title: Transcriptional interactions suggest niche segregation among microorganisms in the human gut.
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 H2and CO2homeostasis, 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.
authors: Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.|Clinical-Microbiomics A/S, DK-2200 Copenhagen, Denmark.
authors: Damian Rafal
authors: http://orcid.org/0000-0002-6555-2557
authors: DR
authors: Plichta
authors: Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
authors: Agnieszka Sierakowska
authors: http://orcid.org/0000-0002-0732-1291
authors: AS
authors: Juncker
authors: Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
authors: Marcelo
authors: M
authors: Bertalan
authors: The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
authors: Elizabeth
authors: E
authors: Rettedal
authors: Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.|Department of Systems Biology, DTU Multi-Assay Core, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
authors: Laurent
authors: L
authors: Gautier
authors: Digestive System Research Unit, University Hospital Vall d'Hebron, Ciberehd, 08035 Barcelona, Spain.
authors: Encarna
authors: E
authors: Varela
authors: Digestive System Research Unit, University Hospital Vall d'Hebron, Ciberehd, 08035 Barcelona, Spain.
authors: Chaysavanh
authors: C
authors: Manichanh
authors: INRA, Institut National de la Recherche Agronomique, Metagenopolis, Cedex 78350 Jouy en Josas, France.
authors: Charlène
authors: C
authors: Fouqueray
authors: INRA, Institut National de la Recherche Agronomique, Metagenopolis, Cedex 78350 Jouy en Josas, France.|MGP, MetaGenoPolis, INRA, UniversitÃ© Paris-Saclay, Cedex 78350 Jouy en Josas, France.
authors: Florence
authors: F
authors: Levenez
authors: The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.
authors: Trine
authors: T
authors: Nielsen
authors: MGP, MetaGenoPolis, INRA, UniversitÃ© Paris-Saclay, Cedex 78350 Jouy en Josas, France.|MICALIS, INRA, Université Paris-Saclay, Cedex 78350 Jouy en Josas, France.
authors: Joël
authors: J
authors: Doré
authors: The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
authors: Ana Manuel Dantas
authors: AM
authors: Machado
authors: The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
authors: Mari Cristina Rodriguez
authors: MC
authors: de Evgrafov
authors: The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.|Faculty of Health Sciences, University of Southern Denmark, DK-5230 Odense, Denmark.
authors: Torben
authors: T
authors: Hansen
authors: Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.|Research Centre for Prevention and Health, Capital region, Glostrup Hospital, DK-2600 Glostrup, Denmark.|Faculty of Medicine, Aalborg University, DK-9220 Aalborg, Denmark.
authors: Torben
authors: T
authors: Jørgensen
authors: European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
authors: Peer
authors: P
authors: Bork
authors: Digestive System Research Unit, University Hospital Vall d'Hebron, Ciberehd, 08035 Barcelona, Spain.
authors: Francisco
authors: F
authors: Guarner
authors: The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.|Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.
authors: Oluf
authors: O
authors: Pedersen
authors: The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
authors: Morten O A
authors: http://orcid.org/0000-0003-4005-5674
authors: MO
authors: Sommer
authors: MGP, MetaGenoPolis, INRA, UniversitÃ© Paris-Saclay, Cedex 78350 Jouy en Josas, France.|MICALIS, INRA, Université Paris-Saclay, Cedex 78350 Jouy en Josas, France.|King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London SE1 9RT, UK.
authors: S Dusko
authors: SD
authors: Ehrlich
authors: Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
authors: Thomas
authors: T
authors: Sicheritz-Pontén
authors: Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.|Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, Disease Systems Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
authors: Søren
authors: S
authors: Brunak
authors: Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.|Clinical-Microbiomics A/S, DK-2200 Copenhagen, Denmark.
authors: H Bjørn
authors: HB
authors: Nielsen
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000235:genetics; D000069985:Bifidobacterium bifidum / Q000235:genetics / Q000378:metabolism; D002087:Butyrates / Q000378:metabolism; D002245:Carbon Dioxide / Q000378:metabolism; D003718:Denmark; D005243:Feces / Q000382:microbiology; D000069196:Gastrointestinal Microbiome / Q000235:genetics* / Q000502:physiology; D020869:Gene Expression Profiling; D006801:Humans; D053858:Metabolic Networks and Pathways / Q000235:genetics; D054892:Metagenome; D056265:Microbial Interactions / Q000235:genetics / Q000502:physiology; D013030:Spain; D013597:Systems Analysis
chemical_list: D018528:ATP-Binding Cassette Transporters; D002087:Butyrates; D002245:Carbon Dioxide