D. A. Relman

Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities

This study shows how initial population size and resource competition shape gut microbial community coalescence, with dose-dependent effects persisting even after many generations.

A short course of antibiotics selects for persistent resistance in the human gut

This study shows that short antibiotic use in humans leads to persistent resistance in gut bacteria through convergent evolution and selective sweeps.

Longitudinal dynamics of the human vaginal ecosystem across the reproductive cycle

This study tracks changes in the vaginal microbiome and inflammation across the reproductive cycle, finding that childbirth disrupts microbial communities and reduces Lactobacillus dominance, with limited recovery over one year.

Gardnerella Diversity and Ecology in Pregnancy and Preterm Birth

This study examines Gardnerella diversity in vaginal microbiomes across populations and its association with preterm birth, revealing intra-species variation and its impact on microbial composition.

Sub-communities of the vaginal ecosystem in pregnant and non-pregnant women.

The paper identifies non-Lactobacillus-dominated sub-communities in vaginal ecosystems of pregnant and non-pregnant women using mixed membership models, revealing associations with preterm birth and menstrual cycle changes.

Previously uncharacterized rectangular bacterial structures in the dolphin mouth

The paper discovers novel rectangular bacterial structures in dolphin mouths and characterizes their morphology and potential bacterial origin through multiple methods.

Short-Term Dairy Elimination and Reintroduction Minimally Perturbs the Gut Microbiota in Self-Reported Lactose Intolerant Adults

This study examines the impact of short-term dairy elimination and reintroduction on gut microbiota and lactose tolerance in self-reported lactose intolerant adults, finding minimal microbiota changes and improved symptom tolerance.

Combined use of metagenomic sequencing and host response profiling for the diagnosis of suspected sepsis.

This study combines metagenomic sequencing and host response profiling to improve sepsis diagnosis by detecting pathogens and guiding clinical decisions.

Microbiota Assembly, Structure, and Dynamics Among Tsimane Horticulturalists of the Bolivian Amazon

This study examines microbiota assembly in Tsimane infants and adults, finding that neutral processes dominate infant colonization, but are reduced in villages with more market access.

Treatment-Specific Composition of Gut Microbiota Is Associated with Disease Remission in a Pediatric Crohn’s Disease Cohort

This study examines how gut microbiota changes with metronidazole and metronidazole plus azithromycin treatments in pediatric Crohn’s disease and finds that microbiota profiles can predict disease remission.

Tracking microbial evolution in the human gut using Hi-C

The paper uses Hi-C and probabilistic modeling to track microbial evolution in the human gut, revealing accessory element exchange and core genome adaptation over time.

Clades of huge phage from across Earth’s ecosystems

The paper identifies major clades of large phage genomes across diverse ecosystems and highlights their expanded genetic repertoires and potential functional roles.

Microbial biogeography and ecology of the mouth and implications for periodontal diseases

This paper explores microbial biogeography in the human mouth, linking spatial patterns to periodontal diseases and proposing methods to test hypotheses about subgingival microbiota variation.

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome

This study uses metagenomic analysis with strain-level resolution to examine the human pregnancy microbiome, revealing gestational age and health complications influence microbial community composition and function.

Early transcriptional responses after dengue vaccination mirror the response to natural infection and predict neutralizing antibody titers