Transcriptional interactions suggest niche segregation among microorganisms in the human gut
Damian Rafal Plichta
(1, 2)
,
Agnieszka Sierakowska Juncker
(1)
,
Marcelo Bertalan
(1)
,
Elizabeth Rettedal
(3)
,
Laurent Gautier
(4, 1)
,
Encarna Varela
(5)
,
Chaysavanh Manichanh
(5)
,
Charlène Fouqueray
(6)
,
Florence Levenez
(6)
,
Trine Nielsen
(7)
,
Joel Dore
(8, 6)
,
Ana Manuel Dantas Machado
(3)
,
Mari Cristina Rodriguez de Evgrafov
(3)
,
Torben Hansen
(9)
,
Torben Jorgensen
(10, 11, 12)
,
Peer Bork
(13)
,
Francisco Guarner
(5)
,
Oluf Pedersen
(7, 12)
,
Metahit Consortium
,
Morten O. A. Sommer
(3)
,
S. Dusko Ehrlich
(14)
,
Thomas Sicheritz-Ponten
(1)
,
Soren Brunak
(1, 15)
,
H. Bjorn Nielsen
(1, 16)
,
Mathieu Almeida
(8)
,
Jean-Michel Batto
(8)
,
Herve Blottiere
(8)
,
Antonietta Cultrone
(8)
,
Christine Delorme
(8)
,
Rozenn Derwyn
(8)
,
Eric Guédon
(8)
,
Florence Haimet
(6)
,
Alexandre Jamet
(8)
,
Catherine Juste
(8)
,
Sean P. Kennedy
(8)
,
Ghalia Kaci
(8)
,
Séverine Layec
(17)
,
Marion Leclerc
(8)
,
Pierre Léonard
(6)
,
Emmanuelle Maguin
(8)
,
Nicolas Pons
(6)
,
Pierre Renault
(8)
,
Nicolas Sanchez
(8)
,
Maarten van de Guchte
(8)
,
Johan van Hylckama Vlieg
(8)
,
Gaetana Vandemeulebrouck
(8)
,
Yohanan Winogradsky
(8)
1
Department of Systems Biology, Center for Biological Sequence Analysis
2 A/S
3 Novo Nordisk Foundation Center for Biosustainability
4 Department of Systems Biology, DTU Multi-Assay Core
5 Digestive System Research Unit
6 MetaGenoPolis
7 CBMR - Novo Nordisk Foundation Center for Basic Metabolic Research
8 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé
9 Faculty of Health Sciences
10 Faculty of Medicine
11 Research Centre for Prevention and Health, Capital region
12 Faculty of Health and Medical Sciences
13 EMBL - European Molecular Biology Laboratory [Hamburg]
14 Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy’s Hospital
15 Disease Systems Biology [Copenhagen]
16 Clinical Microbiomics
17 GMPA - Génie et Microbiologie des Procédés Alimentaires
2 A/S
3 Novo Nordisk Foundation Center for Biosustainability
4 Department of Systems Biology, DTU Multi-Assay Core
5 Digestive System Research Unit
6 MetaGenoPolis
7 CBMR - Novo Nordisk Foundation Center for Basic Metabolic Research
8 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé
9 Faculty of Health Sciences
10 Faculty of Medicine
11 Research Centre for Prevention and Health, Capital region
12 Faculty of Health and Medical Sciences
13 EMBL - European Molecular Biology Laboratory [Hamburg]
14 Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy’s Hospital
15 Disease Systems Biology [Copenhagen]
16 Clinical Microbiomics
17 GMPA - Génie et Microbiologie des Procédés Alimentaires
Trine Nielsen
- Fonction : Auteur
- PersonId : 770024
- ORCID : 0000-0002-2066-7895
Joel Dore
- Fonction : Auteur
- PersonId : 1206301
- IdHAL : joel-dore
- ORCID : 0000-0002-8756-0718
- IdRef : 069752249
Torben Hansen
- Fonction : Auteur
- PersonId : 758676
- ORCID : 0000-0001-8748-3831
Oluf Pedersen
- Fonction : Auteur
- PersonId : 1070332
Metahit Consortium
- Fonction : Auteur
- PersonId : 1172956
- IdHAL : julien-tap
- ORCID : 0000-0001-8998-5413
S. Dusko Ehrlich
- Fonction : Auteur
- PersonId : 1068832
- ORCID : 0000-0002-7563-4046
Herve Blottiere
- Fonction : Collaborateur
- PersonId : 747227
- IdHAL : herve-blottiere
- ORCID : 0000-0002-8390-0607
- IdRef : 076955648
Christine Delorme
- Fonction : Collaborateur
- PersonId : 736589
- IdHAL : christine-delorme
- ORCID : 0000-0002-5208-7238
- IdRef : 124303129
Eric Guédon
- Fonction : Collaborateur
- PersonId : 743950
- IdHAL : eguedon35
- ORCID : 0000-0002-0901-4447
- IdRef : 140101888
Alexandre Jamet
- Fonction : Collaborateur
- PersonId : 737690
- IdHAL : alexandre-jamet
- IdRef : 253129699
Catherine Juste
- Fonction : Collaborateur
- PersonId : 1204549
Sean P. Kennedy
- Fonction : Auteur
- PersonId : 734860
- IdHAL : sean-kennedy
- ORCID : 0000-0002-3932-8922
Séverine Layec
- Fonction : Collaborateur
- PersonId : 754110
- IdHAL : severine-layec
- ORCID : 0000-0001-5053-8712
Marion Leclerc
- Fonction : Collaborateur
- PersonId : 748825
- IdHAL : marion-leclerc
- ORCID : 0000-0001-8684-2847
- IdRef : 142653721
Emmanuelle Maguin
- Fonction : Collaborateur
- PersonId : 751613
- IdHAL : e-maguin
- ORCID : 0000-0001-5452-3382
- IdRef : 032881487
Maarten van de Guchte
- Fonction : Collaborateur
- PersonId : 735862
- IdHAL : maarten-van-de-guchte
- ORCID : 0000-0002-5980-4631
Johan van Hylckama Vlieg
- Fonction : Collaborateur
Gaetana Vandemeulebrouck
- Fonction : Collaborateur
- PersonId : 969463
Résumé
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 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.