The very first 2023 digest features HMOs, antimicrobials and the neonatal gut microbiota, cheese community, cow rumen microbiome, SemiBin2, and more. Happy Friday and see you next week at #MVIF!
Food microbiome
*Longitudinal, Multi-Platform Metagenomics Yields a High-Quality Genomic Catalog and Guides an In Vitro Model for Cheese Communities β Christina C. Saak β mSystems
Gut microbiome
*Human milk oligosaccharides, antimicrobial drugs, and the gut microbiota of term neonates: observations from the KOALA birth cohort study β D.J.M Barnett β Gut microbes
The gut microbiota in multiple sclerosis varies with disease activity β Florence Thirion β Genome Medicine
Review: Intestinal gas production by the gut microbiota: A review β Erasme Mutuyemungu β Journal of Functional Foods
Gestational diabetes is driven by microbiota-induced inflammation months before diagnosis β Yishay Pinto β Gut
Review: The gut microbiota is an emerging target for improving brain health during ageing β Marcus Boehme β Gut microbiome
Vaginal microbiome
Commensal Lactobacilli Metabolically Contribute to Cervical Epithelial Homeostasis in a Species-Specific Manner β Nicole R. Jimenez β mSphere
Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome β William F. Kindschuh β Nature Microbiology
Animal experiment
Gut microbiota of the young ameliorates physical fitness of the aged in mice β Kwang H. Kim β Microbiome
Catheterization of mice triggers resurgent urinary tract infection seeded by a bladder reservoir of Acinetobacter baumannii β Jennie E. Hazen β Science Translational Medicine
Prebiotic intervention with HAMSAB in untreated essential hypertensive patients assessed in a phase II randomized trial β Hamdi A. Jama β Nature Cardiovascular Research
Akkermansia muciniphila protects mice against an emerging tick-borne viral pathogen β Jinyan Xie β Nature Microbiology
Animal microbiome
Beehives possess their own distinct microbiomes β Lorenzo A. Santorelli β Environmental Microbiome
*Differential carbon utilization enables co-existence of recently speciated Campylobacteraceae in the cow rumen epithelial microbiome β Cameron R. Strachan β Nature Microbiology
Bioinformatics
Ecological landscapes guide the assembly of optimal microbial communities β Ashish B. George and Kirill S. Korolev β Plos Computational Biology
Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering β Theresa Ullmann β Plos Computational Biology
Ten simple rules for using public biological data for your research β Vishal H. Oza β Plos Computational Biology
*SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing β Shaojun Pan β bioRxiv
Microbiome Digest - Bik's Picks 