title: Longitudinal study of murine microbiota activity and interactions with the host during acute inflammation and recovery.
abstract: Although alterations in gut microbiota composition during acute colitis have been repeatedly observed, associated functional changes and the recovery from dysbiosis received little attention. In this study, we investigated structure and function of the gut microbiota during acute inflammation and recovery in a dextran sodium sulfate (DSS)-colitis mouse model using metatranscriptomics, bacterial 16S rRNA gene amplicon sequencing and monitoring of selected host markers. Parallel to an increase of host markers of inflammation during acute colitis, we observed relative abundance shifts and alterations in phylotype composition of the dominant bacterial orders Clostridiales and Bacteroidales, and an increase of the low abundant Enterobacteriales, Deferribacterales, Verrucomicrobiales and Erysipelotrichales. During recovery, the microbiota began to resume, but did not reach its original composition until the end of the experiment. Microbial gene expression was more resilient to disturbance, with pre-perturbation-type transcript profiles appearing quickly after acute colitis. The decrease of Clostridiales during inflammation correlated with a reduction of transcripts related to butyrate formation, suggesting a disturbance in host-microbe signalling and mucosal nutrient provision. The impact of acute inflammation on the Clostridiales was also characterized by a significant downregulation of their flagellin-encoding genes. In contrast, the abundance of members of the Bacteroidales increased along with an increase in transcripts related to mucin degradation. We propose that acute inflammation triggered a selective reaction of the immune system against flagella of commensals and temporarily altered murine microbiota composition and functions relevant for the host. Despite changes in specific interactions, the host-microbiota homeostasis revealed a remarkable ability for recovery.
authors.affiliation: Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Wien, Austria.
authors.forename: Clarissa
authors.initials: C
authors.lastname: Schwab
authors.affiliation: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Faculty of Life Sciences, University of Vienna, Wien, Austria.
authors.forename: David
authors.identifier: 000000028997608X
authors.initials: D
authors.lastname: Berry
authors.affiliation: Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Wien, Austria.
authors.forename: Isabella
authors.initials: I
authors.lastname: Rauch
authors.affiliation: Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Wien, Austria.
authors.forename: Ina
authors.initials: I
authors.lastname: Rennisch
authors.affiliation: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Faculty of Life Sciences, University of Vienna, Wien, Austria.
authors.forename: Julia
authors.initials: J
authors.lastname: Ramesmayer
authors.affiliation: Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Wien, Austria.
authors.forename: Eva
authors.initials: E
authors.lastname: Hainzl
authors.affiliation: Ludwig Boltzmann Institute for Cancer Research, Medical University of Vienna, Wien, Austria.
authors.forename: Susanne
authors.initials: S
authors.lastname: Heider
authors.affiliation: Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Wien, Austria.
authors.forename: Thomas
authors.initials: T
authors.lastname: Decker
authors.affiliation: Ludwig Boltzmann Institute for Cancer Research, Medical University of Vienna, Wien, Austria.
authors.forename: Lukas
authors.initials: L
authors.lastname: Kenner
authors.affiliation: Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Wien, Austria.
authors.forename: Mathias
authors.initials: M
authors.lastname: Müller
authors.affiliation: Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Wien, Austria.
authors.forename: Birgit
authors.initials: B
authors.lastname: Strobl
authors.affiliation: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Faculty of Life Sciences, University of Vienna, Wien, Austria.
authors.forename: Michael
authors.initials: M
authors.lastname: Wagner
authors.affiliation: Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Wien, Austria.
authors.forename: Christa
authors.initials: C
authors.lastname: Schleper
authors.affiliation: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Faculty of Life Sciences, University of Vienna, Wien, Austria.
authors.forename: Alexander
authors.initials: A
authors.lastname: Loy
authors.affiliation: Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Wien, Austria.
authors.forename: Tim
authors.initials: T
authors.lastname: Urich
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D002087:Butyrates / Q000378:metabolism; D003092:Colitis / Q000139:chemically induced / Q000235:genetics / Q000382:microbiology*; D016264:Dextran Sulfate; D004195:Disease Models, Animal; D005408:Flagellin / Q000235:genetics; D008137:Longitudinal Studies; D051379:Mice; D064307:Microbiota; D009077:Mucins / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D002087:Butyrates; D009077:Mucins; D012336:RNA, Ribosomal, 16S; D005408:Flagellin; D016264:Dextran Sulfate