Monthly Archives: January 2023

January 27, 2023

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General Microbiome

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies – Kennedy et al. Nature

Microbial foods for improving human and planetary health – Jahn et al. Cell

A tissue atlas of ulcerative colitis revealing evidence of sex-dependent differences in disease-driving inflammatory cell types and resistance to TNF inhibitor therapy – Mayer et al. Science Advances

Associations of the skin, oral and gut microbiome with aging, frailty and infection risk reservoirs in older adults – Larson et al. Nature Aging

Bacteriophage / Virome

Phage therapy: From biological mechanisms to future directions – Strathdee et al. Cell

Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs – Lee et al. Cell

Water and extremophile microbiome

High-resolution metagenomic reconstruction of the freshwater spring bloom – Kavagutti et al. Microbiome

Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria – Sereika et al. ISME

Bioinformatics

Enhanced correlation-based linking of biosynthetic gene clusters to their metabolic products through chemical class matching – Louwen et al. Microbiome

PLSDA-batch: a multivariate framework to correct for batch effects in microbiome data – Wang & Cao. Briefings in Bioinformatics

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine – Heinken et al. Nature Biotechnology

Non-Microbiome picks

Infection infidelities drive innate immunity – Kagan. Science

Functional T cells are capable of supernumerary cell division and longevity – Soerens et al. Nature

Genetic adaptation to pathogens and increased risk of inflammatory disorders in post-Neolithic Europe – Kerner et al. Cell Genomics

January 25, 2023

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Human oral microbiome

Microbiological profile of peri-implantitis: Analyses of microbiome within dental implants – Kensara et al. – Journal of Prosthodontics

Human gut microbiome

Integrated Multi-Cohort Analysis of the Parkinson’s Disease Gut Metagenome – Boktor et al. – Movement Disorders

Gut microbiota and microbiota-derived metabolites promotes endometriosis – Chadchan et al. – Cell Death Discovery

Immune communication between the intestinal microbiota and the cardiovascular system – Ren et al. – Immunology Letters

Animal microbiome

The structure and diversity of microbial communities in Paederus fuscipes (Coleoptera: Staphylinidae): from ecological paradigm to pathobiome – Chamanakar et al. – Microbiome

The gastrointestinal microbiome in dairy cattle is constrained by the deterministic driver of the region and the modified effect of diet – Lin et al. – Microbiome

Fecal Microbiota Was Reshaped in UCP1 Knock-In Pigs via the Adipose-Liver-Gut Axis and Contributed to Less Fat Deposition – Pan et al. – Microbiology Spectrum

Gut microbiota of skywalker hoolock gibbons (Hoolock tianxing) from different habitats and in captivity: Implications for gibbon health – Lan et al. – American Journal of Primatology

Housing temperature plays a critical role in determining gut microbiome composition in research mice: Implications for experimental reproducibility – Hylander et al. – Biochimie

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

The biogeography and co-occurrence network patterns of bacteria and microeukaryotes in the estuarine and coastal waters – Wu et al. – Marine Environmental Research

Bioinformatics

[PREPRINT]Capturing the dynamics of microbiomes using individual-specific networks – Yousefi et al. – bioRxiv

PhaTYP: predicting the lifestyle for bacteriophages using BERT – Shang, Tang & Sun – Briefings in Bioinformatics

January 18, 2023

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Human oral microbiome

[PRIMER]A possible role for taste receptor cells in surveying the oral microbiome – Heisey & McCluskey – PLOS Biology

Type II taste cells participate in mucosal immune surveillance – Qin et al. – PLOS One

Human gut microbiome

[NEWS]How our microbiome is shaped by family, friends and even neighbours – Callaway – Nature

The person-to-person transmission landscape of the gut and oral microbiomes – Valles-Colomer et al. – Nature

[REVIEW]The gut microbiota in obesity and weight management: microbes as friends or foe? – van Hul & Cani – Nature Reviews Endocrinology

Dynamics of the gut microbiome, IgA response, and plasma metabolome in the development of pediatric celiac disease – Girdhar et al. – Microbiome

Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes – Jacobs et al. – Microbiome

Microbiome Features Differentiating Unsupervised-Stratification-Based Clusters of Patients with Abnormal Glycometabolism – Xu et al. – mBio

Gut Bacterial Dysbiosis in Irritable Bowel Syndrome: a Case-Control Study and a Cross-Cohort Analysis Using Publicly Available Data Sets – Kim, Lee & Shim – Microbiology Spectrum

Harnessing gut microbes for glycan detection and quantification – Modesto, Pearce & Townsend Il – Nature Communications

The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles – Malan – Müller et al. – Gut Microbes

Animal microbiome

Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse – Li et al. – Microbiome

The bovine foot skin microbiota is associated with host genotype and the development of infectious digital dermatitis lesions – Bay et al. – Microbiome

Plant, root, and soil microbiome

A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data – Merihu et al. – Microbiome

Diversity and functional analysis of rumen and fecal microbial communities associated with dietary changes in crossbreed dairy cattle – Kibegwa et al. – PLOS One

Bioinformatics

Multi-amplicon microbiome data analysis pipelines for mixed orientation sequences using QIIME2: Assessing reference database, variable region and pre-processing bias in classification of mock bacterial community samples – Maki et al. – PLOS One

January 13, 2023

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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