<i>Rothia</i>

Austin, Brian

doi:10.1002/9781118960608.gbm00124

Cited by 3 publications

(4 citation statements)

References 77 publications

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“…represents Isolate SG at the whole genome level, and R. dentocariosa ATCC17931 T , which represents the type species of Rothia (Austin, 2015), are members of different monophyletic groups separated by intergeneric AAI values < 65%. Thus, when the strains belonging to such groups are appropriately verified , priority in the genus name Rothia should be given to the cluster with a member of the type species R. dentocariosa.…”

Section: Discussionmentioning

confidence: 99%

“…Rothia is a genus of gram-positive, aerobic, coccoid or bacillary, nonmotile, non-sporeforming bacteria of the family Micrococcaceae, phylum Actinobacteria (Austin, 2015). To date, 15 Rothia species have been identified.…”

Section: Introductionmentioning

confidence: 99%

“…Rothia are part of the normal microflora of the gastrointestinal tract (especially the oral cavity and stomach) of humans and animals, but they can cause gastric atrophy and intestinal metaplasia and induce opportunistic infections of the upper respiratory tract in immunocompromised people (Nardone and Compare, 2015;Odeberg et al, 2023). Various Rothia have been recovered from soil, water sources, benthos, rocks, atmosphere, and other sources (Austin, 2015).…”

Section: Introductionmentioning

confidence: 99%

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Quantitative intra- and intergeneric taxonomic relationships among Micrococcaceae strains reveal contradictions in the historical assignments of the strains and indicate the need for species reclassification

Shchyogolev,

Dykman,

Sokolov

et al. 2024

Arch Microbiol

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We report phylogenetic studies of a bacterial isolate (Isolate SG) recovered from a suspension culture of Arabidopsis thaliana (L.) Heynh. In doing this, we use the known results acquired by whole genome sequencing of the DNA of Micrococcaceae strains closely related to Isolate SG in the 16S rRNA gene test and we evaluate the intra-and intergeneric taxonomic relationships between them using a set of five whole genome tests (ANI, AAI, MiGA, GTDB-Tk, and AAIprofiler). Quantitative analysis of the clustering of the proteomes of these strains by the average amino acid identity (AAI)-based test showed the need to clarify (with possible renaming) the generic assignment of the strains both within and between the identified monophyletic groups. The need for such reclassification was also shown by the AAI-profiler test (Medlar et al., 2018) against the UniProt database (250 million records) with the proteome of Rothia sp. ND6WE1A -a strain most evolutionarily similar to Isolate SG. The contradictions in the historically given names of strains and metagenomic objects at the genus and family levels, which were identified by using sets of the genomes and proteomes of the strains related to Isolate SG, can be eliminated with appropriate reclassification of the objects by using quantitative criteria in the AAI-based tests.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Quantitative intra- and intergeneric taxonomic relationships among Micrococcaceae strains reveal contradictions in the historical assignments of the strains and indicate the need for species reclassification

Shchyogolev,

Dykman,

Sokolov

et al. 2024

Arch Microbiol

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“…3-7, Rothia sp. ND6WE1A, which represents Isolate SG at the whole genome level, and R. dentocariosa ATCC17931 T , which represents the type species of Rothia (Austin, 2015), are members of different monophyletic groups separated by intergeneric AAI values < 65%. Thus, when the strains belonging to such groups are appropriately verified (Figs.…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic Analysis of a Bacterial Strain of the GenusRothiaDetected in Suspension Culture Cells ofArabidopsis thaliana(L.) Heynh as a Member of the FamilyMicrococcaceae

Shchyogolev

Дыкман

Sokolov

et al. 2023

Preprint

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We report phylogenetic studies of a bacterial isolate (Isolate SG) recovered from a suspension culture of Arabidopsis thaliana (L.) Heynh. In doing this, we use the known results acquired by whole genome sequencing of the DNA of Micrococcaceae strains closely related to Isolate SG in the 16S rRNA gene test and we evaluate the intra– and intergeneric taxonomic relationships between them using a set of five whole genome tests (ANI, AAI, MiGA, GTDB–Tk, and AAI–profiler). Quantitative analysis of the clustering of the proteomes of these strains by the average amino acid identity (AAI)–based test showed the need to clarify (with possible renaming) the generic assignment of the strains both within and between the identified monophyletic groups. The need for such reclassification was also shown by the AAI–profiler test (Medlar et al., 2018) against the UniProt database (250 million records) with the proteome of Rothia sp. ND6WE1A — a strain most evolutionarily similar to Isolate SG. The contradictions in the historically given names of strains and metagenomic objects at the genus and family levels, which were identified by using sets of the genomes and proteomes of the strains related to Isolate SG, can be eliminated with appropriate reclassification of the objects by using quantitative criteria in the AAI–based tests.

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Comparison of the gut microbiota in the groundwater amphipod Crangonyx islandicus Svavarsson & Kristjánsson, 2006 (Amphipoda: Crangonyctidae) to biofilms in its spring-source habitat

Guðmundsdóttir

Björnsdóttir

Marteinsson

et al. 2020

Journal of Crustacean Biology

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Crangonyx islandicus Svavarsson & Kristjánsson, 2006 is a groundwater amphipod endemic to Iceland and restricted to spring sources at edges of lava fields in the volcanically active zone. Genetic analysis indicate that the amphipod has survived in subglacial refugia in the groundwater in Iceland during past Ice Ages. We investigated the gut bacteria of C. islandicus and compared them with the bacterial diversity identified in biofilms from its groundwater habitat. The diversity of both uncultivated and cultivated bacteria was analyzed using partial 16S rRNA gene sequences. The results show that iron-oxidizing bacteria such as Sideroxydans and Gallionella and the methanotroph Methylobacter are common in the biofilm but absent from the gut samples. Thiomonas was common in both the biofilm and the gut samples. The cultivation of gut bacteria revealed that most of the taxa could be linked with terrestrial soil and/or freshwater habitat based on available database entries. This indicates that the food source for the amphipods is partly of terrestrial origin. The presence of primary producers in the subsurface habitat of C. islandicus indicate that microbial chemolithotrophic activity might fuel the system at least partly and thus explain the amphipod survival in the subsurface of Iceland during repeated glaciation for the past 5 mya.

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Rothia

Cited by 3 publications

References 77 publications

Quantitative intra- and intergeneric taxonomic relationships among Micrococcaceae strains reveal contradictions in the historical assignments of the strains and indicate the need for species reclassification

Quantitative intra- and intergeneric taxonomic relationships among Micrococcaceae strains reveal contradictions in the historical assignments of the strains and indicate the need for species reclassification

Phylogenetic Analysis of a Bacterial Strain of the GenusRothiaDetected in Suspension Culture Cells ofArabidopsis thaliana(L.) Heynh as a Member of the FamilyMicrococcaceae

Comparison of the gut microbiota in the groundwater amphipod Crangonyx islandicus Svavarsson & Kristjánsson, 2006 (Amphipoda: Crangonyctidae) to biofilms in its spring-source habitat

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