Description of Alloprevotella rava gen. nov., sp. nov., isolated from the human oral cavity, and reclassification of 
               
                  Prevotella tannerae
               
             Moore et al. 1994 as Alloprevotella tannerae gen. nov., comb. nov.

The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.

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“…The description is as given by Downes et al (2013) with the following modification. The genomic G+C content of the type strain is 46.6%.…”

Section: Discussionmentioning

confidence: 99%

Genome-Based Taxonomic Classification of Bacteroidetes

et al. 2016

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“…One predicament is the large and growing number of databases containing genome sequences from which to choose from, as well as the quality of the contents of these repositories and maintenance of up-to-date naming and taxonomic information. An example was that the Alloprevotella tannerae genomes in this study initially annotated as Prevotella tannerae due to the naming used by the RefSeq database, despite the recognition of Alloprevotella as a distinct genus for several years (76). This is a particularly difficult issue to address, as changes to established phylogeny are frequent and occasionally controversial; in fact a recent study proposed a large overhaul of the bacterial tree of life, with 58% of taxa being reclassified (77).…”

Section: Discussionmentioning

confidence: 99%

Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules

Baker

Morton

Dinis³

et al. 2019

Preprint

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45Dental caries is the most common chronic infectious disease globally. The microbial communities 46 associated with caries have mainly been examined using relatively low-resolution 16S rRNA gene 47 amplicon sequencing and/or using downstream analyses that are unsound for the compositional 48 nature of the data provided by sequencing. Additionally, the relationship between caries, oral 49 microbiome composition, and host immunological markers has not been explored. In this study, 50 the oral microbiome and a panel of 38 host markers was analyzed across the saliva from 23 51 children with dentin caries and 24 children with healthy dentition. Metagenomic sequencing, 52 followed by investigation using tools designed to be robust for compositional data, illustrated 53 that several Prevotella spp. were prevalent in caries, while Rothia spp. were associated with the 54 health. The contributional diversity (extent to which multiple taxa contribute to each pathway) 55 of functional pathways present in the oral microbiome was decreased in the caries group. This 56 decrease was especially noticeable in several pathways known to impede caries pathogenesis, 57 including arginine and branched-chain amino acid biosynthesis. 10 host immunological markers 58 were found to be significantly elevated in the saliva of the caries group, and microbe-metabolite 59 co-occurrence analysis provided an atlas of relationships contributing to the bi-directional 60 influence between the oral microbiome and the host immune system. Finally, 527 metagenome-61 assembled genomes were obtained from the metagenomics data, representing 151 species. 23 62 taxa were novel genera/species and a further 20 taxa were novel species. This study thus serves 63 as a model analysis pipeline that will tremendously expand our knowledge of the oral microbiome 64 and its relationship to dental caries once applied to large populations. 65 67Dental caries is the most common chronic infectious disease and will afflict well over half of the 68 global human population at some point in their lives. Dental caries is particularly problematic in 69 children, where it is five times more common than asthma, the second most common chronic 70 disease. This extreme prevalence translates to an extraordinary economic burden. Caries 71 disproportionally afflicts vulnerable populations least able to access and afford proper treatment 72(1). Historically, members of the acid-producing and acid-tolerant mutans group of streptococci, 73 particularly the paradigm species of the group, Streptococcus mutans, were considered the 74 etiologic agents of the disease (2). While caries is certainly an infectious and transmissible 75 disease caused by the oral microbiota, it is now understood to be multifactorial and ecology-76 based, because although mutans streptococci are commonly associated with caries, they are 77 neither necessary nor sufficient to cause disease (3). Interplay between host genetic and 78 immunological factors, diet and hygiene habits, and the oral microbiota affect clinica...

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“…Prevotella produces acetate and succinate from glucose fermentation (Willems & Collins, ), and cultivable species of Alloprevotella are saccharolytic, producing acetate and major amounts of succinate. Moreover, their growth in liquid media is stimulated by fermentable carbohydrates (Downes, Dewhirst, Tanner, & Wade, ).…”

Section: Discussionmentioning

confidence: 99%