Zachary C. Holmes
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View article: Untargeted metabolomic analysis of human milk from healthy mothers reveals drivers of metabolite variability
Untargeted metabolomic analysis of human milk from healthy mothers reveals drivers of metabolite variability Open
Understanding the human milk metabolome can help inform infant nutrition and health. Untargeted metabolomics was used to study breast milk from 31 healthy participants to assess the shared metabolites in milk from participants with various…
View article: Interplay between particle size and microbial ecology in the gut microbiome
Interplay between particle size and microbial ecology in the gut microbiome Open
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. H…
View article: Interplay between particle size and microbial ecology in the gut microbiome
Interplay between particle size and microbial ecology in the gut microbiome Open
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. H…
View article: A genetic system for Akkermansia muciniphila reveals a role for mucin foraging in gut colonization and host sterol biosynthesis gene expression
A genetic system for Akkermansia muciniphila reveals a role for mucin foraging in gut colonization and host sterol biosynthesis gene expression Open
View article: Prebiotic galactooligosaccharides interact with mouse gut microbiota to attenuate acute graft-versus-host disease
Prebiotic galactooligosaccharides interact with mouse gut microbiota to attenuate acute graft-versus-host disease Open
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 …
View article: Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake
Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake Open
View article: Ecological memory of prior nutrient exposure in the human gut microbiome
Ecological memory of prior nutrient exposure in the human gut microbiome Open
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 structur…
View article: Additional file 12 of Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake
Additional file 12 of Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake Open
Additional file 12.
View article: Additional file 9 of Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake
Additional file 9 of Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake Open
Additional file 9.
View article: Additional file 8 of Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake
Additional file 8 of Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake Open
Additional file 8.
View article: Additional file 10 of Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake
Additional file 10 of Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake Open
Additional file 10.
View article: Additional file 11 of Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake
Additional file 11 of Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake Open
Additional file 11.
View article: Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake
Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake Open
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 …
View article: Ecological memory of prior nutrient exposure in the human gut microbiome
Ecological memory of prior nutrient exposure in the human gut microbiome Open
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 diet…
View article: Genotypic and Phenotypic Diversity among Human Isolates of Akkermansia muciniphila
Genotypic and Phenotypic Diversity among Human Isolates of Akkermansia muciniphila Open
The abundance of Akkermansia muciniphila in the gastrointestinal (GI) tract is linked to multiple positive health outcomes. There are four known A. muciniphila phylogroups, yet the prevalence of these phylogroups and how they vary in their…
View article: Conserved anti-inflammatory effects and sensing of butyrate in zebrafish
Conserved anti-inflammatory effects and sensing of butyrate in zebrafish Open
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 diseas…
View article: Short-Chain Fatty Acid Production by Gut Microbiota from Children with Obesity Differs According to Prebiotic Choice and Bacterial Community Composition
Short-Chain Fatty Acid Production by Gut Microbiota from Children with Obesity Differs According to Prebiotic Choice and Bacterial Community Composition Open
Pediatric obesity remains a major public health problem in the United States, where 17% of children and adolescents are obese, and rates of pediatric “severe obesity” are increasing. Children and adolescents with obesity face higher health…
View article: Conserved anti-inflammatory effects and sensing of butyrate in zebrafish
Conserved anti-inflammatory effects and sensing of butyrate in zebrafish Open
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 diseas…
View article: Short-chain fatty acid production by gut microbiota from children with obesity is linked to bacterial community composition and prebiotic choice
Short-chain fatty acid production by gut microbiota from children with obesity is linked to bacterial community composition and prebiotic choice Open
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 …
View article: Bayesian Multinomial Logistic Normal Models through Marginally Latent Matrix-T Processes
Bayesian Multinomial Logistic Normal Models through Marginally Latent Matrix-T Processes Open
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. Howev…
View article: Consistency of trematode infection prevalence in host populations across large spatial and temporal scales
Consistency of trematode infection prevalence in host populations across large spatial and temporal scales Open
Parasites can impart heavy fitness costs on their hosts. Thus, understanding the spatial and temporal consistency in parasite pressure can elucidate the likeliness of parasites’ role as agents of directional selection, as well as revealing…
View article: <i>Toxoplasma gondii</i> Toc75 Functions in Import of Stromal but not Peripheral Apicoplast Proteins
<i>Toxoplasma gondii</i> Toc75 Functions in Import of Stromal but not Peripheral Apicoplast Proteins Open
Apicomplexa are unicellular parasites causing important human and animal diseases, including malaria and toxoplasmosis. Most of these pathogens possess a relict but essential plastid, the apicoplast. The apicoplast was acquired by secondar…