Tag Archives: human microbiome

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 29, 2024

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Human microbiomes

Gut microbiome remodeling and metabolomic profile improves in response to protein pacing with intermittent fasting versus continuous caloric restriction – Alex E. Mohr – Nature Communications

[PREPRINT] Towards a Health-Associated Core Keystone (HACK) index for the human gut microbiome – Abishek Goel – bioRxiv

Exposure to environmental pollutants selects for xenobiotic-degrading functions in the human gut microbiome – Francesca De Fillipis – Nature Communications

The interrelation between microbial immunoglobulin coating, vaginal microbiota, ethnicity, and preterm birth – H.J. Schuster – BMC Microbiome

Porphyromonas gingivalis, a bridge between oral health and immune evasion in gastric cancer – Matías Muñoz-Medel – Frontiers in Oncology

Differences in maternal subgingival microbiome between preterm and term births: The MOHEPI study – Jung Soo Park – Journal of Periodontal Resaerch

Animal microbiome

Integrating uterine microbiome and metabolome to advance the understanding of the uterine environment in dairy cows with metritis – S. Casaro – BMC Animal Microbiome

Responses of nutrient utilization, rumen fermentation and microorganisms to different roughage of dairy buffaloes – Shichun He – BMC Microbiology

Identification of the mutual gliding locus as a factor for gut colonization in non-native bee hosts using the ARTP mutagenesis – Yujie Meng – BMC Microbiome

Co-habiting ants and silverfish display a converging feeding ecology – Thomas Parmentier – BMC Biology

Temperature-dependent differences in mouse gut motility are mediated by stress – Alvin Han – Nature Lab Animal

Food microbiome

Evaluation of microbiota-induced changes in biochemical, sensory properties and volatile profile of kombucha produced by reformed microbial community – Hilal Kilmanoglu – Food Chemistry X

Plant, soil, and root microbiome

Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle – Bridget B. McGivern – Nature Microbiology

[PREPRINT] Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils – Samuel E. Barnett & Ashley Shade – bioRxiv

Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome – Yoko Masuda – BMC Microbiome

Water & extremophile microbiome

Bacterial dynamics of the plastisphere microbiome exposed to sub-lethal antibiotic pollution – Brune Jounnard & Concepcion Sanchez-Cid – BMC Microbiome

Exploring potential polysaccharide utilization loci involved in the degradation of typical marine seaweed polysaccharides by Bacteroides thetaiotaomicron – Biao Yu – Frontiers in Microbiology

Organic matter degradation in the deep, sulfidic waters of the Black Sea: insights into the ecophysiology of novel anaerobic bacteria – Subhash Yadav – BMC Microbiome

May 26, 2024

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Human Microbiome in General

Microbiome research in Africa must be based on equitable partnerships – Ovokeraye H Oduaran – Nature Medicine

Human Gut Microbiome

IL-33 controls IL-22-dependent antibacterial defense by modulating the microbiota – Ivo Röwekamp – PNAS

Meta-analysis of shotgun sequencing of gut microbiota in Parkinson’s disease – Hiroshi Nishiwaki – NPJ Parkinson’s Disease

Systematic review of associations between gut microbiome composition and stunting in under-five children – Mwelwa Chibuye – NPJ Biofilms and Microbiomes

Production of deoxycholic acid by low-abundant microbial species is associated with impaired glucose metabolism – Annika Wahlström – Nature Communications

Altered gut microbiota is associated with the formation of occult hepatitis B virus infection – Bochao Liu – Microbiology Spectrum

Metagenome-assembled genomes (MAGs) suggest an acetate-driven protective role in gut microbiota disrupted by Clostridioides difficile – Giovanny Herrera – Microbiological Research

Review: From gut microbiota to brain: implications on binge eating disorders – Weiwei Guo – Gut Microbes

Review: Pathogenesis and therapeutic opportunities of gut microbiome dysbiosis in critical illness – Nicole A Cho – Gut Microbes

Human Respiratory Tract Microbiome

Pathobiological signatures of dysbiotic lung injury in pediatric patients undergoing stem cell transplantation – Matt S Zinter – Nature Medicine

Human Genitourinary Tract Microbiome

Leveraging existing 16S rRNA gene surveys to decipher microbial signatures and dysbiosis in cervical carcinogenesis – Xiaoxiao Li – Scientific Reports

Targeting Megasphaera species to promote cervicovaginal health – Mariano A Molina – Trends in Microbiology

Beneficial Microbes and Compounds

Prodrug-conjugated tumor-seeking commensals for targeted cancer therapy – Haosheng Shen – Nature Communications

Fecal microbiota transplantation significantly improved respiratory failure of amyotrophic lateral sclerosis – Jingshuang Yan – Gut Microbes

The use of probiotics and prebiotics in decolonizing pathogenic bacteria from the gut; a systematic review and meta-analysis of clinical outcomes – Md Nannur Rahman – Gut Microbes

Review: Advanced microbiome therapeutics as a novel modality for oral delivery of peptides to manage metabolic diseases – Ruben Vazquez-Uribe – Trends in Endocrinology and Metabolism

Animal Microbiome

Identification of the mutual gliding locus as a factor for gut colonization in non-native bee hosts using the ARTP mutagenesis – Yujie Meng – Microbiome

Symbiotic bacteria and fungi proliferate in diapause and may enhance overwintering survival in a solitary bee – Shawn M Christensen – The ISME Journal

Plant Microbiome

Phages enhance both phytopathogen density control and rhizosphere microbiome suppressiveness – Xiaofang Wang – mBio

Environmental Microbiome

Global epistasis and the emergence of function in microbial consortia – Juan Diaz-Colunga – Cell

Bacterial dynamics of the plastisphere microbiome exposed to sub-lethal antibiotic pollution – Brune Joannard – Microbiome

Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome – Yoko Masuda – Microbiome

A global initiative for ecological and evolutionary hologenomics – Aoife Leonard – Trends in Ecology & Evolution

Built Environment Microbiome

Fungal diversity differences in the indoor dust microbiome from built environments on earth and in space – Nicholas Nastasi – Scientific Reports

Microbiome Analysis: Tools, Techniques and Resources

A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease – Katherine Do – mSphere

A comparative study of supervised and unsupervised machine learning algorithms applied to human microbiome – E Kalluçi – La Clinica Terapeutica

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

May 12, 2024

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Human and General Microbiome

Preservation of conjugated primary bile acids by oxygenation of the small intestinal microbiota in vitro – Jenni Firrman – mBio

HIV rebound in HIV controllers is associated with a specific fecal microbiome profile – Yanhui Cai – European Journal of Immunology

Comparative analysis of the tumor microbiome, molecular profiles, and immune cell abundances by HPV status in mucosal head and neck cancers and their impact on survival – Rituraj Upadhyay – Cancer Biology & Therapy

Metatranscriptome and resistome of the endodontic microbiome – Ericka T Pinheiro – Journal of Endodontics

Microbiome of periodontitis and peri-implantitis before and after therapy: Long-read 16S rRNA gene amplicon sequencing – Pei-Shiuan Yu – Journal of Periodontal Research

Review: Akkermansia muciniphila: a deworming partner independent of type 2 immunity – Jiaqi Wang – Gut Microbes

Review: The gut microbiome in alcohol use disorder and alcohol-associated liver disease: A systematic review of clinical studies – Erica N Grodin – Alcohol, Clinical & Experimental Research

Review: Bile acid-microbiota crosstalk in hepatitis B virus infection – Jiaxin Wang – Journal of Gastroenterology and Hepatology

Review: Ecological insights into hematopoiesis regulation: unraveling the influence of gut microbiota – Kaiwen Zheng – Gut Microbes

Review: Interactions between host and gut microbiota in gestational diabetes mellitus and their impacts on offspring – Shuxian Wang – BMC Microbiology

Beneficial Microbes and Compounds

Review: Mechanisms of microbiota modulation: Implications for health, disease, and therapeutic interventions – Okechukwu Paul-Chima Ugwu – Medicine

Lactobacillus paracasei Jlus66 relieves DSS-induced ulcerative colitis in a murine model by maintaining intestinal barrier integrity, inhibiting inflammation, and improving intestinal microbiota structure – Fazheng Yu – European Journal of Nutrition

Conjugated linoleic acid metabolite impact in colorectal cancer: a potential microbiome-based precision nutrition approach – Adriana González – Nutrition Reviews

Microbiome in Animal Models

Aging amplifies a gut microbiota immunogenic signature linked to heightened inflammation – Maria Elisa Caetano-Silva – Aging Cell

Bacteroidota inhibit microglia clearance of amyloid-beta and promote plaque deposition in Alzheimer’s disease mouse models – Caroline Wasén – Nature Communications

Prevotella copri promotes vascular calcification via lipopolysaccharide through activation of NF-κB signaling pathway – Qing-Yun Hao – Gut Microbes

Non-Model Animal Microbiome

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

Characterizing the blood microbiota in healthy and febrile domestic cats via 16s rRNA sequencing – Liam Kitson – Scientific Reports

Plant/Rhizosphere Microbiome

Metagenomic sequencing and reconstruction of 82 microbial genomes from barley seed communities – Kalonji A Tshisekedi – Scientific Data

Modulation of rhizosphere microbial community and metabolites by bio-functionalized nanoscale silicon oxide alleviates cadmium-induced phytotoxicity in bayberry plants – Temoor Ahmed – The Science of the Total Environment

Phyllosphere fungal diversity generates pervasive nonadditive effects on plant performance – Brianna K Almeida – The New Phytologist

Environmental Microbiome

Deciphering the functional and structural complexity of the Solar Lake flat mat microbial benthic communities – Rehab Z Abdallah – mSystems

Microbiome processing of organic nitrogen input supports growth and cyanotoxin production of Microcystis aeruginosa cultures – Wei Li – The ISME Journal

Genomic fingerprints of the world’s soil ecosystems – Emily B Graham – mSystems

Review: Insights into cyanobacterial blooms through the lens of omics – Ve Van Le – The Science of the Total Environment

Microbiome Analysis

fastCCLasso: a fast and efficient algorithm for estimating correlation matrix from compositional data – Shen Zhang – Bioinformatics

Review: A Standard Pipeline for Analyzing the Endometrial Microbiome – Mychelle de Medeiros Garcia Torres – Reproductive Sciences 

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

May 5, 2024

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Human and General Microbiome

Paternal microbiome perturbations impact offspring fitness – Ayele Argaw-Denboba – Nature

Oral bacteria relative abundance in faeces increases due to gut microbiota depletion and is linked with patient outcomes – Chen Liao – Nature Microbiology

Human gut microbiota and their production of endocannabinoid-like mediators are directly affected by a dietary oil – Charlène Roussel – Gut Microbes

Leveraging genomic signatures of oral microbiome-associated antibiotic resistance genes for diagnosing pancreatic cancer – Xiaojing Shen – PloS ONE

Deciphering the Pancreatic Cancer Microbiome in Mainland China: Impact of Exiguobacterium/Bacillus ratio on Tumor Progression and Prognostic Significance – Zhengyan Zhang – Pharmacological Research

Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism – Xianyi Xiong – The ISME Journal

Microplastics and microbiota: Unraveling the hidden environmental challenge – Jean Demarquoy – World Journal of Gastroenterology

Genome plasticity shapes the ecology and evolution of Phocaeicola dorei and Phocaeicola vulgatus – Emilene Da Silva Morais – Scientific Reports

Review: A catalog of ethanol-producing microbes in humans – Babacar Mbaye – Future Microbiology

Review: Direct metagenomics investigation of non-surgical hard-to-heal wounds: a review – Madjid Morsli – Annals of Clinical Microbiology and Antimicrobials

Beneficial Microbes

A consortium of Hordeum vulgare and gut microbiota against non-alcoholic fatty liver disease via data-driven analysis – Su-Been Lee – Artificial Cells, Nanomedicine, and Biotechnology

Animal Microbiome

Amphibian tolerance to arsenic: microbiome-mediated insights – Isabella Ferreira Cordeiro – Scientific Reports

Combined effect of seasons and life history in an anuran strengthens the response and relationship between their physiology and gut microbiota – Jun-Kyu Park – Scientific Reports

Gut microbiome and resistome characterization of pigs treated with commonly used post-weaning diarrhea treatments – Judith Guitart-Matas – Animal Microbiome

Effects of microbiome transplants on fly microbiome – Jorge Ferreira – Lab Animal

Multi-omics reveal the gut microbiota-mediated severe foraging environment adaption of small wild ruminants in the Three-River-Source National Park, China – Hongjin Liu – Integrative Zoology

Sea cucumber (Holothuria glaberrima) intestinal microbiome dataset from Puerto Rico, generated by shotgun sequencing – Edwin Omar Rivera-Lopez – Data in Brief

Plant Microbiome

Depletion of protective microbiota promotes the incidence of fruit disease – Xue Luo – The ISME Journal

Analysis of Salt Stress on Soil Microbial Community Composition and Its Correlation with Active Components in the Rhizosphere of Acanthopanax senticosus – Wenhui Yuan – Current Microbiology

Environmental Microbiome

Mechanisms and implications of bacterial-fungal competition for soil resources – Chaoqun Wang – The ISME Journal

Potential coupling of microbial methane, nitrogen, and sulphur cycling in the Okinawa Trough cold seep sediments – Ye Chen – Microbiology Spectrum

Microbiome Analysis

mbDecoda: a debiased approach to compositional data analysis for microbiome surveys – Yuxuan Zong – Briefings in Bioinformatics

EnsembleSeq: a workflow towards real-time, rapid, and simultaneous multi-kingdom-amplicon sequencing for holistic and resource-effective microbiome research at scale – Sunil Nagpal – Microbiology Spectrum

mi-Mic: a novel multi-layer statistical test for microbiota-disease associations – Oshrit Shtossel – Genome Biology

Review: Unveiling microbial diversity: harnessing long-read sequencing technology – Daniel P Agustinho – Nature Methods

April 30, 2024

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Human microbiome

Safety and efficacy of faecal microbiota transplantation in patients with mild to moderate Parkinson’s disease (GUT-PARFECT): a double-blind, placebo-controlled, randomised, phase 2 trial – Anout Bruggeman – eClinicalMedicine

Implications of intestinal microecology and immune function alterations for immunotherapy outcomes in advanced unresectable lung adenocarcinoma – Shuang He – Clinical Respiratory Journal

Recipient microbiome-related features predicting metabolic improvement following fecal microbiota transplantation in adults with severe obesity and metabolic syndrome: a secondary analysis of a phase 2 clinical trial – Zhengxiao Zhang – Gut Microbes

Gut microbiome composition and metabolic activity in women with diverticulitis – Wenjie Ma – Nature Communications

Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development – Raúl Y. Tito – Nature Medicine

Prediction and causal inference of hyperuricemia using gut microbiota – Yuna Miyajima – Scientific Reports

Early-life gut microbiota associates with allergic rhinitis during 13-year follow-up in a Finnish probiotic intervention cohort – Sampo Kallio – Microbiology Spectrum

Food microbiome

The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits – Elena A. Alexa – BMC Microbiome

Animal experiments

Sodium Propionate Oral Supplementation ameliorates Depressive-Like Behavior through Gut Microbiome and Histone 3 Epigenetic Regulation – Luiza Marques Prates Behrens – Journal of Nutritional Biochemistry

Colon impairments and inflammation driven by an altered gut microbiota leads to social behavior deficits rescued by hyaluronic acid and celecoxib – Oryan Agronyoni – BMC Medicine

Dissecting the respective roles of microbiota and host genetics in the susceptibility of Card9−/− mice to colitis – C. Danne – BMC Microbiome

Animal microbiome

Synergistic resistance of honeybee (Apis mellifera) and their gut microorganisms to fluvalinate stress – Jianhui Liu – Pesticide Biochemistry and Physiology

Determinants of microbiome composition: Insights from free-ranging hybrid zebras (Equus quagga × grevyi) – Joel O. Abraham – Molecular Ecology

Water & extremophile microbiomes

Phytoplankton-derived polysaccharides and microbial peptidoglycans are key nutrients for deep-sea microbes in the Mariana Trench – Yan-Ru Dang – BMC Microbiome

Rhizospheric bacteria from the Atacama Desert hyper-arid core: cultured community dynamics and plant growth promotion – Juan Castro-Severyn – Microbiology Spectrum

Tools & techniques

Variability and bias in microbiome metagenomic sequencing: an interlaboratory study comparing experimental protocols – Samuel P. Forry – Scientific Reports

Nanopore and Illumina sequencing reveal different viral populations from human gut samples – Ryan Cook – Microbial Genomics

April 28, 2024

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Human and General Microbiome

Genome Analysis of Epsilon CrAss-like Phages – Igor V Babkin – Viruses

Cervical microbiota dysbiosis associated with high-risk Human Papillomavirus infection – Natalia Zeber-Lubecka – PloS ONE

Association of the trimethylamine N-oxide with cardiovascular risk and vascular alterations in middle-aged patients with risk factors for cardiovascular diseases – Natalia Spasova – Bioscience Reports

Insights into microorganisms, associated factors, and the oral microbiome in infective endocarditis patients – Ayden Ismail – Frontiers in Oral Health

Alterations in the fecal microbiota of methamphetamine users with bad sleep quality during abstinence – Zijing Deng – BMC Psychiatry

Gut microbiome predicts cognitive function and depressive symptoms in late life – A Kolobaric – Molecular Psychiatry

Microbial signatures in human periodontal disease: a metatranscriptome meta-analysis – Armen Ovsepian – Frontiers in Microbiology

Gut microbiome composition reveals the distinctiveness between the Bengali people and the Indigenous ethnicities in Bangladesh – Ishtiaque Ahammad – Communications Biology

Comparative analysis of endometrial, vaginal, and gut microbiota in patients with and without adenomyosis – Marta Valdés-Bango – Acta Obstetricia et Gynecologica Scandinavica

Causal effect of gut microbiota and diabetic nephropathy: a Mendelian randomization study – Ganyuan He – Diabetology & Metabolic Syndrome

The characteristics of microbiome in the upper respiratory tract of COVID-19 patients – Xilong Zhang – BMC Microbiology

Review: Interplay of human gastrointestinal microbiota metabolites: Short-chain fatty acids and their correlation with Parkinson’s disease – Jiaji Liu – Medicine

Review: Natural products from the human microbiome: an emergent frontier in organic synthesis and drug discovery – Saumitra Sengupta – Organic & Biomolecular Chemistry

Review: Oligella spp.: A systematic review on an uncommon urinary pathogen – Eric Farfour – European Journal of Clinical Microbiology & Infectious Diseases

Review: The potential importance of the built-environment microbiome and its impact on human health – Thomas C G Bosch – PNAS

Beneficial Microbes and Compounds

Vitamin D regulates microbiome-dependent cancer immunity – Evangelos Giampazolias – Science 

HMOs Impact the Gut Microbiome of Children and Adults Starting from Low Predicted Daily Doses – Danica Bajic – Metabolites

Effects of microbiome-based interventions on neurodegenerative diseases: a systematic review and meta-analysis – Zara Siu Wa Chui – Scientific Reports

A randomized, double-blinded, placebo-controlled clinical trial on Lactobacillus-containing cultured milk drink as adjuvant therapy for depression in irritable bowel syndrome – Marlynna Sarkawi – Scientific Reports

Animal Microbiome

Review: Understanding the Diversity and Roles of the Ruminal Microbiome – Gi Beom Keum – Journal of Microbiology

Plant Microbiome

Impacts of continuous cropping on the rhizospheric and endospheric microbial communities and root exudates of Astragalus mongholicus – Qin Zhou – BMC Plant Biology

Comparative analysis of root associated microbes in tropical cultivated and weedy rice (Oryza spp.) and temperate cultivated rice – Vani Juliyanti – Scientific Reports

Identifying causes and consequences of rhizosphere microbiome heritability – Maggie R Wagner – PLoS Biology

Environmental Microbiome

Acidithiobacillia class members originating at sites within the Pacific Ring of Fire and other tectonically active locations and description of the novel genus ‘Igneacidithiobacillus’ – Dilanaz Arisan – Frontiers in Microbiology

Exploring changes in microplastic-associated bacterial communities with time, location, and polymer type in Liusha Bay, China – Ting Wang – Marine Environmental Research

Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface – Jennifer L Goff – Environmental Microbiome

Phytoplankton-derived polysaccharides and microbial peptidoglycans are key nutrients for deep-sea microbes in the Mariana Trench – Yan-Ru Dang – Microbiome

Microbiome Analysis

Microbiome compositional data analysis for survival studies – Meritxell Pujolassos – NAR Genomics and Bioinformatics

Other

Periportal macrophages protect against commensal-driven liver inflammation – Yu Miyamoto – Nature

A case study to engage students in the research design and ethics of high-throughput metagenomics – Courtney Carroll Alexander – Journal of Microbiology & Biology Education