January 13, 2023

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 – Christina C. Saak – mSystems

Gut microbiome

*Human milk oligosaccharides, antimicrobial drugs, and the gut microbiota of term neonates: observations from the KOALA birth cohort study – D.J.M Barnett – Gut microbes

The gut microbiota in multiple sclerosis varies with disease activity – Florence Thirion – Genome Medicine

Review: Intestinal gas production by the gut microbiota: A review – Erasme Mutuyemungu – Journal of Functional Foods

Gestational diabetes is driven by microbiota-induced inflammation months before diagnosis – Yishay Pinto – Gut

Review: The gut microbiota is an emerging target for improving brain health during ageing – Marcus Boehme – Gut microbiome

Vaginal microbiome

Commensal Lactobacilli Metabolically Contribute to Cervical Epithelial Homeostasis in a Species-Specific Manner – Nicole R. Jimenez – mSphere

Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome – William F. Kindschuh – Nature Microbiology

Animal experiment

Gut microbiota of the young ameliorates physical fitness of the aged in mice – Kwang H. Kim – Microbiome

Catheterization of mice triggers resurgent urinary tract infection seeded by a bladder reservoir of Acinetobacter baumannii – Jennie E. Hazen – Science Translational Medicine

Prebiotic intervention with HAMSAB in untreated essential hypertensive patients assessed in a phase II randomized trial – Hamdi A. Jama – Nature Cardiovascular Research

Akkermansia muciniphila protects mice against an emerging tick-borne viral pathogen – Jinyan Xie – Nature Microbiology

Animal microbiome

Beehives possess their own distinct microbiomes – Lorenzo A. Santorelli – Environmental Microbiome

*Differential carbon utilization enables co-existence of recently speciated Campylobacteraceae in the cow rumen epithelial microbiome – Cameron R. Strachan – Nature Microbiology

Bioinformatics

Ecological landscapes guide the assembly of optimal microbial communities – Ashish B. George and Kirill S. Korolev – Plos Computational Biology

Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering – Theresa Ullmann – Plos Computational Biology

Ten simple rules for using public biological data for your research – Vishal H. Oza – Plos Computational Biology

*SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing – Shaojun Pan – bioRxiv

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