Good morning, everyone! Finally, the microbiome digest is ready after a long break.

In today’s digest, there are several interesting research articles to read specifically from two main sections Gut microbiome and Animal microbiome/Animal experiments. A few of them are highlighted as follows: 1) Use of machine learning approaches to mine functional peptides from metagenomic datasets; 2) An ultimate effort to mine host-microbiome protein-protein interactions which are mostly unexplored to understand mechanistic links with a variety of diseases; 3) Important role of mucosa-associated fungi with host-protective immunity and epithelial barrier function; 4) A fantastic review article summarizes gut microbial regulation of host 5-HT and 5-HT-mediated gut functions and its implications in the microbiota-gut-brain axis; 5) Another study showed; how gut microbiota regulates specific features of microglia from aged mice; 6) A method named MAGISTA to assess intra-bin statistics of metagenome-assembled genomes.

Enjoy reading. Happy Sunday.

General microbiome

Host-microbiome protein-protein interactions capture disease-relevant pathways – Zhou et al. – Genome Biology

Review: Periodontitis, chronic liver diseases, and the emerging oral-gut-liver axis –Albuquerque-Souza et al. – Periodontology 2000

Review: tRNA modification dynamics from individual organisms to metaepitranscriptomics of microbiomes – Zhang et al. – Molecular Cell

Gut microbiome

Socioeconomic disparities and household crowding in association with the fecal microbiome of school-age children – Lapidot et al. – npj biofilms and microbiomes

Oligofructose-Enriched Inulin Intake, Gut Microbiome Characteristics, and the V̇O₂ Peak Response to High-Intensity Interval Training in Healthy Inactive Adults – Williams et al. – The Journal of Nutrition

Helicobacter pylori infection affects the human gastric microbiome, as revealed by metagenomic sequencing – Wang et al. – FEBS Openbio

Microbiota dynamics in a randomized trial of gut decontamination during allogeneic hematopoietic cell transplantation – Severyn et al. – JCI insight

Review: Direct and indirect mechanisms by which the gut microbiota influence host serotonin systems – Legan et al. – Neurogastroenterology & Motility

Tree-Based Analysis of Dietary Diversity Captures Associations Between Fiber Intake and Gut Microbiota Composition in a Healthy US Adult Cohort – Kable et al. – The Journal of Nutrition

Spatial distribution of live gut microbiota and bile acid metabolism in various parts of human large intestine – Chinda et al. – Scientific Reports

Review: Understanding the mechanism underlying the anti-diabetic effect of dietary component: a focus on gut microbiota – Zhao et al. – Critical Reviews in Food Science and Nutrition

Intestinal AMPK modulation of microbiota mediates crosstalk with brown fat to control thermogenesis – Zhang et al. Nature Communications

Impact of wheat aleurone on biomarkers of cardiovascular disease, gut microbiota and metabolites in adults with high body mass index: a double-blind, placebo-controlled, randomized clinical trial – Fava et al. – European Journal of Nutrition

Oral microbiome

Alterations in the oral microbiome of individuals with a healthy oral environment following COVID-19 vaccination – Uehara et al. – BMC Oral Health

Respiratory microbiome

Age-related changes in the nasopharyngeal microbiome are associated with SARS-CoV-2 infection and symptoms among children, adolescents, and young adults – Hurst et al. – Clinical Infectious Diseases

Animal microbiome / Animal experiments

Animal gut microbiome mediates the effects of antibiotic pollution on an artificial freshwater system – Zhu et al. – Journal of Hazardous Materials

Metagenomic analysis explores the interaction of aged microplastics and roxithromycin on gut microbiota and antibiotic resistance genes of Carassius auratus – Zhang et al. – Journal of Hazardous Materials

Identification and functional expression of a new xylose isomerase from the goat rumen microbiome in Saccharomyces cerevisiae – Colombo et al. – Letters in Applied Microbiology

Extensive metagenomic analysis of the porcine gut resistome to identify indicators reflecting antimicrobial resistance – Zhou et al. – Microbiome

Mucosal fungi promote gut barrier function and social behavior via Type 17 immunity – Leonardi et al. – Cell

Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N⁶-carboxymethyllysine – Mossad et al. – Nature Neuroscience

Kaempferol acts on bile acid signaling and gut microbiota to attenuate the tumor burden in ApcMin/+ mice – Li et al.- European Journal of Pharmacology

Changes of gut microbiota in diabetic nephropathy and its effect on the progression of kidney injury – Cai et al. – Endocrine

The Novel Interplay between Commensal Gut Bacteria and Metabolites in Diet-Induced Hyperlipidemic Rats Treated with Simvastatin – Zhang et al. – Journal of Proteome Research

Changes to gut amino acid transporters and microbiome associated with increased E/I ratio in Chd8^+/− mouse model of ASD-like behavior – Yu et al. – Nature Communications

Novel Selenium Peptides Obtained from Selenium-Enriched Cordyceps militarisAlleviate Neuroinflammation and Gut Microbiota Dysbacteriosis in LPS-Injured Mice – Wu et al. – Journal of Agricultural and Food Chemistry

Microbiome-metabolomics analysis of the effects of decreasing dietary crude protein content on goat rumen mictobiota and metabolites – Zhu et al. – Animal Bioscience

Methods/Tools/Pipelines

Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics – Goussarov et al. – Environmental Microbiome