Virgibacillus phasianinus sp. nov., a halophilic bacterium isolated from faeces of a Swinhoe's pheasant, Lophura swinhoii

Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Nondomestic Animals Described in 2018 to 2021

Revisions and new additions to bacterial taxonomy can have a significant widespread impact on clinical practice, infectious disease epidemiology, veterinary microbiology laboratory operations, and wildlife conservation efforts. The expansion of genome sequencing technologies has revolutionized our knowledge of the microbiota of humans, animals, and insects. Here, we address novel taxonomy and nomenclature revisions of veterinary significance that impact bacteria isolated from nondomestic wildlife, with emphasis being placed on bacteria that are associated with disease in their hosts or were isolated from host animal species that are culturally significant, are a target of conservation efforts, or serve as reservoirs for human pathogens.

Virgibacillus ihumii sp. nov., a new bacterium isolated from the stool of healthy African children

During a case–control study on severe acute malnutrition, strain Marseille-Q1233 was isolated. It is a Gram-positive, rod-shaped and halophilic bacillus isolated from a stool sample of Malian child under the age of 5. The fatty acid profile of the strain consisted of C15:0-anteiso and C14:0-iso as major components. Digital DNA-DNA hybridization and average nucleotide identity calculation showed 23.10% and 80.81% similarity respectively between strain Marseille-Q1233 and Virgibacillus siamensis strain Marseille-P2607, the phylogenetically closely related species with standing in nomenclature. On the basis of these results, we report the description of Virgibacillus ihumii sp. nov. strain Marseille-Q1233 as a new bacterial species.

Radiobacillus deserti gen. nov., sp. nov., a UV-resistant bacterium isolated from desert soil

A Gram-stain-positive, aerobic, rod-shaped, non-motile, endospore-forming and UV-resistant bacterial strain, designated strain TKL69^T, was isolated from sandy soil sampled in the Taklimakan Desert. The strain grew at 20-50 °C, pH 6-9 and with 0-12 % (w/v) NaCl. The major fatty acids were anteiso-C_15 : 0, iso-C_15 : 0 and C_16 : 0. The only respiratory quinone was MK-7. The cell-wall peptidoglycan was meso-diaminopimelic acid. Diphosphatidyl glycerol, two unidentified aminophospholipids and one unidentified phospholipid were identified as the major polar lipids. Genomic DNA analysis revealed a G+C content of 38.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain TKL69^T has the highest similarity to Salinibacillus xinjiangensis CGMCC 1.12331^T (96.9 %) but belongs to an independent taxon separated from other genera of the family Bacillaceae. Phylogenetic, phenotypic and chemotaxonomic analyses suggested that strain TKL69^T represents a novel species of a new genus, for which the name Radiobacillus gen. nov., sp. nov. is proposed, with the type strain being Radiobacillus deserti TKL69^T (=JCM 33497^T=CICC 24779^T).

Mining biosynthetic gene clusters in Virgibacillus genomes

Background

Biosynthetic gene clusters produce a wide range of metabolites with activities that are of interest to the pharmaceutical industry. Specific interest is shown towards those metabolites that exhibit antimicrobial activities against multidrug-resistant bacteria that have become a global health threat. Genera of the phylum Firmicutes are frequently identified as sources of such metabolites, but the biosynthetic potential of its Virgibacillus genus is not known. Here, we used comparative genomic analysis to determine whether Virgibacillus strains isolated from the Red Sea mangrove mud in Rabigh Harbor Lagoon, Saudi Arabia, may be an attractive source of such novel antimicrobial agents.

Results

A comparative genomics analysis based on Virgibacillus dokdonensis Bac330, Virgibacillus sp. Bac332 and Virgibacillus halodenitrificans Bac324 (isolated from the Red Sea) and six other previously reported Virgibacillus strains was performed. Orthology analysis was used to determine the core genomes as well as the accessory genome of the nine Virgibacillus strains. The analysis shows that the Red Sea strain Virgibacillus sp. Bac332 has the highest number of unique genes and genomic islands compared to other genomes included in this study. Focusing on biosynthetic gene clusters, we show how marine isolates, including those from the Red Sea, are more enriched with nonribosomal peptides compared to the other Virgibacillus species. We also found that most nonribosomal peptide synthases identified in the Virgibacillus strains are part of genomic regions that are potentially horizontally transferred.

Conclusions

The Red Sea Virgibacillus strains have a large number of biosynthetic genes in clusters that are not assigned to known products, indicating significant potential for the discovery of novel bioactive compounds. Also, having more modular synthetase units suggests that these strains are good candidates for experimental characterization of previously identified bioactive compounds as well. Future efforts will be directed towards establishing the properties of the potentially novel compounds encoded by the Red Sea specific trans-AT PKS/NRPS cluster and the type III PKS/NRPS cluster.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-6065-7) contains supplementary material, which is available to authorized users.