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View article: A global survey of taxa-metabolic associations across mouse microbiome communities
A global survey of taxa-metabolic associations across mouse microbiome communities Open
Host-microbiota mutualism is rooted in the exchange of dietary and metabolic molecules. Microbial diversity broadens the metabolite pool, with each taxon contributing distinct compounds in varying proportions. In the human microbiome, high…
View article: Acetoacetate suppresses colon cancer via an MR1-MAIT axis
Acetoacetate suppresses colon cancer via an MR1-MAIT axis Open
Colorectal cancer (CRC) is a leading cause of cancer mortality and additional preventative, and therapeutic strategies are urgently needed. Ketogenic diets have mixed effects on tumorigenesis and compliance is challenging. Exogenous ketone…
View article: Predicting functions of uncharacterized gene products from microbial communities
Predicting functions of uncharacterized gene products from microbial communities Open
The majority of genes in microbial communities remain uncharacterized. Here we develop a method to infer putative function for microbial proteins at scale by assessing community-wide multiomics data. We predict high-confidence functions fo…
View article: The metabolic sensor LKB1 regulates ILC3 homeostasis and mitochondrial function
The metabolic sensor LKB1 regulates ILC3 homeostasis and mitochondrial function Open
Group 3 innate lymphoid cells (ILC3s) are tissue-resident cells that sense environmental cues, control infections, and promote tissue homeostasis at mucosal surfaces. The metabolic sensor liver kinase B1 (LKB1) integrates intracellular str…
View article: Chronic binge drinking-induced susceptibility to colonic inflammation is microbiome-dependent
Chronic binge drinking-induced susceptibility to colonic inflammation is microbiome-dependent Open
Alterations in intestinal permeability and the gut microbiome caused by alcohol abuse are associated with alcoholic liver disease and with worsening of inflammatory bowel diseases (IBD) symptoms. To resolve the direct effects of chronic et…
View article: A Bacterial Bile Acid Metabolite Modulates T<sub>reg</sub>Activity through the Nuclear Hormone Receptor NR4A1
A Bacterial Bile Acid Metabolite Modulates T<sub>reg</sub>Activity through the Nuclear Hormone Receptor NR4A1 Open
SUMMARY Bile acids act as signaling molecules that regulate immune homeostasis, including the differentiation of CD4 + T cells into distinct T cell subsets. The bile acid metabolite isoallolithocholic acid (isoalloLCA) enhances the differe…
View article: Human gut bacteria produce T<sub>H</sub>17-modulating bile acid metabolites
Human gut bacteria produce T<sub>H</sub>17-modulating bile acid metabolites Open
The microbiota plays a pivotal role in gut immune homeostasis. Bacteria influence the development and function of host immune cells, including T helper cells expressing interleukin-17a (T H 17 cells). We previously reported that the bile a…
View article: <i>Fusobacterium nucleatum</i> drives a pro-inflammatory intestinal microenvironment through metabolite receptor-dependent modulation of IL-17 expression
<i>Fusobacterium nucleatum</i> drives a pro-inflammatory intestinal microenvironment through metabolite receptor-dependent modulation of IL-17 expression Open
The colorectal cancer (CRC)-associated microbiota creates a pro-tumorigenic intestinal milieu and shapes immune responses within the tumor microenvironment. However, how oncomicrobes - like Fusobacterium nucleatum, found in the oral cavity…
View article: Additional file 8 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach
Additional file 8 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach Open
Additional file 7:. All sample taxonomy.
View article: Additional file 3 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach
Additional file 3 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach Open
Additional file 2. bioBakery workflows.
View article: Additional file 9 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach
Additional file 9 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach Open
Additional file 8:. All sample meta.
View article: Additional file 6 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach
Additional file 6 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach Open
Additional file 5. Metadata.
View article: Additional file 5 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach
Additional file 5 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach Open
Additional file 4. PERMANOVA FDR adjusted.
View article: Additional file 7 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach
Additional file 7 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach Open
Additional file 6. Relative abundances of several taxa changed significantly after PMA treatment.
View article: Additional file 4 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach
Additional file 4 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach Open
Additional file 3. Multivariate tests for taxa associated with metadata.
View article: Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach
Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach Open
Background 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 scale. There is as…
View article: Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach
Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach Open
Background: 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 scale. There is a…
View article: Next Gen sequencing tools to derive insights into protein expression and gene function
Next Gen sequencing tools to derive insights into protein expression and gene function Open
Human physiology is heavily influenced by the colonization of microbes in the gastrointestinal tract. A major roadblock to understanding this process is our inability to genetically manipulate new bacterial species and experimentally asses…