Human and General Microbiome

Multi-site microbiota alteration is a hallmark of kidney stone formation – Kait F Al – Microbiome

Culturing the unculturables: strategies, challenges, and opportunities for gut microbiome study – Asha Yadav – Journal of Applied Microbiology

Trans-vaccenic acid reprograms CD8(+) T cells and anti-tumour immunity – Hao Fan – Nature

Multi-omics analysis of hospital-acquired diarrhoeal patients reveals biomarkers of enterococcal proliferation and Clostridioides difficile infection – Marijana Bosnjak – Nature Communications

Why are so many enteric pathogen infections asymptomatic? Pathogen and gut microbiome characteristics associated with diarrhea symptoms and carriage of diarrheagenic E. coli in northern Ecuador – Kelsey J Jesser – Gut Microbes

Gut microbiome and frailty: insight from genetic correlation and mendelian randomization – Guanghui Cui – Gut Microbes

Review: Metabolic exchanges are ubiquitous in natural microbial communities – Christian Kost – Nature Microbiology

Review: Evolution of a Pathogenic Microbiome – Pui Yin Wong – Journal of Clinical Medicine

Review: Evidence for the contribution of the gut microbiome to obesity and its reversal – Douwe F de Wit – Science Translational Medicine

Beneficial Microbes and Compounds

Parabacteroides distasonis ameliorates insulin resistance via activation of intestinal GPR109a – Yonggan Sun – Nature Communications

Galactooligosaccharide Mediates NF-κB Pathway to Improve Intestinal Barrier Function and Intestinal Microbiota – Menglu Xi – Molecules 

A self-stabilized and water-responsive deliverable coenzyme-based polymer binary elastomer adhesive patch for treating oral ulcer – Chunyan Cui – Nature Communications

A key genetic factor governing arabinan utilization in the gut microbiome alleviates constipation – Chengcheng Zhang – Cell Host & Microbe

Meta-analysis: Fiber intake and fiber intervention in depression and anxiety: a systematic review and meta-analysis of observational studies and randomized controlled trials – Hajara Aslam – Nutrition Reviews

Animal Microbiome

Identification of peptides from honeybee gut symbionts as potential antimicrobial agents against Melissococcus plutonius – Haoyu Lang – Nature Communications

A coral-associated actinobacterium mitigates coral bleaching under heat stress – Jie Li – Environmental Microbiome

Symbiodiniaceae photophysiology and stress resilience is enhanced by microbial associations – Jennifer L Matthews – Scientific Reports

Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts – Dan Sun – ISME Communications

Experimental mining plumes and ocean warming trigger stress in a deep pelagic jellyfish – Vanessa I Stenvers – Nature Communications

Gut microbiomes of cycad-feeding insects tolerant to β-methylamino-L-alanine (BMAA) are rich in siderophore biosynthesis – Karina Gutiérrez-García – ISME Communications

Environmental Factors and the Symbiont Cardinium Influence the Bacterial Microbiome of Spider Mites Across the Landscape – Huan-Huan Liu – Microbial Ecology

Animal Model Microbiome

Gut microbiota-bile acid crosstalk regulates murine lipid metabolism via the intestinal FXR-FGF19 axis in diet-induced humanized dyslipidemia – Hongtao Xu – Microbiome

Multi-omics data reveals aberrant gut microbiota-host glycerophospholipid metabolism in association with neuroinflammation in APP/PS1 mice – Xiaohang Qian – Gut Microbes

Plant and Environmental Microbiome

Combined application of microbial inoculant and kelp-soaking wastewater promotes wheat seedlings growth and improves structural diversity of rhizosphere microbial community – Xin Song – Scientific Reports

Contribution of ammonia-oxidizing archaea and bacteria to nitrogen transformation in a soil fertilized with urea and organic amendments – Yajun Yang – Scientific Reports

Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost – Karl J Romanowicz – ISME Communications

Microbiome Analysis: tools, techniques, and resources

PanDelos-frags: A methodology for discovering pangenomic content of incomplete microbial assemblies – Vincenzo Bonnici – Journal of Biomedical Informatics

PLM-ARG: antibiotic resistance gene identification using a pretrained protein language model – Jun Wu – Bioinformatics

Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes – Shreya Arya – PNAS

Vaccinomics-aided next-generation novel multi-epitope-based vaccine engineering against multidrug resistant Shigella sonnei: Immunoinformatics and chemoinformatics approaches – Sara Aiman – PloS One

Detecting host responses to microbial stimulation using primary epithelial organoids – Jette Bornholdt – Gut Microbes

Review: Exploring microbial worlds: a review of whole genome sequencing and its application in characterizing the microbial communities – Suleiman Aminu – Critical Reviews in Microbiology

Human Gut Microbiome

Altered Gut Microbiota and Short-chain Fatty Acids in Chinese Children with Constipated Autism Spectrum Disorder – Jianquan He – Scientific Reports

Clostridium butyricum and Clostridium tyrobutyricum: angel or devil for necrotizing enterocolitis? – Ruizhi Tao – mSystems

Gut microbiota composition and diversity before, during, and two months after rifamycin-based tuberculosis preventive therapy – Marie Nancy Séraphin – Scientific Reports

Genomic analyses of Bacteroides fragilis: subdivisions I and II represent distinct species – Jamie English – Journal of Medical Microbiology

Bacterial SNPs in the human gut microbiome associate with host BMI – Liron Zahavi – Nature Medicine

Fecal short-chain fatty acids in non-constipated irritable bowel syndrome: a potential clinically relevant stratification factor based on catabotyping analysis – Giorgio Gargari – Gut Microbes

Characterizing alterations in the gut microbiota following postpartum weight change – Bridget N Chalifour – mSystems

Core-genome multilocus sequence typing and core-SNP analysis of Clostridium neonatale strains isolated in different spatio-temporal settings – Victoria Mesa – Microbiology Spectrum

Human Microbiome (outside the gut)

Identification of root canal microbiota profiles of periapical tissue diseases using matrix-assisted laser desorption/ionization time-of-flight mass spectrometer – Mete Ahlat – Anaerobe

Gardnerella pickettii sp. nov. (formerly Gardnerella genomic species 3) and Gardnerella greenwoodii sp. nov. (formerly Gardnerella genomic species 8) isolated from female urinary microbiome – Márcia Sousa – International Journal of Systematic and Evolutionary Microbiology

Smoking and salivary microbiota: a cross-sectional analysis of an Italian alpine population – Giacomo Antonello – Scientific Reports

Prolonged mask wearing changed nasal microbial characterization of young adults during the COVID-19 pandemic in Shanghai, China – Guoxiu Xiang – Frontiers in Immunology

Beneficial Microbes, Compounds and Interventions

Inulin-enriched Megamonas funiformis ameliorates metabolic dysfunction-associated fatty liver disease by producing propionic acid – Xinyue Yang – NPJ Biofilms and Microbiomes

A gut microbial metabolite of linoleic acid ameliorates liver fibrosis by inhibiting TGF-β signaling in hepatic stellate cells – Nanaho Kasahara – Scientific Reports

Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement – Michael H Woodworth – Science Translational Medicine

Animal Microbiome

Revealing the developmental characterization of rumen microbiome and its host in newly received cattle during receiving period contributes to formulating precise nutritional strategies – Yanjiao Li – Microbiome

Shifts in the coral microbiome in response to in situ experimental deoxygenation – Rachel D Howard – Applied and Environmental Microbiology

Limitation of amino acid availability by bacterial populations during enhanced colitis in IBD mouse model – Tanner G Richie – mSystems

Estradiol mediates colonic epithelial protection in aged mice after stroke and is associated with shifts in the gut microbiome – Juneyoung Lee – Gut Microbes

Functional potential and evolutionary response to long-term heat selection of bacterial associates of coral photosymbionts – Justin Maire – mSystems

Gut bacteria mediated adaptation of diamondback moth, Plutella xylostella, to secondary metabolites of host plants – Xiaofeng Xia – mSystems

Environmental Microbiome

Microbial hitchhikers harbouring antimicrobial-resistance genes in the riverine plastisphere – Vinko Zadjelovic – Microbiome

Taxonomic distribution of metabolic functions in bacteria associated with Trichodesmium consortia – Coco Koedooder – mSystems

Review: Microbial ecology of drinking water from source to tap – Leili Abkar – The Science of the Total Environment

Microbiome Analysis: Tools, Techniques and Resources

Food4healthKG: Knowledge graphs for food recommendations based on gut microbiota and mental health – Chengcheng Fu – Artificial Intelligence in Medicine

Testing latent classes in gut microbiome data using generalized Poisson regression models – Xinhui Qiao – Statistics in Medicine