Transcriptional interactions suggest niche segregation among microorganisms in the human gut

TY - JOUR

T1 - Transcriptional interactions suggest niche segregation among microorganisms in the human gut

AU - Plichta, Damian Rafal

AU - Juncker, Agnieszka Sierakowska

AU - Bertalan, Marcelo

AU - Rettedal, Elizabeth

AU - Gautier, Laurent

AU - Varela, Encarna

AU - Manichanh, Chaysavanh

AU - Fouqueray, Charlène

AU - Levenez, Florence

AU - Nielsen, Trine

AU - Doré, Joël

AU - Machado, Ana Manuel Dantas

AU - de Evgrafov, Mari Cristina Rodriguez

AU - Hansen, Torben

AU - Jørgensen, Torben

AU - Bork, Peer

AU - Guarner, Francisco

AU - Pedersen, Oluf

AU - Metagenomics of the Human Intestinal Tract (MetaHIT) Consortium

AU - Sommer, Morten O A

AU - Ehrlich, S Dusko

AU - Sicheritz-Pontén, Thomas

AU - Brunak, Søren

AU - Nielsen, H Bjørn

PY - 2016/8/26

Y1 - 2016/8/26

N2 - 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.

AB - 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.

KW - Journal Article

U2 - 10.1038/nmicrobiol.2016.152

DO - 10.1038/nmicrobiol.2016.152

M3 - Letter

C2 - 27564131

SN - 2058-5276

VL - 1

SP - 1

EP - 6

JO - Nature Microbiology

JF - Nature Microbiology

M1 - 16152

ER -