J. Aron-wisnewsky, J. Dore, C. , and K. , The importance of the gut microbiota after bariatric surgery, Nat. Rev. Gastroenterol. Hepatol, vol.9, pp.590-598, 2012.

M. C. Arrieta, L. T. Stiemsma, P. A. Dimitriu, L. Thorson, S. Russell et al., Early infancy microbial and metabolic alterations affect risk of childhood asthma, Sci. Transl. Med, vol.7, pp.307-152, 2015.

G. Biesbroek, E. A. Sanders, G. Roeselers, X. Wang, M. P. Caspers et al., Deep sequencing analyses of low density microbial communities: working at the boundary of accurate microbiota detection, PLoS One, vol.7, p.32942, 2012.

G. Biesbroek, E. Tsivtsivadze, E. A. Sanders, R. Montijn, R. H. Veenhoven et al., Early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children, Am. J. Respir. Crit. Care Med, vol.190, pp.1283-1292, 2014.

R. Bingula, M. Filaire, N. Radosevic-robin, M. Bey, J. Y. Berthon et al., Desired Turbulence? gut-lung axis, immunity, and lung cancer, J. Oncol, p.5035371, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01652921

M. J. Blaser and M. G. Dominguez-bello, The human microbiome before birth, Cell. Host Microbe, vol.20, 2016.

A. Bosch, E. Levin, M. A. Van-houten, R. Hasrat, G. Kalkman et al., Development of upper respiratory tract microbiota in infancy is affected by mode of delivery, vol.9, pp.336-345, 2016.

K. F. Budden, S. L. Gellatly, D. L. Wood, M. A. Cooper, M. Morrison et al., Emerging pathogenic links between microbiota and the gut-lung axis, Nat. Rev. Microbiol, vol.15, pp.55-63, 2017.

C. Cherbuy, E. Honvo-houeto, A. Bruneau, C. Bridonneau, C. Mayeur et al., Microbiota matures colonic epithelium through a coordinated induction of cell cycle-related proteins in gnotobiotic rat, Am. J. Physiol. Gastrointest. Liver Physiol, vol.299, pp.348-357, 2009.

H. H. Chou, W. H. Chien, L. L. Wu, C. H. Cheng, C. H. Chung et al., Age-related immune clearance of hepatitis B virus infection requires the establishment of gut microbiota, Proc. Natl. Acad. Sci. U.S.A, vol.112, pp.2175-2180, 2015.

D. M. Chu, J. Ma, A. L. Prince, K. M. Antony, M. D. Seferovic et al., Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery, Nat. Med, vol.23, pp.314-326, 2017.

J. De-dios-caballero, R. Vida, M. Cobo, L. Maiz, L. Suarez et al., Individual patterns of complexity in cystic fibrosis lung microbiota, including predator bacteria, over a 1-year period, mBio, vol.8, pp.959-976, 2017.

C. De-filippo, D. Cavalieri, M. Di-paola, M. Ramazzotti, J. B. Poullet et al., Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa, Proc. Natl. Acad. Sci. U.S.A, vol.107, pp.14691-14696, 2010.

J. C. Deschemin, M. L. Noordine, A. Remot, A. Willemetz, C. Afif et al., The microbiota shifts the iron sensing of intestinal cells, FASEB J, vol.30, pp.252-261, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02632319

D. Stefano, A. Ricciardolo, F. L. Caramori, G. Adcock, I. M. Chung et al., Bronchial inflammation and bacterial load in stable COPD is associated with TLR4 overexpression, Eur. Respir. J, vol.49, p.1602006, 2017.

R. P. Dickson and G. B. Huffnagle, The lung microbiome: new principles for respiratory bacteriology in health and disease, PLoS Pathog, vol.11, p.1004923, 2015.

R. P. Dickson, F. J. Martinez, and G. B. Huffnagle, The role of the microbiome in exacerbations of chronic lung diseases, Lancet, vol.384, issue.14, pp.61136-61139, 2014.

J. Douwes, N. Travier, K. Huang, S. Cheng, J. Mckenzie et al., Lifelong farm exposure may strongly reduce the risk of asthma in adults, Allergy, vol.62, pp.1158-1165, 2007.

C. Drajac, D. Laubreton, S. Riffault, and D. Descamps, Pulmonary susceptibility of neonates to respiratory syncytial virus infection: a problem of innate immunity?, J. Immunol. Res, p.8734504, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02628884

J. Durack, N. E. Kimes, D. L. Lin, M. Rauch, M. Mckean et al., Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation, Nat. Commun, vol.9, p.707, 2018.

S. C. Eisenbarth, D. A. Piggott, J. W. Huleatt, I. Visintin, C. A. Herrick et al., Lipopolysaccharide-enhanced, toll-like receptor 4-dependent T helper cell type 2 responses to inhaled antigen, J. Exp. Med, vol.196, pp.1645-1651, 2002.

A. C. Ericsson, A. R. Personett, M. E. Grobman, H. Rindt, and C. R. Reinero, Composition and predicted metabolic capacity of upper and lower airway microbiota of healthy dogs in relation to the fecal microbiota, PLoS One, vol.11, 2016.

S. E. Evans, Y. Xu, M. J. Tuvim, and B. F. Dickey, Inducible innate resistance of lung epithelium to infection, Annu. Rev. Physiol, vol.72, pp.413-435, 2010.

J. M. Flynn, D. Niccum, J. M. Dunitz, and R. C. Hunter, Evidence and role for bacterial mucin degradation in cystic fibrosis airway disease, PLoS Pathog, vol.12, p.1005846, 2016.

K. E. Fujimura and S. V. Lynch, Microbiota in allergy and asthma and the emerging relationship with the gut microbiome, Cell Host Microbe, vol.17, pp.592-602, 2015.

K. E. Fujimura, A. R. Sitarik, S. Havstad, D. L. Lin, S. Levan et al., Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation, Nat. Med, vol.22, pp.1187-1191, 2016.

V. Gaboriau-routhiau, S. Rakotobe, E. Lecuyer, I. Mulder, A. Lan et al., The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses, Immunity, vol.31, pp.677-689, 2009.

R. L. Gallo and L. V. Hooper, Epithelial antimicrobial defence of the skin and intestine, Nat. Rev. Immunol, vol.12, pp.503-516, 2012.

S. Gauguet, S. D'ortona, K. Ahnger-pier, B. Duan, N. K. Surana et al., Intestinal microbiota of mice influences resistance to Staphylococcus aureus pneumonia, Infect. Immun, vol.83, pp.4003-4014, 2015.

L. Glendinning, S. Wright, J. Pollock, P. Tennant, D. Collie et al., Variability of the Sheep Lung Microbiota, Appl. Environ. Microbiol, vol.82, pp.3225-3238, 2016.

E. Goleva, L. P. Jackson, J. K. Harris, C. E. Robertson, E. R. Sutherland et al., The effects of airway microbiome on corticosteroid responsiveness in asthma, Am. J. Respir. Crit. Care Med, vol.188, pp.1193-1201, 2013.

E. S. Gollwitzer, S. Saglani, A. Trompette, K. Yadava, R. Sherburn et al., Lung microbiota promotes tolerance to allergens in neonates via PD-L1, Nat. Med, vol.20, pp.642-647, 2014.

H. Hammad, M. Chieppa, F. Perros, M. A. Willart, R. N. Germain et al., House dust mite allergen induces asthma via Tolllike receptor 4 triggering of airway structural cells, Nat. Med, vol.15, pp.410-416, 2009.

H. Hammad and B. N. Lambrecht, Dendritic cells and epithelial cells: linking innate and adaptive immunity in asthma, Nat. Rev. Immunol, vol.8, pp.193-204, 2008.

S. Hapfelmeier, M. A. Lawson, E. Slack, J. K. Kirundi, M. Stoel et al., Reversible microbial colonization of germ-free mice reveals the dynamics of IgA immune responses, Science, vol.328, pp.1705-1709, 2010.

M. Hilty, C. Burke, H. Pedro, P. Cardenas, A. Bush et al., Disordered microbial communities in asthmatic airways, PLoS One, vol.5, p.8578, 2010.

K. B. Hooks and M. A. Malley, Dysbiosis and Its Discontents, vol.8, pp.1492-1509, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01677295

Y. J. Huang, C. E. Nelson, E. L. Brodie, T. Z. Desantis, M. S. Baek et al., Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma, J. Allergy Clin. Immunol, vol.127, 2011.

T. Ichinohe, I. K. Pang, Y. Kumamoto, D. R. Peaper, J. H. Ho et al., Microbiota regulates immune defense against respiratory tract influenza A virus infection, Proc. Natl. Acad. Sci. U.S.A, vol.108, pp.5354-5359, 2011.

I. I. Ivanov, K. Atarashi, N. Manel, E. L. Brodie, T. Shima et al., Induction of intestinal Th17 cells by segmented filamentous bacteria, Cell, vol.139, pp.485-498, 2009.

Y. Ji, S. Sun, J. K. Goodrich, H. Kim, A. C. Poole et al., Diet-induced alterations in gut microflora contribute to lethal pulmonary damage in TLR2/TLR4-deficient mice, Cell Rep, vol.8, pp.137-149, 2014.

R. M. Jones, L. Luo, C. S. Ardita, A. N. Richardson, Y. M. Kwon et al., Symbiotic lactobacilli stimulate gut epithelial proliferation via Nox-mediated generation of reactive oxygen species, EMBO J, vol.32, pp.3017-3028, 2013.

J. W. Jung, J. C. Choi, J. W. Shin, J. Y. Kim, I. W. Park et al., Lung microbiome analysis in steroid-nasmall yi, ukrainianve asthma patients by using whole sputum, Tuberc. Respir. Dis, vol.79, pp.165-178, 2016.

M. Kilpelainen, E. O. Terho, H. Helenius, and M. Koskenvuo, Farm environment in childhood prevents the development of allergies, Clin. Exp. Allergy, vol.30, pp.201-208, 2000.

C. V. Lal, C. Travers, Z. H. Aghai, P. Eipers, T. Jilling et al., The Airway Microbiome at, Birth. Sci. Rep, vol.6, p.31023, 2016.

C. A. Lozupone, J. I. Stombaugh, J. I. Gordon, J. K. Jansson, and R. Knight, Diversity, stability and resilience of the human gut microbiota, Nature, vol.489, pp.220-230, 2012.

A. J. Macpherson and T. Uhr, Induction of protective IgA by intestinal dendritic cells carrying commensal bacteria, Science, vol.303, pp.1662-1665, 2004.

B. J. Marsland, Influences of the microbiome on the early origins of allergic asthma, Ann. Am. Thorac. Soc, vol.10, pp.165-169, 2013.

B. J. Marsland, A. Trompette, and E. S. Gollwitzer, The gut-lung axis in respiratory disease, Ann. Am. Thorac. Soc, vol.12, pp.150-156, 2015.

M. Mennini, L. Dahdah, M. C. Artesani, A. Fiocchi, and A. Martelli, Probiotics in asthma and allergy prevention, Front. Pediatr, vol.5, p.165, 2017.

S. Miquel, M. Leclerc, R. Martin, F. Chain, M. Lenoir et al., Identification of metabolic signatures linked to anti-inflammatory effects of Faecalibacterium prausnitzii, vol.6, pp.300-315, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01226343

J. Miyoshi and Y. Takai, Molecular perspective on tight-junction assembly and epithelial polarity, Adv. Drug Deliv. Rev, vol.57, pp.815-855, 2005.

A. Morris, J. M. Beck, P. D. Schloss, T. B. Campbell, K. Crothers et al., Comparison of the respiratory microbiome in healthy nonsmokers and smokers, Am. J. Respir. Crit. Care Med, vol.187, pp.1067-1075, 2013.

I. Nicola, F. Cerutti, E. Grego, I. Bertone, P. Gianella et al., Characterization of the upper and lower respiratory tract microbiota in Piedmontese calves, vol.5, p.152, 2017.

T. Olszak, D. An, S. Zeissig, M. P. Vera, J. Richter et al., Microbial exposure during early life has persistent effects on natural killer T cell function, Science, vol.336, pp.489-493, 2012.

L. Portengen, T. Sigsgaard, O. Omland, C. Hjort, D. Heederik et al., Low prevalence of atopy in young Danish farmers and farming students born and raised on a farm, Clin. Exp. Allergy, vol.32, pp.247-253, 2002.

D. Proud, L. , and R. , Epithelial cells and airway diseases, Immunol. Rev, vol.242, pp.186-204, 2011.

K. Pütsep, G. Carlsson, H. G. Boman, A. , and M. , Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study, Lancet, vol.360, pp.1144-1149, 2002.

S. Rakoff-nahoum, J. Paglino, F. Eslami-varzaneh, S. Edberg, and R. Medzhitov, Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis, Cell, vol.118, pp.229-241, 2004.

A. Remot, D. Descamps, M. L. Noordine, A. Boukadiri, E. Mathieu et al., Bacteria isolated from lung modulate asthma susceptibility in mice, ISME J, vol.11, pp.1061-1074, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01595509

J. Riedler, W. Eder, G. Oberfeld, and M. Schreuer, Austrian children living on a farm have less hay fever, asthma and allergic sensitization, Clin. Exp. Allergy, vol.30, pp.194-200, 2000.

D. Rodriguez, A. C. Keller, E. L. Faquim-mauro, M. S. De-macedo, F. Q. Cunha et al., Bacterial lipopolysaccharide signaling through toll-like receptor 4 suppresses asthma-like responses via nitric oxide synthase 2 activity, J. Immunol, vol.171, pp.1001-1008, 2014.

S. P. Rosshart, B. G. Vassallo, D. Angeletti, D. S. Hutchinson, A. P. Morgan et al., Wild mouse gut microbiota promotes host fitness and improves disease resistance, Cell, vol.171, 2017.

S. H. Ryu and T. S. Stappenbeck, Gut-pancreatic axis AMPlified in islets of langerhans, Immunity, vol.43, pp.216-218, 2015.

C. Sabatel, C. Radermecker, L. Fievez, G. Paulissen, S. Chakarov et al., Exposure to bacterial CpG DNA protects from airway allergic inflammation by expanding regulatory lung interstitial macrophages, Immunity, vol.46, pp.457-473, 2017.
URL : https://hal.archives-ouvertes.fr/inserm-01529380

M. J. Schuijs, M. A. Willart, K. Vergote, D. Gras, K. Deswarte et al., Farm dust and endotoxin protect against allergy through A20 induction in lung epithelial cells, Science, vol.349, pp.1106-1110, 2015.

L. N. Segal, J. C. Clemente, J. C. Tsay, S. B. Koralov, B. C. Keller et al., Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype, Nat. Microbiol, vol.1, p.16031, 2016.

L. N. Segal, W. N. Rom, and M. D. Weiden, Lung microbiome for clinicians. New discoveries about bugs in healthy and diseased lungs, Ann. Am. Thorac. Soc, vol.11, pp.108-116, 2014.

A. Shade, Diversity is the question, not the answer, ISME J, vol.11, pp.1-6, 2017.

N. Singh, A. Vats, A. Sharma, A. Arora, and A. Kumar, The development of lower respiratory tract microbiome in mice, vol.5, p.61, 2017.

F. M. Siqueira, E. Perez-wohlfeil, F. M. Carvalho, O. Trelles, I. S. Schrank et al., Microbiome overview in swine lungs, PLoS One, vol.12, p.181503, 2017.

J. Stokholm, M. J. Blaser, J. Thorsen, M. A. Rasmussen, J. Waage et al., Maturation of the gut microbiome and risk of asthma in childhood, Nat. Commun, vol.9, p.141, 2018.

H. Tashiro, K. Takahashi, H. Sadamatsu, G. Kato, K. Kurata et al., Saturated fatty acid increases lung macrophages and augments house dust mite-induced airway inflammation in mice fed with high-fat diet, Inflammation, vol.40, pp.1072-1086, 2017.

N. Thevaranjan, A. Puchta, C. Schulz, A. Naidoo, J. C. Szamosi et al., Age-associated microbial dysbiosis promotes intestinal permeability, systemic inflammation, and macrophage dysfunction, Cell Host Microbe, vol.21, 2017.

J. Tomas, J. Reygner, C. Mayeur, R. Ducroc, S. Bouet et al., Early colonizing Escherichia coli elicits remodeling of rat colonic epithelium shifting toward a new homeostatic state, ISME J, vol.9, pp.46-58, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01194140

J. Tomas, L. Wrzosek, N. Bouznad, S. Bouet, C. Mayeur et al., Primocolonization is associated with colonic epithelial maturation during conventionalization, FASEB J, vol.27, pp.645-655, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01003327

A. Trompette, E. S. Gollwitzer, K. Yadava, A. K. Sichelstiel, N. Sprenger et al., Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis, Nat. Med, vol.20, pp.159-166, 2014.

M. K. Tulic, M. Vivinus-nebot, A. Rekima, S. Rabelo-medeiros, C. Bonnart et al., Presence of commensal house dust mite allergen in human gastrointestinal tract: a potential contributor to intestinal barrier dysfunction, Gut, vol.65, pp.757-766, 2016.

N. D. Ubags and B. J. Marsland, Mechanistic insight into the function of the microbiome in lung diseases, Eur. Respir. J, vol.50, pp.2467-2016, 2017.

A. Venkataraman, C. M. Bassis, J. M. Beck, V. B. Young, J. L. Curtis et al., Application of a neutral community model to assess structuring of the human lung microbiome, vol.6, pp.2284-2214, 2015.

A. I. Vientos-plotts, A. C. Ericsson, H. Rindt, M. E. Grobman, A. Graham et al., Dynamic changes of the respiratory microbiota and its relationship to fecal and blood microbiota in healthy young cats, PLoS One, vol.12, p.173818, 2017.

A. I. Vientos-plotts, A. C. Ericsson, H. Rindt, and C. R. Reinero, Oral probiotics alter healthy feline respiratory microbiota, Front. Microbiol, vol.8, p.1287, 2017.

L. Wrzosek, S. Miquel, M. L. Noordine, S. Bouet, M. Chevalier-curt et al., Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent, BMC Biol, vol.11, p.61, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01001072

G. Yu, M. H. Gail, D. Consonni, M. Carugno, M. Humphrys et al., Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features, Genome Biol, vol.17, p.163, 2016.

Y. Yun, G. Srinivas, S. Kuenzel, M. Linnenbrink, S. Alnahas et al., Environmentally determined differences in the murine lung microbiota and their relation to alveolar architecture, PLoS One, vol.9, p.113466, 2014.

E. T. Zemanick, B. D. Wagner, C. E. Robertson, R. C. Ahrens, J. F. Chmiel et al., Airway microbiota across age and disease spectrum in cystic fibrosis, Eur. Respir. J, vol.50, p.1700832, 2017.