Tag Archives: soil microbiome

December 19, 2025

Posted on by

Animal microbiome

The innate immune IMD pathway is a key regulator of gut microbiome and metabolic homeostasis in the black tiger shrimp (Penaeus monodon) – Premruethai Supungul – PLOS ONE

Human gut microbiome & nutrition

The evaluation of indoxyl sulfate in the general population in Kanegasaki Iwate: A cross-sectional study (KANEGASAKI study) – Mizuki Hisano – PLOS ONE

The relationship between dietary intake of B vitamins and Helicobacter pylori seropositivity – Yuexia Lu – PLOS ONE

Plant, soil & ecological microbiome

Zinc ion increases the effectiveness of phosphorus in agricultural soils through microbial solubilization – Lanxin Tang – PLOS ONE

Optimizing soil quality and rhizosphere ecology to enhance Annona squamosa yield and quality through water–fertilizer–mulching synergy – Weihua Wang – PLOS ONE

Concentration-dependent effects of fermented spent coffee grounds and contrasting effects of earthworms on growth and phytochemicals in medicinal plant Glechoma longituba – Bing-Nan Zhao – PLOS ONE

Animal experiments (model organisms)

The Drosophila G protein-coupled receptor, GulpR, is essential for lipid mobilization in response to nutrient limitation – Daniela Barraza – PLOS Genetics

High-protein diets reduce plasma pro-inflammatory cytokines following lipopolysaccharide challenge in Swiss Albino mice – Hellen W Kinyi – PLOS ONE

Clinical research & public health

Impact of an integrated intervention package during preconception, pregnancy, and early childhood on inflammation, IGF-1, IGFBP3 during first 6 months of life: Findings from the WINGS randomized controlled trial – Ranadip Chowdhury – PLOS Global Public Health

Lack of association between loneliness, social isolation and inflammation in people living with HIV aged ≥50 years – Jose-Ramon Blanco – PLOS ONE

Effect of obesity and exercise training on circulating lipids in American Indian adolescents – Charles F Hojjat – PLOS ONE

From mental health detention to health systems reform: Co-producing policy and practice recommendations with Black men and their communities – Elaine Craig – PLOS Mental Health

Microbial genetics & bacterial physiology

Whole-genome analysis of Lysinibacillus boronitolerans MSR1: A dairy-isolated multidrug-resistant and non-pathogenic strain – Md Shahedur Rahman – PLOS ONE

A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and intra-species cooperation – Ben Vezina – PLOS Biology

Clinical biomarkers & immunology

Blood RNA biomarkers and a point-of-care elastase assay for detecting host immune activation in suspected sepsis – John E Lafleur – PLOS ONE

Multi-omics analysis reveals diagnostic and therapeutic biomarkers for aging phenotypes in ulcerative colitis – Lei Guo – PLOS ONE

Oral health & microbiome

The impact of diet and oral hygiene on dental caries among Turkish children: A cross-sectional study – Ozge Yesildemir – PLOS ONE

Molecular biology & immunity

LIPL-1 and LIPL-2 are TCER-1-regulated lysosomal lipases with distinct roles in immunity and fertility – Laura Bahr – PLOS Genetics

October 24, 2025

Posted on by

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

August 11, 2024

Posted on by

Human and General Microbiome

B cell senescence promotes age-related changes in oral microbiota – Hiroya Mizuno – Aging Cell

Exploring the relationship between gut microbiota and breast cancer risk in European and East Asian populations using Mendelian randomization – Wei Lin – BMC Cancer

Intratumoral microbiome promotes liver metastasis and dampens adjuvant imatinib treatment in gastrointestinal stromal tumor – Yanze Li – Cancer Letters

Comparison of Vaginal microbiota in HPV-negative and HPV-positive pregnant women using a culture-based approach – Podoprigora Irina – Diagnostic Microbiology and Infectious Disease

The gut-microbiome in adult Attention-deficit/hyperactivity disorder – A Meta-analysis – Babette Jakobi – European Neuropsychopharmacology

An Empirical Dietary Pattern Associated with the Gut Microbial Features in Relation to Colorectal Cancer Risk – Kai Wang – Gastroenterology

Species-level characterization of gut microbiota and their metabolic role in kidney stone formation using full-length 16S rRNA sequencing – Bashir Hussain – Urolithiasis

Review: Game of microbes: the battle within – gut microbiota and multiple sclerosis – Ti-Ara Turner – Gut Microbes

Review: The early life exposome and autism risk: a role for the maternal microbiome? – Claudia M Di Gesù – Gut Microbes

Review: Gut mycobiome alterations and implications for liver diseases – Suling Zeng – PLoS Pathogens

Beneficial Microbes and Compounds

A novel intervention of molecular hydrogen on the unbalance of the gut microbiome in opioid addiction: Experimental and human studies – Bing Xie – Biomedicine & Pharmacotherapy

Lower fecal microbiota transplantation ameliorates ulcerative colitis by eliminating oral-derived Fusobacterium nucleatum and virulence factor – Dong-Hao Li – Gut Pathogens

Induction of Cell Death by Bifidobacterium infantis DS1685 in Colorectal and Breast Cancers via SMAD4/TGF-Beta Activation – In Hwan Tae – Journal of Microbiology and Biotechnology

Review: Peptide GLP-1 receptor agonists: From injection to oral delivery strategies – Zhiqiang Ke – Biochemical Pharmacology

Animal Microbiome (including model experiments)

Stress-sensitive neural circuits change the gut microbiome via duodenal glands – Hao Chang – Cell

Effect of Hafnia alvei on Morphophysiologic Parameters and Gut Microbiota of Mice with Inherited Type 2 Diabetes Mellitus – V A Zolotarev – Bulletin of Experimental Biology and Medicine

Spatial analysis of murine microbiota and bile acid metabolism during amoxicillin treatment – Chapman N Beekman – Cell Reports

Evaluating impacts of radiation-induced sterilization on the performance and gut microbiome of mass-reared Mediterranean fruit fly (Ceratitis capitata) in Hawai’i – Charles J Mason – Journal of Economic Entomology

Plant Microbiome

Disease Resistance Correlates with Core Microbiome Diversity in Cotton – Rhea Aqueel – Current Microbiology

Environmental Microbiome

The symbiotic alga Trebouxia fuels a coherent soil ecosystem on the landscape scale in the Atacama Desert – Patrick Jung – Environmental Microbiome

Relationships between radiation, wildfire and the soil microbial communities in the Chornobyl Exclusion Zone – Alexandre Barretto de Menezes – The Science of the Total Environment

The first large scale rDNA amplicon database of soil microbiomes from Pamir Plateau, China – Jing Zhu – Scientific Data

Food and Beverage Microbiome

Changes in the solid-associated bacterial and fungal communities following ruminal in vitro fermentation of winery by-products: aspects of the bioactive compounds and feed safety – Ratchaneewan Khiaosa-Ard – Anaerobe

16S amplicon-based microbiome biomapping of a commercial broiler hatchery – Michael J Jr Rothrock – Animal Microbiome

Analyzing the gut microbiota and microbial-associated metabolites of tomato-based sauces – Alicia Paulina Cárdenas-Castro – Food Chemistry

August 4, 2024

Posted on by

Human Gut Microbiome

Exploring the interplay between antiretroviral therapy and the gut-oral microbiome axis in people living with HIV – Aswathy Narayanan – Scientific Reports

Human Gut Microbiota Composition Associated with International Travels – D Henares – Travel Medicine and Infectious Disease

Respiratory microbiome and clinical course of carbapenem-resistant Acinetobacter baumannii pneumonia in critically Ill patients – Jin Gu Yoon – Medicine

Review: Gut Microbiota and Autism Spectrum Disorder: A Neuroinflammatory Mediated Mechanism of Pathogenesis? – Fatemeh Zarimeidani – Inflammation

Review: Gut microbiota and eating behaviour in circadian syndrome – Jorge R Soliz-Rueda – Trends in Endocrinology and Metabolism

Beneficial Microbes and Compounds

Staphylococcus aureus/Staphylococcus epidermidis from skin microbiota are balanced by Pomegranate peel extract: An eco-sustainable approach – Sara D’Arcangelo – PloS One

Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities – Francesca De Filippis – NPJ Biofilms and Microbiomes

Bugs as drugs: Extended clinical applications and potential translational trends of Akkermansia muciniphila in oncology and comprehensive clinical investigation panorama of therapeutic microbiome modulators in gastric cancer treatment – Yuning Wang – Pharmacological Research

Polyphenols: potent protectors against chronic diseases – Geetha Shanmugam – Natural Product Research

Animal Microbiome

Effects of berberine hydrochloride on antioxidant response and gut microflora in the Charybdis japonica infected with Aeromonas hydrophila – Mingming Han – BMC Microbiology

Design of an agro-industrial by-products-based media for the production of probiotic bacteria for fish nutrition – Marcelo Fernando Valle Vargas – Scientific Reports

Association of microbial community structure with gill disease in marine-stage farmed Atlantic salmon (Salmo salar); a yearlong study – Morag Clinton – BMC Veterinary Research

Selection for stress tolerance and longevity in Drosophila melanogaster have strong impacts on microbiome profiles – Torsten Nygaard Kristensen – Scientific Reports

Novel insights on microbiome dynamics during a gill disease outbreak in farmed rainbow trout (Oncorhynchus mykiss) – Samuele Zamparo – Scientific Reports

Gut Microbiome-Driven metabolites influence skin pigmentation in TYRP1 mutant Oujiang color common carp – Roland Nathan Mandal – Gene

Plant and Soil Microbiome

From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology – Winston E Anthony – Environmental Microbiome

An acidophilic fungus promotes prey digestion in a carnivorous plant – Pei-Feng Sun – Nature Microbiology

A novel strategy of artificially regulating plant rhizosphere microbial community to promote plant tolerance to cold stress – Jianfeng Zhang – The Science of the Total Environment

A bud’s life: Metabarcoding analysis to characterise hazelnut big buds microbiome biodiversity – Silvia Turco – Microbiological Research

Perspective: Integrating viruses into soil food web biogeochemistry – Cátia Carreira – Nature Microbiology

Review: Rhizosphere microbiome assembly, drivers and functions in perennial ligneous plant health – Morgane Duret – Microbiological Research

Environmental Microbiome

Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses – Alexandra K Stiffler – Microbiome

June 26, 2024

Posted on by

Human gut microbiome

Microbial community-scale metabolic modelling predicts personalized short-chain fatty acid production profiles in the human gut – Nick Quinn-Bohmann et al – Nature Microbiology

Island biogeography theory provides a plausible explanation for why larger vertebrates and taller humans have more diverse gut microbiomes – Katherine Ramos Sarmiento et al – ISME Journal

Dietary fibre directs microbial tryptophan metabolism via metabolic interactions in the gut microbiota – Anurag K. Sinha – Nature Microbiology

Animal models

The zebrafish gut microbiome influences benzo[a]pyrene developmental neurobehavioral toxicity – Keaton Stagaman et al – Nature Scientific Reports

Modulation of gut microbiota composition due to early weaning stress induces depressive behavior during the juvenile period in mice – Itsuka Kamimura et al – BMC Animal Microbiome

Antibiotics affect the pharmacokinetics of n-butylphthalide in vivo by altering the intestinal microbiota – Xiangchen Li et al – PLOS One

Trilobatin ameliorates dextran sulfate sodium-induced ulcerative colitis in mice via the NF-κB pathway and alterations in gut microbiota – Nanbo Wang et al – PLOS One

Animal microbiome

Gut microbiota and immune profiling of microbiota-humanised versus wildtype mouse models of hepatointestinal schistosomiasis – K.A. Stark et al – BMC Animal Microbiome

Analysis of differences in the rumen microbiome and metabolic function in prepartum dairy cows with different body condition scores – Dewei Du et al – BMC Animal Microbiome

Improvement of insulin sensitivity by dietary fiber consumption during late pregnant sows is associated with gut microbiota regulation of tryptophan metabolism – Yang Li – BMC Animal Microbiome

Gut microbiota diversity in a dung beetle (Catharsius molossus) across geographical variations and brood ball-mediated microbial transmission – Hao-Yu Chen et al – PLOS One

Water & extremophile microbiomes

Metagenomic insights into Heimdallarchaeia clades from the deep-sea cold seep and hydrothermal vent – Rui Liu – BMC Environmental Microbiome

Metagenomic insights into microbial adaptation to the salinity gradient of a typical short residence-time estuary – Ziheng Wu et al – BMC Microbiome

Plant, root, & soil microbiome

Microbial consortium assembly and functional analysis via isotope labelling and single-cell manipulation of polycyclic aromatic hydrocarbon degraders – Jibing Li – ISME Journal

Chemolithoautotrophic diazotrophs dominate dark nitrogen fixation in mangrove sediments – Shasha Wang et al – ISME Journal

Other microbes

Cellular interactions and evolutionary origins of endosymbiotic relationships with ciliates – Qi Song et al – ISME Journal

Bioinformatics & tools

Entourage: all-in-one sequence analysis software for genome assembly, virus detection, virus discovery, and intrasample variation profiling – Worakorn Phumiphanjarphak & Pakorn Aiewsakun – BMC Bioinformatics

Methods

Soft autonomous ingestible device for sampling the small-intestinal microbiome – Ruben Del-Rio-Ruiz et al – Cell Device

December 18, 2023

Posted on by

Human and General Microbiome

Microbiome diversity protects against pathogens by nutrient blocking – Frances Spragge – Science 

Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients – Zixuan Xie – Microbiome

Functional alterations and predictive capacity of gut microbiome in type 2 diabetes – Nihar Ranjan Dash – Scientific Reports

Fecal metabolite profiling identifies liver transplant recipients at risk for postoperative infection – Christopher J Lehmann – Cell Host & Microbe

Establishment of oral microbiome in very low birth weight infants during the first weeks of life and the impact of oral diet implementation – Pedro A R Vanzele – PloS One

Infant gut DNA bacteriophage strain persistence during the first 3 years of life – Yue Clare Lou – Cell Host & Microbe

Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition – Elias R Gerrick – Cell

Poly-omic risk scores predict inflammatory bowel disease diagnosis – Christopher H Arehart – mSystems

Review: Impact of glyphosate (Roundup(TM)) on the composition and functionality of the gut microbiome – Lauren Walsh – Gut Microbes

Rapid turnover and short-term blooms of Escherichia coli in the human gut – Na Han – Journal of Bacteriology

Designing a multi-epitope vaccine against Peptostreptococcus anaerobius based on an immunoinformatics approach – Yudan Mao – Synthetic and Systems Biotechnology

Twnbiome: a public database of the healthy Taiwanese gut microbiome – Amrita Chattopadhyay – BMC Bioinformatics

Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting – Alessandra Riva – Nature Communications

Review: Application of omics technologies in cariology research: A critical review with bibliometric analysis – Josie Shizhen Zhang – Journal of Dentistry

Dysbiosis and associated stool features improve prediction of response to biological therapy in inflammatory bowel disease – Clara Caenepeel – Gastroenterology

Highlight: Female Reproductive Tract Microbiome

Review: Culturomics in Unraveling the Upper Female Reproductive Tract Microbiota – Robin Vanstokstraeten – Seminars in Reproductive Medicine

A manifold-based framework for studying the dynamics of the vaginal microbiome – Mor Tsamir-Rimon – NPJ Biofilms and Microbiomes

Culturomics reveals a hidden world of vaginal microbiota with the isolation of 206 bacteria from a single vaginal sample – Linda Abou Chacra – Archives of Microbiology

Effects of variation in sample storage conditions and swab order on 16S vaginal microbiome analyses – Tanya Kumar – Microbiology Spectrum

Non-Model Animal Microbiome

Activity budget and gut microbiota stability and flexibility across reproductive states in wild capuchin monkeys in a seasonal tropical dry forest – Shasta E Webb – Animal Microbiome

Validation of method for faecal sampling in cats and dogs for faecal microbiome analysis – Xavier Langon – BMC Veterinary Research

Transmission of antimicrobial resistance in the gut microbiome of gregarious cockroaches: the importance of interaction between antibiotic exposed and non-exposed populations – Amalia Bogri – mSystems

Plant and Soil Microbiome

Fungal community composition changes and reduced bacterial diversity drive improvements in the soil quality index during arable land restoration – Pingxing Wan – Environmental Research

Two-for-one: root microbiota orchestrates both soil pH and plant nutrition – João Antonio Siqueira – Trends in Plant Science

Cotton microbiome profiling and Cotton Leaf Curl Disease (CLCuD) suppression through microbial consortia associated with Gossypium arboreum – Rhea Aqueel – NPJ Biofilms and Microbiomes

Environmental Microbiome

Benthic microbial biogeographic trends in the North Sea are shaped by an interplay of environmental drivers and bottom trawling effort – Guido Bonthond – ISME Communications

Increased prokaryotic diversity in the Red Sea deep scattering layer – Tamara Megan Huete-Stauffer – Environmental Microbiome

August 28, 2023

Posted on by

Human and General Microbiome

The respiratory tract microbiome, the pathogen load, and clinical interventions define severity of bacterial pneumonia – Ana Elena Pérez-Cobas – Cell Reports. Medicine

A phenome-wide association study (PheWAS) to identify the health impacts of 4-cresol sulfate in the Nagahama Study – Huiting Ou – Scientific Reports

A meta-analysis of tissue microbial biomarkers for recurrence and metastasis in multiple cancer types – Xuebo Li – Journal of Medical Microbiology 

Microbe Profile: Ruminococcus gnavus: the yin and yang of human gut symbionts – Nathalie Juge – Microbiology

Oral Porphyromonas gingivalis infection affects intestinal microbiota and promotes atherosclerosis – Sowon Park – Journal of Clinical Periodontology

Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: the METS-microbiome study – Gertrude Ecklu-Mensah – Nature Communications

Very early life microbiome and metabolome correlates with primary vaccination variability in children – Michael Shaffer – mSystems

Carbohydrate quality, fecal microbiota and cardiometabolic health in older adults: a cohort study – Alessandro Atzeni – Gut Microbes

Multi-omics analysis revealing the interplay between gut microbiome and the host following opioid use – Udhghatri Kolli – Gut Microbes

The gut microbiota reprograms intestinal lipid metabolism through long noncoding RNA Snhg9 – Yuhao Wang – Science

Staphylococcus epidermidis activates keratinocyte cytokine expression and promotes skin inflammation through the production of phenol-soluble modulins – Michael R Williams – Cell Reports

Review: Targeting nonalcoholic fatty liver disease via gut microbiome-centered therapies – Mijra Koning – Gut Microbes

Review: Intracellular Fusobacterium nucleatum infection increases METTL3-mediated m6A methylation to promote the metastasis of esophageal squamous cell carcinoma – Songhe Guo – Journal of Advanced Research

Beneficial Microbes and Compounds

Characteristics of gut microbiota determine effects of specific probiotics strains in patients with functional constipation – Haohao Zhang – Chinese Medical Journal

Lacticaseibacillus rhamnosus TF318 prevents depressive behavior in rats by inhibiting HPA-axis hyperactivity and upregulating BDNF expression – Yujuan Zhao – Neuroscience Letters

Animal Model Microbiome

Role of mucin glycosylation in the gut microbiota-brain axis of core 3 O-glycan deficient mice – Erika Coletto – Scientific Reports

Non-Model Animal Microbiome

Outer membrane vesicles from a mosquito commensal mediate targeted killing of Plasmodium parasites via the phosphatidylcholine scavenging pathway – Han Gao – Nature Communications

Whole genome analyses of toxicants tolerance genes of Apis mellifera gut-derived Enterococcus faecium strains – Heba A H Zaghloul – BMC Genomics

Fungal Microbiome

The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research – Julia M Kelliher – Microbiome

Plant Microbiome

Microbiome dataset of bacterial and fungal communities in anthosphere of twelve different wild plants in South Korea – Jihoon Kim – Data in Brief 

Environmental and Soil Microbiome

Anthropogenic activities mediate stratification and stability of microbial communities in freshwater sediments – Xiaotian Zhou – Microbiome

Long-term agro-management strategies shape soil bacterial community structure in dryland wheat systems – Shikha Singh – Scientific Reports

Microbial community structure and functional prediction in five full-scale industrial park wastewater treatment plants – Tujun Tong – The Science of the Total Environment

Deterministic Development of Soil Microbial Communities in Disturbed Soils Depends on Microbial Biomass of the Bioinoculum – Yuri Pinheiro Alves de Souza – Microbial Ecology

Microbial communities related to the sulfur cycle in the Sansha Yongle Blue Hole – Kai Sun – Microbiology Spectrum

A study of microbial diversity in a biofertilizer consortium – Cristóbal Hernández-Álvarez – PloS One

Microbiome Research: Resources, Tools and Techniques

Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data – Aubrey R Odom – Scientific Reports

Amplicon-Based Microbiome Profiling: From Second- to Third-Generation Sequencing for Higher Taxonomic Resolution – Elisabetta Notario – Genes

A flexible quasi-likelihood model for microbiome abundance count data – Yiming Shi – Statistics in Medicine

Identification of multivariable Boolean patterns in microbiome and microbial gene composition data – George Golovko – Bio Systems

Machine learning classification by fitting amplicon sequences to existing OTUs – Courtney R Armour – mSphere

Review: Statistical normalization methods in microbiome data with application to microbiome cancer research – Yinglin Xia – Gut Microbes

Book Chapter: Elucidating the role of microbes in celiac disease through gnotobiotic modeling – Alberto Caminero – Methods in Cell Biology