Happy Holidays, from the MicrobiomeDigest team!

Human and General Microbiome

Gut microbiota predicts severity and reveals novel metabolic signatures in acute pancreatitis – Christoph Ammer-Herrmenau – Gut

Human gut microbiota from hepatitis B virus-infected individuals is associated with reduced triglyceride level in mice: faecal transplantation study – Han-Na Kim – Microbes and Infection

Commensal bacteria maintain a Qa-1(b)-restricted unconventional CD8(+) T population in gut epithelium – Jian Guan – eLife

Akkermansia muciniphila – friend or foe in colorectal cancer? – Ekaterina O Gubernatorova – Frontiers in Immunology

Association between erythrocyte membrane fatty acids and gut bacteria in obesity-related cognitive dysfunction – Tong Zhao – AMB Express

Impact of the gut microbiome on immunological responses to COVID-19 vaccination in healthy controls and people living with HIV – Shilpa Ray – NPJ Biofilms and Microbiomes

The relationship between sleep, gut microbiota, and metabolome in patients with depression and anxiety: A secondary analysis of the observational study – Arisa Tanaka – PloS ONE

Persistence of gut dysbiosis in individuals with anorexia nervosa – Yukiko Morisaki – PloS ONE

Unique microbial diversity, community composition, and networks among Pacific Islander endocervical and vaginal microbiomes with and without Chlamydia trachomatis infection in Fiji – Sankhya Bommana – mBio

Gut microbiome-based machine learning for diagnostic prediction of liver fibrosis and cirrhosis: a systematic review and meta-analysis – Xiaopei Liu – BMC Medical Informatics and Decision Making

Targeting gut microbial nitrogen recycling and cellular uptake of ammonium to improve bortezomib resistance in multiple myeloma – Yinghong Zhu – Cell Metabolism

Variations in the oral microbiome and metabolome of methamphetamine users – Dawei Wang – mSystems

Investigating the causal impact of gut microbiota on glioblastoma: a bidirectional Mendelian randomization study – Chuan Zeng – BMC Genomics

Alterations of oral and gut viromes in hypertension and/or periodontitis – Hui-Lin Ye – mSystems

Heterogeneous associations of gut microbiota with Crohn’s disease activity – Susanne Pinto – Gut Microbes

Early / Infant / Children Microbiome

Gut-resident microorganisms and their genes are associated with cognition and neuroanatomy in children – Kevin S Bonham – Science Advances

The association of tonsillar microbiota with biochemical indices based on obesity and tonsillar hypertrophy in children – Jiwon Park – Scientific Reports

Synergistic horizontal transfer of antibiotic resistance genes and transposons in the infant gut microbial genome – Yanwen Ding – mSphere

Beneficial Microbes and Compounds

Potential therapeutic implications of histidine catabolism by the gut microbiota in NAFLD patients with morbid obesity – Sergio Quesada-Vázquez – Cell Reports Medicine

Attenuation of allergen-specific immunotherapy for atopic dermatitis by ectopic colonization of Brevundimonas vesicularis in the intestine – Xiaochun Liu – Cell Reports Medicine

Model and Non-Model Animal Microbiome

The influence of diet on gut microbiome and body mass dynamics in a capital-breeding migratory bird – Isabelle Jones – PeerJ

Autophagic dysfunction and gut microbiota dysbiosis cause chronic immune activation in a Drosophila model of Gaucher disease – Magda L Atilano – PLoS Genetics

Cytolethal distending toxin B inoculation leads to distinct gut microtypes and IBS-D-like microRNA-mediated gene expression changes in a rodent model – Gabriela Leite – Gut Microbes

Microbiome and Evolution

Evolutionary patterns and processes in animal microbiomes – Florent Mazel – Journal of Evolutionary Biology

Plant and Soil Microbiome

Wheat fungal endophyte communities are inseparable from the host and influence plant development – Or Sharon – mBio

Environmental Microbiome

Metagenomics-Based Microbial Ecological Community Threshold and Indicators of Anthropogenic Disturbances in Estuarine Sediments – Yingyu Bao – Environmental Science & Technology

Microbiome Analysis: Tools, Techniques and Resources

Review: Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology – Corinne Walsh – mBio

SOHPIE: Statistical Approach via Pseudo-Value Information and Estimation for Differential Network Analysis of Microbiome Data – Seungjun Ahn – Bioinformatics

Examining the functional space of gut microbiome-derived peptides – Ying-Chiang J Lee – MicrobiologyOpen

A new absolute quantitative method for peptide and metabolite detection – Carlo Brogna – Journal of Mass Spectrometry

Next steps in studying host-microbiome interactions in apical periodontitis – Athina C Georgiou – Frontiers in Oral Health

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