55 Result(s)
within
Curtis Huttenhower
Bioinformatics
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Article
Open AccessBugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures
The literature of human and other host-associated microbiome studies is expanding rapidly, but systematic comparisons among published results of host-associated microbiome signatures of differential abundance ...
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Open AccessExtending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4
Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms from most metagenomes. Here we present MetaPhlAn 4, which integrates information f...
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Open AccessMetagenomic assessment of gut microbial communities and risk of severe COVID-19
The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alteration...
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Open AccessRNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities
Characterization of microbial activity is essential to the understanding of the basic biology of microbial communities, as the function of a microbiome is defined by its biochemically active (“viable”) communi...
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Open AccessThe gut microbiome modifies the associations of short- and long-term physical activity with body weight changes
The gut microbiome regulates host energy balance and adiposity-related metabolic consequences, but it remains unknown how the gut microbiome modulates body weight response to physical activity (PA).
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Open AccessPopulation structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin
Microbiome studies of inflammatory bowel diseases (IBD) have achieved a scale for meta-analysis of dysbioses among populations. To enable microbial community meta-analyses generally, we develop MMUPHin for nor...
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Open AccessDietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men
A higher intake of dietary fiber is associated with a decreased risk of chronic inflammatory diseases such as cardiovascular disease and inflammatory bowel disease. This may function in part due to abrogation ...
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Open AccessThe colorectal cancer-associated faecal microbiome of develo** countries resembles that of developed countries
The incidence of colorectal cancer (CRC) is increasing in develo** countries, yet limited research on the CRC- associated microbiota has been conducted in these areas, in part due to scarce resources, facili...
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Open AccessWhole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach
High-throughput sequencing provides a powerful window into the structural and functional profiling of microbial communities, but it is unable to characterize only the viable portion of microbial communities at...
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Open AccessDeterminants of Staphylococcus aureus carriage in the develo** infant nasal microbiome
Staphylococcus aureus is a leading cause of healthcare- and community-associated infections and can be difficult to treat due to antimicrobial resistance. About 30% of individuals carry S. aureus asymptomatically...
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Open AccessStrain-level epidemiology of microbial communities and the human microbiome
The biological importance and varied metabolic capabilities of specific microbial strains have long been established in the scientific community. Strains have, in the past, been largely defined and characteriz...
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Open AccessAnalysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations
Eubacterium rectale is one of the most prevalent human gut bacteria, but its diversity and population genetics are not well understood because large-scale whole-genome investigations of this microbe have not been...
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PICRUSt2 for prediction of metagenome functions
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Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
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Open AccessNext steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16–17, 2017
The National Cancer Institute (NCI) sponsored a 2-day workshop, “Next Steps in Studying the Human Microbiome and Health in Prospective Studies,” in Bethesda, Maryland, May 16–17, 2017. The workshop brought tog...
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Translating microbiome futures
A group of microbiome researchers discuss some of the challenges in develo** a new generation of microbiome therapies.
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Species-level functional profiling of metagenomes and metatranscriptomes
Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious map**, and often...
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Open AccessDaylight exposure modulates bacterial communities associated with household dust
Microbial communities associated with indoor dust abound in the built environment. The transmission of sunlight through windows is a key building design consideration, but the effects of light exposure on dust...
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Open AccessContinuity of transcriptomes among colorectal cancer subtypes based on meta-analysis
Previous approaches to defining subtypes of colorectal carcinoma (CRC) and other cancers based on transcriptomes have assumed the existence of discrete subtypes. We analyze gene expression patterns of colorect...
