Draft Genome Sequencing of Methanobrevibacter oralis Strain JMR01, Isolated from the Human Intestinal Microbiota

Khelaifia, Saber; Garibal, Marc; Robert, Caroline; Raoult, Didier; Drancourt, Michel

doi:10.1128/genomea.00073-14

Cited by 16 publications

(6 citation statements)

References 7 publications

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“…In the second step, specific quantitative amplification of the M . oralis strain JMR0 14 DNA was achieved using a specific real-time PCR assay targeting M . oralis heat-shock protein cnp 60 gene as previously described 3 .…”

Section: Methodsmentioning

confidence: 99%

RETRACTED ARTICLE: Peri-implantitis-associated methanogens: a preliminary report

Belkacemi¹,

Mazel²,

Tardivo³

et al. 2018

Sci Rep

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Methanogens have already been described in periodontitis but not in peri-implantitis. Thirty peri-implantitis samples and 28 control samples were collected in 28 consenting peri-implantitis patients. PCR-sequencing of the 16S rRNA gene was used as a broad-spectrum screening method and results were further confirmed by real-time quantitative PCR targeting the mcrA genes. Results showed a methanogen community dominated by Methanobrevibacter oralis in 31/58 (51%) samples including 16/28 (57%) control samples and 15/30 (50%) peri-implantitis samples. Methanobrevibacter massiliense was detected in 5/58 (8.6%) samples including 3/28 (1%) control samples and 2/30 (6.7%) peri-implantitis samples. The prevalence of M. oralis or M. massiliense did not significantly differ in peri-implantitis and control samples (exact Fisher test, P = 0.61 and P = 0.67, respectively). Further ponderation of the methanogen load by the real-time quantitative PCR for actin human gene again indicated non-significant difference (Wilcoxon-Mann-Whitney test, P = 0.48 and P = 0.40, respectively). These data show that the prevalence of methanogens does not differ in peri-implantitis lesions and healthy sites, when individuals are their own control. These data do not allow assigning a specific pathogenic role to methanogens in peri-implantitis; methanogens rather are part of the commensal and normal flora of the oral cavity.

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Section: Methodsmentioning

confidence: 99%

RETRACTED ARTICLE: Peri-implantitis-associated methanogens: a preliminary report

Belkacemi¹,

Mazel²,

Tardivo³

et al. 2018

Sci Rep

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“…Among the genera found, a high prevalence of Methanobrevibacter ( Fig 7 ) was observed, representing almost 60% of all Archaea in each group. This genus is one of the most important organisms in bovine rumen—having a central role in the metabolism of plant compounds [ 27 , 39 , 40 ]—and is also present in the GIT of other animals, including humans [ 41 – 43 ]. Individual analysis confirms a great relative abundance of Methanobrevibacter in each animal, and a significant number of Unclassified Euryarchaeota ( S4 Fig ).…”

Section: Resultsmentioning

confidence: 99%

Vaginal Microbiome Characterization of Nellore Cattle Using Metagenomic Analysis

et al. 2015

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Understanding of microbial communities inhabiting cattle vaginal tract may lead to a better comprehension of bovine physiology and reproductive health being of great economic interest. Up to date, studies involving cattle microbiota are focused on the gastrointestinal tract, and little is known about the vaginal microbiota. This study aimed to investigate the vaginal microbiome in Nellore cattle, heifers and cows, pregnant and non-pregnant, using a culture independent approach. The main bacterial phyla found were Firmicutes (~40–50%), Bacteroidetes (~15–25%) and Proteobacteria (~5–25%), in addition to ~10–20% of non-classified bacteria. 45–55% of the samples were represented by only ten OTUs: Aeribacillus, Bacteroides, Clostridium, Ruminococcus, Rikenella, Alistipes, Bacillus, Eubacterium, Prevotella and non-classified bacteria. Interestingly, microbiota from all 20 animals could be grouped according to the respiratory metabolism of the main OTUs found, creating three groups of vaginal microbiota in cattle. Archaeal samples were dominated by the Methanobrevibacter genus (Euryarchaeota, ~55–70%). Ascomycota was the main fungal phylum (~80–95%) and Mycosphaerella the most abundant genus (~70–85%). Hormonal influence was not clear, but a tendency for the reduction of bacterial and increase of archaeal populations in pregnant animals was observed. Eukaryotes did not vary significantly between pregnant and non-pregnant animals, but tended to be more abundant on cows than on heifers. The present work describes a great microbial variability in the vaginal community among the evaluated animals and groups (heifers and cows, pregnant and non-pregnant), which is significantly different from the findings previously reported using culture dependent methods, pointing out the need for further studies on this issue. The microbiome found also indicates that the vaginal colonization appears to be influenced by the gastrointestinal community.

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“…Most Methanobrevibacter species generally thrive in nutrient-rich environments, such as animal digestive tracts. M. oralis [37], which was isolated from the human mouth-cavity in a subgingival plaque [38], has the potential to obtain aromatic amino acids from its local environment. Similarly, living inside the anaerobic ciliate may provide the endosymbiont with access to nutrients and vitamins either from the eukaryotic host, or, in the case of cobalamin, from the bacterial and archaeal cells ingested as food.…”

Section: Methanogenic Endosymbiont Genomes Undergo Pseudogenizationmentioning

confidence: 99%

Genomes of two archaeal endosymbionts show convergent adaptations to an intracellular lifestyle

et al. 2018

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Endosymbiosis is a widespread phenomenon in the microbial world and can be based on diverse interactions between endosymbiont and host cell. The vast majority of the known endosymbiotic interactions involve bacteria that have invaded eukaryotic host cells. However, methanogenic archaea have been found to thrive in anaerobic, hydrogenosome-containing protists and it was suggested that this symbiosis is based on the transfer of hydrogen. Here, we used culture-independent genomics approaches to sequence the genomes of two distantly related methanogenic endosymbionts that have been acquired in two independent events by closely related anaerobic ciliate hosts Nyctotherus ovalis and Metopus contortus, respectively. The sequences obtained were then validated as originating from the ciliate endosymbionts by in situ probing experiments. Comparative analyses of these genomes and their closest free-living counterparts reveal that the genomes of both endosymbionts are in an early stage of adaptation towards endosymbiosis as evidenced by the large number of genes undergoing pseudogenization. For instance, the observed loss of genes involved in amino acid biosynthesis in both endosymbiont genomes indicates that the endosymbionts rely on their hosts for obtaining several essential nutrients. Furthermore, the endosymbionts appear to have gained significant amounts of genes of potentially secreted proteins, providing targets for future studies aiming to elucidate possible mechanisms underpinning host-interactions. Altogether, our results provide the first genomic insights into prokaryotic endosymbioses from the archaeal domain of life.

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Draft Genome Sequencing of Methanobrevibacter oralis Strain JMR01, Isolated from the Human Intestinal Microbiota

Cited by 16 publications

References 7 publications

RETRACTED ARTICLE: Peri-implantitis-associated methanogens: a preliminary report

RETRACTED ARTICLE: Peri-implantitis-associated methanogens: a preliminary report

Vaginal Microbiome Characterization of Nellore Cattle Using Metagenomic Analysis

Genomes of two archaeal endosymbionts show convergent adaptations to an intracellular lifestyle

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