ConferenceAmerican Journal of Respiratory and Critical Care Medicine · May 1, 2026
AbstractRationalePeople living with HIV are at increased risk of respiratory infections. The nasopharyngeal microbiome plays an ...
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Journal ArticleFood Funct · April 14, 2026
Ready-to-use therapeutic and supplementary foods (RUTF/RUSF) are a primary treatment for childhood malnutrition in Community Management of Acute Malnutrition (CMAM) programs. However, measuring intervention compliance is labor intensive and unreliable. We ...
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Journal ArticleNat Commun · March 31, 2026
Celiac disease (CeD) is an immune-mediated condition driven by dietary gluten resulting in small intestinal mucosal inflammation and injury, along with myriads of symptoms. The only treatment is a lifelong gluten-free diet (GFD) and although most patients ...
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Journal ArticleJ Nutr · March 2026
BACKGROUND: Ultraprocessed food (UPF) intake is associated with increased type 2 diabetes (T2D) risk. No controlled feeding trial has investigated UPF exposure and T2D risk or performed chemical analysis of UPF study diets. OBJECTIVES: To design and chemic ...
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Journal ArticlebioRxiv · December 3, 2025
Microbial growth dynamics contain rich information about microbial populations, which support applications from antibiotic testing to microbiome engineering. However, the high dimensionality of growth data and the scarcity of large, task-specific datasets ...
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Journal ArticleJ Infect Dis · October 15, 2025
Children living with HIV (CLWH) are at high risk of colonization and infection by respiratory pathogens, though this risk can be reduced by other microbes in the upper respiratory microbiome. The impact of HIV infection on the pediatric upper respiratory m ...
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Journal ArticlemSystems · July 22, 2025
Diet plays a pivotal role in human health and disease. Yet, nutrition studies have long relied on self-report methods for collecting dietary intake data despite known limitations. Although new technologies for dietary intake assessment and biomarker identi ...
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Journal ArticlemedRxiv · June 9, 2025
BACKGROUND: Obesity and weight loss in adults have been associated with distinct metabolome and gut microbiome features, but the extent to which those associations apply to adolescent stages remain unclear. METHODS: The Pediatric Obesity Microbiome and Met ...
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Journal ArticlemedRxiv · May 14, 2025
Despite established links between the infant gut microbiome and health, how complementary feeding shapes colonization remains unclear. Using FoodSeq, a DNA-based dietary assessment technique, we surveyed food intake across 729 children (0-3 y) from North a ...
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Journal ArticleNature · February 2025
Metabolites derived from the intestinal microbiota, including bile acids (BA), extensively modulate vertebrate physiology, including development1, metabolism2-4, immune responses5-7 and cognitive function8. However, to what extent host responses balance th ...
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Journal ArticleObesity (Silver Spring) · February 2025
OBJECTIVE: We assessed the impact of a food-provisioning intervention on diet quality in children with obesity. METHODS: Participants (n = 33, aged 6-11 years) were randomly assigned to either usual care (intensive health behavior and lifestyle treatment) ...
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Journal ArticleFood Funct · January 2, 2025
Objective biomarkers of food intake are a sought-after goal in nutrition research. Most biomarker development to date has focused on metabolites detected in blood, urine, skin, or hair, but detection of consumed foods in stool has also been shown to be pos ...
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Journal ArticleInt J Food Sci Nutr · September 2024
Fructans are commonly used as dietary fibre supplements for their ability to promote the growth of beneficial gut microbes. However, fructan consumption has been associated with various dosage-dependent side effects. We characterised side effects in an exp ...
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Journal ArticlebioRxiv · April 27, 2024
Physical particles can serve as critical abiotic factors that structure the ecology of microbial communities. For non-human vertebrate gut microbiomes, fecal particle size (FPS) has been known to be shaped by chewing efficiency and diet. However, little is ...
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Journal ArticleInt J Mol Sci · February 22, 2024
Antibodies to DNA are a diverse set of antibodies that bind sites on DNA, a polymeric macromolecule that displays various conformations. In a previous study, we showed that sera of normal healthy subjects (NHS) contain IgG antibodies to Z-DNA, a left-hande ...
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Journal ArticleContemp Clin Trials · February 2024
BACKGROUND: Aging is associated with gut dysbiosis, low-grade inflammation, and increased risk of type 2 diabetes (T2D). Prediabetes, which increases T2D and cardiovascular disease risk, is present in 45-50% of mid-life adults. The gut microbiota may link ...
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Journal ArticleISME J · January 8, 2024
Physical particles can serve as critical abiotic factors that structure the ecology of microbial communities. For non-human vertebrate gut microbiomes, fecal particle size (FPS) has been known to be shaped by chewing efficiency and diet. However, little is ...
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Journal ArticlePLoS One · 2024
The infant gut microbiome is a crucial factor in health and development. In preterm infants, altered gut microbiome composition and function have been linked to serious neonatal complications such as necrotizing enterocolitis and sepsis, which can lead to ...
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Journal ArticleNat Microbiol · August 2023
Akkermansia muciniphila, a mucophilic member of the gut microbiota, protects its host against metabolic disorders. Because it is genetically intractable, the mechanisms underlying mucin metabolism, gut colonization and its impact on host physiology are not ...
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Journal ArticleProc Natl Acad Sci U S A · July 4, 2023
Eating a varied diet is a central tenet of good nutrition. Here, we develop a molecular tool to quantify human dietary plant diversity by applying DNA metabarcoding with the chloroplast trnL-P6 marker to 1,029 fecal samples from 324 participants across two ...
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Journal ArticleBlood · November 24, 2022
Previous studies suggest that gut microbiome disruption induced by chemotherapy, dietary deficiencies, and/or antibiotics are associated with increased incidence of acute graft-versus-host disease (aGVHD) following hematopoietic stem cell transplantation ( ...
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Journal ArticleISME J · November 2022
Many ecosystems have been shown to retain a memory of past conditions, which in turn affects how they respond to future stimuli. In microbial ecosystems, community disturbance has been associated with lasting impacts on microbiome structure. However, wheth ...
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Journal ArticleNat Chem Biol · November 2022
The functions of many microbial communities exhibit remarkable stability despite fluctuations in the compositions of these communities. To date, a mechanistic understanding of this function-composition decoupling is lacking. Statistical mechanisms have bee ...
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Journal ArticleMicrobiome · July 29, 2022
BACKGROUND: Short-chain fatty acids (SCFAs) derived from gut bacteria are associated with protective roles in diseases ranging from obesity to colorectal cancers. Intake of microbially accessible dietary fibers (prebiotics) lead to varying effects on SCFA ...
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Journal ArticleNat Chem Biol · April 2022
Microbial communities inhabit spatial architectures that divide a global environment into isolated or semi-isolated local environments, which leads to the partitioning of a microbial community into a collection of local communities. Despite its ubiquity an ...
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Journal ArticlemSystems · February 22, 2022
Whether a microbe is free-living or associated with a host from across the tree of life, its existence depends on a limited number of elements and electron donors and acceptors. Yet divergent approaches have been used by investigators from different fields ...
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Journal ArticleJ Mach Learn Res · 2022
Bayesian multinomial logistic-normal (MLN) models are popular for the analysis of sequence count data (e.g., microbiome or gene expression data) due to their ability to model multivariate count data with complex covariance structure. However, existing impl ...
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Journal ArticleFront Microbiol · 2022
Cross feeding between microbes is ubiquitous, but its impact on the diversity and productivity of microbial communities is incompletely understood. A reductionist approach using simple microbial communities has the potential to detect cross feeding interac ...
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Journal ArticlePLoS Comput Biol · July 2021
PCR amplification plays an integral role in the measurement of mixed microbial communities via high-throughput DNA sequencing of the 16S ribosomal RNA (rRNA) gene. Yet PCR is also known to introduce multiple forms of bias in 16S rRNA studies. Here we prese ...
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Journal ArticlemBio · May 18, 2021
The mucophilic anaerobic bacterium Akkermansia muciniphila is a prominent member of the gastrointestinal (GI) microbiota and the only known species of the Verrucomicrobia phylum in the mammalian gut. A high prevalence of A. muciniphila in adult humans is a ...
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Journal ArticleObesity (Silver Spring) · March 2021
OBJECTIVE: The purpose of this study was to establish a biorepository of clinical, metabolomic, and microbiome samples from adolescents with obesity as they undergo lifestyle modification. METHODS: A total of 223 adolescents aged 10 to 18 years with BMI ≥9 ...
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Journal ArticleJ Infect Dis · February 3, 2021
BACKGROUND: Susceptibility to Vibrio cholerae infection is affected by blood group, age, and preexisting immunity, but these factors only partially explain who becomes infected. A recent study used 16S ribosomal RNA amplicon sequencing to quantify the comp ...
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Journal Article · 2021
Many ecosystems retain an ecological memory of past conditions that affects responses to future stimuli. However, it remains unknown what mechanisms and dynamics may govern such a memory in microbial communities. Here, in both a human dietary intervention ...
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Journal Article · 2021
Background Short-chain fatty acids (SCFAs) derived from gut bacteria are associated with protective roles in diseases ranging from obesity to colorectal cancers. Intake of microbially accessible dietary fibers (prebiotics) lead to varying effects ...
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Journal ArticleGut Microbes · November 9, 2020
Short-chain fatty acids (SCFAs) are produced by microbial fermentation of dietary fiber in the gut. Butyrate is a particularly important SCFA with anti-inflammatory properties and is generally present at lower levels in inflammatory diseases associated wit ...
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Journal ArticlemBio · August 11, 2020
Pediatric obesity remains a public health burden and continues to increase in prevalence. The gut microbiota plays a causal role in obesity and is a promising therapeutic target. Specifically, the microbial production of short-chain fatty acids (SCFA) from ...
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Journal ArticlemSystems · June 30, 2020
Culture and screening of gut bacteria enable testing of microbial function and therapeutic potential. However, the diversity of human gut microbial communities (microbiota) impedes comprehensive experimental studies of individual bacterial taxa. Here, we c ...
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Journal Article · April 17, 2020
ABSTRACTBackgroundHow human-associated microbial communities resist and respond to perturbations remains incompletely understood. Vir ...
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Journal Article · 2020
ABSTRACTBackground Susceptibility to Vibrio cholerae infection is impacted by blood group, age, and pre-existing immunity, but these factors only partially explain who becomes infected. A recent study used 16S rRNA amplicon sequencing ...
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Journal ArticleComput Struct Biotechnol J · 2020
Genomic studies feature multivariate count data from high-throughput DNA sequencing experiments, which often contain many zero values. These zeros can cause artifacts for statistical analyses and multiple modeling approaches have been developed in response ...
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Journal ArticlemSystems · October 8, 2019
Dietary intake is difficult to measure reliably in humans because approaches typically rely on self-reporting, which can be incomplete and biased. In field studies of animals, DNA sequencing-based approaches such as metabarcoding have been developed to cha ...
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Journal ArticleEcological Monographs · May 1, 2019
The problem of pattern and scale is a central challenge in ecology. In community ecology, an important scale is that at which we aggregate species to define our units of study, such as aggregation of “nitrogen fixing trees” to understand patterns in carbon ...
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Journal ArticleNat Microbiol · December 2018
Resource limitation is a fundamental factor governing the composition and function of ecological communities. However, the role of resource supply in structuring the intestinal microbiome has not been established and represents a challenge for mammals that ...
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Journal ArticleMicrobiome · November 27, 2018
AbstractFollowing publication of the original article [1], the authors noticed an error in the presentation of equations in the PDF version. ...
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Journal ArticleMicrobiome · November 12, 2018
BACKGROUND: Artificial gut models provide unique opportunities to study human-associated microbiota. Outstanding questions for these models' fundamental biology include the timescales on which microbiota vary and the factors that drive such change. Answeri ...
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Journal ArticleJ Infect Dis · July 13, 2018
BACKGROUND: Cholera is a public health problem worldwide, and the risk factors for infection are only partially understood. METHODS: We prospectively studied household contacts of patients with cholera to compare those who were infected to those who were n ...
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Journal ArticleElife · June 19, 2018
How host and microbial factors combine to structure gut microbial communities remains incompletely understood. Redox potential is an important environmental feature affected by both host and microbial actions. We assessed how antibiotics, which can impact ...
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Journal ArticleEcol Evol · January 2018
Soils harbor large, diverse microbial communities critical for local and global ecosystem functioning that are controlled by multiple and poorly understood processes. In particular, while there is observational evidence of relationships between both biotic ...
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Journal ArticlemSystems · 2018
A key challenge in microbiology will be developing tools for manipulating human gut bacterial communities. Our ability to predict and control the dynamics of these communities is now in its infancy. To manage human gut microbiota, I am developing methods i ...
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Journal Article · 2018
ABSTRACT Artificial gut models provide unique opportunities to study human-associated microbiota. Outstanding questions for these models’ fundamental biology include the timescales on which microbiota vary and the factors that drive such change. A ...
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Journal ArticleElife · February 15, 2017
Surveys of microbial communities (microbiota), typically measured as relative abundance of species, have illustrated the importance of these communities in human health and disease. Yet, statistical artifacts commonly plague the analysis of relative abunda ...
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Journal ArticlePeerJ · 2017
Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunitie ...
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ConferenceProceedings IEEE International Conference on Data Mining Icdm · July 2, 2016
We introduce a novel dynamic model for discrete time-series data, in which the temporal sampling may be nonuniform. The model is specified by constructing a hierarchy of Poisson factor analysis blocks, one for the transitions between latent states and the ...
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Journal ArticleHepatology · March 2016
UNLABELLED: Several animal studies have emphasized the role of gut microbiota in nonalcoholic fatty liver disease (NAFLD). However, data about gut dysbiosis in human NAFLD remain scarce in the literature, especially studies including the whole spectrum of ...
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Journal Article · 2016
ABSTRACT High-throughput DNA sequencing technologies have revolutionized the study of microbial communities (microbiota) and have revealed their importance in both human health and disease. However, due to technical limitations, data from microbi ...
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Journal Article · 2016
Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunitie ...
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Journal ArticlemBio · September 29, 2015
UNLABELLED: Gut microbiota influence the development and physiology of their animal hosts, and these effects are determined in part by the composition of these microbial communities. Gut microbiota composition can be affected by introduction of microbes fr ...
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Journal ArticlemBio · May 19, 2015
UNLABELLED: Disability after childhood diarrhea is an important burden on global productivity. Recent studies suggest that gut bacterial communities influence how humans recover from infectious diarrhea, but we still lack extensive data and mechanistic hyp ...
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Journal ArticleNature · January 23, 2014
Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we s ...
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Journal ArticleGenome Biol · 2014
BACKGROUND: Disturbance to human microbiota may underlie several pathologies. Yet, we lack a comprehensive understanding of how lifestyle affects the dynamics of human-associated microbial communities. RESULTS: Here, we link over 10,000 longitudinal measur ...
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Journal ArticleISME J · March 2013
How reproducibly microbial populations assemble in the wild remains poorly understood. Here, we assess evidence for ecological specialization and predictability of fine-scale population structure and habitat association in coastal ocean Vibrionaceae across ...
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Journal ArticleNature · October 30, 2011
Horizontal gene transfer (HGT), the acquisition of genetic material from non-parental lineages, is known to be important in bacterial evolution. In particular, HGT provides rapid access to genetic innovations, allowing traits such as virulence, antibiotic ...
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Journal ArticleNature · January 6, 2011
The natural history of Precambrian life is still unknown because of the rarity of microbial fossils and biomarkers. However, the composition of modern-day genomes may bear imprints of ancient biogeochemical events. Here we use an explicit model of macroevo ...
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Journal ArticleEnviron Microbiol · January 2011
Although animal-associated microbial communities (microbiomes) are increasingly recognized to influence health, the extent to which animals represent highly selective habitats for microbes leading to predominance of high host specificity remains poorly und ...
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Journal ArticleTrends Microbiol · May 2009
As we observe the 200th anniversary of Charles Darwin's birth, microbiologists interested in the application of Darwin's ideas to the microscopic world have a lot to celebrate: an emerging picture of the (mostly microbial) Tree of Life at ever-increasing r ...
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Journal ArticleScience · May 23, 2008
Identifying ecologically differentiated populations within complex microbial communities remains challenging, yet is critical for interpreting the evolution and ecology of microbes in the wild. Here we describe spatial and temporal resource partitioning am ...
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Journal ArticlePLoS One · 2008
Actin-based cell motility and force generation are central to immune response, tissue development, and cancer metastasis, and understanding actin cytoskeleton regulation is a major goal of cell biologists. Cell spreading is a commonly used model system for ...
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Journal ArticleAnn N Y Acad Sci · December 2007
We seek to quantify the failure and success of dynamic Bayesian networks (DBNs), a popular tool for reverse-engineering networks from time-series data. In particular, we focus on data generated by continuous time processes (e.g., genetic expression) and sa ...
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Journal ArticleJ Gerontol A Biol Sci Med Sci · December 2004
Many behavioral responses require the coordination of sensory inputs with motor outputs. Aging is associated with progressive declines in both motor function and muscle structure. However, the consequences of age-related motor deficits on behavior have not ...
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