Methanobrevibacter smithii, a methanogen consistently colonising the newborn stomach

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.

Changes in Intestinal Microbiota and Predicted Metabolic Pathways During Colonic Fermentation of Mango (Mangifera indica L.)—Based Bar Indigestible Fraction

“…As for Methanobrevibacter, it is the main human methanogen that is almost always found in the digestive tract of adults, with colonization taking place just after birth. Methanobrevibacter is also the main CH 4 /H 2 O producer, which is carried out by transforming H 2 and CO 2 [41].…”

Exploring the archaeome: detection of archaeal signatures in the human body

“…Nevertheless, (methanogenic) archaea are part of the commensal microorganisms inhabiting the human body, being regularly detected in the oral cavity and the gastrointestinal tract (Chaudhary et al, 2015;Gaci et al, 2014;Horz and Conrads, 2011;Nkamga et al, 2017); in the latter they sometimes even outnumber the most abundant bacterial species (14%, (Tyakht et al, 2013);). Most human archaea studies use either cultivation or qPCR methods (Grine et al, 2017;Koskinen et al, 2017;van de Pol et al, 2017;Wampach et al, 2017) and only a few, 16S rRNA gene-based archaeacentric studies are available Moissl-Eichinger et al, 2017). These new studies have shown that archaea are also present in the human respiratory tract and on human skin in considerable amounts Probst et al, 2013).…”

Gut Microbiota beyond Bacteria—Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD

“…Although the research on the commensal viral and fungal constituents of human microbiota gained momentum recently, most microbiota studies still fail to include the archaea. The studies on human archaeome usually employ either cultivation or qPCR methodology [118,119,148], while 16S rRNA gene-based research often uses bacterial-targeted protocols and universal primer pairs to cover the broadest prokaryotic diversity [119,149]. The low abundance of archaeal DNA in human samples, inefficient cell lysis and DNA extraction, failure of the universal primers to fully detect archaeal signatures, as well as incomplete 16S rRNA gene databases, all represent methodological pitfalls of human archaeome analysis [112,150,151].…”