Human and General Microbiome

Gut microbiome for predicting immune checkpoint blockade-associated adverse events – Muni Hu – Genome Medicine

The fusion of multi-omics profile and multimodal EEG data contributes to the personalized diagnostic strategy for neurocognitive disorders – Yan Han – Microbiome

Prediction of lung cancer using novel biomarkers based on microbiome profiling of bronchoalveolar lavage fluid – Gihyeon Kim – Scientific Reports

Exploring the intestinal ecosystem: from gut microbiota to associations with subtypes of inflammatory bowel disease – Fan Li – Frontiers in Cellular and Infection Microbiology

Simulated digestions of free oligosaccharides and mucin-type O-glycans reveal a potential role for Clostridium perfringens – Andrew G McDonald – Scientific Reports

Oral microbiome associated with differential ratios of Porphyromonas gingivalis and Streptococcus cristatus – Qingguo Wang – Microbiology Spectrum

Impact of intratumoral microbiome on tumor immunity and prognosis in human pancreatic ductal adenocarcinoma – Shohei Abe – Journal of Gastroenterology

Evaluation of gut microbiota predictive potential associated with phenotypic characteristics to identify multifactorial diseases – Danielle Cristina Fonseca – Gut Microbes

Review: The Gut Microbiome Affects Atherosclerosis by Regulating Reverse Cholesterol Transport – Yangyang Jiang – Journal of Cardiovascular Translational Research

Review: Role of vertical and horizontal microbial transmission of antimicrobial resistance genes in early life: insights from maternal-infant dyads – Manuel Bernabeu – Current Opinion in Microbiology

Beneficial Microbes and Compounds

Complement in breast milk modifies offspring gut microbiota to promote infant health – Dongqing Xu – Cell

An Oral Nanomedicine Elicits In Situ Vaccination Effect against Colorectal Cancer – Menghang Zu – ACS Nano

Model and Non-Model Animal Microbiome 

Oral bacteria accelerate pancreatic cancer development in mice – Elias Saba – Gut

Bacterial community and diversity in the rumen of 11 Mongolian cattle as revealed by 16S rRNA amplicon sequencing – Yijiu Jia – Scientific Reports

Novel taxonomic and functional diversity of eight bacteria from the upper digestive tract of chicken – Bibiana Rios-Galicia – International Journal of Systematic and Evolutionary Microbiology

Plant Microbiome

A tripartite bacterial-fungal-plant symbiosis in the mycorrhiza-shaped microbiome drives plant growth and mycorrhization – Changfeng Zhang – Microbiome

Host genotype, soil composition, and geo-climatic factors shape the fonio seed microbiome – Naheed Tabassum – Microbiome

The role of plants in ironstone evolution: iron and aluminium cycling in the rhizosphere – Anat Paz – The Science of the Total Environment

Consistent effects of independent domestication events on the plant microbiota – Riccardo Soldan – Current Biology 

Inactivation of siderophore iron-chelating moieties by the fungal wheat root symbiont Pyrenophora biseptata – Katie S French – Environmental Microbiology Reports

Environmental Microbiome

New insights into inhibition of high Fe(III) content on anaerobic digestion of waste-activated sludge – Xuepeng Wang – The Science of the Total Environment

Microbiome Analysis: Tools, Techniques and Resources

Drying as an effective method to store soil samples for DNA-based microbial community analyses: a comparative study – Emily Smenderovac – Scientific Reports

Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines – E Michael Valencia – Scientific Data

Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics – Georgios Marinos – Microbiology Spectrum

Metagenomes and metagenome-assembled genomes from ex vivo fecal incubations of six unique donors – Adrienne B Narrowe – Microbiology Resource Announcements

Bioinformatic Approach to Investigate Larvae Gut Microbiota Cellulosimicrobium protaetiae via Whole-Genome Analysis – Han Le Ho – Molecular Biotechnology

Human and General Microbiome

Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults – Xuanji Li – Nature Communications

Social anxiety disorder-associated gut microbiota increases social fear – Nathaniel L Ritz – PNAS

Plasmid-encoded toxin defence mediates mutualistic microbial interactions – Sarah Moraïs – Nature Microbiology

Oral microbiome-driven virulence factors: A novel approach to pancreatic cancer diagnosis – Xuemin Zeng – Biomolecules & Biomedicine

The Gut Microbiome: A Primer for the Clinician – Olga C Aroniadis – The American Journal of Gastroenterology

Exploring the role of gut microbiota in migraine risk: a two-sample Mendelian randomization study – Xiangyue Meng – Scandinavian Journal of Gastroenterology

High-Throughput Combined Analysis of Saliva Microbiota and Metabolomic Profile in Chinese Periodontitis Patients: A Pilot Study – Jing Ding – Inflammation

Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research – Jonathan L Golob – Cell Reports. Medicine

Impact of dietary inflammatory index on gingival health – Roberta Andrade Reis – Journal of Periodontology

Air particulate pollution exposure associated with impaired cognition via microbiota gut-brain axis: an evidence from rural elderly female in northwest China – Jia Yuan – Environmental Science and Pollution Research International

Metabolic flux and catabolic kinetics of prebiotic-like dietary polyphenol phlorizin in association with gut microbiota in vitro – Jiang Chen – Food Chemistry

Review: Genital tract microbiota composition profiles and use of prebiotics and probiotics in gynaecological cancer prevention: review of the current evidence, the European Society of Gynaecological Oncology prevention committee statement – Anita Mitra – The Lancet. Microbe

Review: Wound Microbiota and Its Impact on Wound Healing – Małgorzata Zielińska – International Journal of Molecular Sciences

Review: Microbial collaborations and conflicts: unraveling interactions in the gut ecosystem – Shuang Wang – Gut Microbes

Animal Model Studies

Gut microbiome responds to alteration in female sex hormone status and exacerbates metabolic dysfunction – Tzu-Wen L Cross – Gut Microbes

Oral fecal transplantation enriches Lachnospiraceae and butyrate to mitigate acute liver injury – Chun-Ju Yang – Cell Reports 

Impact of various high fat diets on gene expression and the microbiome across the mouse intestines – Jose Martinez-Lomeli – Scientific Reports

Non-Model Animal Microbiome

Characteristics of gut microbiota in captive Asian elephants (Elephas maximus) from infant to elderly – Sarisa Klinhom – Scientific Reports

Honeybee symbiont Bombella apis could restore larval-to-pupal transition disrupted by antibiotic treatment – Chen Xiaowen – Journal of Insect Physiology

Toll receptor ligand Spätzle 4 responses to the highly pathogenic Enterococcus faecalis from Varroa mites in honeybees – Wenhao Zhang – PLoS Pathogens

Plant Microbiome

Review: Unveiling the significance of rhizosphere: Implications for plant growth, stress response, and sustainable agriculture – Wogene Solomon – Plant Physiology and Biochemistry

Environmental Microbiome

Connecting molecular biomarkers, mineralogical composition, and microbial diversity from Mars analog lava tubes – Vera Palma – The Science of the Total Environment

The undiscovered biosynthetic potential of the Greenland Ice Sheet microbiome – Ate H Jaarsma – Frontiers in Microbiology

Review: A global review on the abundance and threats of microplastics in soils to terrestrial ecosystem and human health – Wenshan Shi – The Science of the Total Environment

Microbiome analysis: tools, techniques and resources

VIBES: A consensus subtyping of the vaginal microbiota reveals novel classification criteria – Diego Fernández-Edreira – Computational and Structural Biotechnology Journal

Generalized matrix decomposition regression: estimation and inference for two-way structured data – Yue Wang – The Annals of Applied Statistics

Single-cell and spatiotemporal transcriptomic analyses reveal the effects of microorganisms on immunity and metabolism in the mouse liver – Ruizhen Zhao – Computational and Structural Biotechnology Journal

PETR: A novel peristaltic mixed tubular bioreactor simulating human colonic conditions – David Vorländer – Biotechnology and Bioengineering

Mock microbial community meta-analysis using different trimming of amplicon read lengths – Diana Haider – Environmental Microbiology

Review: In Vitro Models for Investigating Intestinal Host-Pathogen Interactions – Reece McCoy – Advanced Science

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