Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single Amino-acid Polymorphisms of Human Gut Ecosystem

ABSTRACT: Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation in gut microbial metagenome and host genome but they could not adequately represent the protein-level variants. Single amino-acid polymorphisms (SAP) derived from non-synonymous SNPs can cause functional changes of proteins and are important forces of adaption. However, SAP remain quite unexplored for human gut microbiome. Here, we present a comprehensive large-scale analysis of SAP in the gut ecosystem, introducing a rigorous computational pipeline for detecting such protein variation from 992 published human metaproteomes.

ORGANISM(S): Homo Sapiens

SUBMITTER: Zhixiang Yan

PROVIDER: PXD062661 | iProX | Sat Apr 05 00:00:00 BST 2025

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

Pan-analysis of Single Amino-acid Polymorphism

Project description:Uncovering dark mass in population proteomics: Pan-analysis of Single Amino-acid Polymorphism (Pan-SAP) revealed quantitative relevance with cognition and aging

2024-12-31 | PXD059327 |

Healthy peripheral neutrophils total RNA-Seq: Serum Amyloid P component is an essential element of resistance against Aspergillus fumigatus

Project description:Serum amyloid P component (SAP; APCS gene, also known as Pentraxin 2, PTX2), is a component of the humoral arm of innate immunity involved in resistance to bacterial infection and regulation of tissue remodeling. The present study was designed to investigate the role of SAP/PTX2 in antifungal resistance. SAP-deficient Apcs-/- mice showed a dramatic increase in susceptibility to A. fumigatus infection. The defective anti-fungal resistance of gene targeted mice was rescued by in vitro opsonization of A. fumigatus conidia and in vivo administration of murine SAP. Mouse and human SAP bound conidia, activated the complement cascade and increased phagocytosis by mouse and human neutrophils. Defective resistance of Apcs-/- SAP-deficient mice was associated with defective in vivo recruitment of neutrophils and phagocytosis in the lungs. The opsonic activity of SAP was dependent on the classical pathway of complement activation. In immunosuppressed mice, SAP administration protected hosts against A. fumigatus infection and death. In the context of a study of hematopoietic stem-cell transplantation, genetic variation in the human APCS gene was associated with susceptibility to invasive pulmonary aspergillosis. Thus, SAP is a fluid phase pattern recognition molecule essential for resistance against A. fumigatus. The results reported here also suggest that SAP has therapeutic potential against an infectious agent which represents a formidable clinical challenge.

2021-04-20 | GSE163533 | GEO

GV-971 prevents severe acute pancreatitis by remodeling the microbiota-metabolic-immune axis

Project description:Despite recent advances, severe acute pancreatitis (SAP) remains an extremely lethal inflammation with limited treatment options. Here, we provide compelling evidence of GV-971 (sodium oligomannate), an anti-Alzheimer's medication, as being a protective agent in various mouse SAP models. Microbiome sequencing, along with fecal microbiota transplantation and mass cytometry technology, unveiled that GV-971 reshapes the gut microbiota, increasing Faecalibacterium populations and modulating both peripheral and intestinal immune systems. A metabolomics analysis of cecal contents from GV-971–treated SAP mice further identified short-chain fatty acids, including propionate and butyrate, as key metabolites in inhibiting macrophage M1 polarization and subsequent lethal inflammation by blocking the MAPK pathway. These findings suggest GV-971 as a promising therapeutic for SAP by targeting the microbiota metabolic immune axis.

2024-07-04 | GSE271034 | GEO

The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. (COPRO-Seq)

Project description:Understanding how the human gut microbiota and host are impacted by probiotic bacterial strains requires carefully controlled studies in humans, and in mouse models of the gut ecosystem where potentially confounding variables that are difficult to control in humans can be constrained. Therefore, we characterized the fecal microbiomes and metatranscriptomes of adult female monozygotic twin pairs through repeated sampling 4 weeks prior to, 7 weeks during, and 4 weeks following consumption of a commercially-available fermented milk product (FMP) containing a consortium of Bifidobacterium animalis subsp. lactis, two strains of Lactobacillus delbrueckii subsp. bulgaricus, Lactococcus lactis subsp. cremoris, and Streptococcus thermophilus. In addition, gnotobiotic mice harboring a 15-species model human gut microbiota whose genomes contain 58,399 known or predicted protein-coding genes were studied prior to and after gavage with all five sequenced FMP strains. 140 samples total. Evaluation of changes in a model community's structure over time after exposure to a consortium of 5 fermented milk product (FMP) strains.

2011-11-01 | E-GEOD-31943 | biostudies-arrayexpress

Xylem sap shotgun proteomics from Mn-excess tomato plants

Project description:The aim of this work was to study the effects of Mn excess on the protein profile of the xylem sap of tomato (Solanum lycopersicum), with the aim of elucidating plant response mechanisms to these nutritional stresses. Tomato was chosen as a model plant because the tomato genome has been published and this plant species has adequate root pressure and turgid stems that permit xylem sap sampling in sufficient amounts by de-topping. The high- throughput shotgun analysis has permitted to identify and quantitate a large number of low abundance proteins in the tomato xylem sap.

2020-12-10 | PXD021973 | Pride

Xylem sap shotgun proteomics from Fe- and Mn-deficient and Mn-toxic tomato plants

Project description:The aim of this work was to study the effects of Fe and Mn deficiencies and Mn toxicity on the protein profile of the xylem sap of tomato (Solanum lycopersicum), with the aim of elucidating plant response mechanisms to these nutritional stresses. Tomato was chosen as a model plant because the tomato genome has been published and this plant species has adequate root pressure and turgid stems that permit xylem sap sampling in sufficient amounts by de-topping. The high-throughput shotgun analysis has permitted to identify and quantitate a large number of low abundance proteins in the tomato xylem sap.

2017-11-30 | PXD007517 | Pride

A selective gut bacterial bile salt hydrolase alters host metabolism

Project description:The human gut microbiota impacts host metabolism and has been implicated in the pathophysiology of obesity and metabolic syndromes. However, defining the roles of specific microbial activities and metabolites on host phenotypes has proven challenging due to the complexity of the microbiome-host ecosystem. Here, we identify strains from the abundant gut bacterial phylum Bacteroidetes that display selective bile salt hydrolase (BSH) activity. Using isogenic strains of wild-type and BSH-deleted Bacteroides thetaiotaomicron, we selectively modulated the levels of the bile acid tauro-b-muricholic acid in monocolonized gnotobiotic mice. B. thetaiotaomicron BSH mutant-colonized mice displayed altered metabolism, including reduced weight gain and respiratory exchange ratios, as well as transcriptional changes in metabolic, circadian rhythm, and immune pathways in the gut and liver. Our results demonstrate that metabolites generated by a single microbial gene and enzymatic activity can profoundly alter host metabolism and gene expression at local and organism-level scales.

2018-07-19 | GSE112571 | GEO

Strongyloides stercoralis infection reduces bacteria producing short-chain fatty acids and increases bacterial amino-acid biosynthesis in early CKD patients

Project description:Controlling the progression of chronic kidney disease (CKD) at an early stage is critical for reducing disease severity. A cross-sectional study of chronic kidney disease (CKD) patients at all stages with S. stercoralis infection found that helminth infection caused gut dysbiosis, which may be involved in CKD progression. Because of the variation of gut microbiome results with helminth infection, the cross-sectional study of 16S rRNA sequencing, therefore, is insufficient to draw valid conclusions and correct the effects of S. stercoralis on the early stages of CKD. Combination with other omics approach is warrant to be better understand the disease.

2024-01-24 | PXD039656 | JPOST Repository