Description of an Unusual Neisseria meningitidis Isolate Containing and Expressing Neisseria gonorrhoeae-Specific 16S rRNA Gene Sequences

Walcher, Marion; Skvoretz, Rhonda; Montgomery-Fullerton, Megan; Jonas, Vivian; Brentano, Steve

doi:10.1128/jcm.00309-13

“…polysaccharea, N. cinerea, and the meningococci, and some meningococci contain a 16S rRNA gene sequence identical to that found in gonococci (6). Further, public 16S rRNA databases, such as the Human Oral Microbiome database (32) and the EzTaxon-e database (3), can provide misleading results.…”

Section: Discussionmentioning

confidence: 95%

Identifying Neisseria Species by Use of the 50S Ribosomal Protein L6 ( rplF ) Gene

Bennett

¹

,

Watkins

²

,

Jolley

³

et al. 2014

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The comparison of 16S rRNA gene sequences is widely used to differentiate bacteria; however, this gene can lack resolution among closely related but distinct members of the same genus. This is a problem in clinical situations in those genera, such as Neisseria, where some species are associated with disease while others are not. Here, we identified and validated an alternative genetic target common to all Neisseria species which can be readily sequenced to provide an assay that rapidly and accurately discriminates among members of the genus. Ribosomal multilocus sequence typing (rMLST) using ribosomal protein genes has been shown to unambiguously identify these bacteria. The PubMLST Neisseria database (http://pubmlst.org/neisseria/) was queried to extract the 53 ribosomal protein gene sequences from 44 genomes from diverse species. Phylogenies reconstructed from these genes were examined, and a single 413-bp fragment of the 50S ribosomal protein L6 (rplF) gene was identified which produced a phylogeny that was congruent with the phylogeny reconstructed from concatenated ribosomal protein genes. Primers that enabled the amplification and direct sequencing of the rplF gene fragment were designed to validate the assay in vitro and in silico. Allele sequences were defined for the gene fragment, associated with particular species names, and stored on the PubMLST Neisseria database, providing a curated electronic resource. This approach provides an alternative to 16S rRNA gene sequencing, which can be readily replicated for other organisms for which more resolution is required, and it has potential applications in high-resolution metagenomic studies.

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“…Firstly, 16S rRNA gene sequences can differ at their various loci within a strain’s genome. This has been observed in the genus Elizabethkingia [32] as well as the genera Pseudomonas [56], Prevotella [57] and Neiserria [58]. Secondly, while a 16S rRNA gene sequence similarity below 98.5 % can ensure that two organisms will have less than 70 % DDH and therefore be separate species [59], the converse is not true.…”

Section: Full-textmentioning

confidence: 99%

Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens

Nicholson

¹

,

Gulvik

²

,

Whitney

³

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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The genus Chryseobacterium in the family Weeksellaceae is known to be polyphyletic. Amino acid identity (AAI) values were calculated from whole-genome sequences of species of the genus Chryseobacterium, and their distribution was found to be multi-modal. These naturally-occurring non-continuities were leveraged to standardise genus assignment of these species. We speculate that this multi-modal distribution is a consequence of loss of biodiversity during major extinction events, leading to the concept that a bacterial genus corresponds to a set of species that diversified since the Permian extinction. Transfer of nine species ( Chryseobacterium arachidiradicis , Chryseobacterium bovis , Chryseobacterium caeni , Chryseobacterium hispanicum , Chryseobacterium hominis , Chryseobacterium hungaricum , Chryseobacterium molle , Chryseobacterium pallidum and Chryseobacterium zeae ) to the genus Epilithonimonas and eleven ( Chryseobacterium anthropi , Chryseobacterium antarcticum , Chryseobacterium carnis , Chryseobacterium chaponense , Chryseobacterium haifense, Chryseobacterium jeonii, Chryseobacterium montanum , Chryseobacterium palustre , Chryseobacterium solincola , Chryseobacterium treverense and Chryseobacterium yonginense ) to the genus Kaistella is proposed. Two novel species are described: Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. Evidence is presented to support the assignment of Planobacterium taklimakanense to a genus apart from Chryseobacterium, to which Planobacterium salipaludis comb nov. also belongs. The novel genus Halpernia is proposed, to contain the type species Halpernia frigidisoli comb. nov., along with Halpernia humi comb. nov., and Halpernia marina comb. nov.

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“…However, due to the conserved nature of the 16S rRNA gene, the resolution is often too low to adequately resolve different species and sometimes is not even adequate for genus delineation (5,6). Furthermore, many prokaryotic genomes contain several copies of the 16S rRNA gene with substantial intergene variation (7,8). It is also considered problematic that this gene represents only a tiny fraction, roughly about 0.1% or less, of the coding part of a microbial genome (9).…”

mentioning

confidence: 99%

Benchmarking of Methods for Genomic Taxonomy

Larsen

¹

,

Cosentino

²

,

Lukjancenko

³

et al. 2014

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One of the first issues that emerges when a prokaryotic organism of interest is encountered is the question of what it is-that is, which species it is. The 16S rRNA gene formed the basis of the first method for sequence-based taxonomy and has had a tremendous impact on the field of microbiology. Nevertheless, the method has been found to have a number of shortcomings. In the current study, we trained and benchmarked five methods for whole-genome sequence-based prokaryotic species identification on a common data set of complete genomes: (i) SpeciesFinder, which is based on the complete 16S rRNA gene; (ii) Reads2Type that searches for species-specific 50-mers in either the 16S rRNA gene or the gyrB gene (for the Enterobacteraceae family); (iii) the ribosomal multilocus sequence typing (rMLST) method that samples up to 53 ribosomal genes; (iv) TaxonomyFinder, which is based on species-specific functional protein domain profiles; and finally (v) KmerFinder, which examines the number of cooccurring k-mers (substrings of k nucleotides in DNA sequence data). The performances of the methods were subsequently evaluated on three data sets of short sequence reads or draft genomes from public databases. In total, the evaluation sets constituted sequence data from more than 11,000 isolates covering 159 genera and 243 species. Our results indicate that methods that sample only chromosomal, core genes have difficulties in distinguishing closely related species which only recently diverged. The KmerFinder method had the overall highest accuracy and correctly identified from 93% to 97% of the isolates in the evaluations sets.

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Description of an Unusual Neisseria meningitidis Isolate Containing and Expressing Neisseria gonorrhoeae-Specific 16S rRNA Gene Sequences

Cited by 15 publications

References 76 publications

Identifying Neisseria Species by Use of the 50S Ribosomal Protein L6 ( rplF ) Gene

Identifying Neisseria Species by Use of the 50S Ribosomal Protein L6 ( rplF ) Gene

Benchmarking of Methods for Genomic Taxonomy

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