David A. Relman

Prehistoric Global Migration of Vanishing Gut Microbes With Humans

The paper compares gut microbiomes of Tsimane and Hadza populations to show that many microbes co-migrated with humans globally, but are now vanishing in industrialized populations.

CUPID-seq enables highly multiplexed amplicon sequencing via combinatorial in-line dual indexing

CUPID-seq improves amplicon sequencing by reducing costs and increasing multiplexing through combinatorial indexing, enabling efficient use of high-throughput sequencing platforms.

Fifteen-year microbiome survey of endangered killer whales (Orcinus orca) reveals declining diversity and population differences

This study analyzes 15-year fecal microbiome data from endangered killer whales to show declining diversity and population-specific differences.

Effects of parental care on skin microbial community composition in poison frogs

This study shows that parental care in poison frogs transfers skin microbes to offspring, influencing their microbial communities, but not necessarily their similarity to adult microbiotas.

VIRGO2: Unveiling the Functional and Ecological Complexity of the Vaginal Microbiome with an Enhanced Non-Redundant Gene Catalog

This study introduces VIRGO2, an enhanced gene catalog for the vaginal microbiome, revealing new bacterial species, mycobiome features, and gene expression patterns.

Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized

This study examines oral microbiomes of Nepali individuals with different lifestyles, finding that lifestyle, not geography, shapes microbiome composition across a gradient from foraging to industrialized.

Precise genotyping of circular mobile elements uncovers human associated plasmids with surprisingly recent common ancestors

The paper develops an algorithm to accurately reconstruct circular mobile genomes from metagenomic data, revealing plasmids with recently diverged common ancestors.

Strategies for understanding dynamic, personalized profiles of host-derived proteins and microbes from human stool

This study quantifies variability in host proteins and bacterial taxa in stool samples from healthy individuals, showing greater inter-subject variation than temporal or technical variation.

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

decontam, an R package, classifies contaminant sequences in marker-gene and metagenomic data by their inverse frequency-DNA concentration relationship and higher prevalence in negative controls.

Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients

This study examines how bacterial composition and function change over a year after fecal microbiota transplantation in immunocompromised patients, finding limited long-term donor strain persistence and complex functional shifts.