General microbiome
The evolution of coexistence from competition in experimental co-cultures of Escherichia coli and Saccharomyces cerevisiae – Jake N. Barber – ISME Journal
Human microbiome
Quantifying the effects of antibiotic treatment on the extracellular polymer network of antimicrobial resistant and sensitive biofilms using multiple particle tracking – Lydia C. Powell – npj Biofilms and Microbiomes
Biofilms harbour Clostridioides difficile, serving as a reservoir for recurrent infection – Charmaine Normington – npj Biofilms and Microbiomes
Gut microbiome
REVIEW: The contribution of gut bacterial metabolites in the human immune signaling pathway of non-communicable diseases – F. Hosseinkhani – Gut Microbes
The effect of acute moderate-intensity exercise on the serum and fecal metabolomes and the gut microbiota of cross-country endurance athletes – Mariangela Tabone – Scientific Reports
Oral microbiome
Candida albicans promotes tooth decay by inducing oral microbial dysbiosis – Qian Du – ISME Journal
Characterization of oral virome and microbiome revealed distinctive microbiome disruptions in paediatric patients with hand, foot and mouth disease – Si Xian Ho – npj Biofilms and Microbiomes
Skin microbiome
Characterization of the human skin resistome and identification of two microbiota cutotypes – Zhiming Li – Microbiome
Animal experiment
A gene co-association network regulating gut microbial communities in a Duroc pig population – Antonio Reverter – Microbiome
Modulating gut microbiota in a mouse model of Graves’ orbitopathy and its impact on induced disease – Sajad Moshkelgosha – Microbiome
Multi-compartment metabolomics and metagenomics reveal major hepatic and intestinal disturbances in cancer cachectic mice – Sarah A. Pötgens – Journal of Cachexia, Sarcopenia and Muscle
Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome – Congying Chen – Nature Communications
Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection – Franziska A. Stressmann – ISME Journal
Plant, root, and soil microbiome
REVIEW: From exploration to remediation: A microbial perspective for innovation in mining – Alan Levett – Earth-Science Reviews
Food microbiology
A Combined Metagenomics and Metatranscriptomics Approach to Unravel Costa Rican Cocoa Box Fermentation Processes Reveals Yet Unreported Microbial Species and Functionalities – Marko Verce – Frontiers in Microbiology
Water and extremophile microbiome
Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh – Daniel R. Leadbeater – Microbiome
Taxonomic and functional analyses of intact microbial communities thriving in extreme, astrobiology-relevant, anoxic sites – Alexandra Kristin Bashir – Microbiome
Genomic evidence for sulfur intermediates as new biogeochemical hubs in a model aquatic microbial ecosystem – Adrien Vigneron – Microbiome
REVIEW: The Seagrass Holobiont: What We Know and What We Still Need to Disclose for Its Possible Use as an Ecological Indicator – Chiara Conte – Water
Spatiotemporal variations and relationships of phosphorus, phosphomonoesterases, and bacterial communities in sediments from two Chilean rivers – Marco Camposa – Science of The Total Environment
Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy – Frank Xavier Ferrer-González – ISME Journal
Phages and virues
Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2 – Claudia Wylezich – Microbiome
Preliminary Assessment of Viral Metagenome from Cancer Tissue and Blood from Patients with Lung Adenocarcinoma – Hua‐Zhong Cai – Journal of Medical Virology
Bioinformatics
PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data – Laura de Nies – Microbiome
CANTARE: finding and visualizing network-based multi-omic predictive models – Janet C. Siebert – BMC Bioinformatics
kLDM: Inferring Multiple Metagenomic Association Networks based on the Variation of Environmental Factors – Yuqing Yang – Genomics, Proteomics & Bioinformatics
Methods
REVIEW: Cross-species RNA-seq for deciphering host–microbe interactions – Alexander J. Westermann – Nature Review Genetics
A community resource for paired genomic and metabolomic data mining – Michelle A. Schorn – Nature Chemical Biology
Pre-prints
Cross-sectional analysis of the microbiota of the human gut and their direct environment (exposome) in a household cohort in northern Vietnam – Bich Vu Thi Ngoc – bioRxiv
HumGut: A comprehensive Human Gut prokaryotic genomes collection filtered by metagenome data – Pranvera Hiseni – bioRxiv
Comparative analysis of 16S rRNA gene and metagenome sequencing in pediatric gut microbiomes – Danielle Peterson – bioRxiv
Unifying the known and unknown microbial coding sequence space – Chiara Vanni – bioRxiv
Microbiome Digest - Bik's Picks 