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Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach
Open accessAbstract
Background and aim: A role for the intestinal microbial community (microbiota) in the onset and chronicity of Crohn’s disease (CD) is strongly suspected. However, investigation of such a complex ecosystem is difficult, even with culture independent molecular approaches. Methods: We used, for the first time, a comprehensive metagenomic approach to investigate the full range of intestinal microbial diversity. We used a fosmid vector to construct two libraries of genomic DNA isolated directly from faecal samples of six healthy donors and six patients with CD. Bacterial diversity was analysed by screening the two DNA libraries, each composed of 25 000 clones, for the 16S rRNA gene by DNA hybridisation. Results: Among 1190 selected clones, we identified 125 non-redundant ribotypes mainly represented by the phyla Bacteroidetes and Firmicutes. Among the Firmicutes, 43 distinct ribotypes were identified in the healthy microbiota, compared with only 13 in CD (p<0.025). Fluorescent in situ hybridisation directly targeting 16S rRNA in faecal samples analysed individually (n = 12) confirmed the significant reduction in the proportion of bacteria belonging to this phylum in CD patients (p<0.02). Conclusion: The metagenomic approach allowed us to detect a reduced complexity of the bacterial phylum Firmicutes as a signature of the faecal microbiota in patients with CD. It also indicated the presence of new bacterial species.
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“The microbiome has long been implicated in IBD, potentially as a causative or risk factor66,67”
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Cites
Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.22.4673 · Cited by 64,617
Kimura, M. (1980) · Journal of Molecular Evolution · doi:10.1007/bf01731581 · Cited by 29,778
PHYLIP-Phylogeny inference package (Version 3.2)
Felsenstein, J. (1989) · Cladistics · Cited by 17,682
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
Castresana, J. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026334 · Cited by 10,633
Tree View: An application to display phylogenetic trees on personal computers
Page, R. (1996) · Computer applications in the biosciences · doi:10.1093/bioinformatics/12.4.357 · Cited by 10,223
Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease
Hugot, J.-P., Chamaillard, M., Zouali, H., Lesage, S., Cézard, J.-P., Belaiche, J., Almer, S., Tysk, C., O'Morain, C. A., Gassull, M., et al. (2001) · Nature · doi:10.1038/35079107 · Cited by 5,591
Environmental genome shotgun sequencing of the sargasso sea
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376
Gut flora in health and disease
Guarner, F., & Malagelada, J. (2003) · The Lancet · doi:10.1016/s0140-6736(03)12489-0 · Cited by 3,479
THE POPULATION FREQUENCIES OF SPECIES AND THE ESTIMATION OF POPULATION PARAMETERS
Good, I. J. (1953) · Biometrika · doi:10.1093/biomet/40.3-4.237 · Cited by 3,427
Commensal Host-Bacterial Relationships in the Gut
Hooper, L. V., & Gordon, J. I. (2001) · Science · doi:10.1126/science.1058709 · Cited by 2,362
Suau, A., Bonnet, R., Sutren, M., Godon, J.-J., Gibson, G. R., Collins, M. D., & Doré, J. (1999) · Applied and Environmental Microbiology · doi:10.1128/aem.65.11.4799-4807.1999 · Cited by 1,490
Self-citationThe species concept for prokaryotes
Rossello-Mora, R. A., & Amann, R. (2001) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2001.tb00571.x · Cited by 1,475
Cole, J. R. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg039 · Cited by 1,432
Butyrate inhibits inflammatory responses through NFκB inhibition: implications for Crohn's disease
Segain, J.-P., de la Blétière, D. R., Bourreille, A., Leray, V., Gervois, N., Rosales, C., Ferrier, L., Bonnet, C., Blottière, H. M., & Galmiche, J.-P. (2000) · Gut · doi:10.1136/gut.47.3.397 · Cited by 1,357
Ott, S. J., Musfeldt, M., Wenderoth, D. F., Hampe, J., Brant, O., Fölsch, U. R., Timmis, K. N., & Schreiber, S. (2004) · Gut · doi:10.1136/gut.2003.025403 · Cited by 1,311
Rondon, M. R., August, P. R., Bettermann, A. D., Brady, S. F., Grossman, T. H., Liles, M. R., Loiacono, K. A., Lynch, B. A., MacNeil, I. A., Minor, C., et al. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.6.2541-2547.2000 · Cited by 1,235
Human Fecal Flora: The Normal Flora of 20 Japanese-Hawaiians
Moore, W. E. C., & Holdeman, L. V. (1974) · Applied Microbiology · doi:10.1128/am.27.5.961-979.1974 · Cited by 1,144
Sartor, R. B. (2004) · Gastroenterology · doi:10.1053/j.gastro.2004.03.024 · Cited by 1,053
Phylogenetic Relationships of Butyrate-Producing Bacteria from the Human Gut
Barcenilla, A., Pryde, S. E., Martin, J. C., Duncan, S. H., Stewart, C. S., Henderson, C., & Flint, H. J. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.4.1654-1661.2000 · Cited by 996
Godon, J., Zumstein, E., Dabert, P., Habouzit, F., & Moletta, R. (1997) · Applied and Environmental Microbiology · doi:10.1128/aem.63.7.2802-2813.1997 · Cited by 924
Culture-Independent Analysis of Gut Bacteria: the Pig Gastrointestinal Tract Microbiota Revisited
Leser, T. D., Amenuvor, J. Z., Jensen, T. K., Lindecrona, R. H., Boyé, M., & Møller, K. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.2.673-690.2002 · Cited by 868
Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon
Seksik, P., Rigottier‐Gois, L., Gramet, G., BRIEND‐SUTREN, M., Pochart, P., Marteau, P. R., Jian, R., & Dore, J. M. (2003) · Gut · doi:10.1136/gut.52.2.237 · Cited by 746
Self-citationDysbiosis in inflammatory bowel disease
Tamboli, C. P., Neut, C., Desreumaux, P., & Colombel, J. F. (2004) · Gut · doi:10.1136/gut.53.1.1 · Cited by 743
Duncan, S. H., Barcenilla, A., Stewart, C. S., Pryde, S. E., & Flint, H. J. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.10.5186-5190.2002 · Cited by 743
The species concept for prokaryotes
Rossello-Mora, R. A. (2001) · FEMS Microbiology Reviews · doi:10.1016/s0168-6445(00)00040-1 · Cited by 721
Stein, J. L., Marsh, T., Wu, K., Shizuya, H., & Delong, E. (1996) · Journal of Bacteriology · doi:10.1128/jb.178.3.591-599.1996 · Cited by 460
Hayashi, H., Sakamoto, M., & Benno, Y. (2002) · Microbiology and Immunology · doi:10.1111/j.1348-0421.2002.tb02731.x · Cited by 458
The Population Frequencies of Species and the Estimation of Population Parameters
Good, I. J. (1953) · Biometrika · doi:10.2307/2333344 · Cited by 442
Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis
Hold, G. L., Pryde, S. E., Russell, V. J., Furrie, E., & Flint, H. J. (2002) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2002.tb00904.x · Cited by 406
Courtois, S., Cappellano, C., Ball, M. M., Francou, F., Normand, P., Helynck, G., Martinez, A., Kolvek, S. J., Hopke, J., Osburne, M. S., et al. (2003) · Applied and Environmental Microbiology · doi:10.1128/aem.69.1.49-55.2003 · Cited by 351
Self-citationPhylogenetic and Ecological Analysis of Novel Marine Stramenopiles
Massana, R., Castresana, J., Balagué, V., et al. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.6.3528-3534.2004 · Cited by 326
Colonic Microbiota Signatures across Five Northern European Countries
Lay, C., Rigottier‐Gois, L., Holmstrøm, K., Rajilić-Stojanović, M. D., Vaughan, E. E., de Vos, W. M., Collins, M. D., Thiel, R., Namsolleck, P., Blaut, M., et al. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.7.4153-4155.2005 · Cited by 296
Self-citationMolecular inventory of faecal microflora in patients with Crohn's disease.
Mangin, I., Bonnet, R., Seksik, P., Rigottier-Gois, L., Sutren, M., Bouhnik, Y., Neut, C., Collins, M., Colombel, J., Marteau, P., et al. (2003) · FEMS Microbiology Ecology · doi:10.1016/j.femsec.2004.05.005 · Cited by 160
Self-citationTargeting enteric bacteria in treatment of inflammatory bowel diseases
Sartor, R. B. (2003) · Current Opinion in Gastroenterology · doi:10.1097/00001574-200307000-00006 · Cited by 93
FISH (Fluorescent In Situ Hybridisation)
Englert, Y., & Hottois, G. (2001) · Dépôt institutionnel de l'Université libre de Bruxelles (Université Libre de Bruxelles) · Cited by 1
Research works printed but not linked: 2
- 2003, Lancet, 360, 512
- 2004, Appl Environ Microbiol, 64, 171
Cited by
Sorted by citations
Metagenomic biomarker discovery and explanation
Segata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L., Garrett, W. S., & Huttenhower, C. (2011) · Genome Biology · doi:10.1186/gb-2011-12-6-r60 · Cited by 16,192
A human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624
Self-citationA metagenome-wide association study of gut microbiota in type 2 diabetes
Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., Liang, S., Zhang, W., Guan, Y., Shen, D., et al. (2012) · Nature · doi:10.1038/nature11450 · Cited by 6,762
Cryan, J. F., O'Riordan, K. J., Cowan, C. S. M., Sandhu, K. V., Bastiaanssen, T. F. S., Boehme, M., Codagnone, M. G., Cussotto, S., Fulling, C., Golubeva, A. V., et al. (2019) · Physiological Reviews · doi:10.1152/physrev.00018.2018 · Cited by 5,286
Richness of human gut microbiome correlates with metabolic markers
Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., Almeida, M., Arumugam, M., Batto, J.-M., Kennedy, S., et al. (2013) · Nature · doi:10.1038/nature12506 · Cited by 4,662
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Metadata
- Authors
- Manichanh, C., Rigottier-Gois, L., Bonnaud, E., Gloux, K., Pelletier, E., Frangeul, L., Nalin, R., Jarrin, C., Chardon, P., Marteau, P., Roca, J., & Dore, J.
- Affiliations
- Institut National de la Recherche Agronomique (FR)
- Institut Pasteur (FR)
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR)
- Hôpital Européen Georges-Pompidou (FR)
- Consejo Superior de Investigaciones Científicas (ES)
- Corresponding author
- Dore, J
- Venue
- Gut
- Publisher
- BMJ
- Published
- 2005-09-27
- Volume
- 55
- Issue
- 2
- Pages
- 205-211
- ISSN
- 0017-5749 (ISSN-L)
- 1468-3288
- PMC
- PMC1856500
- OpenAlex
- W2156145269
- Cited by
- 2,277
- References
- 35
- Citations by year
- 2026: 35 · 2025: 76 · 2024: 100 · 2023: 114 · 2022: 134 · 2021: 198 · 2020: 172 · 2019: 157 · 2018: 148 · 2017: 127 · 2016: 143 · 2015: 145 · 2014: 148 · 2013: 111 · 2012: 107
- FWCI
- 16.50
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Gut (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- HAL (submittedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Institut National de la Recherche Agronomique
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Gastroenterology › Inflammatory Bowel Disease
- Health Sciences › Medicine › Infectious Diseases › Clostridium difficile and Clostridium perfringens research
- Keywords
- Crohn's disease, gut microbiota, fecal microbiota, bacterial diversity, Firmicutes, Bacteroidetes, 16S rRNA gene, metagenomics, fosmid library, ribotypes, novel bacterial species, fluorescence in situ hybridization
- MeSH terms
- Adolescent, Adult, Bacteria, Crohn Disease, DNA, Bacterial, Feces, Female, Humans, Male, Phylogeny, RNA, Bacterial, RNA, Ribosomal, 16S, Bacterial Typing Techniques, Gene Library, In Situ Hybridization, Fluorescence, Ecosystem
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