Good morning from New Jersey! A broad selection of papers to share with you today—highlights include several new bioinformatics papers and an examination of the effect of storage method on the composition of microbiome samples:
General microbiome
A global metagenomic map of urban microbiomes and antimicrobial resistance, David Danko et al., Cell
Ecology and molecular targets of hypermutation in the global microbiome, Simon Roux et al., Nature Communications
Human oral microbiome
A cocoa (Theobroma cacao L.) extract impairs the growth, virulence properties, and inflammatory potential of Fusobacterium nucleatum and improves oral epithelial barrier function, Amel Ben Lagha et al., PLOS ONE
Human skin microbiome
Composition of cutaneous bacterial microbiome in seborrheic dermatitis patients: A cross-sectional study, Martijn G.H. Sanders et al., PLOS ONE
Human gut microbiome
Gene-level metagenomic architectures across diseases yield high-resolution microbiome diagnostic indicators, Braden T. Tierney et al., Nature Communications
Altered faecal microbiome and metabolome in IgG4-related sclerosing cholangitis and primary sclerosing cholangitis, Qiaoyan Liu et al., Gut
Animal experiments
Gut microbiome variation modulates the effects of dietary fiber on host metabolism, Sofia M. Murga-Garrido et al., Microbiome
Real-time monitoring of ruminal microbiota reveals their roles in dairy goats during subacute ruminal acidosis, Xiaodong Chen et al., npj Biofilms and Microbiomes
Animal microbiome
The microbiome and mosquito vectorial capacity: rich potential for discovery and translation, Cintia Cansado-Utrilla et al., Microbiome
Bioinformatics
Preprint: A metabolomics pipeline enables mechanistic interrogation of the gut microbiome, Shuo Han et al., bioRxiv
Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing, Zachary D. Wallen, BMC Bioinformatics
Reads Binning Improves the Assembly of Viral Genome Sequences From Metagenomic Samples, Kai Song, Frontiers in Microbiology
Techniques
Preprint: Standard Sample Storage Conditions Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns, Casper Sahl Poulsen et al., bioRxiv