November 12, 2021

Today’s digest features the study on the Amazon River microbiome, Spanish gut microbiome, review on nanopore sequencing, 16S rRNA metabarcoding study to characterize the responses of the active gut microbiome of fathead minnows to exposure with a model contaminant (benzo[a]pyrene), and more. Happy Friday!

Lung microbiome

Review: The composition of lung microbiome in lung cancer: a systematic review and meta-analysis – Sadaf Najafi – BMC Microbiology

Skin microbiome

Charting host-microbe co-metabolism in skin aging and application to metagenomics data – Wynand Alkema – PlosOne

Gut microbiome

*The Spanish gut microbiome reveals links between microorganisms and Mediterranean diet – Adriel Latorre-Pérez – Scientific Reports

Autism-related dietary preferences mediate autism-gut microbiome associations – Chloe X. Yap – Cell

Animal microbiome

*16S rRNA metabarcoding unearths responses of rare gut microbiome of fathead minnows exposed to benzo[a]pyrene – Abigail DeBofsky – Science of The Total Environment

Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs – Morag Clinton – BMC Microbiology

Rabbit microbiota across the whole body revealed by 16S rRNA gene amplicon sequencing – Xiaofen Hu – BMC Microbiology

Animal experiment

The composition of human vaginal microbiota transferred at birth affects offspring health in a mouse model – Eldin Jašarević – Nature Communications

Polyamine metabolism links gut microbiota and testicular dysfunction – Qi Zhao – Microbiome

A fiber-deprived diet causes cognitive impairment and hippocampal microglia-mediated synaptic loss through the gut microbiota and metabolites – Hongli Shi – Microbiome

Water microbiome

*Microbial population genomes from the Amazon River reveal possible modulation of the organic matter degradation process in tropical freshwaters – Célio Dias Santos-Júnior – Molecular Ecology

Bioinformatics

*Review: Nanopore sequencing technology, bioinformatics and applications – Yunhao Wang – Nature Biotechnology

mBodyMap: a curated database for microbes across human body and their associations with health and diseases – Hanbo Jin – Nucleic Acids Research

Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper – Alexander G McFarland – Bioinformatics

OptiFit: an improved method for fitting amplicon sequences to existing OTUs – Kelly L Sovacool – bioRxiv

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