Tag Archives: animal models

July 21, 2024

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Human and General Microbiome

Akkermansia muciniphila and Parabacteroides distasonis as prognostic markers for relapse in ulcerative colitis patients – Ana Mendes-Frias – Frontiers in Cellular and Infection Microbiology

Obesity-enriched gut microbe degrades myo-inositol and promotes lipid absorption – Chao Wu – Cell Host & Microbe

Gut microbiome in endometriosis: a cohort study on 1000 individuals – Inmaculada Pérez-Prieto – BMC Medicine

Metagenomic analysis reveals altered gut virome and diagnostic potential in pancreatic cancer – Pan Zhang – Journal of Medical Virology

The tumor microbiome as a predictor of outcomes in patients with metastatic melanoma treated with immune checkpoint inhibitors – Caroline E Dravillas – Cancer Research Communications

Gut microbiome diversity within Clostridia is negatively associated with human obesity – Laura Salazar-Jaramillo – mSystems

Early depletion of gut microbiota shape oligodendrocyte response after traumatic brain injury – Kirill Shumilov – Journal of Neuroinflammation

Effect of progestin-based contraceptives on HIV-associated vaginal immune biomarkers and microbiome in adolescent girls – Mélodie A Nasr – PloS One

Review: Microbiome and pancreatic cancer: time to think about chemotherapy – Juliana de Castilhos – Gut Microbes

Review: Host control of the microbiome: Mechanisms, evolution, and disease – Jacob Wilde – Science

Review: Connecting microbial community assembly and function – Leonora S Bittleston – Current Opinion in Microbiology

Review: Microbiota of Saliva: A Non-invasive Diagnostic Tool – Dasharath B Shinde – Indian Journal of Microbiology

Beneficial Microbes, Compounds and Interventions

Topical prebiotic nitrate: optimizing the ‘hang-time’, source and dose for specific oral or systemic effects – Bob T Rosier – NPJ Biofilms and Microbiomes

An improved diet-based nutritional interventions can improve childhood obesity with the synergistic regulation of gut microbiota – M Zhou – Beneficial Microbes

Intermittent fasting, calorie restriction, and a ketogenic diet improve mitochondrial function by reducing lipopolysaccharide signaling in monocytes during obesity: A randomized clinical trial – Martha Guevara-Cruz – Clinical Nutrition 

Food Microbiome

Influence of the initial microbiota on eggplant shibazuke pickle and eggplant juice fermentation – Kazunori Sawada – Microbiology Spectrum

Metatranscriptomics reveals microbial community function succession and characteristic flavor formation mechanisms during black rice wine fermentation – Aoxing Tang – Food Chemistry

Animal Model Microbiome

Gα13 restricts nutrient driven proliferation in mucosal germinal centers – Hang T Nguyen – Nature Immunology

Gut microbiota mediates ambient PM(2.5) exposure-induced abnormal glucose metabolism via short-chain fatty acids – Wenpu Shao – Journal of Hazardous Materials

Non-Model Animal Microbiome

Domestication and evolutionary histories of specialized gut symbionts across cephalotine ants – Christian Cabuslay – Molecular Ecology

Review: The interplay between gut symbionts and behavioral variation in social insects – Joanito Liberti – Current Opinion in Insect Science

Meta-transcriptomic analysis of companion animal infectomes reveals their diversity and potential roles in animal and human disease – Wei-Chen Wu – mSphere

Alcohol consumption during pregnancy differentially affects the fecal microbiota of dams and offspring – Tamara S Bodnar – Scientific Reports

Environmental Microbiome

Meta-omics analysis reveals the marine arsenic cycle driven by bacteria – Zhao-Jie Teng – Journal of Hazardous Materials

Using Machine Learning to Identify Environmental Factors that Collectively Determine Microbial Community Structure of Activated Sludge – Lu Wang – Environmental Research

Microplastic pollution promotes soil respiration: A global-scale meta-analysis – Shuling Zhao – Global Change Biology

SMMP: A Deep-Coverage Marine Metaproteome Method for Microbial Community Analysis throughout the Water Column Using 1 L of Seawater – Songduo Wang – Analytical Chemistry

Metagenomic insights into microbial community structure and metabolism in alpine permafrost on the Tibetan Plateau – Luyao Kang – Nature Communications

Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass – Xuejiao Lyu – Journal of Industrial Microbiology & Biotechnology

Microbiome Analysis

GSearch: ultra-fast and scalable genome search by combining K-mer hashing with hierarchical navigable small world graphs – Jianshu Zhao – Nucleic Acids Research

Multi-omics machine learning to study host-microbiome interactions in early-onset colorectal cancer – Thejus T Jayakrishnan – NPJ Precision Oncology

3D printed rectal swabs for assessing the gut microbiome, metabolome and inflammation – Robert W Perry – Scientific Reports

AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides – Amin Darabi – BMC Bioinformatics

JASPER: Fast, powerful, multitrait association testing in structured samples gives insight on pleiotropy in gene expression – Joelle Mbatchou – American Journal of Human Genetics

Microbial Evolution

The nature of the last universal common ancestor and its impact on the early Earth system – Edmund R R Moody – Nature Ecology & Evolution

June 26, 2024

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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

June 23, 2024

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Human and General Microbiome

Custom scoring based on ecological topology of gut microbiota associated with cancer immunotherapy outcome – Lisa Derosa – Cell

News: Gut microbiome discovery provides roadmap for life-saving cancer therapies – Giorgia Guglielmi – Nature

Faecal microbiota transplantation for sleep disturbance in post-acute COVID-19 syndrome – Raphaela I Lau – Clinical Gastroenterology and Hepatology

Pan-cancer atlas of tumor-resident microbiome, immunity and prognosis – Dashuang Sheng – Cancer Letters

Gut metagenomic analysis of gastric cancer patients reveals Akkermansia, Gammaproteobacteria, and Veillonella microbiota as potential non-invasive biomarkers – Anju R Nath – Genomics & Informatics

A Bioinformatic Analysis of Gut Microbiota Related with Immune Cell Infiltration in Colorectal Cancer – Dan Liu – Cancer Investigation

An alternative broad-specificity pathway for glycan breakdown in bacteria – Seyed Amirhossein Nasseri – Nature

The association of maternal factors with the neonatal microbiota and health – Bin Zhu – Nature Communications

Revealing the gut microbiome mystery: A meta-analysis revealing differences between individuals with autism spectrum disorder and neurotypical children – Changjiang Yang – Bioscience Trends

Propionic acid promotes neurite recovery in damaged multiple sclerosis neurons – Barbara Gisevius – Brain Communications

Review: What is the impact of microbiota on dry eye: a literature review of the gut-eye axis – Jiaping Song – BMC Ophthalmology

Review: Cross-feeding of bifidobacteria promotes intestinal homeostasis: a lifelong perspective on the host health – Meifang Xiao – NPJ Biofilms and Microbiomes

Review: Peyer’s Patch: Possible target for modulating the Gut-Brain-Axis through microbiota – Reza Asgari – Cellular Immunology

Animal Model Microbiome

Alterations in gut microbiota and inflammatory cytokines after administration of antibiotics in mice – Wang Gao – Microbiology Spectrum

Environmental Microbiome

A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts – Emily B Graham – Nature Microbiology

Resistance to freezing conditions of endemic Antarctic polychaetes is enhanced by cryoprotective proteins produced by their microbiome – Emanuela Buschi – Science Advances

Microbial co-occurrence network demonstrates spatial and climatic trends for global soil diversity – Nikos Pechlivanis – Scientific Data

Other Microbes

Strain dynamics of contaminating bacteria modulate the yield of ethanol biorefineries – Felipe Senne de Oliveira Lino – Nature Communications

Microbiome Analysis: tools, techniques and resources

A multi-kingdom collection of 33,804 reference genomes for the human vaginal microbiome – Liansha Huang – Nature Microbiology

Deep learning for predicting 16S rRNA gene copy number – Jiazheng Miao – Scientific Reports

GEM-based computational modeling for exploring metabolic interactions in a microbial community – Soraya Mirzaei – PLoS Computational Biology

Review: Techniques, procedures, and applications in microbiome analysis – Adriana González – Advances in Genetics

June 16, 2024

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Human and General Microbiome

Mouse IgA modulates human gut microbiota with inflammatory bowel disease patients – Keishu Takahashi – Journal of Gastroenterology

Distinct characteristics of the gut virome in patients with osteoarthritis and gouty arthritis – Chang-Ming Chen – Journal of Translational Medicine

The microbial composition of pancreatic ductal adenocarcinoma: A systematic review of 16S rRNA gene sequencing – Nabeel Merali – International Journal of Surgery

Therapeutic microbiome modulation: new frontiers in HIV treatment – Rene Bulnes – Current Opinion in HIV and AIDS

Untargeted metabolomics reveal signatures of a healthy lifestyle – Wimal Pathmasiri – Scientific Reports

In-depth microbiological characterization of urine from subjects with type 2 diabetes – Marco Calvigioni – The Journal of Clinical Endocrinology and Metabolism

Study on intestinal parasitic infections and gut microbiota in cancer patients at a tertiary teaching hospital in Malaysia – Sidi Omar Siti Farah Norasyikeen – Scientific Reports

The vaginal microbial signatures of preterm birth woman – Huan Li – BMC Pregnancy and Childbirth

Review: Gut microbiome and cardiometabolic comorbidities in people living with HIV – Marius Trøseid – Microbiome

Review: Nontoxigenic Bacteroides fragilis: A double-edged sword – Yumei Huang – Microbiological Research

Review: Vaginal microbiota and gynecological cancers: a complex and evolving relationship – Kasra Javadi – Infectious Agents and Cancer

Review: Microbial genomics: a potential toolkit for forensic investigations – Pooja Tripathi – Forensic Science, Medicine, and Pathology

Beneficial Microbes and Compounds

Metformin-induced changes in the gut microbiome and plasma metabolome are associated with cognition in men – Marisel Rosell-Díaz – Metabolism: Clinical and Experimental

Effects of Bifidobacterium breve 207-1 on regulating lifestyle behaviors and mental wellness in healthy adults based on the microbiome-gut-brain axis: a randomized, double-blind, placebo-controlled trial – Jinxing Li – European Journal of Nutrition

Bacteria of healthy periodontal tissues as candidates of probiotics: a systematic review – María Del Pilar Angarita-Díaz – European Journal of Medical Research

Animal Model Microbiome

Investigating the influence of perinatal fluoxetine exposure on murine gut microbial communities during pregnancy and lactation – Katelyn Desorcy-Scherer – Scientific Reports

Microbiota dictate T cell clonal selection to augment graft-versus-host disease after stem cell transplantation – Albert C Yeh – Immunity

Non-Model Animal Microbiome

Do fish gut microbiotas vary across spatial scales? A case study of Diplodus vulgaris in the Mediterranean Sea – Lilli Ginevra – Animal Microbiome

Plant Microbiome

Plant growth promotion and biocontrol properties of a synthetic community in the control of apple disease – Rongye Qiao – BMC Plant Biology

Review: Microbial Consortia: Promising Tool as Plant Bioinoculants for Agricultural Sustainability – Rajeshwari Negi – Current Microbiology

Environmental Microbiome

Anthropogenic pollution may enhance natural transformation in water, favouring the spread of antibiotic resistance genes – Periyasamy Sivalingam – Journal of Hazardous Materials

Microbiome Analysis: Tools, Techniques and Resources

mbtransfer: Microbiome intervention analysis using transfer functions and mirror statistics – Kris Sankaran – PLoS Computational Biology

Other

Editorial: Direct-to-consumer microbiome testing needs regulation  – The Lancet Gastroenterology & Hepatology

June 12, 2024

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Human gut microbiome

Persistence and Sexual Dimorphism of Gut Dysbiosis and Pathobiome after Sepsis and Trauma – Jennifer A. Munley – Annals of Surgery

[REVIEW] COVID-19 influenced gut dysbiosis, post-acute sequelae, immune regulation, and therapeutic regimens – Sterlin T. Raj – Frontiers in Cellular and Infection Microbiology

Novel probiotic preparation with in vivo gluten-degrading activity and potential modulatory effects on the gut microbiota – Olga Nikoloudaki – Microbiology Spectrum

Adaptation to tolerate high doses of arabinoxylan is associated with fecal levels of Bifidobacterium longum – Edward C. Deehan – Gut Microbes

Vaginal microbiome

Co-evolution of vaginal microbiome and cervical cancer – Menglu Hu – BMC Journal of Translational Medicine

Animal experiments

Establishment of a novel obesity mouse model: the induction of intestinal microbiota dysbiosis – Qiuju Li – Scientific Reports

Bacteroides uniformis CECT 7771 requires adaptive immunity to improve glucose tolerance but not to prevent body weight gain in diet-induced obese mice – Marina Romaní-Pérez – BMC MIcrobiome

Animal microbiome

Oral microbiome sequencing revealed the enrichment of Fusobacterium sp., Porphyromonas sp., Campylobacter sp., and Neisseria sp. on the oral malignant fibroma surface of giant panda – Xiaowan Wang – Frontiers in Microbiology

Effect of microplastics pollution on the gut microbiome of anecic and endogeic earthworms – Christina Papazlatani – FEMS Microbiology Letters

Evolutionary history of tyrosine-supplementing endosymbionts in pollen-feeding beetles – Jürgen C Wierz – ISME Journal

Compendium of 5810 genomes of sheep and goat gut microbiomes provides new insights into the glycan and mucin utilization – Ke Zhang – BMC MIcrobiome

Plant, root, and soil microbiome

Fungal biomass and ectomycorrhizal community assessment of phosphorus responsive Pinus taeda plantations – Jacob Hackman – Frontiers in Fungal Biology

Soil conditioner improves soil properties, regulates microbial communities, and increases yield and quality of Uncaria rhynchophylla – Qian Liu – Scientific Reports

Genetic control of rhizosphere microbiome of the cotton plants under field conditions – Feng Wei – Applied Microbiology and Biotechnology

Genomic insights into redox-driven microbial processes for carbon decomposition in thawing Arctic soils and permafrost – Yaoming Li – mSphere

Sewage Sludge Promotes the Accumulation of Antibiotic Resistance Genes in Tomato Xylem – Wen-Jing Li – Environmental Science and Technology

Water and extremophile microbiome

Plastic and terrestrial organic matter degradation by the humic lake microbiome continues throughout the seasons – Jussi S. Vesamäki – Environmental Microbiology Reports

Coral microbiomes are structured by environmental gradients in deep waters – Samuel A. Vohsen – BMC Environmental Microbiome

June 9, 2024

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Human and General Microbiome

Divergent age-associated and metabolism-associated gut microbiome signatures modulate cardiovascular disease risk – Tiange Wang – Nature Medicine

Quantifying variation across 16S rRNA gene sequencing runs in human microbiome studies – Andrew J Hoisington – Applied Microbiology and Biotechnology

Gut microbiome changes associated with chronic pancreatitis and pancreatic cancer: A systematic review and Meta-analysis – Jiaze Hong – International Journal of Surgery

Gut microbial signatures of patients with diarrhea-predominant irritable bowel syndrome and their healthy relatives – Jie Chen – Journal of Applied Microbiology

Two weeks of acarbose treatment show no effect on gut microbiome composition in patients with type 2 diabetes: a randomised, placebo-controlled, double-blind, crossover study – Niels B Dalsgaard – Endocrine Connections

A conserved inhibitory interdomain interaction regulates DNA-binding activities of hybrid two-component systems in Bacteroides – Rong Gao – mBio

Multi-omics Analysis Reveals Key Gut Microbiota and Metabolites Closely Associated with Huntington’s Disease – Shu-Xia Qian – Molecular Neurobiology

Review: Unravelling the role of intratumoral bacteria in digestive system cancers: current insights and future perspectives – Weiqin Lu – Journal of Translational Medicine

Model and Non-model Animal Microbiome

Effect of microplastics pollution on the gut microbiome of anecic and endogeic earthworms – Christina Papazlatani – FEMS Microbiology Letters

Novel indigenous probiotic isolated from healthy Pacific White shrimp Litopenaeus vannamei intestine in differing stages based on metagenomic and screening approach – Sutanti Sutanti – Fish & Shellfish Immunology

Citrobacter rodentium infection impairs dopamine metabolism and exacerbates the pathology of Parkinson’s disease in mice – Yongtao He – Journal of Neuroinflammation

Gut microbiota depletion delays somatic peripheral nerve development and impairs neuromuscular junction maturation – Matilde Cescon – Gut Microbes

Plant Microbiome

Review: Unravelling the impact of environmental factors in shaping plant microbiomes – Alicia Isabel Pérez-Lorente – Microbial Biotechnology

Microbiome Analysis

GROND: a quality-checked and publicly available database of full-length 16S-ITS-23S rRNA operon sequences – Calum J Walsh – Microbial Genomics

Machine learning enabled design features of antimicrobial peptides selectively targeting peri-implant disease progression – Kyle Boone – Frontiers in Dental Medicine

Review: An exploratory in silico analysis of bacteriocin gene clusters in the urobiome – Jennifer Jones – Microbiome Research Reports

June 5, 2024

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Human gut microbiome

Gut microbiome and inflammation among athletes in wheelchair in a crossover randomized pilot trial of probiotic and prebiotic interventions – Ezra Valido – Nature Scientific Reports

A microbiota-directed complementary food intervention in 12-18-month-old Bangladeshi children improves linear growth – Ishita Mostafa – eBioMedicine

Gut microbiome shifts in people with type 1 diabetes are associated with glycaemic control: an INNODIA study – Tommi Vatanen – Diabetologia

Association of methyl donor nutrients dietary intake and sleep disorders in the elderly revealed by the intestinal microbiome – Qianqian Chen – Food & Function

[REVIEW] The human gut microbiome and aging – Evan Bradley & John Haran – Gut Microbes

[REVIEW] Nurturing gut health: role of m6A RNA methylation in upholding the intestinal barrier – Shuaijie Wang – Cell Death Discovery

Persistent dysbiosis of duodenal microbiota in patients with controlled pediatric Crohn’s disease after resolution of inflammation – Rebecca Pierce – Nature Scientific Reports

Dysfunctional circadian clock accelerates cancer metastasis by intestinal microbiota triggering accumulation of myeloid-derived suppressor cells – Jing-Lin Liu – Cell Metabolism

Human respiratory microbiome

Longitudinal multicompartment characterization of host-microbiota interactions in patients with acute respiratory failure – Georgios D. Kitsios – Nature Communications

Lack of correlation between in vitro and within patient measures of P. aeruginosa biofilms in cystic fibrosis – Amanda J Morris – Cell Heliyon

Human oral microbiome

The oral microbiome and oral and upper gastrointestinal diseases – Sifan Liu – Journal of Oral Microbiology

Comprehensive analysis of the oral microbiota and metabolome change in patients of burning mouth syndrome with psychiatric symptoms – Shihong Luo – Journal of Oral Microbiology

Candida albicans natural diversity: a resource to dissect fungal commensalism and pathogenesis – Elena Lindemann-Perez – Current Opinion in Microbiology

Animal experiments

Prevotella copri transplantation promotes neurorehabilitation in a mouse model of traumatic brain injury – Nina Gu – Journal of Neuroinflammation

Spatial recovery of the murine gut microbiota after antibiotics perturbation – M. Taguer – mBio

Water and extremophile microbiome

Global biogeography of microbes driving ocean ecological status under climate change – Zhenyan Zhang – Nature Communications

Macroalgal eukaryotic microbiome composition indicates novel phylogenetic diversity and broad host spectrum of oomycete pathogens – Natalia Timanikova – Environmental Microbiology

Viruses & phages

Personalized bacteriophage therapy outcomes for 100 consecutive cases: a multicentre, multinational, retrospective observational study – Jean-Paul Pirnay – Nature Microbiology

Built environment microbiome

Environmental and structural factors associated with bacterial diversity in household dust across the Arizona-Sonora border – Lauren D. Benton – Nature Scientific Reports

Plant, root and soil microbiome

Tibetan Plateau grasslands might increase sequestration of microbial necromass carbon under future warming – Qinwei Zhang – Nature Communications Biology

Assembly of Endophytic Communities of Setaria viridis Plants when Grown in Different Soils and Derived from Different Seeds – Carolina Escobar Rodríguez – Phytobiomes

[PREPRINT] Hybrid xyloglucan utilisation loci are prevalent among plant-associated Bacteroidota – Hannah Martin – bioRxiv

Microbial ecology

Cooperative growth in microbial communities is a driver of multistability – William Lopes – Nature Communications

Bioenergetic mapping of ‘healthy microbiomes’ via compound processing potential imprinted in gut and soil metagenomes – Craig Liddicoat – Science of the Total Environment

Temporal dynamics of fecal microbiota community succession in broiler chickens, calves, and piglets under aerobic exposure – Paul Oladele – Microbiology Spectrum

June 2, 2024

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Human Microbiome

Commensal bacterial outer membrane protein A induces interleukin-22 production – Yanling Wang – Cell Reports

Mucus production, host-microbiome interactions, hormone sensitivity, and innate immune responses modeled in human cervix chips – Zohreh Izadifar – Nature Communications

Gut microbiome and symptoms in females with irritable bowel syndrome: a cross-sectional analysis – K J Kamp – Beneficial Microbes

Gut microbiome in the Graves’ disease: Comparison before and after anti-thyroid drug treatment – Chaiho Jeong – PloS ONE

Guild-level signature of gut microbiome for diabetic kidney disease – Shasha Tang – mBio

Gut microbiome correlates of recurrent urinary tract infection: a longitudinal, multi-center study – JooHee Choi – EClinicalMedicine

Gut microbiota-derived butyrate induces epigenetic and metabolic reprogramming in myeloid-derived suppressor cells to alleviate primary biliary cholangitis – Rui Wang – Gastroenterology

Review: Gut microbiota research nexus: One Health relationship between human, animal, and environmental resistomes – Yuhao Fu – mLife

Review: Exploring the Impact of Airway Microbiome on Asthma Morbidity: A Focus on the Constructing a ‘Eubiosis Reinstatement Therapy’ for Asthma-CURE Project – Paraskevi Xepapadaki – Pulmonary Therapy

Beneficial Microbes and Compounds

A Gram-negative-selective antibiotic that spares the gut microbiome – Kristen A Muñoz – Nature

Bifidobacterium adolescentis-derived hypaphorine alleviates acetaminophen hepatotoxicity by promoting hepatic Cry1 expression – Ping Qin – Journal of Translational Medicine

Chrysanthemum morifolium attenuates metabolic and alcohol-associated liver disease via gut microbiota and PPARα/γ activation – Dan Liu – Phytomedicine

Animal Model Microbiome

Transgenerational effects of early life stress on the fecal microbiota in mice – Nize Otaru – Communications Biology

Metagenomics and metaproteomics alterations are associated with kidney disease in opisthorchiasis hamsters fed a high-fat and high-fructose diet – Keerapach Tunbenjasiri – PloS ONE

Animal Microbiome

Spatial profiles of the bacterial microbiota throughout the gastrointestinal tract of dairy goats – Qingyong Hu – Applied Microbiology and Biotechnology

Interaction between methanotrophy and gastrointestinal nematodes infection on the rumen microbiome of lambs – Patricia Spoto Corrêa – FEMS Microbiology Ecology

Antibiotic-altered gut microbiota explain host memory plasticity and disrupt pace-of-life covariation for an aquatic snail – Gabrielle L Davidson – The ISME Journal

Food Microbiome

Metagenome-assembled genomes from microbiomes fermenting dairy coproducts – Kevin A Walters – Microbiology Resource Announcements

Environmental Microbiome

Global biogeography of microbes driving ocean ecological status under climate change – Zhenyan Zhang – Nature Communications

Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling – Zhepu Ruan – Nature Communications

Interpretable machine learning decodes soil microbiome’s response to drought stress – Michelle Hagen – Environmental Microbiome

Macroalgal eukaryotic microbiome composition indicates novel phylogenetic diversity and broad host spectrum of oomycete pathogens – Natalia Timanikova – Environmental Microbiology

Microbiome Analysis

Combining compositional data sets introduces error in covariance network reconstruction – James D Brunner – ISME Communications

How to Obtain and Compare Metagenome-Assembled Genomes – Fabio Beltrame Sanchez – Methods in Molecular Biology

A strategy for differential abundance analysis of sparse microbiome data with group-wise structured zeros – Fentaw Abegaz – Scientific Reports

Review: A review of machine learning methods for cancer characterization from microbiome data – Marco Teixeira – NPJ Precision Oncology

May 19, 2024

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Human Gut Microbiome

Genetic association between gut microbiome and blood pressure and blood cell count as mediator: A two-step Mendelian randomization analysis – Jiyu Zhang – Gene

Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia – Tianjin Yang – BMC Microbiology

Environmental Factors Associated with Risk of Crohn’s Disease Development in the CCC-GEM Project – Mingyue Xue – Clinical Gastroenterology and Hepatology

Cohort profile of an early life observational cohort in China: Bone and MicroBiOme onset (BAMBOO) study – Jing Wang – BMJ Open

Framework for exploring the sensory repertoire of the human gut microbiota – Patricia A Ross – mBio

Metformin-induced changes of the gut microbiota in patients with type 2 diabetes mellitus: results from a prospective cohort study – Yuting Gao – Endocrine

Review: Host-microbiota interaction in intestinal stem cell homeostasis – Haiqin Wu – Gut Microbes

Review: Gut dysbiosis and neurological modalities: An engineering approach via proteomic analysis of gut-brain axis – Meenakshi Kandpal – Advances in Protein Chemistry and Structural Biology

Human Respiratory Tract Microbiome

Comparative microbiome analysis in cystic fibrosis and non-cystic fibrosis bronchiectasis – Heryk Motta – Respiratory Research

Indole-3-Acetic Acid Protects Against Lipopolysaccharide-induced Endothelial Cell Dysfunction and Lung Injury through the Activation of USP40 – Nargis Shaheen – American Journal of Respiratory cell and Molecular Biology

Human Oral Microbiome

Quantitative analysis of the effects of brushing, flossing, and mouthrinsing on supragingival and subgingival plaque microbiota: 12-week clinical trial – Kyungrok Min – BMC Oral Health

Human Skin Microbiome

Review: Exploring the skin microbiome in atopic dermatitis pathogenesis and disease modification – Claudia Hülpüsch – The Journal of Allergy and Clinical Immunology

Beneficial Microbes and Compounds

Isobutyric acid enhances the anti-tumour effect of anti-PD-1 antibody – Masakazu Murayama – Scientific Reports

Effects of fructooligosaccharides and Saccharomyces boulardii on the compositional structure and metabolism of gut microbiota in students – Hao Fu – Microbiological Research

Urolithin A’s Role in Alleviating Severe Acute Pancreatitis via Endoplasmic Reticulum-Mitochondrial Calcium Channel Modulation – Hongxin Kang – ACS Nano

Animal Model Microbiome

Oral microbiota transplantation for intra-oral halitosis: a feasibility analysis based on an oral microbiota colonization trial in Wistar rats – Zhiqiang Huang – BMC Microbiology

NOD2 contributes to Parvimonas micra-induced bone resorption in diabetic rats with experimental periodontitis – Ying-Yi Chen – Molecular oral Microbiology

Non-Model Animal Microbiome

Microbiome depletion and recovery in the sea anemone, Exaiptasia diaphana, following antibiotic exposure – Sophie MacVittie – mSystems

Environmental Microbiome

Giant viral signatures on the Greenland ice sheet – Laura Perini – Microbiome

Photosynthetic carbon allocation in native and invasive salt marshes undergoing hydrological change: A mesocosm experiment – Ya-Lei Li – The Science of the Total Environment

Ibuprofen degradation by mixed bacterial consortia: metabolic pathway and microbial community analysis – A Rastogi – Chemosphere

Examining the impacts of salt specificity on freshwater microbial community and functional potential following salinization – Jonathon B Van Gray – Environmental Microbiology

Habitat conditions and not moss composition mediate microbial community structure in Swiss peatlands – Rachel Korn – Environmental Microbiology

May 15, 2024

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Human gut microbiome

A shared group of bacterial taxa in the duodenal microbiota of undernourished Pakistani children with environmental enteric dysfunction – Najeeha T Iqbal – mSphere

Gut microbiota, blood metabolites, and left ventricular diastolic dysfunction in US Hispanics/Latinos – Kai Luo – BMC Microbiome

Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition – Xuanji Li – BMC Microbiome

Impact of the gut microbiome composition on social decision-making – Marie Falkenstein – PNAS Nexus

Veillonella and Bacteroides are associated with gestational diabetes mellitus exposure and gut microbiota immaturity – Fernanda Valdez-Palomares – PLOS One

[REVIEW] The neonatal gut microbiome and global health – Pinaki Panigrahi – Gut Microbes

Functional characterization of helminth-associated Clostridiales reveals covariates of Treg differentiation – Shusan Sargisan – BMC Microbiome

Vaginal microbiome

16S rRNA female reproductive microbiome investigation reveals Dalfopristin, Clorgyline, and Hydrazine as potential therapeutics for the treatment of bacterial vaginosis – Sudeepti Kulshrestha – Diagnostic Microbiology and Infectious Disease

Fecal transplant from vaginally seeded infants decreases intraabdominal adiposity in mice – Sivaranjani Namasivayam – Gut Microbes

Animal microbiome

Viruses contribute to microbial diversification in the rumen ecosystem and are associated with certain animal production traits – Ming Yan & Zhongtang Yu – BMC Microbiome

Quantitative microbiome profiling of honey bee (Apis mellifera) guts is predictive of winter colony loss in northern Virginia (USA) – David B. Carlini – Nature Scientific Reports

How do phytophagous insects affect phyllosphere fungi? Tracking fungi from milkweed to monarch caterpillar frass reveals communities dominated by fungal yeast – Ryoko Oono – Environmental Microbiology

Beneficial microbes & compounds

The gut lactic acid bacteria metabolite, 10-oxo- cis-6, trans-11-octadecadienoic acid, suppresses inflammatory bowel disease in mice by modulating the NRF2 pathway and GPCR-signaling – Miki Ando – Frotiers in Immunology

Effect of weight loss program using prebiotics and probiotics on body composition, physique, and metabolic products: longitudinal intervention study – Nayera E Hassan – Nature Scientific Reports

Origin of the neonatal gut microbiota and probiotic intervention: a randomized controlled trial – Zhe Li – Frontiers in Nutrition

Effectiveness of probiotic- and fish oil-loaded water-in-oil-in-water (W1/O/W2) emulsions at alleviating ulcerative colitis – Qingzhao Gu – Food & Function

Plant, root, and soil microbiome

Competition mode and soil nutrient status shape the role of soil microbes in the diversity–invasibility relationship – Haokun Li – Ecology and Evolution

Dynamics and drivers of fungal communities in a multipartite ant-plant association – Veronica Barrajon-Santos – BMC Biology

Quorum sensing related activities of beneficial and pathogenic bacteria have important implications for plant and human health – Anton Hartmann – FEMS Microbiology Ecology

Impacts of vegetable processing and cheese making effluent on soil microbial functional diversity, community structure, and denitrification potential of land treatment systems – Geoffrey S. Siemering – Water Environment Research

Role of Bacillus subtilis exopolymeric genes in modulating rhizosphere microbiome assembly – Caroline Sayuri Nishisaka – BMC Environmental Microbiome

The predominant lactic acid bacteria and yeasts involved in the spontaneous fermentation of millet during the production of the traditional porridge Hausa koko in Ghana – Amy Atter – BMC Microbiology

Bioinformatics & Tools

Multi-class boosting for the analysis of multiple incomplete views on microbiome data – Andrea Simeon – BMC Bioinformatics

PrimerEvalPy: a tool for in-silico evaluation of primers for targeting the microbiome – Lara Vázquez-González – BMC Bioinformatics

Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches – Ryan Kuster – BMC Bioinformatics