Project description:We performed single cell RNAseq of liver cells in acute liver failure model in mice with different microbiome states to unravel cellular changes in the disease and the impact of gut microbiota on the physiology in this disease.

2020-08-18 | E-MTAB-8263 | biostudies-arrayexpress

Lysine acetylation of microbiome

Project description:This project study and comprehensively characterize the lysine acetyltion in the human gut microbiome using antibody-based enrichment strategry and Orbitrap mass spectrometer. The technique has also been applied to study the microbiome in pediatric Crohn's disease and control subjects in order to understand the functional alterations of microbiome in IBD.

2020-07-08 | PXD013427 | Pride

Metaproteomic analysis of the infant fecal microbiome

Project description:A metaproteomics analysis was conducted on the infant fecal microbiome to characterize global protein expression in 8 samples obtained from infants with a range of early-life experiences. Samples included breast-, formula- or mixed-fed, mode of delivery, and antibiotic treatment and one set of monozygotic twins. Although label-free mass spectrometry-based proteomics is routinely used for the identification and quantification of thousands of proteins in complex samples, the metaproteomic analysis of the gut microbiome presents particular technical challenges. Among them: the extreme complexity and dynamic range of member taxa/species, the need for matched, well-annotated metagenomics databases, and the high inter-protein sequence redundancy/similarity between related members. In this study, a metaproteomic approach was developed for assessment of the biological phenotype and functioning, as a complement to 16S rRNA sequencing analysis to identify constituent taxa. A sample preparation method was developed for recovery and lysis of bacterial cells, followed by trypsin digestion, and pre-fractionation using Strong Cation Exchange chromatography. Samples were then subjected to high performance LC-MS/MS. Data was searched against the Human Microbiome Project database, and a homology-based meta-clustering strategy was used to combine peptides from multiple species into representative proteins. Bacterial taxonomies were also identified, based on species-specific protein sequences, and protein metaclusters were assigned to pathways and functional groups. The results obtained demonstrate the applicability of this approach for performing qualitative comparisons of human fecal microbiome composition, physiology and metabolism, and also provided a more detailed assessment of microbial composition in comparison to 16S rRNA.

2019-03-29 | PXD006033 | Pride

Indo_mother-infant microbiome

Project description:Indonesian mother-infant microbiome

| PRJEB34323 | ENA

Relationships of neighborhood blight, urban green remediation and the postmortem human microbiome

Project description:Relationships of neighborhood blight, urban green remediation and the postmortem human microbiome

| PRJEB19323 | ENA

Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States.

Project description: Not available

| S-EPMC7820601 | biostudies-literature