Comparative genomics reconciliations of genus Streptococcus resolves its taxonomy and elucidates biotechnological importance of their constituent species
{"title":"Comparative genomics reconciliations of genus Streptococcus resolves its taxonomy and elucidates biotechnological importance of their constituent species","authors":"Sanjeet Kumar , Kanika Bansal , Santosh Kumar Sethi","doi":"10.1016/j.egg.2023.100205","DOIUrl":null,"url":null,"abstract":"<div><p>The current taxonomy of <em>Streptococcus</em> is primarily based on low-resolution methods such as biochemical analysis, single housekeeping gene-based phylogeny, or conserved sequence identity of species groups resulting in various amendments in the taxonomic positioning of their constituent species.. We reported genome similarities assessment and phylogeny using several methods to provide a robust taxonomic framework with inclusion of 115 type strains and 23 unclassified species. Phylogeny based on the 16S rRNA gene suggests no integrity of the earlier classified species groups, which cannot be used for taxonomic classification. The whole genome phylogeny does not support the existence of the earlier defined species groups. Genome similarity assessment suggests the presence of sixteen novel genomospecies, including some of the amendments in the earlier classified species and subspecies. A highly stringent antibiotic resistance gene search resulted in widespread fluoroquinolones resistance. It is noteworthy that among the 42 genomes analyzed, which include strains of probiotic significance such as <em>S. thermophilus</em> NCTC 12958T and S<em>. salivarius</em> NCTC 8618T, no properly curated antibiotic resistance genes were discovered. However, the presence of partial hits for resistance genes in such strains requires further experimental validation before their downstream application.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2023-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Ecological Genetics and Genomics","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2405985423000460","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"Agricultural and Biological Sciences","Score":null,"Total":0}
引用次数: 0
Abstract
The current taxonomy of Streptococcus is primarily based on low-resolution methods such as biochemical analysis, single housekeeping gene-based phylogeny, or conserved sequence identity of species groups resulting in various amendments in the taxonomic positioning of their constituent species.. We reported genome similarities assessment and phylogeny using several methods to provide a robust taxonomic framework with inclusion of 115 type strains and 23 unclassified species. Phylogeny based on the 16S rRNA gene suggests no integrity of the earlier classified species groups, which cannot be used for taxonomic classification. The whole genome phylogeny does not support the existence of the earlier defined species groups. Genome similarity assessment suggests the presence of sixteen novel genomospecies, including some of the amendments in the earlier classified species and subspecies. A highly stringent antibiotic resistance gene search resulted in widespread fluoroquinolones resistance. It is noteworthy that among the 42 genomes analyzed, which include strains of probiotic significance such as S. thermophilus NCTC 12958T and S. salivarius NCTC 8618T, no properly curated antibiotic resistance genes were discovered. However, the presence of partial hits for resistance genes in such strains requires further experimental validation before their downstream application.
期刊介绍:
Ecological Genetics and Genomics publishes ecological studies of broad interest that provide significant insight into ecological interactions or/ and species diversification. New data in these areas are published as research papers, or methods and resource reports that provide novel information on technologies or tools that will be of interest to a broad readership. Complete data sets are shared where appropriate. The journal also provides Reviews, and Perspectives articles, which present commentary on the latest advances published both here and elsewhere, placing such progress in its broader biological context. Topics include: -metagenomics -population genetics/genomics -evolutionary ecology -conservation and molecular adaptation -speciation genetics -environmental and marine genomics -ecological simulation -genomic divergence of organisms