Genome Mining and Characterization of Biosynthetic Gene Clusters in Two Cave Strains of Paenibacillus sp.

The genome sequencing and mining of microorganisms from unexplored and extreme environments has become important in the process of identifying novel biosynthetic pathways. In the present study, the biosynthetic potential of Paenibacillus sp. strains 23TSA30-6 and 28ISP30-2 was investigated. Both strains were isolated from the deep oligotrophic Krubera-Voronja Cave and were found to be highly active against both Gram-positive and Gram-negative bacteria. Genome mining revealed a high number of biosynthetic gene clusters in the cave strains: 21 for strain 23TSA30-6 and 19 for strain 28ISP30-2. Single clusters encoding the biosynthesis of phosphonate, terpene, and siderophore, as well as a single trans-AT polyketide synthase/non-ribosomal peptide synthetase, were identified in both genomes. The most numerous clusters were assigned to the biosynthetic pathways of non-ribosomal peptides and ribosomally synthesized and post-translationally modified peptides. Although four non-ribosomal peptide synthetase gene clusters were predicted to be involved in the biosynthesis of known compounds (fusaricidin, polymyxin B, colistin A, and tridecaptin) of the genus Paenibacillus, discrepancies in the structural organization of the clusters, as well as in the substrate specificity of some adenylation domains, were detected between the reference pathways and the clusters in our study. Among the clusters involved in the biosynthesis of ribosomally synthesized peptides, only one was predicted to be involved in the biosynthesis of a known compound: paenicidin B. Most biosynthetic gene clusters in the genomes of the cave strains showed a low similarity with the reference pathways and were predicted to represent novel biosynthetic pathways. In addition, the cave strains differed in their potential to encode the biosynthesis of a few unique, previously unknown compounds (class II lanthipeptides and three non-ribosomal peptides). The phenotypic characterization of proteinaceous and volatile compounds produced by strains 23TSA30-6 and 28ISP30-2 was also performed, and the results were compared with those of genome mining.

Draft Genome Sequences of Two Geobacillus Species Strains, Isolated from Oil Wells and Surface Soil above Oil Pools.

Here, we present the draft genome sequences of two Geobacillus species strains isolated from oil wells and surface soil above oil pools in Lithuania.

Combining prebiotics with probiotic bacteria can enhance bacterial growth and secretion of bacteriocins.

There is a growing interest in supporting human health by using prebiotics, such as oligosaccharides, and beneficial bacteria, also called probiotics. Combining these two components we can develop synbiotics. In order to create successful combination of synbiotic it is very important to evaluate the influence of prebiotic oligosaccharides to probiotic bacteria and their behavior, such as growth and secretion of health related biomolecules, including bacteriocins. In this study seven type strains of probiotic bacteria (five Lactobacillus sp. and two Lactococcus sp.) and two Lactobacillus sp. strains, isolated from probiotic yoghurt, were cultivated with various commercially available and extracted oligosaccharides (OS). The aim of this study was to evaluate the influence of these OS on type and isolated bacterial strains growth and antibacterial activity. Obtained results suggest that combination of certain OS with probiotic strains may considerably improve their growth and/or antibacterial activity. We also determined the antibacterial activity spectrum of investigated strains with combination of OS against common food borne pathogens. Results of this work show that prebiotic OS can be useful for modulating probiotic bacteria growth, antibacterial activity and even specificity of this activity.

Development of synbiotics with inulin, palatinose, alpha-cyclodextrin and probiotic bacteria.

Success in creating a synbiotic depends on compatibility between the chosen components--prebiotic and probiotic. In this work the interactions between Lactobacillus sp. strains isolated from yogurts and type strains of Lactobacillus sp. and Lactococcus sp., and the dependence of their growth and antibacterial activity on three oligosaccharides (OS)--palatinose, inulin and alpha-cyclodextrin were investigated. All isolated lactobacilli produce antibacterial compounds, which possibly are the bacteriocins of Lactobacillus casei ATCC334 strain. Results of growth analysis with different OS revealed that part of lactobacilli isolated from yogurts can effectively ferment inulin and may be used for the development of synbiotics. Palatinose and Lactobacillus acidophilus could be used as symbiotics with effective antibacterial activity. One of the types of Lactococcus sp. strains can assimilate palatinose and alpha-cyclodextrin, so they both can be used as components of synbiotics with the investigated lactococci. Results of this analysis suggest that the investigated isolated and type strains of Lactobacillus sp. and Lactoccocus sp. can be useful as probiotics in the development of synbiotics. Together with prebiotics--palatinose, inulin and alpha-cyclodextrin, the synbiotics, which could regulate not only the growth of beneficial bacteria in the gastrointestinal tract, but also their antibacterial activity, can be created.