title: The outer mucus layer hosts a distinct intestinal microbial niche.
abstract: The overall composition of the mammalian intestinal microbiota varies between individuals: within each individual there are differences along the length of the intestinal tract related to host nutrition, intestinal motility and secretions. Mucus is a highly regenerative protective lubricant glycoprotein sheet secreted by host intestinal goblet cells; the inner mucus layer is nearly sterile. Here we show that the outer mucus of the large intestine forms a unique microbial niche with distinct communities, including bacteria without specialized mucolytic capability. Bacterial species present in the mucus show differential proliferation and resource utilization compared with the same species in the intestinal lumen, with high recovery of bioavailable iron and consumption of epithelial-derived carbon sources according to their genome-encoded metabolic repertoire. Functional competition for existence in this intimate layer is likely to be a major determinant of microbiota composition and microbial molecular exchange with the host.
authors.affiliation: Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland.
authors.forename: Hai
authors.initials: H
authors.lastname: Li
authors.affiliation: Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland.
authors.forename: Julien P
authors.initials: JP
authors.lastname: Limenitakis
authors.affiliation: Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, Auguste-Piccard-Hof 1, 8093 Zürich, Switzerland.
authors.forename: Tobias
authors.initials: T
authors.lastname: Fuhrer
authors.affiliation: Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland.
authors.forename: Markus B
authors.initials: MB
authors.lastname: Geuking
authors.affiliation: Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland.
authors.forename: Melissa A
authors.initials: MA
authors.lastname: Lawson
authors.affiliation: Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland.
authors.forename: Madeleine
authors.initials: M
authors.lastname: Wyss
authors.affiliation: Max-von-Pettenkofer Institute, German Center for Infection Research (DZIF), Pettenkoferstrasse 9a, Partner site LMU Munich, D-80336 Munich, Germany.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Brugiroux
authors.affiliation: Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland.
authors.forename: Irene
authors.initials: I
authors.lastname: Keller
authors.affiliation: Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland.
authors.forename: Jamie A
authors.initials: JA
authors.lastname: Macpherson
authors.affiliation: Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland.
authors.forename: Sandra
authors.initials: S
authors.lastname: Rupp
authors.affiliation: Theodor Kocher Institute, Freiestrasse 1, University of Bern, 3012 Bern, Switzerland.
authors.forename: Bettina
authors.initials: B
authors.lastname: Stolp
authors.affiliation: Theodor Kocher Institute, Freiestrasse 1, University of Bern, 3012 Bern, Switzerland.
authors.forename: Jens V
authors.initials: JV
authors.lastname: Stein
authors.affiliation: Max-von-Pettenkofer Institute, German Center for Infection Research (DZIF), Pettenkoferstrasse 9a, Partner site LMU Munich, D-80336 Munich, Germany.
authors.forename: Bärbel
authors.initials: B
authors.lastname: Stecher
authors.affiliation: Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, Auguste-Piccard-Hof 1, 8093 Zürich, Switzerland.
authors.forename: Uwe
authors.initials: U
authors.lastname: Sauer
authors.affiliation: Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland.
authors.forename: Kathy D
authors.initials: KD
authors.lastname: McCoy
authors.affiliation: Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Macpherson
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D015964:Gene Expression Regulation, Bacterial; D005856:Germ-Free Life; D007413:Intestinal Mucosa / Q000382:microbiology*; D007501:Iron / Q000378:metabolism; D051379:Mice; D008810:Mice, Inbred C57BL; D005810:Multigene Family; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D059467:Transcriptome
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D007501:Iron