Genome-based reclassification of Paenibacillus panacisoli DSM 21345T as Paenibacillus massiliensis subsp. panacisoli subsp. nov. and description of Paenibacillus massiliensis subsp. massiliensis subsp. nov.

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 1 mol%, overall genome relatedness index values higher than the species circumscription thresholds (average nucleotide identity, 95.57 %; genome-wide ANI, =96.51 %; and orthologous ANI, 96.25 %), 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).

Genomic metrics analyses indicate that Paenibacillus azotofixans is not a later synonym of Paenibacillus durus.

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 92 %, 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.

Genomic metrics made easy: what to do and where to go in the new era of bacterial taxonomy.

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.

Genome-based reclassification of Paenibacillus dauci as a later heterotypic synonym of Paenibacillus shenyangensis.

Paenibacillus shenyangensis and Paenibacillus dauci are Gram-stain-positive, rod-shaped and endospore-forming bacteria originally isolated from soil and carrot samples, respectively, in China. Preliminary comparative genomic analysis showed that these bacteria could constitute a single species. Therefore, in this study, their taxonomic statuses were clarified through distinct genomic metrics and phylogenetic analyses. Paenibacillus shenyangensis A9T and P. dauci H9T presented values of average nucleotide identity (ANI) and its derivative metrics (gANI and OrthoANI) ranging from 97.88 to 98.08 %, and digital DNA-DNA hybridization equal to 89.08 %. Furthermore, the identities of 16S rRNA, gyrB, rpoB, recA and recN genes were all equal or higher than 98.7 %. Phylogenies of these marker genes and the concatenated core proteome were congruent in the sense that P. shenyangensis A9T and P. dauci H9T are the closest type-strains of the genus Paenibacillus. A review of their profiles revealed that these strains do not present pronounced differences at the phenotypic and chemotaxonomic levels. Considering phylogenetic, genomic, phenotypic and chemotaxonomic data, P. dauci should be reclassified as a later heterotypic synonym of P. shenyangensis.

Guanosine Protects Against Cortical Focal Ischemia. Involvement of Inflammatory Response.

Stroke is the major cause of death and the most frequent cause of disability in the adult population worldwide. Guanosine plays an important neuroprotective role in several cerebral ischemic models and is involved in the modulation of oxidative responses and glutamatergic parameters. Because the excessive reactive oxygen species produced during an ischemic event can trigger an inflammatory response, the purpose of this study was to evaluate the hypothesis that guanosine is neuroprotective against focal cerebral ischemia, inhibits microglia/macrophages activation, and mediates an inflammatory response ameliorating the neural damage. Permanent focal cerebral ischemia was induced in adult rats, and guanosine was administered immediately, 1, 3, and 6 h after surgery. Twenty-four hours after ischemia, the asymmetry scores were evaluated by the cylinder test; neuronal damage was evaluated by Fluoro-Jade C (FJC) staining and propidium iodide (PI) incorporation; microglia and immune cells were evaluated by anti-Iba-1 antibody; and inflammatory parameters such as interleukins (IL): IL-1, IL-6, IL-10; tumor necrosis factors alpha (TNF-α); and interferon-gamma (INF-γ) were evaluated in the brain tissue and cerebrospinal fluid. The ischemic event increased the levels of Iba-1-positive cells and pro-inflammatory cytokines and decreased IL-10 levels (an anti-inflammatory cytokine) in the lesion periphery. The guanosine treatment attenuated the changes in these inflammatory parameters and also reduced the infarct volume, PI incorporation, and number of FJC-positive cells, improving the functional recovery. Thus, guanosine may have been a promising therapeutic agent for the treatment of ischemic brain injury by reduction of inflammatory process triggered in an ischemic event.