These authors contributed equally to this work.
Microbial culturomics: paradigm shift in the human gut microbiome study
Article first published online: 3 OCT 2012
© 2012 The Authors. Clinical Microbiology and Infection © 2012 European Society of Clinical Microbiology and Infectious Diseases
Clinical Microbiology and Infection
Volume 18, Issue 12, pages 1185–1193, December 2012
How to Cite
Lagier, J.-C., Armougom, F., Million, M., Hugon, P., Pagnier, I., Robert, C., Bittar, F., Fournous, G., Gimenez, G., Maraninchi, M., Trape, J.-F., Koonin, E. V., La Scola, B. and Raoult, D. (2012), Microbial culturomics: paradigm shift in the human gut microbiome study. Clinical Microbiology and Infection, 18: 1185–1193. doi: 10.1111/1469-0691.12023
- Issue published online: 13 NOV 2012
- Article first published online: 3 OCT 2012
- Accepted manuscript online: 4 SEP 2012 09:55AM EST
- Original Submission: 20 August 2012; Revised Submission: 28 August 2012; Accepted: 29 August 2012 Editor: G. GreubArticle published online: 4 September 2012
Figure S1. A comparison of the speciesidentified from the cultures of the different samples. The outsidecircles correspond to the classification of the species at thephylum level. The yellow, red, blue, green, purple, orange andblack colors indicate Actinobacteria, Bacteroidetes, Firmicutes,Proteobacteria, Fungi, Deinococcus-Thermus and Fusobacteria, respectively. For the inside circles: red indicates a species not previously described in gut. Green indicates a species already identified in gut. Blue indicates a new species found in this study.
Figure S2. The protocol used for the rumen fluid preparati on.
Figure S3. A genomic comparison between the Marseillevirus, Senegalvirus and Lausanne viruses.
Figure S4. A Venn diagram representing the number of species cultivated from each of the stool samples.
Figure S5. The number of species that werecultivated in 10–70 conditions out of the 212 tested cultureconditions.
Figure S6. The percentage of new species and of the total number of species cultured that grew in only one culture condition or in multiple culture conditions.
Table S1. Culture conditions for microbialculturomics characterization from the stool samples of theN’Diop, Dielmo and obese French individuals. The applicationof a culture condition to a stool sample is indicated in gray.
Table S2. The 345 bacterial and fungal speciescultured from the N’Diop, Dielmo and obese-patient stoolsamples. The use of a red font for the species label indicates anew bacterial species. Whether a given species was found or not ina given sample is indicated by a green or red square,respectively.
Table S3. The 20 best culture conditions that facilitated the identification of 73% of the bacterial species.
Table S4. Cultivated species identified in aSenegalese stool sample from the Dielmo village.The asterisks inred indicate a bootstrap confidence of 100% based on the RDPclassifier. All of the phylotypes were identified with a bootstrapconfidence >0.80, except for the Synergistes group.
Table S5. Cultivated phylotypes identified in the stool sample from an obese patient. The red asterisks indicate a bootstrap confidence of 100% based on the RDP classifier. All of the identified phylotypes had a bootstrap confidence >0.80.
Table S6. Cultivated phylotypes identified in aSenegalese stool sample from N’Diop village. The redasterisks indicate a bootstrap confidence of 100% based on the RDPclassifier. All of the identified phylotypes have a bootstrapconfidence >0.80.
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