Phylogenetic characterization and proposal of a new pigmented species to the genus Prevotella: Prevotella pallens sp. 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 Könönen et al (1998) with the following addition. The genomic G+C content of the type strain is 37.4%.…”

Section: Discussionmentioning

confidence: 99%

Genome-Based Taxonomic Classification of Bacteroidetes

et al. 2016

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“…In addition, at the species level, we found the relative abundance of Prevotella_pallens _ATCC_700821 was significantly decreased after 6‐month Invisalign orthodontic treatment (Group P) compared with that in Group B. Prevotella pallens , included in Prevotella intermedia group, is both biochemically and phylogenetically related to Prevotella intermedia and Prevotella nigrescens (Könönen, Eerola, & Frandsen, ). Könönen found that Prevotella pallens was common in oral findings from early childhood (Könönen et al, ).…”

Section: Discussionmentioning

confidence: 94%

The dynamics of the oral microbiome and oral health among patients receiving clear aligner orthodontic treatment

et al. 2020

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Objectives This 6‐month prospective clinical study assessed the impacts of Invisalign appliances on the oral bacterial community and oral health of patients. Methods Salivary samples were obtained from twenty‐five adult patients receiving Invisalign aligner treatment before the treatment (Group B) and at a 6‐month follow‐up (Group P). The bacterial composition of each sample was determined using Illumina MiSeq sequencing of the bacterial 16S rRNA. Intra‐ and intergroup biodiversity was analyzed. Clinical periodontal parameters and daily oral hygiene habits were recorded. Results Reduction in plaque, increased daily brushing frequency, and decreased dessert intake were observed in Group P compared with that in Group B. A total of 1,853,952 valid reads were obtained from the 50 salivary samples, with 37,904 sequences per sample. No significant differences were detected in the intra‐ and intergroup biodiversity comparisons between the two groups. By clustering, 8,885 OTUs were identified and categorized into six major phyla: Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria, Actinobacteria, and Candidate_division_TM7_norank. At the genus level, compared with Group B, Group P demonstrated significantly increased Bacillus abundance and decreased Prevotella abundance. Conclusions Our results suggested that the general biodiversity and salivary microbial community structure did not change significantly and that patients had increased beneficial oral hygiene habits and awareness during the first six months of Invisalign treatment. Hence, on the basis of this study, it appears that Invisalign aligner treatment did not induce deterioration of oral health nor significant biodiversity changes in oral bacterial communities, assuming that detailed oral hygiene instructions for both teeth and aligners were provided.

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“…JF122, Pseudomonas gessardii strain LZ‐E and Pseudomonas taiwanensis would be a potential applicant for chromium (Cr) remediation (Huang et al ., ; Majumder et al ., ; Zhou and Chen, ). Prevotella is a genus of Gram‐negative bacteria, which is closely related to various infections as introduced above (Könönen et al ., ). No studies have shown that Prevotella contributes to heavy metal speciation changes during composting.…”

Section: Discussionmentioning

confidence: 99%

Chrysomya megacephala larvae feeding favourably influences manure microbiome, heavy metal stability and greenhouse gas emissions

Wang

Gao

et al. 2018

Microbial Biotechnology

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Summary Chrysomya megacephala is a saprophagous fly whose larvae can compost manure and yield biomass and bio‐fertilizer simultaneously. However, there are concerns for the safety of the composting system, that is risk of diseases spread by way of manure pathogens, residue of harmful metals and emission of greenhouse gases. Microbiota analysis and heavy metal speciation by European Communities Bureau of Reference were evaluated in raw, C. megacephala‐composted and natural stacked swine manure to survey pathogenic bacterial changes and mobility of lead and cadmium in manure after C. megacephala feeding; the emission rate of CH4 and N2O from manure during C. megacephala composting and natural stacking was also measured. C. megacephala composting altered manure microbiota, reduced the risk of pathogenic bacteria and maintained the stability, and microbiota changes might be associated with heavy metal fractions, especially in Pseudomonas and Prevotella. In addition, C. megacephala‐composting significantly reduced the emission rate of CH4 and N2O in comparing with natural stacking situation and the first two days should be the crucial period for CH4 and N2O emission measurement for manure treatment by C. megacephala. Moreover, OTU26 and Betaproteobacteria were changed after C. megacephala composting which might play a role in emission of CH4 and N2O, respectively.

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Phylogenetic characterization and proposal of a new pigmented species to the genus Prevotella: Prevotella pallens sp. nov.

Cited by 41 publications

References 12 publications

Genome-Based Taxonomic Classification of Bacteroidetes

Genome-Based Taxonomic Classification of Bacteroidetes

The dynamics of the oral microbiome and oral health among patients receiving clear aligner orthodontic treatment

Chrysomya megacephala larvae feeding favourably influences manure microbiome, heavy metal stability and greenhouse gas emissions

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