Transcriptional interactions suggest niche segregation among microorganisms in the human gut

Autor: Plichta, Damian Rafal, Juncker, Agnieszka Sierakowska, Bertalan, Marcelo, Rettedal, Elizabeth, Gautier, Laurent, Varela, Encarna, Manichanh, Chaysavanh, Fouqueray, Charlène, Levenez, Florence, Nielsen, Trine, Dore, Joel, Machado, Ana Manuel Dantas, de Evgrafov, Mari Cristina Rodriguez, Hansen, Torben, Jorgensen, Torben, Bork, Peer, Guarner, Francisco, Pedersen, Oluf, Consortium, MetaHit, Sommer, Morten O. A., Ehrlich, S. Dusko, Sicheritz-Ponten, Thomas, Brunak, Soren, Nielsen, H. Bjorn, Almeida, Mathieu, Batto, Jean-Michel, Blottiere, Herve, Cultrone, Antonietta, Delorme, Christine, derwyn, rozenn, Guédon, Eric, Haimet, Florence, Jamet, Alexandre, Juste, Catherine, Kennedy, Sean P., Kaci, Ghalia, Layec, Séverine, Leclerc, Marion, Léonard, Pierre, Maguin, Emmanuelle, Pons, Nicolas, Renault, Pierre, Sanchez, Nicolas, Van De Guchte, Maarten, Van Hylckama Vlieg, Johan, Vandemeulebrouck, Gaetana, Winogradsky, Yohanan
Přispěvatelé: Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark [Lyngby] (DTU), A/S, Clinical-Microbiomics, Novo Nordisk Foundation Center for Biosustainability, Department of Systems Biology, DTU Multi-Assay Core, Digestive System Research Unit, Vall d'Hebron University Hospital, MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Faculty of Health Sciences, University of Southern Denmark (SDU), Faculty of Medicine, Aalborg University [Denmark] (AAU), Research Centre for Prevention and Health, Capital region, Glostrup University Hospital, University of Copenhagen = Københavns Universitet (KU), European Molecular Biology Laboratory [Hamburg] (EMBL), Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy’s Hospital, King‘s College London, Disease Systems Biology [Copenhagen], Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, Clinical Microbiomics, International Human Microbiome Standards [FP7-HEALTH-2010-261376], Metagenopolis [ANR-11-DPBS-0001], Novo Nordisk Foundation, Lundbeck Foundation, European Project: 201052, Vall d'Hebron University Hospital [Barcelona], Génie et Microbiologie des Procédés Alimentaires (GMPA), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), University of Copenhagen = Københavns Universitet (UCPH), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences
Jazyk: angličtina
Rok vydání: 2016
Předmět:
0301 basic medicine
Microbiology (medical)
Feces/microbiology
Systems Analysis
ATP-Binding Cassette Transporters/genetics
Denmark
[SDV]Life Sciences [q-bio]
Microbial Interactions/genetics
030106 microbiology
Immunology
Gastrointestinal Microbiome/genetics
Biology
Applied Microbiology and Biotechnology
Microbiology
03 medical and health sciences
Feces
Microbial ecology
Journal Article
Genetics
Humans
Butyrates/metabolism
Microbiome
Regulation of gene expression
Ecology
Metabolic Networks and Pathways/genetics
Gene Expression Profiling
Niche segregation
Chemotaxis
Cell Biology
Carbon Dioxide
Gastrointestinal Microbiome
Gene expression profiling
Butyrates
030104 developmental biology
Metagenomics
Spain
Bifidobacterium bifidum/genetics
Metagenome
Microbial Interactions
Carbon Dioxide/metabolism
ATP-Binding Cassette Transporters
Bifidobacterium bifidum
Adaptation
Metabolic Networks and Pathways
Zdroj: Nature Microbiology
Nature Microbiology, Nature Publishing Group, 2016, 1 (11), pp.1-6. ⟨10.1038/NMICROBIOL.2016.152⟩
Plichta, D R, Juncker, A S, Bertalan, M, Rettedal, E, Gautier, L, Varela, E, Manichanh, C, Fouqueray, C, Levenez, F, Nielsen, T, Doré, J, Machado, A M D, De Evgrafov, M C R, Hansen, T, Jørgensen, T, Bork, P, Guarner, F, Pedersen, O, Sommer, M O A, Ehrlich, S D, Sicheritz-Ponten, T, Brunak, S & Nielsen, H B 2016, ' Transcriptional interactions suggest niche segregation among microorganisms in the human gut ', Nature Microbiology, vol. 1, no. 11, 16152 . https://doi.org/10.1038/nmicrobiol.2016.152
Plichta, D R, Juncker, A S, Bertalan, M, Rettedal, E, Gautier, L, Varela, E, Manichanh, C, Fouqueray, C, Levenez, F, Nielsen, T, Doré, J, Machado, A M D, de Evgrafov, M C R, Hansen, T, Jørgensen, T, Bork, P, Guarner, F, Pedersen, O, Sommer, M O A, Ehrlich, S D, Sicheritz-Pontén, T, Brunak, S & Nielsen, H B 2016, ' Transcriptional interactions suggest niche segregation among microorganisms in the human gut ', Nature Microbiology, vol. 1, 16152 . https://doi.org/10.1038/nmicrobiol.2016.152
Nature Microbiology, 2016, 1 (11), pp.1-6. ⟨10.1038/NMICROBIOL.2016.152⟩
ISSN: 2058-5276
Popis: 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 H 2 and CO 2 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.
Databáze: OpenAIRE
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