RESUMO
Microsporidia are obligatory intracellular parasites related to fungi and since their discovery their classification and origin has been controversial due to their unique morphology. Early taxonomic studies of microsporidia were based on ultrastructural spore features, characteristics of their life cycle and transmission modes. However, taxonomy and phylogeny based solely on these characteristics can be misleading. SSU rRNA is a traditional marker used in taxonomical classifications, but the power of SSU rRNA to resolve phylogenetic relationships between microsporidia is considered weak at the species level, as it may not show enough variation to distinguish closely related species. Overall genome relatedness indices (OGRI), such as average nucleotide identity (ANI), allows fast and easy-to-implement comparative measurements between genomes to assess species boundaries in prokaryotes, with a 95% cutoff value for grouping genomes of the same species. Due to the increasing availability of complete genomes, metrics of genome relatedness have been applied for eukaryotic microbes taxonomy such as microsporidia. However, the distribution of ANI values and cutoff values for species delimitation have not yet been fully tested in microsporidia. In this study we examined the distribution of ANI values for 65 publicly available microsporidian genomes and tested whether the 95% cutoff value is a good estimation for circumscribing species based on their genetic relatedness.
Assuntos
Microsporídios , Filogenia , Nucleotídeos , RNA Ribossômico/genética , Fungos/genéticaRESUMO
Bacteria of the genus Paenibacillus are relevant to humans, animals and plants. The species Paenibacillus massiliensis and Paenibacillus panacisoli are Gram-stain-positive and endospore-forming bacilli isolated from a blood culture of a leukemia patient and from soil of a ginseng field, respectively. Comparative analyses of their 16S rRNA genes revealed that the two Paenibacillus species could be synonyms (99.3% sequence identity). In the present study we performed different genomic analyses in order to evaluate the phylogenetic relationship of these micro-organisms. Paenibacillus massiliensis DSM 16942T and P. panacisoli DSM 21345T presented a difference in their G+C content lower than 1âmol%, overall genome relatedness index values higher than the species circumscription thresholds (average nucleotide identity, 95.57â%; genome-wide ANI, =96.51â%; and orthologous ANI, 96.25â%), and a monophyletic grouping pattern in the phylogenies of the 16S rRNA gene and the proteome core. Considering that these strains present differential biochemical capabilities and that their computed digital DNA-DNA hybridization value is lower than the cut-off for bacterial subspecies circumscription, we suggest that each of them form different subspecies of P. massiliensis, Paenibacillus massiliensis subsp. panacisoli subsp. nov. (type strain DSM 21345T) and Paenibacillus massiliensis subsp. massiliensis subsp. nov. (type strain DSM 16942T).
Assuntos
Paenibacillus/classificação , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Genes Bacterianos , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNARESUMO
Paenibacillus durusand Paenibacillus azotofixans, both Gram-stain-positive and endospore-forming bacilli, have been considered to be a single species. However, a preliminary computation of their average nucleotide identity (ANI) values suggested that these species are not synonyms. Given this, the taxonomic attributions of these species were evaluated through genomic and phylogenomic approaches. Although the identity of 16S rRNA gene sequences of P. durus DSM 1735T and P. azotofixans ATCC 35681T are above the circumscription species threshold, genomic metrics analyses indicate otherwise. ANI, gANI and OrthoANI values computed from their genome sequences were around 92â%, below the species limits. Digital DNA-DNA hybridization and MUMi estimations also corroborated these observations. In fact, in all metrics, Paenibacillus zanthoxyli JH29T seemed to be more similar to Paenibacillus azotofixans. ATCC 35681T than P. durus DSM 1735T. Phylogenetic analyses based on concatenated core-proteome and concatenated gyrB, recA, recN and rpoB genes confirmed that P. zanthoxyli is the closest Paenibacillus species to P. azotofixans. A review of the phenotypic profiles from these three species revealed that their biochemical repertoires are very similar, although P. azotofixans ATCC 35681T can be differentiated from P. durus DSM1735T in 13 among more than 90 phenotypic traits. Considering phylogenetic and genomic analyses, Paenibacillus azotofixans should be considered as an independent species, and not as a later synonym of Paenibacillus durus.
Assuntos
Paenibacillus/classificação , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Genes Bacterianos , Genômica , Tipagem de Sequências Multilocus , Hibridização de Ácido Nucleico , Fenótipo , RNA Ribossômico 16S/genética , Análise de Sequência de DNARESUMO
With the advent of high-throughput DNA sequencing technologies, traditional methodologies for taxonomic classification of bacteria as DNA-DNA hybridization and 16S rRNA identity analyses are being challenged by the development of a fast-growing number of genomic metrics. The large amount of portable and digitized genome sequences available in public repositories constitutes an invaluable data for bacterial classification. Consequently, several genomic metrics and tools were developed to aid the interpretation of these massive data. Genomic metrics are based on the assumption that higher genome similarities would reflect closer phylogenetic relationships. Different metrics would vary in their methodology of analysis, resolution power, limitations and easiness of use. The aim of this review is to highlight the differences among available genome-based methods and tools to provide a guide for in silico bacterial identification and classification.