title: A metaproteomic approach to study human-microbial ecosystems at the mucosal luminal interface.
abstract: Aberrant interactions between the host and the intestinal bacteria are thought to contribute to the pathogenesis of many digestive diseases. However, studying the complex ecosystem at the human mucosal-luminal interface (MLI) is challenging and requires an integrative systems biology approach. Therefore, we developed a novel method integrating lavage sampling of the human mucosal surface, high-throughput proteomics, and a unique suite of bioinformatic and statistical analyses. Shotgun proteomic analysis of secreted proteins recovered from the MLI confirmed the presence of both human and bacterial components. To profile the MLI metaproteome, we collected 205 mucosal lavage samples from 38 healthy subjects, and subjected them to high-throughput proteomics. The spectral data were subjected to a rigorous data processing pipeline to optimize suitability for quantitation and analysis, and then were evaluated using a set of biostatistical tools. Compared to the mucosal transcriptome, the MLI metaproteome was enriched for extracellular proteins involved in response to stimulus and immune system processes. Analysis of the metaproteome revealed significant individual-related as well as anatomic region-related (biogeographic) features. Quantitative shotgun proteomics established the identity and confirmed the biogeographic association of 49 proteins (including 3 functional protein networks) demarcating the proximal and distal colon. This robust and integrated proteomic approach is thus effective for identifying functional features of the human mucosal ecosystem, and a fresh understanding of the basic biology and disease processes at the MLI.
authors: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, United States of America.
authors: Xiaoxiao
authors: X
authors: Li
authors: James
authors: J
authors: LeBlanc
authors: Allison
authors: A
authors: Truong
authors: Ravi
authors: R
authors: Vuthoori
authors: Sharon S
authors: SS
authors: Chen
authors: Jonathan L
authors: JL
authors: Lustgarten
authors: Bennett
authors: B
authors: Roth
authors: Jeff
authors: J
authors: Allard
authors: Andrew
authors: A
authors: Ippoliti
authors: Laura L
authors: LL
authors: Presley
authors: James
authors: J
authors: Borneman
authors: William L
authors: WL
authors: Bigbee
authors: Vanathi
authors: V
authors: Gopalakrishnan
authors: Thomas G
authors: TG
authors: Graeber
authors: David
authors: D
authors: Elashoff
authors: Jonathan
authors: J
authors: Braun
authors: Lee
authors: L
authors: Goodglick
mesh_terms: D001706:Biopsy; D017753:Ecosystem; D005260:Female; D006262:Health; D006801:Humans; D007413:Intestinal Mucosa / Q000382:microbiology* / Q000473:pathology; D008297:Male; D008875:Middle Aged; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D013048:Specimen Handling; D059467:Transcriptome / Q000235:genetics
chemical_list: D020543:Proteome