Pan‐genome analysis of Exiguobacterium reveals species delineation and genomic similarity with Exiguobacterium profundum PHM 11

Abstract

The stint of the bacterial species is convoluting, but the new algorithms to calculate genome-to-genome distance (GGD) and DNA-DNA hybridization (DDH) for comparative genome analysis have rejuvenated the exploration of species and sub-species characterization. The present study reports the first whole genome sequence of Exiguobacterium profundum PHM11. PHM11 genome consist of~2.92 Mb comprising 48 contigs, 47.93% G + C content. Functional annotations revealed a total of 3033 protein coding genes and 33 non-protein coding genes. Out of these, only 2316 could be characterized and others reported as hypothetical proteins. The comparative analysis of predicted proteome of PHM11 with five other Exiguobacterium sp. identified 3806 clusters, out of which the PHM11 shared a total of 2723 clusters having 1664 common clusters, 131 singletons and 928 distributed between five species. The pan-genome analysis of 70 different genomic sequences of Exigubacterium strains devoid of a species taxon was done on the basis of GGD and the DDH which identified eight genomes analogous to the PHM11 at species level and may be characterized as E. profundum. The ANI value and phylogenetic tree analysis also support the same. The results regarding pan-genome analysis provide a convincing insight for delineation of these eight strains to species.

Analysis of Biosynthetic Gene Clusters, Secretory, and Antimicrobial Peptides Reveals Environmental Suitability of Exiguobacterium profundum PHM11

“…JLM2, HVEsp1, AT1b, ZOR0005, and NG55; E. marinum DSM 16307; and E. chiriqhucha RW-2 (Figure 2C). The results indicated that all the genes present in this cluster are ∼100% similar in the Exiguobacterium species which has been characterized for the isolates closely related with E. profundum PHM11 in our previous studies (Srivastava et al, 2020).…”

“…These studies have also described the impact of salinity on the expression of these genes. Further, we reported the presence of several pathways and its comparison with the already sequenced genome of Exiguobacterium (Srivastava et al, 2020). In the present study, different BGCs, secretory peptides (SPs), TMHs, and AMPs were mined from the genome of PHM11 with the aim to decipher its environmental suitability for PGP applications under salt stress.…”

Genomic Reclassification and Phenotypic Characterization of <i>Pseudomonas putida</i> Strains Deposited in Japanese Culture Collections

“…Whole-genome similarity with P. putida type strain NBRC 14164 T (=JCM 13063 T ) was calculated using ANI and dDDH values. ANI ≥95% and dDDH ≥70% are classified as the same species ( Goris et al , 2007 ; Srivastava et al , 2020 ). Based on the results of calculations of the ANI and dDDH values of P. putida strains against the genome sequence of the P. putida type strain, three strains, JCM 20005, JCM 21368, and JCM 13061, were identified with the same species as that of the P. putida type strain ( Table 2 ).…”