probiotics, and synbiotics on hemoglobin and anemia in the pediatric population: A systematic review and meta-analysis – Gladys Estheysi Elías Solís – PLOS ONE

Pharmacokinetic model selection for infliximab based on inflammatory bowel disease phenotype and severity: Toward model-informed precision dosing – Ana Homšek Ilić – PLOS ONE

Pathogens, Infection & Host–Microbe Interactions

Neotropical bats as sentinels for emerging zoonoses in Central America: A case study identifying Trypanosoma cruzi in bats from Belize using metagenomic next-generation sequencing – Elissa G. Torgerson – PLOS Neglected Tropical Diseases

Viral replication dynamics: Coinfection and superinfection of Vero cells with Zika virus and West Nile virus or Zika virus and Mayaro virus – Larissa Krokovsky – PLOS ONE

Phenotypic and molecular characterization of Salmonella enterica isolated from retail beef in Peshawar, Pakistan – Muhammad Jawad Ullah – PLOS ONE

Longitudinal study of a rodent invasion reveals shifts in host pathogen interactions – Andrew McManus – PLOS ONE

Noncanonical bactericidal activity of teleost type I interferon is conferred by a membrane-targeting C-terminal peptide – Han Zhang – PLOS Pathogens

A single DNA methylation site regulates cell fate during Clostridioides difficile sporulation – Pola Kuhn – PLOS Genetics

Microbial Genomics & Systems Biology

A systems biology approach to find representative genes in Acute Myeloid Leukemia– Behnam Aghajan – PLOS ONE

Aquatic & Animal Microbiology

Influence of salinity on growth, nutrient utilization, and gene expression of giant freshwater prawn (Macrobrachium rosenbergii) – Farhana Ahamed Shanila – PLOS ONE

Metabolism, Inflammation & Human Health

Integrated computational analysis identifies FABP4, PTGS2, and HPGD as key molecular targets linking PET microplastic exposure to metabolic dysfunction-associated steatotic liver disease – Yi Zhang – PLOS ONE

Exploring the mechanism of Shuangyu Granule in regulating immune-inflammatory responses in influenza through UPLC-Orbitrap-MS/MS, GC-MS, and network target analysis – Ling Sun – PLOS ONE

Cardiometabolic risk pathways in adults with disabilities: A structural equation model of diet quality and functional ability – Radwan Qasrawi – PLOS ONE

Neuroscience & Neurodegeneration

Research advances in key genes and regulatory mechanisms of posttranslational modifications in Parkinson’s disease – Bangzhi Wang – PLOS ONE

Clinical & Healthcare Research

HF-OCAQ: Oral comfort assessment in heart failure patients – Mei Lu – PLOS ONE

Mental Health

Spirituality as a coping resource: Towards integration into mental health framework – Sajama Nepali – PLOS Mental Health

June 4 , 2026

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Gut Microbiome

Associations between body composition and gut microbiota in female college students with and without dance training – Caifang Qiu – PLOS ONE

Imaging the impact of rotifer consumption on bacterial behaviors in the zebrafish gut – Susana Marquez Rosales – PLOS ONE

Environmental Microbiome

The livestock drinking water system as an active reservoir for antimicrobial resistance: A systematic review and one health gap analysis – Sujan Adhikar – PLOS ONE

Viral Microbiome

ViralMultiNet: A structure-aware multimodal framework for viral protein function prediction in wastewater surveillance – FuGuo Liu – PLOS ONE

Virological investigation and comparative genomic analysis of elephant endotheliotropic herpesvirus 1B infection in an Australian captive herd of Asian elephants (Elephas maximus) – Jack W Wheelahan – PLOS ONE

Expanding diversity of tick-borne phleboviruses (Phlebovirus mukawaense, Mudanjiang phlebovirus, Gomselga Virus, and Onega tick phlebovirus) in Russia – Mikhail Y Kartasho – PLOS ONE

Phage / Mobile Genetic Elements

Phage-plasmid-like elements are found throughout diverse environments and encode niche-specific functional traits – James I Mulle – PLOS ONE

Microbiological quality assessment of potential pathogenic bacteria and multidrug resistance patterns in commercial electrolyte drinks in Dhaka, Bangladesh – Sananda Saha – PLOS ONE

Pathogen & Disease-related Microbiology

Leishmania major virulence attenuation in vitro: An old conundrum revisited in the omics era – Evgeny S Gerasimov – PLOS ONE

Microbiological quality assessment of potential pathogenic bacteria and multidrug resistance patterns in commercial electrolyte drinks in Dhaka, Bangladesh – Sananda Saha – PLOS ONE

Microbiome Tools / Bioinformatics / Methods

TIPP-SD: A new method for species detection in microbiomes – Chengze Shen – PLOS ONE

AgrOmicSo: A client-server interface for accessible large-scale analysis of next-generation sequencing data – Dong-Jun Lee – PLOS ONE

Antimicrobial Resistance (AMR Microbiome)

The livestock drinking water system as an active reservoir for antimicrobial resistance: A systematic review and one health gap analysis
Sujan Adhikar

April 29 , 2026

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Gut microbiome

Gut microbiota induces dysspermatogenesis via microbial-derived phenylacetylglycine in Ggt1-deficient mice – Jinhua Tang – Microbiome

Puerarin modulates the gut-liver-ovarian axis to ameliorate reproductive aging in breeder hens – Zhenwu Huang – microbiome

Gastrointestinal microbial nitrogen metabolic landscape underlies nitrogen utilization efficiency of goats fed distinct dietary protein sources – Yechan Zhao – microbiome

Environmental Microbiome

Unveiling microbial risks in Chinese household dust: a comprehensive analysis from absolute abundance to virulence unit – Lu Long – microbiome

Livestock Microbiome

Curcumin modulates hepatic pyroptosis-autophagy crosstalk induced by aflatoxin B1 via rumen microbiota-blood-liver axis – Tongwei Liu – microbiome

Plant Microbiome

Metabolome-driven rhizosphere microbiome assembly determining the health of medicinal herb (Angelica sinensis) against root rot – Chuan You – microbiome

Microbiome & Cancer / Immunology

Trimethylamine-producing microbe Bacillus megaterium KCTC 3007 promotes antitumor immunity in endometrial cancer via type I interferon response pathways – Kyungchan Min – microbiome

February 26 , 2026

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Gut Microbiome

Association between the gut microbiome and plasma metabolites linked to vocalization-based temperament in Merino sheep – Luoyang Ding – microbiome

Cross-kingdom genomic variation in chicken gut microbiomes: insights from China’s diverse local breeds – Jiayu Zhang – microbiome

Microbiota-derived propionate suppresses Salmonella virulence gene expression via LuxS quorum sensing – Qianyun Zhang – microbiome

rumen microbiome

Comparative analysis of rumen metagenomes with dietary supplementation of 3-nitrooxypropanol revealed divergent modes of action in hydrogen metabolism and reductant pathways between beef and dairy cattle – Youyoung Choi – microbiome

January 29, 2026

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Animal microbiome

Host genetic background and environment have different effects on the establishment and structure of the adult worker honey bee gut microbiota – Breven Stark – PLOS ONE

Microbiota discovered in scorpion venom – Barbara Murdoch – PLOS ONE

Animal experiments / Disease models

Intestinal decontamination with rifaximin attenuates LSEC dysfunction and liver fibrosis in mice – Tingting Su – PLOS ONE

Periplaneta americana extract ameliorates recurrent oral ulcers in rats by enhancing the intestinal epithelial barrier and regulating gut microbiota – Kailing Li – PLOS ONE

Formononetin ameliorates SP-induced urticaria in mice via suppressing TAK1/MAK signaling pathway -Yan Wu –PLOS ONE

Lipopolysaccharide induced mouse depression model can better simulate changes in peripheral blood FFAs in alMDD -Jincai Pan –PLOS ONE

Human microbiome (gut & reproductive)

Stool and vaginal microbiome profiles patterns among Black and White endometrial cancer survivors: A pilot study in North Carolina – Mu Jin – PLOS ONE

Infection, immunity & host–microbe interactions

Examining the role of IgA in a persistent model of Staphylococcus aureus colonization – Yunys Perez-Betancourt – PLOS Pathogens

Diversify and conquer: How effector diversity is shaped by host–microbe co-evolution -Marion C Müller – PLOS Pathogens

Oo-No: Ophidiomyces ophidiicola–bacterial interactions and the role of skin lipids in development of ophidiomycosis – Jason W Dallas – PLOS Pathogens

Probiotics & food microbiology

In-vitro evaluation of probiotic potential of gut microbes isolated from retail chicken – Sangram Biswas – PLOS ONE

Antimicrobial resistance & clinical microbiology

Extended-spectrum β-lactamase and carbapenemase-producing Enterobacterales among adult patients and their family members at Tikur Anbessa Specialized Hospital, Addis Ababa, Ethiopia – Dessie Abera – PLOS ONE

Microbiome methods & bioinformatics

PCR bias impacts microbiome ecological analyses – Dharmik R Rathod – PLOS Computational Biology

CoSMIC: A hybrid approach for large-scale, high-resolution microbial profiling of novel niches – Maor Knafo – PLOS ONE

Environmental & applied microbiology

Developing a simple, cost-effective proof-of-concept vaccine candidate against EHEC for cattle – Cecilia M Duarte – PLOS ONE

Preventive effect of bentonite against pyoderma via direct binding capability of staphylococci – Mao Kaneki – PLOS ONE

Ultraviolet light and polyethylene glycol as environmental cleaning agents to reduce contamination of Pseudogymnoascus destructans in bat hibernacula – Alyssa J Stulberg – PLOS ONE

Water, pollution & human exposure

Micro- and nanoplastics in biological samples following a drinking water intervention in Barcelona, Spain – Emma Calikanzaros – PLOS Water

Human disease & biomarkers

Evidence of an allostatic response by intestinal tissues following induction of joint inflammation – Meghan M Moran – PLOS ONE

Multi-modal data to identify key factors influencing lung injury in ARDS patients undergoing invasive mechanical ventilation: A prospective multi-center observational study protocol – Zhimei Duan – PLOS ONE

Integrative genomic analysis reveals DHX58 as a key player in gastric cancer – Yan Li – PLOS ONE

Identifying biomarkers for diagnosis and disease activity monitoring in PSC-IBD and UC through proteomic profiling: A prospective study protocol – Ondrej Fabian – PLOS ONE

S100-alarmins, antenatal corticosteroids and the risk of late-onset sepsis in preterm infants – Gloria Kessler – PLOS ONE

Exploring the role of the key gene TNFAIP3 between periodontitis and influenza A through bioinformatic analysis and molecular docking – Mingxiang Xu – PLOS ONE

GC-MS based bioactive profiling of Phyllanthus niruri and its antibacterial potential – Zubair Khalid Labu – PLOS ONE

January 28, 2026

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Reproductive / Urogenital Microbiome & Host–Pathogen Interactions

The interactive relationship between Fusobacterium necrophorum, Bacteroides pyogenes, and Porphyromonas levii in driving inflammatory uterine disease – Dianjun Cao – microbiome

 Gut Microbiome, Diet, and Host Health

Total and different types of olive oil consumption, gut microbiota, and cognitive function changes in older adults –Jiaqi Ni – microbiome

Environmental Microbiome & Antimicrobial Resistance (Resistome)

Beyond borders: plasmids drive a shared antibiotic resistome in European urban water systems

– Wanli He – microbiome

Spatial and temporal patterns of public transit aerobiomes – Russell J. S. Or – microbiome

Food Chain, Meat Microbiome & Resistome Dynamics

Microbiome and resistome successions in pig carcasses and fresh pork meat throughout slaughtering, processing and shelf-life – Elena Fernández-Trapote – microbiome

Microbiome–Immune System Interactions

Commensal microbe-derived butyrate enhances T follicular helper cell function to boost mucosal vaccine efficacy – Haeun Ko – microbiome

Animal microbiome

A culturomics approach reveals cross-feeding capacity of intestinal pig bacteria upon release of inositol from phytate – Lena-Sophie Paul – microbiome

November 27, 2025

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Human gut microbiome

Weifuchun alleviates MNNG-induced chronic atrophic gastritis by improving the gastric and intestinal microbiota homeostasis – Yingying Chen – PLOS ONE

Microbiota-supportive diets and hyperlipidemia: The mediating role of systemic inflammation – Wenjing Wang – PLOS ONE

Toxoplasma gondii disrupts intestinal microbiota and host metabolism in a rat model – Ji-Xin Zhao – PLOS NTDs

Body mass index distinctly modulates the associations between Alistipes and CRP/IL-6 – Lourdes Chero-Sandoval – PLOS ONE

Dogs with advanced myxomatous mitral valve disease have evidence of gastrointestinal bacterial translocation – Maria C Jugan – PLOS ONE

Predicting postoperative constipation in middle-aged and elderly fracture patients using machine learning – Xiaoyan Yang – PLOS ONE

Animal microbiome

Cecal microbiota of broilers responds similarly to black soldier fly larvae fat and conventional fat sources – Muhammad Rumman Aslam – PLOS ONE

Sarcopenia modelling by portal vein ligation inducing hyperammonemia in rats – Maria Nadinskaia – PLOS ONE

Oral / GI cancer microbiome

Serum IgG titer for Fusobacterium nucleatum and clinical outcome in esophageal squamous cell carcinoma – Toru Yoshikawa – PLOS ONE

Phages & bacterial pathogenesis

Structural determinants of SlpA-mediated phage recognition in Clostridioides difficile – Alexia LM Royer – PLOS Pathogens

Disruption of yqhG attenuates virulence in MRSA by compromising membrane stability – Jianhua Liao – PLOS ONE

Host range of generalist and specialist phages in capsule-diverse Klebsiella hosts – Celia Ferriol-González – PLOS Biology

Immunology / human disease

Large-scale seroepidemiology uncovers nephro-urological pathologies with tau autoimmunity – Andreia D Magalhães – PLOS Biology

Plant, soil & ecological microbiome

Root-associated Streptomyces strains enriched during drought reveal diverse functional traits – Citlali Fonseca-Garcia – PLOS Biology

Co-infections shaping Chlamydia pecorum infection outcomes in northern koalas – Yasmine S S Muir – PLOS Pathogens

Trade-offs between yields and sustainability in winter wheat systems under climate change – Jennifer Michel – PLOS Climate

Clinical microbiology

Clinical impact of prophylactic antibiotics in kidney transplantation – Sang Ah Lee – PLOS ONE

Microbial interactions

Veillonella species increase Listeria monocytogenes growth in broth and biofilms – Fanie Shedleur-Bourguignon – PLOS ONE

October 24, 2025

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Gut & Human Microbiome

The microbiome and gut–lung axis in nontuberculous mycobacterial pulmonary disease – Ria N. Thompson – PLOS Pathogens

Alterations in the gut microbiota of alcoholic cirrhosis patients infected with Clonorchis sinensis in the Pearl River Delta region of China – Aijun Huang – PLOS ONE

Association between dietary B vitamins intake and age-specific blood pressure: A cross-sectional study in American adults – Xianfeng Li – PLOS ONE

Animal & Environmental Microbiomes

Cuts or carcasses? Diet form affects fecal microbial and animal fiber fractions in a large carnivore, the Asiatic lion – Mengmeng Sun – PLOS ONE

From pre-oral secretions to gut digestion: How do Lucilia sericata (Diptera: Calliphoridae) larvae handle Leishmania major? – Azam Malekian – PLOS ONE

Pathogenicity and transmission of Morganella morganii in honey bees – Yijun Chen – PLOS Pathogens

Mitogenomics of the tropical bont tick Amblyomma variegatum reveals vertical and horizontal transmission of Rickettsia africae – Elisha Chatanga – PLOS Neglected Tropical Diseases

Regulation of lipid metabolism in Spodoptera frugiperda by the symbiotic bracovirus of the gregarious parasitoid Cotesia ruficrus – Xian Li – PLOS Pathogens

The genome of Gallaecimonas pentaromativorans strain 10A, isolated from a Pacific oyster, sheds light on an environmentally widespread genus with remarkable metabolic potential – Yasmine Gouin – PLOS ONE

Plant, Soil & Microbial Ecology

Starve or share? Phosphate availability shapes plant–microbe interactions – Maja Schmidt – PLOS Pathogens

PMA-qPCA: Accelerating the market release of high-quality Bradyrhizobium diazoefficiens inoculant – Mariana Cap – PLOS ONE

Ancient & Evolutionary Microbiomes

Targeted pathogen profiling of ancient feces reveals common enteric infections in the Rio Zape Valley, 725–920 CE – Drew Capone – PLOS ONE

Health, Disease & Microbial Interactions

Differential regulation of the eicosanoid biosynthesis pathway in response to Enterocytozoon hepatopenaei infection in Litopenaeus vannamei – Wananit Wimuttisuk – PLOS ONE

Microplastic exposure and allergic rhinitis: Network toxicology and molecular docking insights – Yaojun Wang – PLOS ONE

Comparative evaluation of the antimicrobial, antioxidant, and cytotoxic properties of essential oils from vetiver, lemongrass, and clove buds with implications for topical application – Acharawan Thongmee – PLOS ONE

October 17, 2025

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Gut Microbiome & Health

Lactic acid produced by optimal vaginal Lactobacillus spp. potently and specifically inactivates HIV-1 in vitro by targeting the viral RNA genome and reverse transcriptase
– Muriel Aldunate – PLOS Pathogens

Differential composition of the pulmonary microbiome in HIV-positive versus HIV-negative patients with Pneumocystis jirovecii
– Chang-Run Zhang – PLOS ONE

Risk of atopic dermatitis in periodontitis patients with and without dental scaling: A retrospective cohort study
– Ming-Che Chiang – PLOS ONE

Fecal carriage and associated factors of extended-spectrum beta-lactamase-producing Enterobacteriaceae in children under five years old with diarrhea at a tertiary hospital in Tanzania
– Emily M. Jackson – PLOS ONE

Pathogens, Immunity & Host Interactions

Dietary tannic acid promotes intestinal clearance of Candida albicans by cross-linking hyphal chitosan
– Jia Feng – PLOS Pathogens

Trends in Clostridioides difficile infection prevalence among pediatric cancer patients: A systematic review and meta-analysis
– Muluneh Assefa – PLOS ONE

Multiplex serology for Streptobacillus moniliformis and other ‘rat bite fever-like’ microorganisms for seroprevalence studies in rodents
– Katja Schmidt – PLOS ONE

Animal & Environmental Microbiomes

Effects of rumen-protected or unprotected Clostridium butyricum on growth performance, rumen fermentation, immunity and antioxidation in fattening goats
– Caixia Zhang – PLOS ONE

The intracellular symbiont Wolbachia alters Drosophila development and metabolism to buffer against nutritional stress
– Amelia R. I. Lindsey – PLOS Genetics

Interactive effects of developmental and adult nutrition on lifespan and fecundity in a genetically diverse Drosophila population
– Andrew Jones – PLOS ONE

Metabolism, Health & Disease

Alterations in the serum metabolome in patients with the COVID-19 Omicron variant and in recovered cases
– Feng Gao – PLOS ONE

Humanized monoacylglycerol acyltransferase 2 mice on a high-fat diet exhibit impaired liver detoxification during metabolic dysfunction-associated steatotic liver disease
– J. Jose Corbalan – PLOS ONE

Current and future burden of gynecological cancers attributable to high body-mass index: A comprehensive global analysis and projection study
– Xuanyu Zhao – PLOS ONE

Developing and experimentally validating a glucocorticoid signaling-related gene signature to evaluate the prognosis and immunotherapeutic response in kidney renal clear cell carcinoma
– Yu Zhang – PLOS ONE

Computational & Bioinformatics Advances

ArcDFI: Attention regularization guided by CYP450 interactions for predicting drug–food interactions
– Mogan Gim – PLOS Computational Biology

Advanced deep learning-based brain tumor classification using a novel customized CNN and optimized residual network
– Mehwish Rasheed – PLOS ONE

October 2, 2024

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Gut Microbiome

Gut microbiota wellbeing index predicts overall health in a cohort of 1000 infants – Brandon Hickman et al – Nature Communications

Pangenomes of human gut microbiota uncover links between genetic diversity and stress response – Saar Shoer et al – Cell Host & Microbe

[MINI REVIEW] The human gut microbiome in health and disease: time for a new chapter? – Jee-Yon Lee et al – ASM Infection & Immunity

Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities – Amin Valiei et al – NPJ Biofilms & Microbiomes

A population-scale analysis of 36 gut microbiome studies reveals universal species signatures for common diseases – Wen Sun et al – NPJ Biofilms & Microbiomes

A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome – Tetsuro Kawano-Sugaya et al – BMC Microbiome

Stratification of human gut microbiomes by succinotype is associated with inflammatory bowel disease status – Laura Anthamatten et al – BMC Microbiome

Impact of complementary feeding on infant gut microbiome, metabolites and early development – Yudong Shi et al – Food & Function

Can longer lifespan be associated with gut microbiota involvement in lipid metabolism? – Sára Šardzíková et al – FEMS Microbiology Ecology

Beneficial microbes & compounds

[REVIEW] Preventive effect of probiotics on oral mucositis induced by anticancer therapy: a systematic review and meta-analysis of randomized controlled trials – Bo Yang et al – BMC Oral Health

Animal Microbiome

Bacteria from the Amycolatopsis genus associated with a toxic bird secrete protective secondary metabolites – Elena Seibel et al – Nature Communications

Impact of virginiamycin on the ruminal microbiota of feedlot cattle – Bruna Parapinski Santos – Canadian Journal of Veterinary Research

Microbiome of death

From carrion to soil: microbial recycling of animal carcasses – Jennifer M. DeBruyn et al – Cell Trends in Microbiology

Water & extremophile microbiome

Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient – Viviana Freire-Zapata et al – Nature Microbiology

Prescribed fire regimes influence responses of fungal and bacterial communities on new litter substrates in a brackish tidal marsh – Viet Q. Dao et al – PLOS One

Plant, root & soil microbiome

The phyllosphere of Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii is inhabited by a specific microbiota – Anderson O. Oaikhena et al – Scientific Reports

Water‒soil-air‒plant mutual feedback mechanism under the application of red bed composite polymers – Tianpeng Chen et al – PLOS One

Diversity and community distribution of soil bacterial in the Yellow River irrigation area of Ningxia, China – Xia Wu et al – PLOS One

Bioinformatics & tools

Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs – Annika Jochheim et al – BMC Microbiome