Human and General Microbiome

Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes – Aarthi Ravikrishnan – Nature Communications

Integrated analysis of facial microbiome and skin physio-optical properties unveils cutotype-dependent aging effects – Chuqing Sun – Microbiome

Regulation of Bacteroides acidifaciens by the aryl hydrocarbon receptor in IL-22-producing immune cells has sex-dependent consequential impact on colitis – Chandani Mitchell – Frontiers in Immunology

The role of KLF5 in gut microbiota and lung adenocarcinoma: unveiling programmed cell death pathways and prognostic biomarkers – Qingliang Fang – Discover Oncology

Healthy first-degree relatives from multiplex families versus simplex families have a higher subclinical intestinal inflammation, a distinct fecal microbial signature, and harbor a higher risk of developing Crohn’s disease – Pablo A Olivera – Gastroenterology

Reversions mask the contribution of adaptive evolution in microbiomes – Paul A Torrillo – eLife

Review: The hidden base of the iceberg: gut peptidoglycome dynamics is foundational to its influence on the host – Richard Wheeler – Gut Microbes

Review: Benefits and concerns of probiotics: an overview of the potential genotoxicity of the colibactin-producing Escherichia coli Nissle 1917 strain – Luca Falzone – Gut Microbes

Book Chapter: Microbial Extracellular Vesicles in Host-Microbiota Interactions – Sarah Abubaker – Results and Problems in Cell Differentiation

Beneficial Microbes and Compounds

A probiotic Limosilactobacillus fermentum GR-3 mitigates colitis-associated tumorigenesis in mice via modulating gut microbiome – Tuoyu Zhou – NPJ Science of Food

Review: Pathophysiological and Clinical Potential of Human Microbiome: Microbe-based Therapeutic Insights – Somali Sanyal – Current Pharmaceutical Biotechnology

Plant Microbiome

Soil volatilomics uncovers tight linkage between soybean presence and soil omics profiles in agricultural fields – Hikari Kuchikata – Scientific Report

Review: Meddling with the microbiota: Fungal tricks to infect plant hosts – Fantin Mesny – Current Opinion in Plant Biology

Environmental Microbiome

A comprehensive catalog encompassing 1376 species-level genomes reveals the core community and functional diversity of anammox microbiota – Depeng Wang – Water Research

Revealing the intricate temporal dynamics and adaptive responses of prokaryotic and eukaryotic microbes in the coastal South China Sea – Wenqian Xu – The Science of the Total Environment

Biodegradation of low-density polyethylene by mixed fungi composed of Alternaria sp. and Trametes sp. isolated from landfill sites – Wei-Kang Yang – BMC Microbiology

Using patterns of shared taxa to infer bacterial dispersal in human living environment in urban and rural areas – M Grönroos – Applied and Environmental Microbiology

Annotation-free prediction of microbial dioxygen utilization – Avi I Flamholz – mSystem

Microbiome Analysis: Tools, Techniques and Resources

MRGM: an enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes – Nayeon Kim – Gut Microbes

A unified web cloud computing platform MiMedSurv for microbiome causal mediation analysis with survival responses – Hyojung Jang – Scientific Reports

A quantitative approach to measure and predict microbiome response to antibiotics – Vincent Tu – mSphere

Metagenomic functional profiling: to sketch or not to sketch? – Mahmudur Rahman Hera – Bioinformatics

TolRad, a model for predicting radiation tolerance using Pfam annotations, identifies novel radiosensitive bacterial species from reference genomes and MAGs – Philip Sweet – Microbiology Spectrum

Review: Improving viral annotation with artificial intelligence – Zachary N Flamholz – mBio

Additionally, the Cold Spring Harbor Protocols Journal released a set of protocols covering the study of Maize Microbiome:

Sampling the Maize (Zea mays) Leaf Microbiome – Jason G Wallace – Cold Spring Harbor Protocols

Sampling Root-Associated Microbiome Communities of Maize (Zea mays) – Alonso Favela – Cold Spring Harbor Protocols

Sampling and Analysis of the Maize Microbiome – Jason G Wallace – Cold Spring Harbor Protocols

Manipulating the Maize (Zea mays) Microbiome – Sierra S Raglin – Cold Spring Harbor Protocols