Tag Archives: Microbial Ecology

December 12, 2025

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Animal microbiome

Human-derived fecal virome transplantation (FVT) reshapes the murine gut microbiota and virome, enhancing glucose regulation – Cervantes-Echeverría – PLOS ONE

TTSS-2 virulence drives inflammatory destruction of the gut epithelial barrier and modulates inflammatory response profiles in the Salmonella-infected mouse gut – Enz – PLOS Pathogens

Aspartic protease 2 from Trichinella spiralis excretion/secretion products hydrolyzes tight junctions of intestinal epithelial cells – Long – PLOS NTDs

Endosymbiont hijacking of acylcarnitines regulates insect vector fecundity by suppressing the viability of stored sperm – Weiss – PLOS Genetics

Development and validation of a quantitative real-time PCR assay for enumeration of Clostridium sporogenes in meat products – Schuller – PLOS ONE

Rooting for data: A FAIR research data management environment for Plant-Microbe collaboration – Dröst – PLOS Pathogens (Plant microbiome)

Prolonged starvation deepens quiescence in Vasa2/Piwi1-expressing cells of a sea anemone – Pascual-Carreras – PLOS Biology

Host–microbe interactions / Immunology

Gut bacteria induce heterologous immune priming in Rhodnius prolixus encompassing humoral and cellular responses – Gilliland – PLOS Pathogens

Dietary flavonoids may improve insulin resistance: NHANES + in vitro – Sui – PLOS ONE

Antiviral and immune-modulatory activities of STING agonists in persistent HBV infection – Wang – PLOS Pathogens

Endosymbiont metabolic manipulation affecting insect reproduction – Weiss – PLOS Genetics

Human clinical studies / Metabolism

Effects of risperidone on amino acid metabolism, glucose & kidney function – Oshima – PLOS ONE

Association between Anti-H. pylori IgG and coronary heart disease – Wang – PLOS ONE

Benefits of psychosocial support for adolescent mothers in Uganda – Nakyaze – PLOS ONE

Modifiable risk factors for inflammatory bowel disease in Kuwait – Alhasan – PLOS ONE

Exposure to polystyrene nanoparticles disrupts trophoblast mitochondrial homeostasis – Hao – PLOS ONE

Molecular mechanisms of lipid metabolism abnormalities driving sepsis & atrial fibrillation – Ou – PLOS ONE

Multi-dimensional analysis of global colorectal cancer burden (1990–2021) – Sun – PLOS ONE

Computational / Modeling

Identification of dynamic models of microbial communities – Paredes-Vázquez – PLOS Comp Biol

Accuracy limits of the Lotka–Volterra model in strongly coupled microbial systems – Mustri – PLOS Comp Biol

Plant, soil & ecological microbiome

High-resolution melting assays for discrimination of fungal pathogens in grapevine trunk disease – Azevedo-Nogueira – PLOS ONE

Rooting for data: FAIR data environment for plant–microbe collaboration – Dröst – PLOS Pathogens

Environmental health / Climate / Water

Bridging water, health and climate: A call to action – Hedke – PLOS Water

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

August 14, 2024

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Human microbiome

Major depletion of insulin sensitivity-associated taxa in the gut microbiome of persons living with HIV controlled by antiretroviral drugs – Eugeni Belda et al – BMC Medical Genomics

The impact of breastfeeding on the preterm infant’s microbiome and metabolome: a pilot study – Keriann Schulkers Escalante et al – Nature Pediatric Research

[REVIEW] The human microbiome in space: parallels between Earth-based dysbiosis, implications for long-duration spaceflight, and possible mitigation strategies – Sofia Etlin et al – Clinical Microbiology Reviews

MASS cohort: Multicenter, longitudinal, and prospective study of the role of microbiome in severe pneumonia and host susceptibility – Xin Wei et al – iMeta

Distinctive duodenal microbiomes and bile acid profiles in duodenal tumor patients revealed by prospective observational study – Yoko Kubosawa et al – Nature Scientific Reports

Elucidating the dynamics and impact of the gut microbiome on maternal nutritional status during pregnancy, effect on pregnancy outcomes and infant health in rural Pakistan: study protocol for a prospective, longitudinal observational study – Yaqub Wassan et al – BMJ Open

Time-varying ambient air pollution exposure is associated with gut microbiome variation in the first 2 years of life – Tianlai Qiu et al – Environmental Pollution

Animal experiments

Gut Microbiota-Induced Modulation of the Central Nervous System Function in Parkinson’s Disease Through the Gut-Brain Axis and Short-Chain Fatty Acids – Yiting Ni et al – Molecular Neurobiology

Animal microbiome

Synergistic pectin deconstruction is a prerequisite for mutualistic interactions between honeybee gut bacteria – Junbo Tang et al – Nature Communications

Environmentally acquired gut-associated bacteria are not critical for growth and survival in a solitary bee, Megachile rotundata – Gagandeep Brar et al – Applied & Environmental Microbiology

Duck gut metagenome reveals the microbiome signatures linked to intestinal regional, temporal development, and rearing condition – Lingyan Ma & Wentao Lyu et al – iMeta

Meconium microbiota in naturally delivered canine puppies – Alessia Bertero et al – BMC Veterinary Research

Gut microbiome perturbation and its correlation with tylosin pharmacokinetics in healthy and infected pigs – Eon-Bee Lee et al – Nature Scientific Reports

Beneficial microbes, compounds, & foods

Restriction of growth and biofilm formation of ESKAPE pathogens by caprine gut-derived probiotic bacteria – Prerna Saini et al – Frontiers in Microbiology

[REVIEW] Polyphenols improve non-alcoholic fatty liver disease via gut microbiota: A comprehensive review – Kimia Mohammadhasani et al – Food Science & Nutrition

[REVIEW] Exploring the Potential of Postbiotics for Food Safety and Human Health Improvement – Folayemi Janet Isaac-Bamgboye et al – Journal of Nutrition & Metabolism

Transcriptomics and gut microbiome analysis of the edible herb Bidens pilosa as a functional feed additive to promote growth and metabolism in tilapia (Oreochromis spp.) – Che-Chun Chen et al – BMC Genomics

[REVIEW] A comprehensive review of the characterization, host interactions, and stabilization advancements on probiotics: Addressing the challenges in functional food diversification – Eskindir Getachew Fentie et al – Comp. Rev. in Food Science & Safety

Effects of kefir consumption on gut microbiota and health outcomes in women with polycystic ovary syndrome – Merve Esra Çıtar Dazıroğlu – Food Science & Nutrition

Plant, root, & soil microbiome

Decrease due to pollution in the rhizosphere microbial diversity can be amended by supplementation from adapted plants of another species – Anastasiia Fetsiukh et al – Nature Scientific Reports

Differences in the constituents of bacterial microbiota of soils collected from two fields of diverse potato blackleg and soft rot diseases incidences, a case study – Weronika Babinska-Wensierska et al – Nature Scientific Reports

Variations of soil metal content, soil enzyme activity and soil bacterial community in Rhododendron delavayi natural shrub forest at different elevations – Li Wang et al – BMC Microbiology

Effective microorganism combinations improve the quality of compost-bedded pack products in heifer barns: exploring pack bacteria-fungi interaction mechanisms – Zhenbin Zhang et al – BMC Microbiology

Global patterns in the growth potential of soil bacterial communities – Ernest D. Osburn et al – Nature Communications

Microplastic-contamination can reshape plant community by affecting soil properties – Mengzuan He et al – Ecotoxicology & Environmental Safety

Water & extremophile microbiome

Microbial Succession on Microplastics in Wastewater Treatment Plants: Exploring the Complexities of Microplastic-Microbiome Interactions – Klaudia Kwiatkowska & Paulina Ormaniec – Microbial Ecology

Microbial ecology

Higher-order interactions and emergent properties of microbial communities: The power of synthetic ecology – Oscar Gallardo-Navarro et a – Heliyon

Antibiotic resistance

[NEWS FEATURE] Five ways science is tackling the antibiotic resistance crisis – Amber Dance – Nature

Antibiotic resistance gene dynamics in the commensal infant gut microbiome over the first year of life – Pål Trosvik et al – Nature Scientific Reports

Bioinformatics tools

MetaBakery: a Singularity implementation of bioBakery tools as a skeleton application for efficient HPC deconvolution of microbiome metagenomic sequencing data to machine learning ready information – Boštjan Murovec et al – Frontiers in Microbiology

May 8, 2024

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Happy Wednesday folks, we’re halfway through the week! Today’s blog features a number of interesting articles – it was difficult to pick just a few to highlight. Read on to learn about a new study that unveils the environment-specificity of secondary successional dynamics following microbiota disruption, a review summarizing the literature on how pesticide exposure affects the microbiota-gut-brain-axis, an investigation of how host phylogeny, diet, and anthropogenic factors shape the Cetacea gut microbiome – and more!

Human Microbiome

Diet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort – Tzipi Braun – Nature Communications

Improvements in Gut Microbiome Composition and Clinical Symptoms Following Familial Fecal Microbiota Transplantation in a Nineteen-Year-Old Adolescent With Severe Autism – Sabine Hazan – Journal of Medical Cases

[PREPRINT] Interplay between particle size and microbial ecology in the gut microbiome – Jeffrey Letourneau – bioRxiv

Shotgun metagenomic analysis of saliva microbiome suggests Mogibacterium as a factor associated with chronic bacterial osteomyelitis – Hiroko Yahara – PLOS One

[REVIEW] Pesticide exposure and the microbiota-gut-brain axis – Rie Matsuzaki – ISME Journal

Animal Experiments

Short-term exposure to antibiotics begets long-term disturbance in gut microbial metabolism and molecular ecological networks – Yuehui Hong – BMC Microbiome

Microbial Ecology

Synthesis of recovery patterns in microbial communities across environments – Stephanie D. Jurburg – BMC Microbiome

Cooperative interactions between invader and resident microbial community members weaken the negative diversity-invasion relationship – Johanna Vendermaesen – Ecology Letters

High speciation rate of niche specialists in hot springs – Qing He – ISME Journal

Plant, root, and soil microbiome

Effects of reduced snowpack due to climate warming on abiotic and biotic soil properties in alpine and boreal forest systems – Anastasiia Kosolapova – PLOS Climate

Microbiota recovery in a chronosquences of impoverished Cerrado soils with biosolids applications – Laibin Huang – Science of the Total Environment

Melatonin promotes the recovery of apple plants after waterlogging by shaping the structure and function of the rhizosphere microbiome – Yang Cao – Plant, Cell & Environment

Antimony efflux underpins phosphorus cycling and resistance of phosphate-solubilizing bacteria in mining soils – Shengwei Liu – ISME Journal

Animal Microbiome

Antibiotic exposure alters the honeybee gut microbiota and may interfere with the honeybee behavioral caste transition – Zijing Zhang – Insect Science

Meta-analysis of the Cetacea gut microbiome: Diversity, co-evolution, and interaction with the anthropogenic pathobiome – Elena Radaelli – Science of the Total Environment

Comparative analysis of gut microbiome of mangrove brachyuran crabs revealed patterns of phylosymbiosis and codiversification – Chandlar Tsz To Tsang – Molecular Ecology

Techniques & Methodology

A perfusion host-microbe bioreactor (HMB) system that captures dynamic interactions of secreted metabolites between epithelial cells cocultured with a human gut anaerobe – Jingyun Yang – Biotechnology and Bioengineering

Stable, fluorescent markers for tracking synthetic communities and assembly dynamics – Beatriz Jorrin – BMC Microbiome

Sterile sentinels and MinION sequencing capture active soil microbial communities that differentiate crop rotations – Sonya R. Erlandson – BMC Environmental Microbiome