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Nat Microbiol. 2016 Aug 26;1(11):16152. doi: 10.1038/nmicrobiol.2016.152.

Transcriptional interactions suggest niche segregation among microorganisms in the human gut.

Author information

1
Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
2
Clinical-Microbiomics A/S, DK-2200 Copenhagen, Denmark.
3
The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
4
Department of Systems Biology, DTU Multi-Assay Core, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
5
Digestive System Research Unit, University Hospital Vall d'Hebron, Ciberehd, 08035 Barcelona, Spain.
6
INRA, Institut National de la Recherche Agronomique, Metagenopolis, Cedex 78350 Jouy en Josas, France.
7
MGP, MetaGenoPolis, INRA, Université Paris-Saclay, Cedex 78350 Jouy en Josas, France.
8
The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.
9
MICALIS, INRA, Université Paris-Saclay, Cedex 78350 Jouy en Josas, France.
10
Faculty of Health Sciences, University of Southern Denmark, DK-5230 Odense, Denmark.
11
Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.
12
Research Centre for Prevention and Health, Capital region, Glostrup Hospital, DK-2600 Glostrup, Denmark.
13
Faculty of Medicine, Aalborg University, DK-9220 Aalborg, Denmark.
14
European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
15
King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London SE1 9RT, UK.
16
Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, Disease Systems Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.

Abstract

The human gastrointestinal (GI) tract is the habitat for hundreds of microbial species, of which many cannot be cultivated readily, presumably because of the dependencies between species1. Studies of microbial co-occurrence in the gut have indicated community substructures that may reflect functional and metabolic interactions between cohabiting species2,3. To move beyond species co-occurrence networks, we systematically identified transcriptional interactions between pairs of coexisting gut microbes using metagenomics and microarray-based metatranscriptomics data from 233 stool samples from Europeans. In 102 significantly interacting species pairs, the transcriptional changes led to a reduced expression of orthologous functions between the coexisting species. Specific species-species transcriptional interactions were enriched for functions important for H2 and CO2 homeostasis, butyrate biosynthesis, ATP-binding cassette (ABC) transporters, flagella assembly and bacterial chemotaxis, as well as for the metabolism of carbohydrates, amino acids and cofactors. The analysis gives the first insight into the microbial community-wide transcriptional interactions, and suggests that the regulation of gene expression plays an important role in species adaptation to coexistence and that niche segregation takes place at the transcriptional level.

PMID:
27564131
DOI:
10.1038/nmicrobiol.2016.152
[Indexed for MEDLINE]

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