Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effects of BAFASAL on human microbiome

ABSTRACT: This project aims to examinw the effects of an anti-Salmonella bacteriophage preparation, BAFASAL, on ex vivo human gut microbiome composition and function using a multi-omics approach

INSTRUMENT(S): Q Exactive

ORGANISM(S): Human Gut Metagenome

SUBMITTER: Xu Zhang

LAB HEAD: Daniel Figeys

PROVIDER: PXD027172 | Pride | 2022-02-17

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	MB_20200120_QE_Proteon2_1.raw	Raw
	MB_20200120_QE_Proteon2_10.raw	Raw
	MB_20200120_QE_Proteon2_100.raw	Raw
	MB_20200120_QE_Proteon2_101_200127003306.raw	Raw
	MB_20200120_QE_Proteon2_102_2.raw	Raw

Items per page:

1 - 5 of 125

Publications

Examining the Effects of an Anti-Salmonella Bacteriophage Preparation, BAFASAL<sup>®</sup>, on Ex-Vivo Human Gut Microbiome Composition and Function Using a Multi-Omics Approach.

Mayne Janice J Zhang Xu X Butcher James J Walker Krystal K Ning Zhibin Z Wójcik Ewelina E Dastych Jarosław J Stintzi Alain A Figeys Daniel D

Viruses 20210831 9

<i>Salmonella</i> infections (salmonellosis) pose serious health risks to humans, usually via food-chain contamination. This foodborne pathogen causes major food losses and human illnesses, with significant economic impacts. Overuse of antibiotics in the food industry has led to multidrug-resistant strains of bacteria, and governments are now restricting their use, leading the food industry to search for alternatives to secure food chains. Bacteriophages, viruses that infect and kill bacteria, a ...[more]

PMID: 34578313

Similar Datasets

An in vitro model maintaining taxon-specific functional activities of the gut microbiome

Project description:We developed and validated a 96-deep well plate-based culturing model named Mipro to maintain individuals’ microbiomes. The Mipro model quintupled viable bacteria count while maintained the functional and compositional profiles of individuals’ gut microbiomes.

2019-08-16 | PXD013600 | Pride

Lysine acetylation in human fecal microbiome

Project description:This study characterized the lysine acetylome in human gut microbiome samples. Briefly, the microbial peptides obtained from human mcirobiome cells were used for lysine acetylated peptide enrichment using anti-acetyl-lysine (Kac) antibody cocktail; the enriched Kac peptides were then identified and quantified using mass spectrometry.

2020-07-08 | PXD015482 | Pride

Differential Lysis Approach Enables Selective Extraction of Taxon-Specific Proteins for Gut Metaproteomics

Project description:A differential lysis approach was developed with different strength of lysis buffers (urea and/or sodium dodecyl sulfate) and applied on human stool samples to separate different microbial species to increase the depth of metaproteomic measurements. We showed that the lysates dominating by proteins from Gram-positive (G+) or negative bacteria (G-) can be achieved by differential lysis

2023-03-27 | PXD016787 | Pride

Human gut microbiome cultured over time responsed differently to drug stimulation

Project description:In vitro gut microbiota models are often used to study drug-microbiome interaction. Similar to culturing individual microbial strains, the biomass accumulation of in vitro gut microbiota follows a logistic growth curve. Current studies on in vitro gut microbiome responses introduce drug stimulation during different growth stages, e.g. lag phase or stationary phase. However, in vitro gut microbiota in different growth phases may respond differently to a same stimuli. Therefore, in this study, we used a 96-deep well plate-based culturing model (MiPro) to culture the human gut microbiota. Metformin, as the stimulus, was added at the lag, log and stationary phases of growth. Microbiome samples were collected at different time points for optical density and metaproteomic functional analysis. Results show that in vitro gut microbiota responded differently to metformin added during different growth phases, in terms of the growth curve, alterations of taxonomic and functional compositions. The addition of drugs at log phase leads to the greatest decline of bacterial growth. Metaproteomic analysis suggested that the strength of the metformin effect on the gut microbiome functional profile was ranked as lag phase > log phase > stationary phase. Our results showed that metformin added at lag phase resulted in a significantly reduced abundance of the Clostridiales order as well as an increased abundance of the Bacteroides genus, which was different from stimulation during the rest of the growth phase. Metformin also resulted in alterations of several pathways, including energy production and conversion, lipid transport and metabolism, translation, ribosomal structure and biogenesis. Our results indicate that the timing for drug stimulation should be considered when studying drug-microbiome interactions in vitro.

2022-03-01 | PXD017390 | Pride

Pediatric IBD MLI metaproteomics

Project description:Mucosal-luminal interface (MLI) samples were collected from a cohort of children with new-onset IBD and microbial cells were harvested and processed for metaproteomic analysis. Deep metaproteomics data analysis was then performed for better understanding the MLI microbiota functions in the development of pediatric IBD.

2018-08-03 | PXD007819 | Pride

Hunam gut microbiome metaproteomcis in LP1

Project description:The samples of gut micorbiota were collected in "Lunar Palace 365" experiment. The "Lunar Palace 365" experiment was a 370-day, multicrew, closed experiment carried out in a ground-based experimental BLSS platform named Lunar Palace 1. Deep metaproteomics data analysis was then performed for better understanding the role of gut micorbiota in mood regulation.

2023-05-10 | PXD027661 | Pride

Proteome-Level Functional Redundancy in the Human Gut Microbiome

Project description:Here, we quantify the proteome-level functional redundancy in the human gut microbiome using metaproteomics and network approaches.In particular, we used an ultra-deep metaproteomics approach based on high-pH reverse phase fractionation. The data analysis revealed high protein-level functional redundancy and high nestedness in proteomic content networks - bipartite graphs that connect taxa with their expressed functions.

2023-06-08 | PXD027297 | Pride

Metaproteomic responses of in vitro gut microbiomes to resistant starches

Project description:Resistant starches (RS) are dietary compounds processed by the gut microbiota into metabolites, such as butyrate, that are beneficial to the host. The production of butyrate by the microbiome appears to be affected by the plant source and type of RS as well as the individual’s microbiota. In this study, we used in vitro culture and metaproteomic methods to explore the consistency and variations in individual microbiome's functional responses to three types of RS - RS2(Hi Maize 260), RS3(Novelose 330) and RS4(Fibersym RW). Results showed that RS2 and RS3 significantly altered the levels of protein expression in the individual gut microbiomes, while RS4 did not result in significant protein changes. Significantly elevated protein groups were enriched in carbohydrate metabolism and transport functions of families Eubacteriaceae, Lachnospiraceae and Ruminococcaceae. In addition, Bifidobacteriaceae was significantly increased in response to RS3. We also observed taxon-specific enrichments of starch metabolism and pentose phosphate pathways corresponding to this family. Functions related to starch utilization, ABC transporters and pyruvate metabolism pathways were consistently increased in the individual microbiomes in response to RS2 and RS3; in contrast, the downstream butyrate producing pathway response varied. Our study confirm that different types of RS have markedly variable functional effects on the human gut microbiome, and also found considerable inter-individual differences in microbiome pathway responses.

2021-09-08 | PXD017907 | Pride

Stool metaproteomics of children with islet autoimmunity

Project description:The gastrointestinal ecosystem is a highly complex environment with a profound influence on human health. Inflammation in the gut, linked to an altered gut microbiome has been associated with the development of multiple human conditions including type 1 diabetes (T1D). Viruses infecting the gastrointestinal tract, especially enteroviruses, are also thought to play an important role in T1D pathogenesis possibly via overlapping mechanisms. Here, we apply an integrative approach to combine comprehensive faecal virome, microbiome and metaproteome data sampled before and at the onset of islet autoimmunity in 40 children. We show strong age and antibody related effects across the datasets. Mastadenovirus infection was associated with profound functional changes in the faecal metaproteome. Multiomic factor analysis modelling revealed proteins associated with carbohydrate transport from the genus Faecalibacterium were associated with islet autoimmunity. These findings demonstrate functional remodelling of the gut microbiota accompanies both islet autoimmunity and viral infection.

2022-08-22 | PXD032997 | Pride

Study of human gut microbiota from healthy adults

Project description:The link between the gut microbiota of a human being (a complex group of microorganism including not only bacteria but also fungi, viruses, etc.,) that form an ecosystem in his gastrointestinal tract and his physiological state is nowadays unquestionable. Metaproteomics has emerged as a useful technique to characterize this microbial community, not just taxonomically, but also focusing on specific biological processes carried out by gut microbiota that may have an effect in the host health or pathological state. In order to characterize this host-microbiota inter-relation, we carried out the metaproteomic study of 6 stool samples from 6 healthy adults. A total of 37 080 peptide sequences and 10 686 protein groups were identified in this study. Regarding taxonomic information, we found a total of 247 taxa among 105 were species. Interesting contributions of microbiota metabolism to human host physiology has also been described.

2021-07-06 | PXD020786 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data