Nowadays, the importance of bibliographic databases (DBs) has increased enormously, as they are the main providers of publication metadata and bibliometric indicators universally used both for research assessment practices and for performing daily tasks. Because the reliability of these tasks firstly depends on the data source, all users of the DBs should be able to choose the most suitable one. Web of Science (WoS) and Scopus are the two main bibliographic DBs. The comprehensive evaluation of the DBs’ coverage is practically impossible without extensive bibliometric analyses or literature reviews, but most DBs users do not have bibliometric competence and/or are not willing to invest additional time for such evaluations. Apart from that, the convenience of the DB’s interface, performance, provided impact indicators and additional tools may also influence the users’ choice. The main goal of this work is to provide all of the potential users with an all-inclusive description of the two main bibliographic DBs by gathering the findings that are presented in the most recent literature and information provided by the owners of the DBs at one place. This overview should aid all stakeholders employing publication and citation data in selecting the most suitable DB.

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.

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.

Ability of bacteriocins to inhibit pathogenic bacteria may depend on the environment inhabited by the producing strain. However, there are just few reports on bacteriocin-producing thermophilic bacteria from unconventional environments. Therefore, in this work we investigated differences in antibacterial activity spectra of microorganisms isolated from two different environments: the oil wells (first collection) and surface soil above the oil pools (second collection). All strains were Gram-positive, rod-shaped, thermophilic and endospore forming bacteria. Using spot-on-lawn method we have demonstrated that strains from the second collection possess higher and broader antibacterial activity spectra than first collection strains. Furthermore, all strains were active against at least 1 of 19 tested pathogenic bacteria. Analysis of antibacterial compounds has shown that all of them were stable in broad temperature and pH ranges, sensitive to proteolytic enzymes, proving their proteonaceus nature. They were all secreted during the exponential growth phase and active against closely related thermophilic bacteria, which suggest that these substances are most likely bacteriocins. Most of the bacteriocins had molecular masses under 20 kDa. Plasmid isolation and elimination experiments suggest that bacteriocins are most likely chromosome-encoded. Our results confirm the differences between antibacterial spectra of bacteriocins produced by bacterial strains isolated from different environmental niches.

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