Microbial genomic taxonomy

Thompson, Cristiane C.; Chimetto, Luciane A.; Edwards, Robert A.; Swings, Jean; Stackebrandt, Erko; Thompson, Fabiano L.

doi:10.1186/1471-2164-14-913

Cited by 300 publications

(222 citation statements)

References 70 publications

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“…Based on their high 16S rRNA similarity (Ͼ95%) (35) to N. stetteri, and their overall genome homology, we propose that these cells are N. stetteri and that they share the same A. nanophilum host as previously described (7). All three YNP Nanobsidianus genomes are closely related to each other and quite distinct from N. equitans.…”

Section: Discussionmentioning

confidence: 90%

Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs

Munson-McGee

Field

Bateson

et al. 2015

Appl Environ Microbiol

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e Nanoarchaeota are obligate symbionts with reduced genomes first described from marine thermal vent environments. Here, both community metagenomics and single-cell analysis revealed the presence of Nanoarchaeota in high-temperature (ϳ90°C), acidic (pH Ϸ 2.5 to 3.0) hot springs in Yellowstone National Park (YNP) (United States). Single-cell genome analysis of two cells resulted in two nearly identical genomes, with an estimated full length of 650 kbp. Genome comparison showed that these two cells are more closely related to the recently proposed Nanobsidianus stetteri from a more neutral YNP hot spring than to the marine Nanoarchaeum equitans. Single-cell and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) analysis of environmental hot spring samples identified the host of the YNP Nanoarchaeota as a Sulfolobales species known to inhabit the hot springs. Furthermore, we demonstrate that Nanoarchaeota are widespread in acidic to near neutral hot springs in YNP. An integrated viral sequence was also found within one Nanoarchaeota single-cell genome and further analysis of the purified viral fraction from environmental samples indicates that this is likely a virus replicating within the YNP Nanoarchaeota.

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Section: Discussionmentioning

confidence: 90%

Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs

Munson-McGee

Field

Bateson

et al. 2015

Appl Environ Microbiol

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“…A new species description needs to be based, first of all, on at least one complete genome (Thompson et al 2013a). In this way, the genomic landscape of the novel bacterium becomes available to microbiologists.…”

Section: Paradigm Shiftmentioning

confidence: 99%

“…Taxonomy must adjust to the genomics era, addressing the needs of its users in microbial ecology and clinical microbiology (Preheim et al 2011), in a new paradigm of openaccess genomic taxonomy (Thompson et al 2013a). We witness already the tremendous efforts put into initiatives on prokaryote genomics, such as the Genomic Encyclopedia of Bacteria and Archaeae-GEBA (Wu et al 2009;Klenk and Göker 2010), Genomes OnLine Database-GOLD (Kyrpides 1999; Pagani et al 2012), and the Integrated Microbial Genomes-IMG (Markowitz et al 2006(Markowitz et al , 2014.…”

Section: Paradigm Shiftmentioning

confidence: 99%

Microbial taxonomy in the post-genomic era: Rebuilding from scratch?

et al. 2014

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“…Full genomic information can provide extraordinary opportunities for prokaryotic taxonomy (12,13). Genomic data have already been applied to bacterial species definition and classification on the basis of genomic parameters, such as average amino acid sequence identity (AAI) and average nucleotide sequence identity (ANI) (14,15).…”

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confidence: 99%

A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights

et al. 2014

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Genomic information has already been applied to prokaryotic species definition and classification. However, the contribution of the genome sequence to prokaryotic genus delimitation has been less studied. To gain insights into genus definition for the prokaryotes, we attempted to reveal the genus-level genomic differences in the current prokaryotic classification system and to delineate the boundary of a genus on the basis of genomic information. The average nucleotide sequence identity between two genomes can be used for prokaryotic species delineation, but it is not suitable for genus demarcation. We used the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance. A comprehensive genomic survey indicated that the POCP can serve as a robust genomic index for establishing the genus boundary for prokaryotic groups. Basically, two species belonging to the same genus would share at least half of their proteins. In a specific lineage, the genus and family/order ranks showed slight or no overlap in terms of POCP values. A prokaryotic genus can be defined as a group of species with all pairwise POCP values higher than 50%. Integration of whole-genome data into the current taxonomy system can provide comprehensive information for prokaryotic genus definition and delimitation.

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Microbial genomic taxonomy

Cited by 300 publications

References 70 publications

Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs

Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs

Microbial taxonomy in the post-genomic era: Rebuilding from scratch?

A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights

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