Renee Oles
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View article: Antimicrobial resistance is widespread among intestinal and extra-intestinal <i>Bacteroides fragilis</i> strains
Antimicrobial resistance is widespread among intestinal and extra-intestinal <i>Bacteroides fragilis</i> strains Open
Bacteroides fragilis is an important member of the human gut microbiota, where it contributes to immune modulation, intestinal barrier integrity, and colonization resistance. Despite its beneficial roles as a symbiont in the gut, B. fragil…
View article: Calculating fast differential genome coverages among metagenomic sources using micov
Calculating fast differential genome coverages among metagenomic sources using micov Open
Breadth of coverage, the proportion of a reference genome covered by at least one sequencing read, is critical for interpreting metagenomic data, informing analyses from genome assembly to taxonomic profiling. However, existing tools typic…
View article: IBD-associated Bacteroides fragilis strains drive dysregulated tolerogenic immunity and pro-inflammatory responses 3416
IBD-associated Bacteroides fragilis strains drive dysregulated tolerogenic immunity and pro-inflammatory responses 3416 Open
Description The gut microbiota plays a central role in maintaining immune homeostasis, balancing tolerogenic and pro-inflammatory responses crucial for intestinal health. Among gut bacteria, Bacteroides fragilis is a keystone species known…
View article: A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population
A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population Open
Emerging research suggests that diet plays a vital role in shaping the composition and function of the gut microbiota. Although substantial efforts have been made to identify general patterns linking diet to the gut microbiome, much of thi…
View article: The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns
The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns Open
Space habitation provides unique challenges in built environments isolated from Earth. We produced a 3D map of the microbes and metabolites throughout the United States Orbital Segment (USOS) of the International Space Station (ISS) with 8…
View article: A three-country analysis of the gut microbiome indicates taxon associations with diet vary by location and strain
A three-country analysis of the gut microbiome indicates taxon associations with diet vary by location and strain Open
Emerging research suggests that diet plays a vital role in shaping the composition and function of the gut microbiota. While significant efforts have been made to identify general patterns linking diet to the gut microbiome, much of this r…
View article: Pangenome comparison of <i>Bacteroides fragilis</i> genomospecies unveils genetic diversity and ecological insights
Pangenome comparison of <i>Bacteroides fragilis</i> genomospecies unveils genetic diversity and ecological insights Open
Bacteroides fragilis is a Gram-negative commensal bacterium commonly found in the human colon, which differentiates into two genomospecies termed divisions I and II. Through a comprehensive collection of 694 B. fragilis whole genome sequen…
View article: Pathogenic<i>Bacteroides fragilis</i>strains can emerge from gut-resident commensals
Pathogenic<i>Bacteroides fragilis</i>strains can emerge from gut-resident commensals Open
SUMMARY Bacteroides fragilis is a prominent member of the human gut microbiota, playing crucial roles in maintaining gut homeostasis and host health. Although it primarily functions as a beneficial commensal, B. fragilis can become pathoge…
View article: Pangenome comparison of<i>Bacteroides fragilis</i>genomospecies unveil genetic diversity and ecological insights
Pangenome comparison of<i>Bacteroides fragilis</i>genomospecies unveil genetic diversity and ecological insights Open
Bacteroides fragilis is a Gram-negative commensal bacterium commonly found in the human colon that differentiates into two genomospecies termed division I and II. We leverage a comprehensive collection of 694 B. fragilis whole genome seque…
View article: Commensal bacteria promote type I interferon signaling to maintain immune tolerance in mice
Commensal bacteria promote type I interferon signaling to maintain immune tolerance in mice Open
Type I interferons (IFNs) exert a broad range of biological effects important in coordinating immune responses, which have classically been studied in the context of pathogen clearance. Yet, whether immunomodulatory bacteria operate throug…
View article: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
A bacterial sialidase mediates early life colonization by a pioneering gut commensal Open
The early microbial colonization of the gastrointestinal tract can lead to long-term impacts in development and overall human health. Keystone species, including Bacteroides spp ., play a crucial role in maintaining the structure, diversit…
View article: A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data
A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data Open
MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can s…
View article: A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data
A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data Open
MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can s…