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MuSt multiomics

ABSTRACT: Multiomics of faecal samples collected from individuals in families with multiple cases of type 1 diabetes mellitus (T1DM) over 3 or 4 months. Metagenomic and metatranscriptomic sequencing and metaproteomics were carried out, as well as whole human genome sequencing. Phenotypic data is available.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mixed Culture Metagenome (ncbitaxon:1306859)

SUBMITTER: Paul Wilmes

PROVIDER: MSV000081630 | MassIVE | Thu Oct 19 06:38:00 BST 2017

SECONDARY ACCESSION(S): PXD003791

REPOSITORIES: MassIVE

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Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes.

Heintz-Buschart Anna A May Patrick P Laczny Cédric C CC Lebrun Laura A LA Bellora Camille C Krishna Abhimanyu A Wampach Linda L Schneider Jochen G JG Hogan Angela A de Beaufort Carine C Wilmes Paul P

Nature microbiology 20161010

The gastrointestinal microbiome is a complex ecosystem with functions that shape human health. Studying the relationship between taxonomic alterations and functional repercussions linked to disease remains challenging. Here, we present an integrative approach to resolve the taxonomic and functional attributes of gastrointestinal microbiota at the metagenomic, metatranscriptomic and metaproteomic levels. We apply our methods to samples from four families with multiple cases of type 1 diabetes mel ...[more]

PMID: 27723761

Similar Datasets

MuSt multiomics - Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

Project description:Multiomics of faecal samples collected from individuals in families with multiple cases of type 1 diabetes mellitus (T1DM) over 3 or 4 months. Metagenomic and metatranscriptomic sequencing and metaproteomics were carried out, as well as whole human genome sequencing. Phenotypic data is available.

2016-08-22 | PXD003791 | Pride

Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by multi-omic analysis

Project description:Background Alterations of the gut microbiome have been linked to multiple chronic diseases. However, the drivers of such changes remain largely unknown. The oral cavity acts as a major route of exposure to exogenous factors including pathogens, and processes therein may affect the communities in the subsequent compartments of the gastrointestinal tract. Here, we perform strain-resolved, integrated multi-omic analyses of saliva and stool samples collected from eight families with multiple cases of type 1 diabetes mellitus (T1DM). Results We identified distinct oral microbiota mostly reflecting competition between streptococcal species. More specifically, we found a decreased abundance of the commensal Streptococcus salivarius in the oral cavity of T1DM individuals, which is linked to its apparent competition with the pathobiont Streptococcus mutans. The decrease in S. salivarius in the oral cavity was also associated with its decrease in the gut as well as higher abundances in facultative anaerobes including Enterobacteria. In addition, we found evidence of gut inflammation in T1DM as reflected in the expression profiles of the Enterobacteria as well as in the human gut proteome. Finally, we were able to follow transmitted strain-variants from the oral cavity to the gut at the metagenomic, metatranscriptomic and metaproteomic levels, highlighting not only the transfer, but also the activity of the transmitted taxa along the gastrointestinal tract. Conclusions Alterations of the oral microbiome in the context of T1DM impact the microbial communities in the lower gut, in particular through the reduction of “oral-to-gut” transfer of Streptococcus salivarius. Our results indicate that the observed oral-cavity-driven gut microbiome changes may contribute towards the inflammatory processes involved in T1DM. Through the integration of multi-omic analyses, we resolve strain-variant “mouth-to-gut” transfer in a disease context.

2022-10-05 | PXD031579 | Pride

T1D_MSC

Project description:The oligo microarrays were used to determine mRNA gene expression profiles of mesenchymal stromal cells from type 1 diabetes mellitus (T1DM) patients, before and after autologous hematopoietic stem cell transplantation, and compare to healthy individuals.

2016-12-01 | E-MEXP-3904 | biostudies-arrayexpress

Transcriptional profiling by array of microRNAs of human peripheral blood mononuclear cells - PBMC - from control individuals for Type 2 diabetes mellitus patients

Project description:The microRNA oligo microarrays were used to determine expression profiles of peripheral blood mononuclear cells from control healthy individuals and compare to type 2 diabetes mellitus (T2DM) patients, aiming the identification of possible disease related MicroRNAs.

2015-04-01 | E-MTAB-2902 | biostudies-arrayexpress

Project description:Metagenomic sequencing of diabetes progression in the UC Davis Type 2 Diabetes Mellitus Rat Model

| PRJNA450767 | ENA

Shifts in the Immunoepigenomic Landscape of Monocytes in Response to a Diabetes-Specific Social Support Intervention: A Pilot Study Among Native Hawaiian Adults with Diabetes

Project description:Genome-wide DNA methylation profiling of bead-enriched total monocytes collected from Native Hawaiian participants with known type 2 diabetes mellitus enrolled in a 3 month diabetes-specific social support education intervention. DNA methylation profiling was performed across ~450,000 CpGs from monocytes using the Illumina Infinium HumanMethylation450 BeadChip. Samples included 8 participants with paired DNA methylation data collected at pre-intervention and post-intervention (3 months), and 2 non-diabetic donors.

2022-07-18 | GSE197881 | GEO

human fecal microbiome

Project description:Metagenomic analysis of fecal microbiome from patients with gestational diabetes mellitus

| PRJNA401977 | ENA

RNA-seq of liver tissue from Macaca fascicularis with high fat high sugar treatment or with spontaneous diabetes

Project description:In order to understand the mechanisms underlying diabetes mellitus, we conducted a transcriptomic profiling of the liver from Macaca fascicularis with spontaneously occurred diabetes mellitus at their middle age compared with the monkeys fed with the same food and high-fat and high-sugar diet, respectively.

2022-05-05 | E-MTAB-10493 | biostudies-arrayexpress

Project description:Comparative analysis of gut microbiome among type 2 diabetes mellitus and healthy individuals

| PRJNA588353 | ENA

Macaca fascicularis liver LC-MS/MS

Project description:In order to develop new safe and potent therapeutics, insights into the mechanisms underlying diabetes mellitus are urgently needed. We used proteomics profiling of the liver tissue from Macaca fascicularis with spontaneously occurred diabetes mellitus at their middle age and including two groups of the monkeys fed with the same food and high-fat and high-sugar diet for comparison.We hoped to find something new for diabetes mellitus treatment.

2022-02-17 | PXD025863 | Pride

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