L. Albenberg, T. V. Esipova, C. P. Judge, K. Bittinger, J. Chen et al., Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota, Gastroenterology, vol.147, pp.1055-1063, 2014.

A. Almeida, A. L. Mitchell, M. Boland, S. C. Forster, G. B. Gloor et al., A new genomic blueprint of the human gut microbiota, Nature, vol.568, pp.499-504, 2019.

J. H. Apajalahti, A. Kettunen, P. H. Nurminen, H. Jatila, and W. E. Holben, Selective plating underestimates abundance and shows differential recovery of bifidobacterial species from human feces, Appl. Environ. Microbiol, vol.69, pp.5731-5735, 2003.

K. Ben-amor, H. Heilig, H. Smidt, E. E. Vaughan, T. Abee et al., Genetic diversity of viable, injured, and dead fecal bacteria assessed by fluorescence-activated cell sorting and 16S rRNA gene analysis, Appl. Environ. Microbiol, vol.71, pp.4679-4689, 2005.

M. Bilen, J. Dufour, J. Lagier, F. Cadoret, Z. Daoud et al., The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species, vol.6, p.94, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01858939

H. P. Browne, S. C. Forster, B. O. Anonye, N. Kumar, B. A. Neville et al., Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation, Nature, vol.533, pp.543-546, 2016.

T. Brusa, E. Canzi, N. Pacini, R. Zanchi, and A. Ferrari, Oxygen tolerance of anaerobic bacteria isolated from human feces, Curr. Microbiol, vol.19, pp.39-43, 1989.

C. J. Bunthof, A. , and T. , Development of a flow cytometric method to analyze subpopulations of bacteria in probiotic products and dairy starters, 2002.

, Appl. Environ. Microbiol, vol.68, pp.2934-2942

S. Cardona, A. Eck, M. Cassellas, M. Gallart, C. Alastrue et al., Storage conditions of intestinal microbiota matter in metagenomic analysis, BMC Microbiol, vol.12, p.158, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01190761

J. C. Clemente, L. K. Ursell, L. W. Parfrey, and R. Knight, The impact of the gut microbiota on human health: an integrative view, Cell, vol.148, pp.1258-1270, 2012.

M. A. Conlon and A. R. Bird, The impact of diet and lifestyle on gut microbiota and human health, Nutrients, vol.7, pp.17-44, 2014.

H. M. Davey, Life, death, and in-between: meanings and methods in microbiology, Appl. Environ. Microbiol, vol.77, pp.5571-5576, 2011.

P. B. Eckburg, E. M. Bik, C. N. Bernstein, E. Purdom, L. Dethlefsen et al., Diversity of the human intestinal microbial flora, Science, vol.308, pp.1635-1638, 2005.

S. M. Finegold, Anaerobic infections in humans: an overview, Anaerobe, vol.1, pp.3-9, 1995.

S. C. Forster, N. Kumar, B. O. Anonye, A. Almeida, E. Viciani et al., A human gut bacterial genome and culture collection for improved metagenomic analyses, Nat. Biotechnol, vol.37, pp.186-192, 2019.

A. H. Franks, H. J. Harmsen, G. C. Raangs, G. J. Jansen, F. Schut et al., Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes, Appl. Environ. Microbiol, vol.64, pp.3336-3345, 1998.

M. A. Gorzelak, S. K. Gill, N. Tasnim, Z. Ahmadi-vand, M. Jay et al., Methods for improving human gut microbiome data by reducing variability through sample processing and storage of stool, PLoS One, vol.10, p.134802, 2015.

H. Harmsen, G. Gibson, P. Elfferich, G. Raangs, A. Wildeboer-veloo et al., Comparison of viable cell counts and fluorescence in situ hybridization using specific rRNA-based probes for the quantification of human fecal bacteria, FEMS Microbiol. Lett, vol.183, pp.125-129, 2000.

P. Hugon, J. Lagier, C. Robert, C. Lepolard, L. Papazian et al., Molecular studies neglect apparently gram-negative populations in the human gut microbiota, J. Clin. Microbiol, vol.51, pp.3286-3293, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00964198

P. Jervøe-storm, M. Koltzscher, W. Falk, A. Dörfler, J. et al., Comparison of culture and real-time PCR for detection and quantification of five putative periodontopathogenic bacteria in subgingival plaque samples, J. Clin. Periodontol, vol.32, pp.778-783, 2005.

J. C. Lagier, F. Armougom, M. Million, P. Hugon, I. Pagnier et al., Microbial culturomics: paradigm shift in the human gut microbiome study, Clin. Microbiol. Infect, vol.18, pp.1185-1193, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00964466

J. Lagier, M. Million, P. Hugon, F. Armougom, and D. Raoult, Human gut microbiota: repertoire and variations, Front. Cell. Infect. Microbiol, vol.2, p.136, 2012.

J. Lagier, G. Dubourg, M. Million, F. Cadoret, M. Bilen et al., Culturing the human microbiota and culturomics, Nat. Rev. Microbiol, vol.1, pp.540-550, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01910305

J. Lagier, S. Khelaifia, M. T. Alou, S. Ndongo, N. Dione et al., Culture of previously uncultured members of the human gut microbiota by culturomics, Nat. Microbiol, vol.1, p.16203, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01453324

P. S. Langendijk, F. Schut, G. J. Jansen, G. C. Raangs, G. R. Kamphuis et al., Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA-targeted probes and its application in fecal samples, Appl. Environ. Microbiol, vol.61, pp.3069-3075, 1995.

W. J. Loesche, Oxygen sensitivity of various anaerobic bacteria, Appl. Microbiol, vol.18, pp.723-727, 1969.

G. Macfarlane and G. R. Gibson, Metabolic activities of the normal colonic flora, pp.17-52, 1994.

L. J. Mata, C. Carrillo, and E. Villatoro, Fecal microflora in health persons in a preindustrial region, Appl. Microbiol, vol.17, pp.596-602, 1969.

T. Matsuki, K. Watanabe, J. Fujimoto, Y. Miyamoto, T. Takada et al., Development of 16S rRNA-gene-targeted group-specific primers for the detection and identification of predominant bacteria in human feces, 2002.

, Appl. Environ. Microbiol, vol.68, pp.5445-5451

, Frontiers in Microbiology | www.frontiersin.org

W. Moore, E. Cato, and L. Holdeman, Some current concepts in intestinal bacteriology, Am. J. Clin. Nutr, vol.31, pp.33-42, 1978.

W. E. Moore and L. V. Holdeman, Human fecal flora: the normal flora of 20 Japanese-Hawaiians, Appl. Microbiol, vol.27, pp.961-979, 1974.

W. E. Moore and L. V. Holdeman, Special problems associated with the isolation and identification of intestinal bacteria in fecal flora studies, Am. J. Clin. Nutr, vol.27, pp.1450-1455, 1974.

S. Nayfach, Z. J. Shi, R. Seshadri, K. S. Pollard, N. C. Kyrpides et al., High stability of faecal microbiome composition in guanidine thiocyanate solution at room temperature and robustness during colonoscopy, Nature, vol.568, pp.1574-1575, 2016.

E. Pasolli, F. Asnicar, S. Manara, M. Zolfo, N. Karcher et al., Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle, Cell, vol.176, 2019.

S. Rezasoltani, H. Dabiri, H. A. Aghdaei, A. A. Sepahi, M. H. Modarressi et al., An improved real-time qPCR technique for quantification of intestinal bacteria in human fecal samples, S. Asian J. Exp. Biol, vol.7, pp.201-209, 2017.

C. Rinke, P. Schwientek, A. Sczyrba, N. N. Ivanova, I. J. Anderson et al., Insights into the phylogeny and coding potential of microbial dark matter, Nature, vol.499, pp.431-437, 2013.

R. D. Rolfe, D. J. Hentges, B. J. Campbell, and J. T. Barrett, Factors related to the oxygen tolerance of anaerobic bacteria, Appl. Environ. Microbiol, vol.36, pp.306-313, 1978.

I. Sekirov, S. L. Russell, L. C. Antunes, and B. B. Finlay, Gut microbiota in health and disease, Physiol. Rev, vol.90, pp.859-904, 2009.

J. T. Staley and A. Konopka, Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats, Annu. Rev. Microbiol, vol.39, pp.321-346, 1985.

M. Vital, M. Dignum, A. Magic-knezev, P. Ross, L. Rietveld et al., Flow cytometry and adenosine tri-phosphate analysis: alternative possibilities to evaluate major bacteriological changes in drinking water treatment and distribution systems, Water Res, vol.46, pp.4665-4676, 2012.

G. W. Welling, P. Elfferich, G. C. Raangs, A. C. Wildeboer-veloo, G. J. Jansen et al., 16S ribosomal RNA-targeted oligonucleotide probes for monitoring of intestinal tract bacteria, Scand. J. Gastroenterol. Suppl, vol.222, pp.17-19, 1997.

K. H. Wilson and R. B. Blitchington, Human colonic biota studied by ribosomal DNA sequence analysis, Appl. Environ. Microbiol, vol.62, pp.2273-2278, 1996.

E. Zahavy, R. Ber, D. Gur, H. Abramovich, E. Freeman et al., Application of nanoparticles for the detection and sorting of pathogenic bacteria by flow-cytometry, pp.23-36, 2012.

Y. Zou, W. Xue, G. Luo, Z. Deng, P. Qin et al., 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses, Nat. Biotechnol, vol.37, pp.179-185, 2019.