Genome Sequence of “
            <i>Candidatus</i>
            Methanomassiliicoccus intestinalis” Issoire-Mx1, a Third
            <i>Thermoplasmatales</i>
            -Related Methanogenic Archaeon from Human Feces

Borrel, Guillaume; Harris, Hugh M. B.; Parisot, Nicolas; Gaci, Nadia; Tottey, William; Mihajlovski, Agnès; Deane, Jennifer; Gribaldo, Simonetta; Bardot, Olivier; Peyretaillade, Éric; Peyret, Pierre; O’Toole, Paul W.; Brugère, Jean-François

doi:10.1128/genomea.00453-13

Cited by 91 publications

(85 citation statements)

References 10 publications

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“…Species of the second most abundant genus in the order Methanobacteriales, Methanosphaera, have been characterized as methylotrophs (9, 10). Little is known about substrate requirements of members of the order Methanomassiliicoccales, but evidence is accumulating that some members of this order may grow methylotrophically as well (5,(11)(12)(13).Altogether, at least 40 different strains of methanogens have been isolated from the rumen or other intestinal environments, representing a range of species. Cultivation-independent studies suggest that other potentially important species are yet to be cultured and characterized.…”

mentioning

confidence: 99%

Few Highly Abundant Operational Taxonomic Units Dominate within Rumen Methanogenic Archaeal Species in New Zealand Sheep and Cattle

Seedorf

Kittelmann

Janssen

2015

Appl Environ Microbiol

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Sequencing and analyses of 16S rRNA gene amplicons were performed to estimate the composition of the rumen methanogen community in 252 samples from eight cohorts of sheep and cattle, separated into 16 different sample groups by diet, and to determine which methanogens are most prominent in the rumens of farmed New Zealand ruminants. Methanobacteriales (relative abundance ؎ standard deviation, 89.6% ؎ 9.8%) and Methanomassiliicoccales (10.4% ؎ 9.8%) were the two major orders and contributed 99.98% (؎0.1%) to the rumen methanogen communities in the samples. Sequences from Methanobacteriales were almost entirely from only four different species (or clades of very closely related species). Each was detectable in at least 89% of the samples. These four species or clades were the Methanobrevibacter gottschalkii clade and Methanobrevibacter ruminantium clade with a mean abundance of 42.4% (؎19.5% standard deviation) and 32.9% (؎18.8%), respectively, and Methanosphaera sp. ISO3-F5 (8.2% ؎ 6.7%) and Methanosphaera sp. group5 (5.6% ؎ 5.7%). These four species or clades appeared to be primarily represented by only one or, in one case, two dominant sequence types per species or clade when the sequences were grouped into operational taxonomic units (OTUs) at 99% sequence identity. The mean relative abundance of Methanomassiliicoccales in the samples was relatively low but exceeded 40% in some of the treatment groups. Animal feed affected the apparent methanogen community structure of both orders, as evident from differences in relative abundances of the major OTUs in animals under different feeding regimens.M ethane is the second most significant anthropogenic greenhouse gas, after carbon dioxide, and its concentration in the atmosphere is increasing (1). One major contributor to this is an intensification and expansion of global agricultural activities, in particular increased ruminant livestock numbers. Ruminants, such as cattle, sheep, and domesticated deer, produce large amounts of methane via enteric fermentation and are the most numerous farm animals in New Zealand. It is estimated that methane from these animals accounts for almost 30% of New Zealand's total anthropogenic greenhouse gas emissions (2).Methane is produced in the rumen by methanogenic archaea, here referred to as methanogens. Methanogens comprise a phylogenetically diverse group of microorganisms that are present in the rumen at up to ϳ10 10 cells/g rumen contents (3). Previous analyses have shown that members of the orders Methanobacteriales and Methanomassiliicoccales are dominant in the rumens of domesticated ruminants in New Zealand and many other geographic locations around the world (4). The order name Methanomassiliicoccales has only recently been proposed (5). These methanogens are closely related to the Thermoplasmatales (6) and were previously known as rice cluster III (RC-III) archaea (7), rumen cluster C (RCC) (4), or Methanoplasmatales (8). Within the order Methanobacteriales, hydrogenotrophic methanogens of the genus Methanobrevibacter appe...

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confidence: 99%

Few Highly Abundant Operational Taxonomic Units Dominate within Rumen Methanogenic Archaeal Species in New Zealand Sheep and Cattle

Seedorf

Kittelmann

Janssen

2015

Appl Environ Microbiol

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“…These Euryarchaeota have been detected based on gene biomarker analyses in diverse environments such as lakes, soils, and marine sediments but are particularly abundant in the digestive tracts of ruminants (10-15). A single pure culture, Methanomassiliicoccus luminyensis, as well as a few enrichment cultures, have been obtained, all of which reduce methanol or methylamines with H 2 as the electron donor (6,(16)(17)(18)(19)(20).…”

mentioning

confidence: 99%

Unusual Butane- and Pentanetriol-Based Tetraether Lipids in Methanomassiliicoccus luminyensis, a Representative of the Seventh Order of Methanogens

Becker

Elling

Yoshinaga

et al. 2016

Appl Environ Microbiol

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A new clade of archaea has recently been proposed to constitute the seventh methanogenic order, the Methanomassiliicoccales, which is related to the Thermoplasmatales and the uncultivated archaeal clades deep-sea hydrothermal vent Euryarchaeota group 2 and marine group II Euryarchaeota but only distantly related to other methanogens. In this study, we investigated the membrane lipid composition of Methanomassiliicoccus luminyensis, the sole cultured representative of this seventh order. The lipid inventory of M. luminyensis comprises a unique assemblage of novel lipids as well as lipids otherwise typical for thermophilic, methanogenic, or halophilic archaea. For instance, glycerol sesterpanyl-phytanyl diether core lipids found mainly in halophilic archaea were detected, and so were compounds bearing either heptose or methoxylated glycosidic head groups, neither of which have been reported so far for other archaea. The absence of quinones or methanophenazines is consistent with a biochemistry of methanogenesis different from that of the methanophenazine-containing methylotrophic methanogens. The most distinctive characteristic of the membrane lipid composition of M. luminyensis, however, is the presence of tetraether lipids in which one glycerol backbone is replaced by either butane-or pentanetriol, i.e., lipids recently discovered in marine sediments. Butanetriol dibiphytanyl glycerol tetraether (BDGT) constitutes the most abundant core lipid type (>50% relative abundance) in M. luminyensis. We have thus identified a source for these unusual orphan lipids. The complementary analysis of diverse marine sediment samples showed that BDGTs are widespread in anoxic layers, suggesting an environmental significance of Methanomassiliicoccales and/or related BDGT producers beyond gastrointestinal tracts. IMPORTANCECellular membranes of members of all three domains of life, Archaea, Bacteria, and Eukarya, are largely formed by lipids in which glycerol serves as backbone for the hydrophobic alkyl chains. Recently, however, archaeal tetraether lipids with either butanetriol or pentanetriol as a backbone were identified in marine sediments and attributed to uncultured sediment-dwelling archaea. Here we show that the butanetriol-based dibiphytanyl tetraethers constitute the major lipids in Methanomassiliicoccus luminyensis, currently the only isolate of the novel seventh order of methanogens. Given the absence of these lipids in a large set of archaeal isolates, these compounds may be diagnostic for the Methanomassiliicoccales and/or closely related archaea. Methane is a potent greenhouse gas and an important intermediate in the global carbon cycle (1-3). Biogenic methane is produced predominantly by archaea inhabiting diverse anoxic environments such as sediments, soils, wetlands, and the digestive tracts of termites and ruminants (2, 4). All cultured methanogens to date belong to the phylum Euryarchaeota, while metagenomic sequencing revealed a putative methanogenic metabolism for members of the uncultivated Bathyarc...

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“…Fluorescence in situ hybridization (FISH) confirmed the presence of viable archaeal cells, but this archaeon has not been isolated in pure culture or deposited in public collections (178). Similarly, the use of methanol as the substrate led to the enrichment in stool microbiota of "Candidatus Methanomethylophilus alvus" and "Candidatus Methanomassiliicoccus intestinalis," a Thermoplasmatales-related lineage distantly related to its most closely related species, Methanomassiliicoccus luminyensis (179,180) and Aciduliprofundum boonei (159,174). M. luminyensis appears to be the sole cultured representative of a new, seventh order of methylotrophic methanogens (181).…”

Section: Archaeamentioning

confidence: 96%

“…The availability of colonies allowed antibiotic susceptibility testing, which demonstrated the high natural resistance of Archaea, except against imidazole, its derivatives, and fusidic acid (188,189), and genome sequencing (174,180,190). Several archaeal species remaining uncultured have been detected only by molecular tools (159,161,162,165,178,191,192). Thus far, only strictly anaerobic methanogenic Archaea have been isolated from humans.…”

Section: Archaeamentioning

confidence: 99%

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Current and Past Strategies for Bacterial Culture in Clinical Microbiology

et al. 2015

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SUMMARY A pure bacterial culture remains essential for the study of its virulence, its antibiotic susceptibility, and its genome sequence in order to facilitate the understanding and treatment of caused diseases. The first culture conditions empirically varied incubation time, nutrients, atmosphere, and temperature; culture was then gradually abandoned in favor of molecular methods. The rebirth of culture in clinical microbiology was prompted by microbiologists specializing in intracellular bacteria. The shell vial procedure allowed the culture of new species of Rickettsia . The design of axenic media for growing fastidious bacteria such as Tropheryma whipplei and Coxiella burnetii and the ability of amoebal coculture to discover new bacteria constituted major advances. Strong efforts associating optimized culture media, detection methods, and a microaerophilic atmosphere allowed a dramatic decrease of the time of Mycobacterium tuberculosis culture. The use of a new versatile medium allowed an extension of the repertoire of archaea. Finally, to optimize the culture of anaerobes in routine bacteriology laboratories, the addition of antioxidants in culture media under an aerobic atmosphere allowed the growth of strictly anaerobic species. Nevertheless, among usual bacterial pathogens, the development of axenic media for the culture of Treponema pallidum or Mycobacterium leprae remains an important challenge that the patience and innovations of cultivators will enable them to overcome.

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

Abstract: “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.

Cited by 91 publications

References 10 publications

Few Highly Abundant Operational Taxonomic Units Dominate within Rumen Methanogenic Archaeal Species in New Zealand Sheep and Cattle

Few Highly Abundant Operational Taxonomic Units Dominate within Rumen Methanogenic Archaeal Species in New Zealand Sheep and Cattle

Unusual Butane- and Pentanetriol-Based Tetraether Lipids in Methanomassiliicoccus luminyensis, a Representative of the Seventh Order of Methanogens

Current and Past Strategies for Bacterial Culture in Clinical Microbiology

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