title: Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults.
abstract: Recent metagenomic studies have demonstrated that the overall functional potential of the intestinal microbiome is rather conserved between healthy individuals. Here we assessed the biological processes undertaken in-vivo by microbes and the host in the intestinal tract by conducting a metaproteome analysis from a total of 48 faecal samples of 16 healthy adults participating in a placebo-controlled probiotic intervention trial. Half of the subjects received placebo and the other half consumed Lactobacillus rhamnosus GG for three weeks (1010 cfu per day). Faecal samples were collected just before and at the end of the consumption phase as well as after a three-week follow-up period, and were processed for microbial composition and metaproteome analysis. A common core of shared microbial protein functions could be identified in all subjects. Furthermore, we observed marked differences in expressed proteins between subjects that resulted in the definition of a stable and personalized microbiome both at the mass-spectrometry-based proteome level and the functional level based on the KEGG pathway analysis. No significant changes in the metaproteome were attributable to the probiotic intervention. A detailed taxonomic assignment of peptides and comparison to phylogenetic microarray data made it possible to evaluate the activity of the main phyla as well as key species, including Faecalibacterium prausnitzii. Several correlations were identified between human and bacterial proteins. Proteins of the human host accounted for approximately 14% of the identified metaproteome and displayed variations both between and within individuals. The individually different human intestinal proteomes point to personalized host-microbiota interactions. Our findings indicate that analysis of the intestinal metaproteome can complement gene-based analysis and contributes to a thorough understanding of the activities of the microbiome and the relevant pathways in health and disease.
authors.affiliation: Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.
authors.forename: Carolin A
authors.initials: CA
authors.lastname: Kolmeder
authors.affiliation: Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.
authors.forename: Jarkko
authors.initials: J
authors.lastname: Salojärvi
authors.affiliation: Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.
authors.forename: Jarmo
authors.initials: J
authors.lastname: Ritari
authors.affiliation: Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.|Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
authors.forename: Mark
authors.initials: M
authors.lastname: de Been
authors.affiliation: KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium.|VIB, Center for the Biology of Disease, Leuven, Belgium.
authors.forename: Jeroen
authors.initials: J
authors.lastname: Raes
authors.affiliation: KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium.|VIB, Center for the Biology of Disease, Leuven, Belgium.
authors.forename: Gwen
authors.initials: G
authors.lastname: Falony
authors.affiliation: KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium.|VIB, Center for the Biology of Disease, Leuven, Belgium.
authors.forename: Sara
authors.initials: S
authors.lastname: Vieira-Silva
authors.affiliation: Valio Oy, Helsinki, Finland.
authors.forename: Riina A
authors.initials: RA
authors.lastname: Kekkonen
authors.affiliation: Translational Proteomics, Turku Center for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
authors.forename: Garry L
authors.initials: GL
authors.lastname: Corthals
authors.affiliation: Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.
authors.forename: Airi
authors.initials: A
authors.lastname: Palva
authors.affiliation: Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.|Department of Bacteriology and Immunology, Immunobiology Research Program, University of Helsinki, Helsinki, Finland.
authors.forename: Anne
authors.initials: A
authors.lastname: Salonen
authors.affiliation: Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.|Department of Bacteriology and Immunology, Immunobiology Research Program, University of Helsinki, Helsinki, Finland.|Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Willem M
authors.initials: WM
authors.lastname: de Vos
mesh_terms: D000328:Adult; D001426:Bacterial Proteins / Q000235:genetics / Q000302:isolation & purification; D015331:Cohort Studies; D004311:Double-Blind Method; D005243:Feces / Q000382:microbiology; D005260:Female; D000069196:Gastrointestinal Microbiome / Q000235:genetics; D016680:Genome, Bacterial; D006801:Humans; D008137:Longitudinal Studies; D008297:Male; D008875:Middle Aged; D010449:Peptide Mapping; D010802:Phylogeny; D057285:Precision Medicine; D019936:Probiotics / Q000627:therapeutic use*; D040901:Proteomics; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D055815:Young Adult
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S