Genome Sequence of "Candidatus Methanomassiliicoccus intestinalis" Issoire-Mx1, a Third Thermoplasmatales-Related Methanogenic Archaeon from Human Feces.

"Candidatus Methanomassiliicoccus intestinalis" Issoire-Mx1 is a methanogenic archaeon found in the human gut and is a representative of the novel order of methanogens related to Thermoplasmatales. Its complete genome sequence is presented here.

Genome sequence of "Candidatus Methanomethylophilus alvus" Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens.

We report the draft genome sequence of "Candidatus Methanomethylophilus alvus" Mx1201, a methanogen present in the human gut. It was enriched from human feces under anaerobic conditions with methanol as the substrate. Its circular genome, of around 1.7 Mb, contains genes needed for methylotrophic methanogenesis from methanol and tri-, di-, and monomethylamine.

Molecular evaluation of the human gut methanogenic archaeal microbiota reveals an age-associated increase of the diversity.

The methanogenic diversity of the human intestinal microbiota has long been viewed as composed of two Methanobacteriales: Methanobrevibacter smithii and Methanosphaera stadtmanae. Recently, Mx-01, a new phylotype hypothesized to belong to a putative sixth methanogenic order, was recovered from human faeces. Here we examined the diversity and the distribution of methanogens among healthy people of three age groups by analysing mcrA and 16S rDNA clones. The mcrA analysis of ∼1200 clones revealed that the usual Methanobacteriales were present without any significant difference among adults and elderly (respectively 60% and 80% of carriers, n = 40, P = 0.3). In addition, four new phylotypes that grouped with Mx-01 in the same monophyletic clade were recovered. These phylotypes were significantly more frequently detected in elderly people (40%, n = 20) than in adults (10%, n = 20, P = 0.065). In parallel, new 16S rDNA phylotypes affiliated near or within Thermoplasmatales were recovered. Altogether, these results indicate an age-related apparition of Mx-phylotypes, putatively methanogenic, which are formed of several species carrying a mcrA gene and that are not related to any of the five methanogenic orders. These species may be related to Thermoplasmatales or may cohabit with archaeal species related to Thermoplasmatales.

Tools for stools: the challenge of assessing human intestinal microbiota using molecular diagnostics.

The human GI tract is inhabited by an incredibly complex and abundant microbiota, whose composition is dependent on a variety of factors. The gut microbiota has an influence in the morphological, immunological and nutritional functions of the digestive tract and may be involved in many diseases. This article proposes the rationale behind conducting in vitro diagnostics (IVDs) of the human microbiota, as well as outlining the conceptual and technical difficulties involved in IVD testing. The molecular methods that can be used according to whether the IVD tools are employed to study one individual constituent species or to determine the microbiota as a whole will also be described. In the latter case, these technologies include high-throughput sequencing for metagenomics and DNA microarrays, which can now be efficiently used to study gut ecology and are believed to represent the future of standardized diagnostics.

A putative new order of methanogenic Archaea inhabiting the human gut, as revealed by molecular analyses of the mcrA gene.

The diversity of methanogenic Archaea from the gut of 6 humans was investigated by targeting mcrA, a molecular metabolic marker of methanogenesis. Three operational taxonomic units (OTUs) were recovered from about 400 clones analyzed, two of which were attributed to the expected Methanobacteriales Methanobrevibacter smithii (4 volunteers) and Methanosphaera stadtmanae (1 volunteer). The third OTU (1 volunteer) corresponded to a distant phylotype that does not cluster with any of the five methanogenic orders. This result, also supported by 16S archaeal sequences retrieved from the same volunteer, strongly suggests there may be a sixth order and hence potential underestimation of the role of methanogens in gut physiology.

Influence of cabbage processing methods and prebiotic manipulation of colonic microflora on glucosinolate breakdown in man.

Glucosinolate consumption from brassica vegetables has been implicated in reduction of cancer risk. The isothiocyanate breakdown products of glucosinolates appear to be particularly important as chemoprotective agents. Before consumption, brassica vegetables are generally cooked, causing the plant enzyme, myrosinase, to be denatured, influencing the profile of glucosinolate breakdown products produced. Some human intestinal microflora species show myrosinase-like activity (e.g. bifidobacteria). We aimed to increase bifidobacteria by offering a prebiotic (inulin) in a randomised crossover study. Six volunteers consumed inulin (10 g/d) for 21 d followed by a 21 d control period (no inulin). Treatment periods were reversed for the remaining six volunteers. During the last 5 d of each period two cabbage-containing meals were consumed. Total urine output was collected for 24 h following each meal. Cabbage was microwaved for 2 min (lightly cooked) or 5.5 min (fully cooked). Faecal samples were collected at the start and after the inulin and control treatments. Bifidobacteria were enumerated by real-time PCR. Allyl isothiocyanate production was quantified by measuring urinary excretion of allyl mercapturic acid (AMA). Bifidobacteria increased following prebiotic supplementation (P < 0.001) but there was no impact of this increase on AMA excretion. AMA excretion was greater following consumption of lightly cooked cabbage irrespective of prebiotic treatment (P < 0.001). In conclusion, the most effective way to increase isothiocyanate production may be to limit the length of time that brassica vegetables are cooked prior to consumption.