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Transcriptional interactions suggest niche segregation among microorganisms in the human gut

2016; Nature Portfolio; Volume: 1; Issue: 11 Linguagem: Inglês

10.1038/nmicrobiol.2016.152

2058-5276

Damian R. Plichta, Agnieszka Sierakowska Juncker, Marcelo Bertalan, Elizabeth A. Rettedal, Laurent Gautier, Encarna Varela, Chaysavanh Manichanh, Charlène Fouqueray, Florence Levenez, Trine Nielsen, Joël Doré, Ana Manuel Dantas Machado, Mari Cristina Rodriguez de Evgrafov, Torben Hansen, Torben Jørgensen, Peer Bork, Francisco Guarner, Oluf Pedersen, Metahit Consortium, Morten Otto Alexander Sommer, S. Dusko Ehrlich, Thomas Sicheritz‐Pontén, Søren Brunak, Henrik Bjørn Nielsen, Mathieu Almeida, Jean-Michel Batto, Hervé M. Blottière, Antonietta Cultrone, Christine Delorme, Rozenn Derwyn, Éric Guédon, Florence Haimet, Alexandre Jamet, Catherine Juste, Sean P. Kennedy, Ghalia Kaci, Séverine Layec, Marion Leclerc, Pierre Léonard, Emmanuelle Maguin, Nicolas Pons, Pierre Renault, Nicolás Sánchez, Maarten van de Guchte, Johan van Hylckama Vlieg, Gaetana Vandemeulebrouck, Yohanan Winogradsky,

Bioinformatics and Genomic Networks

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.