2022
DOI: 10.3390/microorganisms10030605
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The Use and Limitations of the 16S rRNA Sequence for Species Classification of Anaplasma Samples

Abstract: With the advent of cheaper, high-throughput sequencing technologies, the ability to survey biodiversity in previously unexplored niches and geographies has expanded massively. Within Anaplasma, a genus containing several intra-hematopoietic pathogens of medical and economic importance, at least 25 new species have been proposed since the last formal taxonomic organization. Given the obligate intracellular nature of these bacteria, none of these proposed species have been able to attain formal standing in the n… Show more

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Cited by 40 publications
(41 citation statements)
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“…and Anaplasma -like bacteria [ 4 , 20 , 22 , 27 29 , 32 , 37 , 40 ]. However, the use of 16S rRNA gene sequences as an exclusive taxonomic marker was recently shown to be inadequate for inferring a reliable phylogeny within the Anaplasmataceae since the tree topology is often poorly resolved and usually unstable because of insufficient sequence polymorphism [ 7 ]. We therefore developed, in the present study, a generic multi-locus sequence typing approach, examining the DNA sequence variation of Ca.…”
Section: Introductionmentioning
confidence: 99%
“…and Anaplasma -like bacteria [ 4 , 20 , 22 , 27 29 , 32 , 37 , 40 ]. However, the use of 16S rRNA gene sequences as an exclusive taxonomic marker was recently shown to be inadequate for inferring a reliable phylogeny within the Anaplasmataceae since the tree topology is often poorly resolved and usually unstable because of insufficient sequence polymorphism [ 7 ]. We therefore developed, in the present study, a generic multi-locus sequence typing approach, examining the DNA sequence variation of Ca.…”
Section: Introductionmentioning
confidence: 99%
“…[ 1 ], rrs and groEL are conserved and do not have sufficient resolution to segregate some groups when short fragments are analyzed, even in different species of the genus. Therefore, the sequenced fragments must be long enough [ 1 , 6 ]. Based on the above argument, our phylogenetic analyses did not include sequences shorter than 600 bp.…”
Section: Discussionmentioning
confidence: 99%
“…The genetic diversity of Anaplasma spp. has been explored using the conserved 16S rRNA ( rrs ) gene [ 1 ]; however, due to its weak intraspecific discriminatory resolution [ 6 ], variable loci such as citrate synthase ( gltA ) and the heat-shock operon ( groEL ) have been selected as suitable markers for single-locus genetic analyses [ 1 , 7 , 8 ]. Based on these markers four ecotypes split into seven phylogenetic clusters have been proposed to compose the A .…”
Section: Introductionmentioning
confidence: 99%
“…sequences downloaded from GenBank using the command line application. Sequences were further filtered and excluded based on sequence length (minimum of 1275 bp), quality, and sequence identity in Microsoft Excel [ 39 , 40 ]. Since some distinct Anaplasma species are known to have more than 98.7% shared sequence identity, and A. platys , Anaplasma sp.…”
Section: Methodsmentioning
confidence: 99%
“…Mymensingh, “ Candidatus Anaplasma camelii” and Anaplasma sp. Omatjenne share more than 99.5% 16S rRNA gene sequence identity, it is not possible to resolve these organisms to species level [ 40 ]. Thus, only 16S rRNA sequences that were identical to previously published sequences were classified to species level; the remainder were reported as putative novel Anaplasma species and/or genotypes.…”
Section: Methodsmentioning
confidence: 99%