October 30, 2023

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Human and General Microbiome

Amino acid auxotrophies in human gut bacteria are linked to higher microbiome diversity and long-term stability – Svenja Starke – The ISME Journal

Gut microbiota impacts bone via Bacteroides vulgatus-valeric acid-related pathways – Xu Lin – Nature Communications

The global burden of antimicrobial resistance – urinary tract infections – Sibylle Von Vietinghoff – Nephrology, Dialysis, Transplantation

Class I HLA Allele Predicted Restricted Antigenic Coverages for Fap2 Protein of Fusobacterium nucleatum Are Associated with Colorectal Cancer Incidence – Mustapha Zeddou – Asian Pacific Journal of Cancer Prevention

Microbial-dependent recruitment of immature myeloid cells promotes intestinal regeneration – Zhengyu Jiang – Cellular and Molecular Gastroenterology and Hepatology

Prior antibiotic administration disrupts anti-PD-1 responses in advanced gastric cancer by altering the gut microbiome and systemic immune response – Chang Gon Kim – Cell Reports Medicine

Gut microbiome dynamics in index patients colonized with extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales after hospital discharge and their household contacts – Janetta Top – Microbiology Spectrum

White-nose syndrome restructures bat skin microbiomes – Meghan Ange-Stark – Microbiology Spectrum

Linking Clinical Blood Metabogram and Gut Microbiota – Petr G Lokhov – Metabolites

A citizen-science-enabled catalogue of the vaginal microbiome and associated factors – Sarah Lebeer – Nature Microbiology

Low-dose ethanol consumption inhibits neutrophil extracellular traps formation to alleviate rheumatoid arthritis – Lin Jin – Communications Biology

Community composition and the environment modulate the population dynamics of type VI secretion in human gut bacteria – Sophie Robitaille – Nature Ecology & Evolution

Extension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions – Aitor Blanco-Míguez – Cell Host & Microbe

Gut microbe-metabolite profiles are associated with microbial pathways of longevity in women: a cross-sectional study conducted in China – Qinren Zhang – Gerontology

Longitudinal analysis of vaginal microbiota during IVF fresh embryo transfer and in early pregnancy – Sofia Väinämö – Microbiology Spectrum

Gut microbiota and autism spectrum disorders: where do we stand? – Sa’ed H Zyoud – Gut Pathogens

Host fecal DNA specific methylation signatures mark gut dysbiosis and inflammation in children affected by autism spectrum disorder – Mariella Cuomo – Scientific Reports

Gut microbiome-derived ammonia modulates stress vulnerability in the host – Pei Wang – Nature Metabolism

Nanobodies against C. difficile TcdA and TcdB reveal unexpected neutralizing epitopes and provide a toolkit for toxin quantitation in vivo – Shannon L Kordus – PLoS Pathogens

Review: Microbiome-based therapies for periodontitis and peri-implantitis – Xindi Wei – Oral Diseases

Animal Microbiome

Distinct gut microbial communities and functional predictions in divergent ophiuroid species: host differentiation, ecological niches, and adaptation to cold-water habitats – Yue Dong – Microbiology Spectrum

Integrated multi-omics analysis reveals the positive leverage of citrus flavonoids on hindgut microbiota and host homeostasis by modulating sphingolipid metabolism in mid-lactation dairy cows consuming a high-starch diet – Yuchao Zhao – Microbiome

More Microbes

Review: Update on novel validly published taxa of bacteria isolated from domestic animals described in 2022 – Sara D Lawhon – Journal of Clinical Microbiology

Plant Microbiome

Location: root architecture structures rhizosphere microbial associations – Tania Galindo-Castañeda – Journal of Experimental Botany

Environmental Microbiome

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem – Clement Coclet – Microbiome

Shotgun metagenomics and computational profiling of the plastisphere microbiome: unveiling the potential of enzymatic production and plastic degradation – Mahnoor Saleem – Archives of Microbiology

Microbiome Analysis: Tools, Techniques and Resources

Machine-learning analysis of cross-study samples according to the gut microbiome in 12 infant cohorts – Petri Vänni – mSystems

Analyzing microbial evolution through gene and genome phylogenies – Sarah Teichman – Biostatistics

AnimalMetaOmics: a multi-omics data resources for exploring animal microbial genomes and microbiomes – Ruirui Hu – Nucleic Acids Research

SPIRE: a Searchable, Planetary-scale mIcrobiome REsource – Thomas S B Schmidt – Nucleic Acids Research

ACR: metagenome-assembled prokaryotic and eukaryotic genome refinement tool – Hoon Je Seong – Briefings in Bioinformatics

dbAPIS: a database of anti-prokaryotic immune system genes – Yuchen Yan – Nucleic Acids Research

Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis – Sinan U Umu – GigaScience

aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow – Zoé Pochon – Genome Biology

October 23, 2023

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Human and General Microbiome

Secretory IgA impacts the microbiota density in the human nose – Rob van Dalen – Microbiome

Disease-specific loss of microbial cross-feeding interactions in the human gut – Vanessa R Marcelino – Nature Communications

Feasibility of a dietary intervention to modify gut microbial metabolism in patients with hematopoietic stem cell transplantation – Mary M Riwes – Nature Medicine

Four functional profiles for fibre and mucin metabolism in the human gut microbiome – Simon Labarthe – Microbiome

The airway microbiota of neonates colonized with asthma-associated pathogenic bacteria – Jonathan Thorsen – Nature Communications

Multiomic profiling of cutaneous leishmaniasis infections reveals microbiota-driven mechanisms underlying disease severity – Camila Farias Amorim – Science Translational Medicine

Tumor-resident Lactobacillus iners confer chemoradiation resistance through lactate-induced metabolic rewiring – Lauren E Colbert – Cancer Cell

Analysis of the influence of host lifestyle (coffee consumption, drinking, and smoking) on Korean oral microbiome – Kyeong-Min Yu – Forensic Science International. Genetics

Potential roles of gut microbiota in metal mixture and bone mineral density and osteoporosis risk association: an epidemiologic study in Wuhan – Jianli Zhang – Environmental Science and Pollution Research International

Characteristics of gut microbiota and metabolic phenotype in patients with major depressive disorder based on multi-omics analysis – Xianpeng Zu – Journal of Affective Disorders

The role of microbial interactions in dental caries: Dental plaque microbiota analysis – Qingyi Shao – Microbial Pathogenesis

A distinctive subgingival microbiome in patients with periodontitis and Alzheimer’s disease compared with cognitively unimpaired periodontitis patients – Hee Sam Na – Journal of Clinical Periodontology

Review: On developmental programming of the immune system – Jun Young Hong – Trends in Immunology

Review: Regulation of pain perception by microbiota in Parkinson’s Disease – Zulmary Manjarres – Pharmacological Reviews

Review: Single-cell analysis and spatial resolution of the gut microbiome – Bhoomi Madhu – Frontiers in Cellular and Infection Microbiology

Beneficial Microbes and Compounds

Synbiotic Sapota-do-Solimões (Quararibea cordata Vischer) Juice Improves Gut Microbiota and Short-Chain Fatty Acid Production in an In Vitro Model – Rhonyele Maciel da Silva – Probiotics and Antimicrobial Proteins

Limosilactobacillus fermentum HF06-derived paraprobiotic and postbiotic alleviate intestinal barrier damage and gut microbiota disruption in mice with ulcerative colitis – Chunhong Liu – Journal of the Science of Food and Agriculture

Animal Microbiome (including Animal Models)

A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs – Mirja Thomsen – Microbiome

High soluble fiber promotes colorectal tumorigenesis through modulating gut microbiota and metabolites in mice – Jia Yang – Gastroenterology

Gut bacterial consortium enriched in a biofloc system protects shrimp against Vibrio parahaemolyticus infection – Haipeng Guo – Microbiome

Environmental Microbiome

Prokaryotic communities inhabiting a high-radon subterranean ecosystem (Castañar Cave, Spain): Environmental and substrate-driven controls – Tamara Martin-Pozas – Microbiological Research

Review: The interplay between microbial communities and soil properties – Laurent Philippot – Nature Reviews. Microbiology

Plant Microbiome

Insights into accumulation of active ingredients and rhizosphere microorganisms between Salvia miltiorrhiza and S. castanea – Zishu Xu – FEMS Microbiology Letters

Microbiome and Evolution

Review: Hierarchical eco-evo dynamics mediated by the gut microbiome – Ellen Decaestecker – Trends in Ecology & Evolution

October 18, 2023

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Human gut microbiome

Association between gut microbiota and influenza: a bidirectional two-sample mendelian randomization study – Xu et al. – BMC Infectious Diseases

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

LACC1 regulates changes in the intestinal flora in a mouse model of inflammatory bowel disease – Xu & Wang – BMC Gastroenterology

Animal microbiome (for animals in the wild)

[PREPRINT]Sex-specific gut bacteria manipulation impacts offspring production in the honeybee parasite small hive beetle, Aethina tumida Murray – Biswas et al. – bioRxiv

Selective enrichment of founding reproductive microbiomes allows extensive vertical transmission in a fungus-farming termite – Sinotte et al. – Proc. R. Soc. B

Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing – Klinsawat et al. – Scientific Reports

Temporal and spatial variations in body mass and thermogenic capacity associated with alterations in the gut microbiota and host transcriptome in mammalian herbivores – Ren et al. – Science of The Total Environment

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Metagenome sequencing and recovery of 444 metagenome-assembled genomes from the biofloc aquaculture system – Rajeev et al. – Scientific Data

Net-spinning caddisflies create denitrifier-enriched niches in the stream microbiome – Bertagnolli et al. – ISME Communications

Parasites, Phages and viruses

Effects of heat tolerance on the gut microbiota of Sarcophaga peregrina (Diptera: Sarcophagidae) and impacts on the life history traits – Ren et al. – Parasites & Vectors

Bioinformatics / Techniques

[PREPRINT]Comprehensive Identification of Pathogenic Microbes and Antimicrobial Resistance Genes in Food Products Using Nanopore Sequencing-Based Metagenomics – Wing-Tung et al. – bioRxiv

Causal inference on microbiome-metabolome relations in observational host-microbiome data via in silico in vivo association pattern analyses – Hertel et al. – Cell Reports Methods

Rank selection for non-negative matrix factorization – Cai, Gu & Kenney

October 16, 2023

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Human and General Microbiome

A Sedentary Lifestyle Changes the Composition and Predicted Functions of the Gut Bacterial and Fungal Microbiota of Subjects from the Same Company – Longwei Xu – Current Microbiology

Animal Microbiome

Effect of urbanization and parasitism on the gut microbiota of Darwin’s finch nestlings – Gabrielle Solomon – Molecular Ecology

Metabarcoding using nanopore long-read sequencing for the unbiased characterization of apicomplexan haemoparasites – Lucas G Huggins – Molecular Ecology Resources

Bacterial networks in Atlantic salmon with Piscirickettsiosis – Yoandy Coca – Scientific Reports

Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions that respond to ovulation regulation in the mouse endometrium – Sisi Pu – BMC Genomics

Beneficial Microbes, Foods and Compounds

Probiotic-fermented tomato alleviates high-fat diet-induced obesity in mice: Insights from microbiome and metabolomics – Benliang Wei – Food Chemistry

Lactobacillus rhamnosus Modulates Lung Inflammation and Mitigates Gut Dysbiosis in a Murine Model of Asthma-COPD Overlap Syndrome – Jéssica Aparecida Vasconcelos – Probiotics and Antimicrobial Proteins

Fermented Goat’s Milk Contributes to the Recovery of Iron Deficiency Anemia via Modulation of the Gut Microbiome – Ana Soriano-Lerma – Journal of Agricultural and Food Chemistry

Environmental Microbiome

Coexistence of specialist and generalist species within mixed plastic derivative-utilizing microbial communities – Laura Schaerer – Microbiome

Review: A critical review of the recent trends in source tracing of microplastics in the environment – Kiruthika K M – Environmental Research

Keystone taxa of phoD-harboring bacteria mediate alkaline phosphatase activity during biochar remediation of Cd-contaminated soil – Qiang Wang – The Science of the Total Environment

Plant Microbiome

Maintaining beneficial alga-associated bacterial communities under heat stress: Insights from controlled co-culture experiments using antibiotic-resistant bacterial strains – Elham Karimi – FEMS Microbiology Ecology

Review: Deep discovery informs difficult deployment in plant microbiome science – Dor Russ – Cell

Highlights: Plant cell wall component induced bacterial development – Ákos T Kovács – Trends in Microbiology

Microbiome Analysis: Tools, Techniques and Resources

MGS2AMR: a gene-centric mining of metagenomic sequencing data for pathogens and their antimicrobial resistance profile – Pieter-Jan Van Camp – Microbiome

Subgroup Identification Using Virtual Twins for Human Microbiome Studies – Hyunwook Koh – IEEE/ACM Transactions on Computational Biology and Bioinformatics

October 13, 2023

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Today’s digest features the Chinese Gut Microbiome Resource, plate readers in the anaerobic chamber, seasonal stability of sponge microbiomes, and more.

Also, you can support the outreachy bugsigdb project by sharing your study to be curated (more info here https://www.outreachy.org/apply/project-selection/#bioconductor or contact me). See you at #MVIF next week!

General

From hype to hope: considerations in conducting robust microbiome science – Amelia J McGuinness – Brain, Behavior, and Immunity

Global

Unraveling the functional dark matter through global metagenomics – Georgios A. Pavlopoulos – Nature

Human gut microbiome

Integration of 168,000 samples reveals global patterns of the human gut microbiome – Richard J. Abdill – bioRxiv

Analysis of strain, sex, and diet-dependent modulation of gut microbiota reveals candidate keystone organisms driving microbial diversity in response to American and ketogenic diets – Anna C. Salvador – Microbiome

Gut microbial genomes with paired isolates from China signify probiotic and cardiometabolic effects – Pan Huang – bioRxiv

Gut microbiota profiles in feces and paired tumor and non-tumor tissues from Colorectal Cancer patients. Relationship to the Body Mass Index – Sofía Tesolato – PlosOne

Tracking gut microbiome and bloodstream infection in critically ill adults – Christopher H. Gu – PlosOne

Human milk

Human milk oligosaccharides modify the strength of priority effects in the Bifidobacterium community assembly during infancy – Martin F. Laursen & Henrik M. Roager – The ISME Journal

Antibiotic Resistome

Metagenome meta-analysis reveals an increase in the abundance of some multidrug efflux pumps and mobile genetic elements in chemically polluted environments – Jessica Subirats – Applied and Environmental Microbiology

Plant microbiome

Characterization of Differences of Seed Endophytic Microbiome in Conventional and Organic Rice by Amplicon-based Sequencing and Culturing Methods – Sabin Khana – bioRxiv

Animal microbiome

Microbiome species diversity and seasonal stability of two temperate marine sponges Hymeniacidon perlevis and Suberites massa – Claire E. Lamb & Joy E. M. Watts – Environmental Microbiome

An observational study of the presence and variability of the microbiota composition of goat herd milk related to mainstream and artisanal farm management – Rita A. H. Hoving-Bolink – PlosOne

Technique

Cultivating efficiency: High-throughput growth analysis of anaerobic bacteria in compact microplate readers – Oona L.O. Snoeyenbos-West – bioRxiv

Bioinformatics

On the relationship between protist metabarcoding and protist metagenome-assembled genomes – Daryna Zavadska – bioRxiv

Track, Analyze, Visualize: Unravel Your Microbiome’s Temporal Tale with MicrobiomeStat – Chen Yang & MicrobiomeStat team

October 11, 2023

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General microbiome

Major data analysis errors invalidate cancer microbiome findings – Gihawi et al. – mBio

Relative abundance data can misrepresent heritability of the microbiome – Bruihning et al. – Microbiome

Human gut microbiome

Discrimination exposure impacts unhealthy processing of food cues: crosstalk between the brain and gut – Zhang et al. – Nature Mental Health

[REVIEW]The impact of acute and chronic stress on gastrointestinal physiology and function: a microbiota–gut–brain axis perspective – Leigh et al. – The Journal of Physiology

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Vertical transmission of gut bacteria in commercial chickens is limited – Shterzer et al. – Animal Microbiome

Animal microbiome (for animals in the wild)

[PREPRINT]The role of family and environment in determining the skin microbiome of captive aquatic frogs, Xenopus laevis – Chapman et al. – bioRxiv

Vertical transmission of gut bacteria in commercial chickens is limited – Shterzer et al. – Animal Microbiome

Bioinformatics/Techiques

[PREPRINT]MetaQuad: Shared Informative Variants Discovery in Metagenomic Samples – Xu et al. – bioRxiv

[PREPRINT]Insertion sequence driven evolution of the microbiota revealed by a novel metagenomics pipeline – Kirsch, Hryckowian & Duerkop

[PREPRINT]A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics – Eisenhofer et al. – bioRxiv

The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling – Zhang et al. – Applied and Environmental Microbiology

[PERSPECTIVE]Challenges and opportunities in sharing microbiome data and analyses – Huttenhower, Finn & McHardy – Nature Microbiology

October 9, 2023

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Human and General Microbiome

Mitochondrial dysfunction promotes microbial composition that negatively impacts on ulcerative colitis development and progression – Ainize Peña-Cearra – NPJ Biofilms and Microbiomes

The recovery of the microbial community after plaque removal depends on periodontal health status – Xiaoqing Li – NPJ Biofilms and Microbiomes

Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 +  – Massimo Bellato – Scientific Reports

COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition – Shilin Zhao – NPJ Vaccines

Spatial diversity of the skin bacteriome – Marcos Pérez-Losada – Frontiers in Microbiology

Microbiota-gut-brain axis drives overeating disorders – Sijia Fan – Cell Metabolism

Review: Human-gut bacterial protein-protein interactions: understudied but impactful to human health – Diana Balint – Trends in Microbiology

Review: Progress of linking gut microbiota and musculoskeletal health: casualty, mechanisms, and translational values – Yu Wang – Gut Microbes

Review: The microbial landscape of colorectal cancer – Maxwell T White – Nature Reviews. Microbiology

Beneficial Microbes and Compounds

Probiogenomics of Leuconostoc Mesenteroides Strains F-21 and F-22 Isolated from Human Breast Milk Reveal Beneficial Properties – Juan Carlos Ariute – Probiotics and Antimicrobial Proteins

Faecalibacterium prausnitzii, Bacteroides faecis and Roseburia intestinalis attenuate clinical symptoms of experimental colitis by regulating Treg/Th17 cell balance and intestinal barrier integrity – Nooshin Mohebali – Biomedicine & Pharmacotherapy 

Simulated gastrointestinal digestion of beer using the simgi® model. Investigation of colonic phenolic metabolism and impact on human gut microbiota – Magaly Rodriquez-Saavedra – Food Research International

Animal Microbiome (Model and Non-model organisms)

High temperatures augment inhibition of parasites by a honey bee gut symbiont – Evan C Palmer-Young – Applied and Environmental Microbiology

The maternal microbiome promotes placental development in mice – Geoffrey N Pronovost – Science Advances

Omics-Based Mathematical Modeling Unveils Pathogenesis of Periodontitis in an Experimental Murine Model – C Fujihara – Journal of Dental Research

Environmental Microbiome

Compost, plants and endophytes versus metal contamination: choice of a restoration strategy steers the microbiome in polymetallic mine waste – Martina Kracmarova-Farren – Environmental Microbiome

Litter decomposition and nutrient release are faster under secondary forests than under Chinese fir plantations with forest development – Shuaijun Li – Scientific Reports

Microbiome Analysis: Tools, Techniques and Resources

PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation – Guangping Huang – Microbiome

The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling – Tianyuan Zhang – Applied and Environmental Microbiology

October 4, 2023

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General microbiome

[OPINION]Toward an integrative framework for microbial community coalescence – Custer, Bresciani & Dini-Andreote – Trends in Microbiology

Statistically learning the functional landscape of microbial communities – Skwara et al. – Nature Ecology & Evolution

Human skin microbiome

Skin microbiota secretomes modulate cutaneous innate immunity against Borrelia burgdorferi s.s – Baquer et al. – Scientific Reports

Human gut microbiome

Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort – Galperine et al. – BMC Infectious Diseases

Association Between Bowel-Movement Pattern and Cognitive Function: Prospective Cohort Study and a Metagenomic Analysis of the Gut Microbiome – Ma et al. – Neurology

[REVIEW]The gut microbiome tango in the progression of chronic kidney disease and potential therapeutic strategies – Tang, Yu & Pan – Journal of Translational Medicine

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Microbiota-gut-brain axis drives overeating disorder – Fan et al. – Cell Metabolism

Animal microbiome (for animals in the wild)

Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics – Wang et al. – Animal Microbiome

Plant, root, and soil microbiome

Using wasps as a tool to restore a functioning vine grape mycobiota and preserve the mycobial “terroir” – Di Paola et al. – Scientific Reports

Soil microbes mediate the effects of resource variability on plant invasion – Zhang et al. – Ecology

Bioinformatics

[PREPRINT]Deepurify: a multi-modal deep language model to remove contamination from metagenome-assembled genomes – Zou et al. – bioRxiv

[PREPRINT]BATTER: Accurate Prediction of Rho-dependent and Rho-independent Transcription Terminators in Metagenomes – Jin et al. – bioRxiv

[PREPRINT]Gut Microbiome Wellness Index 2 for Enhanced Health Status Prediction from Gut Microbiome Taxonomic Profiles – Chang et al. – bioRxiv

Techniques

INVADEseq to identify cell-adherent or invasive bacteria and the associated host transcriptome at single-cell-level resolution – Nino et al. – Nature Protocols

October 2, 2023

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Highlights!

Review: A relational framework for microbiome research with Indigenous communities – Alyssa C Bader – Nature Microbiology

Review: Microbiome ownership for Indigenous peoples – Matilda Handsley-Davis – Nature Microbiology

Human and General Microbiome

Expanded microbiome niches of RAG-deficient patients – Ryan A Blaustein – Cell Reports Medicine

Low dietary fiber intake impairs small intestinal Th17 and intraepithelial T cell development over generations – Charlotte J Royer – Cell Reports

Iron acquisition by a commensal bacterium modifies host nutritional immunity during Salmonella infection – Luisella Spiga – Cell Host & Microbe

Microbiome profile and calprotectin levels as markers of risk of recurrent Clostridioides difficile infection – Silvia Vázquez-Cuesta – Frontiers in Cellular and Infection Microbiology

Safety and tolerability of frozen, capsulized autologous faecal microbiota transplantation. A randomized double blinded phase I clinical trial – Måns Stefansson – PloS One

Metabolism of azo food dyes by bacterial members of the human gut microbiome – Riley Elder – Anaerobe

Genetic risk score in multiple sclerosis is associated with unique gut microbiome – Noha S Elsayed – Scientific Reports

Antisense inhibition of RNA polymerase α subunit of Clostridioides difficile – Rusha Pal – Microbiology Spectrum

Review: Metabolic signature for a dysbiotic microbiome in the female genital tract: A systematic review and meta-analysis – Biban Gill – American Journal of Reproductive Immunology

Review: Influence of Plant-Based Diet on the Cardiovascular System: A Narrative Review – Gurusha Jangid – Cardiology in Review

Review: Bile acid and its bidirectional interactions with gut microbiota: a review – Shuqi He – Critical Reviews in Microbiology

Animal Microbiome

Population mixing mediates the intestinal flora composition and facilitates invasiveness in a globally invasive fruit fly – Yidan Wang – Microbiome

Diet-related factors strongly shaped the gut microbiota of Japanese macaques – Wanyi Lee – American Journal of Primatology

Skin and gut microbiomes of tadpoles vary differently with host and water environment: a short-term experiment using 16S metabarcoding – Bárbara Santos – Scientific Reports

Multi-omics revealed the long-term effect of ruminal keystone bacteria and the microbial metabolome on lactation performance in adult dairy goats – Dangdang Wang – Microbiome

The multi-kingdom microbiome of the goat gastrointestinal tract – Yanhong Cao – Microbiome

Multi-breed host rumen epithelium transcriptome and microbiome associations and their relationship with beef cattle feed efficiency – P A S Fonseca – Scientific Reports

Animal Model Microbiome

Select symbionts drive high IgA levels in the mouse intestine – Shanshan Zhang – Cell Host & Microbe

Blocked conversion of Lactobacillus johnsonii derived acetate to butyrate mediates copper-induced epithelial barrier damage in a pig model – Yang Wen – Microbiome

Laboratory mice with a wild microbiota generate strong allergic immune responses – Junjie Ma – Science Immunology

Plant Microbiome

Host genetic variation drives the differentiation in the ecological role of the native Miscanthus root-associated microbiome – Niuniu Ji – Microbiome

Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial Pseudomonas in the wheat rhizosphere – Daniel Garrido-Sanz – Microbiome

Microbially produced fertilizer provides rhizobacteria to hydroponic tomato roots by forming beneficial biofilms – Yuya Sato – Applied Microbiology and Biotechnology

Terpenes modulate bacterial and fungal growth and sorghum rhizobiome communities – Ming-Yi Chou – Microbiology Spectrum 

Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development – Ella T Sieradzki – mSystems

Environmental Microbiome

The presence of benzene ring activating CoA ligases for aromatics degradation in the ANaerobic MEthanotrophic (ANME) archaea – Wei-Wei Liu – Microbiology Spectrum

Microbial biogeography of pit mud from an artificial brewing ecosystem on a large time scale: all roads lead to Rome – Jun-Lan Mei – mSystems

Stable microbial community in compacted bentonite after 5 years of exposure to natural granitic groundwater – Katja Engel – mSphere

Microbiome Analysis Tools, Techniques and Resources

Impact of Experimental Bias on Compositional Analysis of Microbiome Data – Yingtian Hu – Genes

happi: a hierarchical approach to pangenomics inference – Pauline Trinh – Genome Biology

Integrating a tailored recurrent neural network with Bayesian experimental design to optimize microbial community functions – Jaron C Thompson – PLoS Computational Biology

Review: Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics – Koji Arikawa – Computational and Structural Biotechnology Journal

September 27, 2023

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General microbiome

The Triple Alliance: Microbiome, Mitochondria, and Metabolites in the Context of Age-Related Cognitive Decline and Alzheimer’s Disease – Prajapiti et al. – The Journals of Gerontology: Series A

[REVIEW]Genomic surveillance for antimicrobial resistance — a One Health perspective – Djordjevic et al. – Nature Reviews Genetics

Human respiratory microbiome

[REVIEW]Lung Microbiome as a Treatable Trait in Chronic Respiratory Disorders – Scialo et al. – Lung

Human gut microbiome

[PREPRINT]Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation – Xue et al. – bioRxiv

[PREPRINT]A gut meta-interactome map reveals modulation of human immunity by microbiome effectors – Young et al. – bioRxiv

[PREPRINT]Association of homelessness and diet on the gut microbiome: A United States-Veteran Microbiome Project (US-VMP) study – Hoisington et al. – bioRxiv

Plant, root, and soil microbiome

Tomato growth stage modulates bacterial communities across different soil aggregate sizes and disease levels – Dong et al. – ISME Communications

Soil microbial diversity and network complexity drive the ecosystem multifunctionality of temperate grasslands under changing precipitation – Zhai et al. – Science of The Total Environment

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt, rocks)

Arctic bacterial diversity and connectivity in the coastal margin of the Last Ice Area – Girard, Vincent & Culley – ISME Communications

A glimpse of the paleome in endolithic microbial communities – Wegener et al. – Microbiome

Bioinformatics

A computational method to dissect colonization resistance of the gut microbiota against pathogens – Ke et al. – Cell Reports Methods

[PREPIRNT]SurvBal: Compositional Microbiome Balances for Survival Outcomes – Li et al. – bioRxiv