A novel mathematical modeling framework for antibiotic-resistant bacteria combining within-host microbiome-pathogen interactions with population-level pathogen epidemiology, demonstrating how antibiotic consumption and ecological competition come together to drive the spread of resistance.

In baboon gut microbiota, most pairwise correlations in bacterial abundances are weak and negative, and bacterial correlation patterns are largely shared across hosts, rather than personalized to each hosts.

Microbiome and transcriptomic profiling of genetically selected tropical fish with high and low tolerance to cold exposure revealed host control over microbiome composition and response to temperature changes.

Gut microbial signatures of domestication parallel those of industrialization, implicating shared ecological drivers.

The gut microbiota of East Asians is distinct, dissociated from body mass, and self-sustains compared to White subjects from the same region, and therein may underpin a key health disparity.

A novel multi-omics framework revealed the taxonomic contribution to microbiota oxalate, demontrated O. formigenes as the dominating taxon transcriptionally, and identified specific IBD cohort at risk for oxalte toxicity.

Interactions between fungal and bacterial microbiome members alter Drosophila melanogaster's chemical environment, affecting host behavior and survival.

Modeling weighted transfer ratios enable statistical analysis of maternal–infant transfer at a more general level and can indicate whether any transfer is persistent, transient, or originates from alternate sources.

Computational reaction representations and profile hidden Markov model searches of metagenomics databases can be harnessed to accurately predict bacterial species and enzyme sequences responsible for biotransformations in the human gut microbiome.

Disturbing the microbiota with antibiotics alters gut redox state via changes in electron acceptor availability, setting the stage for post-antibiotic succession.