Transcriptional interactions suggest niche segregation among microorganisms in the human gut

Damian Rafal Plichta, Agnieszka Juncker, Marcelo Bertalan Quintanilha dos Santos, Elizabeth 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, Metagenomics of the Human Intestinal Tract (MetaHIT) Consortium, Morten Otto Alexander SommerS. Dusko Ehrlich, Thomas Sicheritz-Pontén, Søren Brunak, Henrik Bjørn Nielsen

Research output: Contribution to journalJournal articleResearchpeer-review


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 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.
Original languageEnglish
Article number16152
JournalNature Microbiology
Publication statusPublished - 2016


  • Microbial ecology
  • Microbiome
  • Systems analysis


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