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 7, 2024

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Today’s digest features AMPSphere, Candida pathogenesis, rhizosphere microbiome in the Himalayas, imaging of oral microbiome, and more.
See you at #MVIF special event on women’s health!

Global microbiome

Discovery of antimicrobial peptides in the global microbiome with machine learning – Célio Dias Santos-Júnior and Marcelo D.T. Torres – Cell

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

Infant microbiome

The impact of perinatal maternal stress on the maternal and infant gut and human milk microbiomes: A scoping review protocol – Niamh Ryan – Plos One

Oral microbiome

Improved Visualization of Oral Microbial Consortia – S.T. Ramirez-Puebla – Journal of Dental Research

Animal microbiome

Changes of faecal bacterial communities and microbial fibrolytic activity in horses aged from 6 to 30 years old – Marylou Baraille – Plos One

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

Animal experiments

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 – Microbiome

The impact of microplastics polystyrene on the microscopic structure of mouse intestine, tight junction genes and gut microbiota – Qi-Ling Su – Plos One

Epithelial hypoxia maintains colonization resistance against Candida albicans – Hannah P. Savage – Cell Host & Microbe

Viruses and phages

Characterizing the gut phageome and phage-borne antimicrobial resistance genes in pigs – Jun Hu – Microbiome

Water microbiome

Deep long-read metagenomic sequencing reveals niche differentiation in carbon cycling potential between benthic and planktonic microbial populations – Tomeu Viver – bioRxiv

Root, soil, plant microbiome

Altitude-Dependent Influence of Artemisia brevifolia on its Rhizosphere Microbiome in Ladakh Region of the Western Himalayas – Manzoor Hussain – Rhizosphere

Bioinformatics

Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet – Nicolae Sapoval – bioRxiv

Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion – Xiaofan Jin – bioRxiv

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 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 17, 2024

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Today’s digest features bioinformatics binning methods, healthy dogs, lakes in South Africa, and more. For the human gut microbiome studies, check out the latest digest (May 15, 2024) by Grace Deitzler.

See you at #MVIF!

Skin microbiome

Intraspecies warfare restricts strain coexistence in human skin microbiomes – Christopher P. Mancuso – bioRxiv

Oral microbiome

Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study – Memduh Bingöl – Journal of Clinical Periodontology

Urinary microbiome

Microbroth dilution method for antibiotic susceptibility testing of fastidious and anaerobic bacteria of the urinary microbiome – Wilson Geaman – Microbiology Spectrum

Respiratory tract

Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease – Nick Quinn-Bohmann – BMC Biology

Food microbiome

Microbial community structure of plant-based meat alternatives – Franz-Ferdinand Rochn – pj Science of Food

Plan, root, soil

Functional team selection: a framework for local adaptation in plants and their belowground microbiomes – Nancy Collins Johnson and César Marín – ecoevoRxiv

Life on the edge: microbial diversity, resistome, and virulome in soils from the Union Glacier cold desert – Patricio Arros – bioRxiv

Animal microbiome

Microbiota of healthy dogs demonstrate a significant decrease in richness and changes in specific bacterial groups in response to supplementation with resistant starch, but not psyllium or methylcellulose, in a randomized cross-over trial – Silke Salavati Schmitz – Access Microbiology

Early-life factors shaping the gut microbiota of Common buzzard nestlings – Hugo Pereira – Animal Microbiome

Animal experiment

13C-Stable isotope resolved metabolomics uncovers dynamic biochemical landscape of gut microbiome-host organ communications in mice – Xia Xiao – Microbiome

Water microbiome

Metagenomics datasets of water and sediments from eutrophication-impacted artificial lakes in South Africa – Grace Nkechinyere Ijoma – Scientific Data

Bioinformatics

Fairy: fast approximate coverage for multi-sample metagenomic binning – Jim Shaw and Yun William Yu – bioRxiv

Highly accurate metagenome-assembled genomes from human gut microbiota using long-read assembly, binning, and consolidation methods – Daniel M Portik – biorXiv

Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level – Amy S Graham – bioRxiv

Full factorial construction of synthetic microbial communities – Juan Diaz-Colunga – bioRxiv

ARGNet: using deep neural networks for robust identification and classification of antibiotic resistance genes from sequences – Yao Pei – Microbiome