112 Result(s)
within
Curtis Huttenhower
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Article
Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes
The association of gut microbial features with type 2 diabetes (T2D) has been inconsistent due in part to the complexity of this disease and variation in study design. Even in cases in which individual microbi...
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Open AccessAuthor Correction: Optimized model architectures for deep learning on genomic data
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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 AccessOptimized model architectures for deep learning on genomic data
The success of deep learning in various applications depends on task-specific architecture design choices, including the types, hyperparameters, and number of layers. In computational biology, there is no cons...
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Open AccessGut microbiome composition and metabolic activity in women with diverticulitis
The etiopathogenesis of diverticulitis, among the most common gastrointestinal diagnoses, remains largely unknown. By leveraging stool collected within a large prospective cohort, we performed shotgun metageno...
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A host–microbiota interactome reveals extensive transkingdom connectivity
The myriad microorganisms that live in close association with humans have diverse effects on physiology, yet the molecular bases for these impacts remain mostly unknown1–3. Classical pathogens often invade host t...
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Challenges and opportunities in sharing microbiome data and analyses
Microbiome data, metadata and analytical workflows have become ‘big’ in terms of volume and complexity. Although the infrastructure and technologies to share data have been established, the interdisciplinary a...
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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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Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease
For decades, variability in clinical efficacy of the widely used inflammatory bowel disease (IBD) drug 5-aminosalicylic acid (5-ASA) has been attributed, in part, to its acetylation and inactivation by gut mic...
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Microbiome epidemiology and association studies in human health
Studies of the human microbiome share both technical and conceptual similarities with genome-wide association studies and genetic epidemiology. However, the microbiome has many features that differ from genome...
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Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies
Whether the human fetus and the prenatal intrauterine environment (amniotic fluid and placenta) are stably colonized by microbial communities in a healthy pregnancy remains a subject of debate. Here we evaluat...
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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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A biosynthetic pathway for the selective sulfonation of steroidal metabolites by human gut bacteria
Members of the human gut microbiome enzymatically process many bioactive molecules in the gastrointestinal tract. Most gut bacterial modifications characterized so far are hydrolytic or reductive in nature. He...
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Discovery of bioactive microbial gene products in inflammatory bowel disease
Microbial communities and their associated bioactive compounds1–3 are often disrupted in conditions such as the inflammatory bowel diseases (IBD)4. However, even in well-characterized environments (for example, t...
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Open AccessDietary lignans, plasma enterolactone levels, and metabolic risk in men: exploring the role of the gut microbiome
The conversion of plant lignans to bioactive enterolignans in the gastrointestinal tract is mediated through microbial processing. The goal of this study was to examine the relationships between lignan intake,...
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Human gut bacteria produce ΤΗ17-modulating bile acid metabolites
The microbiota modulates gut immune homeostasis. Bacteria influence the development and function of host immune cells, including T helper cells expressing interleukin-17A (TH17 cells). We previously reported that...
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The oral microbiome in relation to pancreatic cancer risk in African Americans
African Americans have the highest pancreatic cancer incidence of any racial/ethnic group in the United States. The oral microbiome was associated with pancreatic cancer risk in a recent study, but no such stu...
