Draft Genome Sequence of Methanobrevibacter smithii Isolate WWM1085, Obtained from a Human Stool Sample

Jennings, Matthew E.; Chia, Nicholas; Boardman, Lisa A.; Metcalf, William W.

doi:10.1128/genomea.01055-17

Cited by 7 publications

(7 citation statements)

References 9 publications

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“…Based on the extent of discriminative features, and an ANI of only 93.95% between the two representative genomes of M. smithii and M. smithii _A, we propose to rename the smithii _A clade, represented by isolate WWM1085 ( GUT_GENOME143185 (ref. 33 )), ‘ Candidatus Methanobrevibacter intestini ’ sp. nov. (in.tes.ti’ni L. gen. neut.…”

Section: Resultsmentioning

confidence: 99%

A catalogue of 1,167 genomes from the human gut archaeome

Mahnert²,

et al. 2021

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The human gut microbiome plays an important role in health, but its archaeal diversity remains largely unexplored. In the present study, we report the analysis of 1,167 nonredundant archaeal genomes (608 high-quality genomes) recovered from human gastrointestinal tract, sampled across 24 countries and rural and urban populations. We identified previously undescribed taxa including 3 genera, 15 species and 52 strains. Based on distinct genomic features, we justify the split of the Methanobrevibacter smithii clade into two separate species, with one represented by the previously undescribed ‘CandidatusMethanobrevibacter intestini’. Patterns derived from 28,581 protein clusters showed significant associations with sociodemographic characteristics such as age groups and lifestyle. We additionally show that archaea are characterized by specific genomic and functional adaptations to the host and carry a complex virome. Our work expands our current understanding of the human archaeome and provides a large genome catalogue for future analyses to decipher its impact on human physiology.

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Section: Resultsmentioning

confidence: 99%

A catalogue of 1,167 genomes from the human gut archaeome

Mahnert²,

et al. 2021

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“…oralis strain MBORA DSM 7256 isolated from the human mouth 23 and M . smithii strain WWM1085 isolated from the human gut 24 .…”

Section: Methodsmentioning

confidence: 99%

Culture of Methanogenic Archaea from Human Colostrum and Milk

Togo¹,

Grine²,

Khelaifia³

et al. 2019

Sci Rep

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Archaeal sequences have been detected in human colostrum and milk, but no studies have determined whether living archaea are present in either of these fluids. Methanogenic archaea are neglected since they are not detected by usual molecular and culture methods. By using improved DNA detection protocols and microbial culture techniques associated with antioxidants previously developed in our center, we investigated the presence of methanogenic archaea using culture and specific Methanobrevibacter smithii and Methanobrevibacter oralis real-time PCR in human colostrum and milk. M. smithii was isolated from 3 colostrum and 5 milk (day 10) samples. M. oralis was isolated from 1 milk sample. For 2 strains, the genome was sequenced, and the rhizome was similar to that of strains previously isolated from the human mouth and gut. M. smithii was detected in the colostrum or milk of 5/13 (38%) and 37/127 (29%) mothers by culture and qPCR, respectively. The different distribution of maternal body mass index according to the detection of M. smithii suggested an association with maternal metabolic phenotype. M. oralis was not detected by molecular methods. Our results suggest that breastfeeding may contribute to the vertical transmission of these microorganisms and may be essential to seed the infant’s microbiota with these neglected critical commensals from the first hour of life.

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“…The variance for each principal coordinate (PC) is shown in parenthesis. The number of MAGs or genomes for each study is n = 729 Unified Human Gastrointestinal Genome (UHGG) collection ( 43 ), n = 14 Singapore Platinum Metagenomes Project (SPMP), n = 20 Hansen et al ( 5 ), n = 1 TLL-48-HuF1 (this study) and n = 1 (WWM1085) ( 12 ). (B) A protein tree of concatenated alignment of 43 translated CDS.…”

Section: Observationmentioning

confidence: 99%

“…These differences were also detected in Ca. Methanobrevibacter intestini strain WWM1085 and 12 isolates from a pan-genomic study of gut M. smithii of related individuals ( 5 , 12 ) (see Table S3B for nucleotide differences between Ca . Methanobrevibacter intestini strains).…”

Section: Observationmentioning

confidence: 99%