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An integrated workflow for enhanced taxonomic and functional coverage of the mouse fecal metaproteome.

Title: An integrated workflow for enhanced taxonomic and functional coverage of the mouse fecal metaproteome.
Authors: Nalpas, N
Hoyles, L
Anselm, V
Ganief, T
Martinez-Gili, L
Grau, C
Droste-Borel, I
Davidovic, L
Altafaj, X
Dumas, M-E
Macek, B
Item Type: Journal Article
Abstract: Intestinal microbiota plays a key role in shaping host homeostasis by regulating metabolism, immune responses and behavior. Its dysregulation has been associated with metabolic, immune and neuropsychiatric disorders and is accompanied by changes in bacterial metabolic regulation. Although proteomics is well suited for analysis of individual microbes, metaproteomics of fecal samples is challenging due to the physical structure of the sample, presence of contaminating host proteins and coexistence of hundreds of taxa. Furthermore, there is a lack of consensus regarding preparation of fecal samples, as well as downstream bioinformatic analyses following metaproteomics data acquisition. Here we assess sample preparation and data analysis strategies applied to mouse feces in a typical mass spectrometry-based metaproteomic experiment. We show that subtle changes in sample preparation protocols may influence interpretation of biological findings. Two-step database search strategies led to significant underestimation of false positive protein identifications. Unipept software provided the highest sensitivity and specificity in taxonomic annotation of the identified peptides of unknown origin. Comparison of matching metaproteome and metagenome data revealed a positive correlation between protein and gene abundances. Notably, nearly all functional categories of detected protein groups were differentially abundant in the metaproteome compared to what would be expected from the metagenome, highlighting the need to perform metaproteomics when studying complex microbiome samples.
Issue Date: 11-Nov-2021
Date of Acceptance: 29-Sep-2021
URI: http://hdl.handle.net/10044/1/93087
DOI: 10.1080/19490976.2021.1994836
ISSN: 1949-0976
Publisher: Taylor & Francis Open Access
Start Page: 1
End Page: 23
Journal / Book Title: Gut Microbes
Volume: 13
Issue: 1
Copyright Statement: © 2021 The Author(s). Published with license by Taylor & Francis Group, LLC. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Sponsor/Funder: Medical Research Council (MRC)
Medical Research Council (MRC)
Funder's Grant Number: MR/L01632X/1
MR/L01632X/1
Keywords: Science & Technology
Life Sciences & Biomedicine
Gastroenterology & Hepatology
Microbiology
Metaproteomics
microbiome
Mus musculus
mass spectrometry
proteogenomics
SAMPLE PREPARATION
MASS-SPECTROMETRY
GUT MICROBIOTA
PROTEOMICS
ENRICHMENT
PEPTIDES
PROTEINS
PACKAGE
MODEL
SUITE
Metaproteomics
Mus musculus
mass spectrometry
microbiome
proteogenomics
Metaproteomics
Mus musculus
mass spectrometry
microbiome
proteogenomics
0605 Microbiology
Publication Status: Published
Conference Place: United States
Open Access location: https://www.tandfonline.com/doi/full/10.1080/19490976.2021.1994836
Online Publication Date: 2021-11-11
Appears in Collections:Department of Metabolism, Digestion and Reproduction
Department of Surgery and Cancer



This item is licensed under a Creative Commons License Creative Commons