Abstract
Methanobrevibacter smithii is the main human methanogen almost always found in the digestive tract of adults. Yet, the age at which M. smithii establishes itself as part of the developing intestinal microflora remains unknown. In order to gain insight into this, we developed a polyphasic approach, including microscopic observation by fluorescence in situ hybridisation, polymerase chain reaction (PCR) sequencing detection, identification and culture, to isolate and genotype M. smithii in one-day-old newborns’ gastric juice specimens. In the presence of negative controls, 50/50 (100%) prospectively analysed newborn gastric juice specimens were PCR-positive for methanogens, all identified as M. smithii by sequencing. We succeeded in cultivating M. smithii in 35/50 (70%) newborn gastric juice specimens, while 15/50 specimens remained sterile. Further, M. smithii was observed by direct microscopic investigation using fluorescence in situ hybridisation. Multispacer sequence typing found one of seven different genotypes per specimen, these genotypes having all been previously described in adult human stools. Methanobrevibacter smithii is an early inhabitant of the human stomach, colonising the gastric mucosa just after birth, and the mother’s gut microbiota is a probable source of colonisation.
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Dridi B, Henry M, El Khéchine A, Raoult D, Drancourt M (2009) High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PLoS One 4(9):e7063
Dridi B, Fardeau ML, Ollivier B, Raoult D, Drancourt M (2012) Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces. Int J Syst Evol Microbiol 62(Pt 8):1902–1907
Khelaifia S, Raoult D, Drancourt M (2013) A versatile medium for cultivating methanogenic archaea. PLoS One 8(4):e61563
Samuel BS, Hansen EE, Manchester JK, Coutinho PM, Henrissat B, Fulton R, Latreille P, Kim K, Wilson RK, Gordon JI (2007) Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc Natl Acad Sci U S A 104(25):10643–10648
Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO (2007) Development of the human infant intestinal microbiota. PLoS Biol 5(7):e177
Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, Angenent LT, Ley RE (2011) Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci U S A 108(Suppl 1):4578–4585
Mihajlovski A, Doré J, Levenez F, Alric M, Brugère JF (2010) Molecular evaluation of the human gut methanogenic archaeal microbiota reveals an age-associated increase of the diversity. Environ Microbiol Rep 2(2):272–280
Gaci N, Borrel G, Tottey W, O’Toole PW, Brugère JF (2014) Archaea and the human gut: new beginning of an old story. World J Gastroenterol 20(43):16062–16078
Odamaki T, Kato K, Sugahara H, Hashikura N, Takahashi S, Xiao JZ, Abe F, Osawa R (2016) Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study. BMC Microbiol 16:90
Hungate RE (1969) A roll tube method for cultivation of strict anaerobes. In: Norris JR, Ribbons DW (eds) Methods in microbiology, vol 3B. Academic Press, Cambridge, pp 117–132
Hungate RE, Macy J (1973) The roll-tube method for cultivation of strict anaerobes. Bulletins from the Ecological Research Committee/NFR, No. 17, Modern Methods in the Study of Microbial Ecology. Oikos Editorial Office, pp 123–126
Khelaifia S, Lagier JC, Nkamga VD, Guilhot E, Drancourt M, Raoult D (2016) Aerobic culture of methanogenic archaea without an external source of hydrogen. Eur J Clin Microbiol Infect Dis 35(6):985–991
Nkamga VD, Drancourt M (2016) Methanomassiliicoccaceae. In: Whitman WB (ed) Bergey’s manual of systematics of Archaea and Bacteria. Wiley, Chichester. doi: 10.1002/9781118960608.fbm00269
Nkamga VD, Huynh HT, Aboudharam G, Ruimy R, Drancourt M (2015) Diversity of human-associated Methanobrevibacter smithii isolates revealed by multispacer sequence typing. Curr Microbiol 70(6):810–815
Raskin L, Stromley JM, Rittmann BE, Stahl DA (1994) Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl Environ Microbiol 60(4):1232–1240
Luton PE, Wayne JM, Sharp RJ, Riley PW (2002) The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology 148(Pt 11):3521–3530
Sondheimer JM, Clark DA, Gervaise EP (1985) Continuous gastric pH measurement in young and older healthy preterm infants receiving formula and clear liquid feedings. J Pediatr Gastroenterol Nutr 4(3):352–355
Mason S (1962) Some aspects of gastric function in the newborn. Arch Dis Child 37:387–391
Belay N, Mukhopadhyay B, Conway de Macario E, Galask R, Daniels L (1990) Methanogenic bacteria in human vaginal samples. J Clin Microbiol 28(7):1666–1668
Bäckhed F, Roswall J, Peng Y, Feng Q, Jia H, Kovatcheva-Datchary P, Li Y, Xia Y, Xie H, Zhong H, Khan MT, Zhang J, Li J, Xiao L, Al-Aama J, Zhang D, Lee YS, Kotowska D, Colding C, Tremaroli V, Yin Y, Bergman S, Xu X, Madsen L, Kristiansen K, Dahlgren J, Wang J (2015) Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe 17(5):690–703
Jiménez E, de Andrés J, Manrique M, Pareja-Tobes P, Tobes R, Martínez-Blanch JF, Codoñer FM, Ramón D, Fernández L, Rodríguez JM (2015) Metagenomic analysis of milk of healthy and mastitis-suffering women. J Hum Lact 31(3):406–415
Hudson MJ, Roberts AK (1993) Establishment of methanogens in the infant intestine. Microbial Ecol Health Dis 6(6):301–308. Available online at: http://informahealthcare.com/doi/abs/10.3109/08910609309141339
Hansen EE, Lozupone CA, Rey FE, Wu M, Guruge JL, Narra A, Goodfellow J, Zaneveld JR, McDonald DT, Goodrich JA, Heath AC, Knight R, Gordon JI (2011) Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins. Proc Natl Acad Sci U S A 108(Suppl 1):4599–4606
Vallès Y, Gosalbes MJ, de Vries LE, Abellán JJ, Francino MP (2012) Metagenomics and development of the gut microbiota in infants. Clin Microbiol Infect 18(Suppl 4):21–26
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This study was funded by IHU Méditerranée Infection, Marseille, France.
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Grine, G., Boualam, M.A. & Drancourt, M. Methanobrevibacter smithii, a methanogen consistently colonising the newborn stomach. Eur J Clin Microbiol Infect Dis 36, 2449–2455 (2017). https://doi.org/10.1007/s10096-017-3084-7
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DOI: https://doi.org/10.1007/s10096-017-3084-7