S. Holmes

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.

Pro-inflammatory feedback loops define immune responses to pathogenic lentivirus infection

This study identifies pro-inflammatory feedback loops in immune responses to pathogenic lentivirus infection, showing that highly pathogenic variants induce delayed, sustained, and amplifying inflammatory circuits.

SARS-CoV-2 escapes direct NK cell killing through Nsp1-mediated downregulation of ligands for NKG2D

This study shows SARS-CoV-2 evades NK cell killing by downregulating NKG2D ligands via Nsp1, reducing NK cell cytotoxicity against infected cells.

Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles

This study compares infant gut microbiome assembly in Hadza hunter-gatherers and industrialized infants, finding distinct microbial trajectories and functional differences.

Dynamic genome plasticity during unisexual reproduction in the human fungal pathogen Cryptococcus deneoformans

This study identifies cell cycle regulators involved in ploidy transitions during unisexual reproduction in C. deneoformans and reveals segmental aneuploidy associated with azole resistance.

Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19

Single-cell multi-omic profiling identifies immune dysregulation in severe COVID-19, including neutrophil hyperactivation and anti-inflammatory monocytes.

Mass cytometry analysis of the NK cell receptor-ligand repertoire reveals unique differences between dengue-infected children and adults

This study uses mass cytometry to compare NK cell receptor-ligand profiles between dengue-infected children and adults, identifying distinct immune signatures associated with infection outcomes.

Treated HIV Infection Alters Phenotype But Not HIV-specific Function of Peripheral Blood Natural Killer Cells

This study examines how treated HIV infection affects NK cell phenotype and function, finding altered repertoires but no increased HIV-specificity.

Targeting BDCA2 suppresses Plasmacytoid dendritic cell dependent interferon response and tissue fibrosis

This study shows that targeting BDCA2 reduces pDC-driven interferon responses and fibrosis in preclinical models of skin inflammation.

TIGIT is upregulated by HIV-1 infection and marks a highly functional adaptive and mature subset of natural killer cells

This study shows that TIGIT is upregulated on NK cells in untreated HIV+ individuals and marks a functional, mature NK cell subset with enhanced responses to HIV-infected targets.

CD38 contributes to human natural killer cell responses through a role in immune synapse formation

This study identifies CD38 as a key receptor in human NK cells that facilitates immune synapse formation, enhancing antiviral and antitumor responses.

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.

Specific Gut Microbiome Members are Associated with Distinct Immune Markers in Allogeneic Hematopoietic Stem Cell Transplantation

The paper identifies associations between gut microbiome taxa and immune markers in HSCT patients, linking specific microbial profiles to clinical outcomes like aGvHD and mortality.

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.

Gut microbiome transition across a lifestyle gradient in Himalaya

The paper examines gut microbiome differences across four Himalayan populations with varying lifestyles, finding that microbiome composition is significantly associated with lifestyle changes rather than genetics or geography.