Journal article
Transcriptional interactions suggest niche segregation among microorganisms in the human gut
Department of Systems Biology, Technical University of Denmark1
Université Paris-Saclay2
Research Groups, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark3
European Molecular Biology Laboratory4
Bacterial Synthetic Biology, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark5
Metagenomics, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark6
Metagenomics of the Human Intestinal Tract (MetaHIT) Consortium7
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark8
Integrative Systems Biology, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark9
Drug Resistance and Community Dynamics, Department of Systems Biology, Technical University of Denmark10
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark11
DTU Multi Assay Core, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark12
University Hospital Vall d’Hebron13
INRAE14
University of Copenhagen15
...and 5 moreThe 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 species 1. Studies of microbial co-occurrence in the gut have indicated community substructures that may reflect functional and metabolic interactions between cohabiting species 2,3.
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.
Language: | English |
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Publisher: | Nature Publishing Group |
Year: | 2016 |
Pages: | 16152 |
ISSN: | 20585276 |
Types: | Journal article |
DOI: | 10.1038/nmicrobiol.2016.152 |
ORCIDs: | 0000-0002-6555-2557 , 0000-0002-0732-1291 , Sommer, Morten Otto Alexander , 0000-0002-2066-7895 , 0000-0001-8748-3831 , 0000-0002-3321-3972 , 0000-0003-0316-5866 , de Evgrafov, Mari Cristina Rodriguez and Nielsen, Henrik Bjørn |