Complete Genome Sequence of “
            <i>Candidatus</i>
            Nanosynbacter” Strain HMT-348_TM7c-JB, a Member of
            <i>Saccharibacteria</i>
            Clade G1

Baker, Jonathon L.

doi:10.1128/mra.00023-22

Cited by 2 publications

(6 citation statements)

References 18 publications

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“…As recently described (Baker, 2022), HMT-348-TM7c-JB was 841,302 bp. This genome represents the first complete genome from Saccharibacteria clade G1 HMT-348, which is one of the most common members of Saccharibacteria present in supra-and subgingival plaque, and on the buccal mucosa (McLean et al, 2020; Shaiber et al, 2020).…”

Section: Results and Discusssionsupporting

confidence: 70%

“…The next genome examined in this dataset was Candidatus Nanosynbacter HMT-348 strain HMT-348-TM7c-JB (contig_847 in the SC33 metaFlye assembly [Table S3]), which was circular and 841,704 bp in length (Baker, 2022). This Flye draft genome appeared to be the cognate long-read draft genome to the original short-read based draft genome, which was Candidatus_Nanosynbacter_sp._isolate_JCVI_32_bin.19, a 793,808 bp assembly fragmented into 7 contigs (Baker et al, 2021).…”

Section: Results and Discusssionmentioning

confidence: 99%

“…Sequencing of 3 saliva samples resulted in 12 complete, circular chromosomes. Among these were 3 genomes, representing two distinct species, of clade G6 Saccharibacteria (HMT-870) (Baker, 2021a, 2021b), 1 genome of clade G1 Saccharibacteria HMT-348 (Baker, 2022), 2 genomes of Actinomyces graevenitzii , 2 genomes of Rothia mucilaginosa , 1 genome of Lachnospiraceae HMT-096, 1 genome of Mogibacterium diversum , 1 genome of Lancefieldella parvula , and also a complete circular chromosome from Ruminococcaceae HMT-075 (this taxon likely has multiple chromosomes). The properties of these genomes are then highlighted.…”

Section: Introductionmentioning

confidence: 99%

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Using nanopore sequencing to obtain complete genomes from saliva samples

Baker

2022

Preprint

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Obtaining complete, high-quality reference genomes is essential to the study of any organism. Recent advances in nanopore sequencing, as well as genome assembly and analysis methods, have made it possible to obtain complete bacterial genomes from metagenomic (i.e. multispecies) samples, including those from the human microbiome. In this study, methods are presented to obtain complete bacterial genomes from human saliva using complementary Oxford Nanopore (ONT) and Illumina sequencing. Applied to 3 human saliva samples, these methods resulted in 11 complete bacterial genomes: 3 Saccharibacteria clade G6 (aka Ca. Nanogingivalaceae HMT-870), 1 Saccharibacteria clade G1 HMT-348, 2 Rothia mucilaginosa, 2 Actinomyces graevenitzii, 1 Mogibacterium diversum, 1 Lachnospiraceae HMT-096, 1 Lancefieldella parvula, and one circular chromosome of Ruminococcaceae HMT-075 (which likely has at least 2 chromosomes). The 4 Saccharibacteria genomes, as well as the Actinomyces graeventizii genomes, represented the first complete genomes from their respective bacterial taxa. Aside from the complete genomes, the assemblies contained 147 contigs of over 500,000 bp each and thousands of smaller contigs, together representing many additional draft genomes including many which are likely near-complete. The complete genomes enabled highly accurate pangenome analysis, which identified unique and missing features of each genome compared to its closest relatives with complete genomes available in public repositories. These features provide clues as to the lifestyle and ecological role of these bacteria within the human oral microbiota, which will be particularly useful in designing future studies of the specific taxa that have never been isolated or cultivated.

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Section: Results and Discusssionsupporting

confidence: 70%

Section: Results and Discusssionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Using nanopore sequencing to obtain complete genomes from saliva samples

Baker

2022

Preprint

Self Cite

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show abstract

“…The next genome examined in this data set was Candidatus Nanosynbacter HMT-348 strain HMT-348-TM7c-JB (contig_847 in the SC33 metaFlye assembly [Table S3]), which was circular and 841,704 bp in length ( 24 ). This Flye draft genome appeared to be the cognate long-read draft genome to the original short-read based draft genome, which was Candidatus_Nanosynbacter_sp._isolate_JCVI_32_bin.19, a 793,808 bp assembly fragmented into 7 contigs ( 27 ).…”

Section: Results and Discusssionmentioning

confidence: 99%

“…Sequencing of 3 saliva samples resulted in 12 complete, circular chromosomes. Among these were 3 genomes representing two distinct species of clade G6 Saccharibacteria (HMT-870) ( 22 , 23 ), 1 genome of clade G1 Saccharibacteria HMT-348 ( 24 ), 2 genomes of Actinomyces graevenitzii , 2 genomes of Rothia mucilaginosa , 1 genome of Lachnospiraceae HMT-096, 1 genome of Mogibacterium diversum , 1 genome of Lancefieldella parvula , and also a complete circular chromosome from Ruminococcaceae HMT-075 (this taxon likely has multiple chromosomes). The properties of these genomes are then highlighted.…”

Section: Introductionmentioning

confidence: 99%

Using Nanopore Sequencing to Obtain Complete Bacterial Genomes from Saliva Samples

Baker

2022

mSystems

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Complete Genome Sequence of “ Candidatus Nanosynbacter” Strain HMT-348_TM7c-JB, a Member of Saccharibacteria Clade G1

Cited by 2 publications

References 18 publications

Using nanopore sequencing to obtain complete genomes from saliva samples

Using nanopore sequencing to obtain complete genomes from saliva samples

Using Nanopore Sequencing to Obtain Complete Bacterial Genomes from Saliva Samples

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