BackgroundThe increasing spectrum of multidrug-resistant bacteria is a major global public health concern, necessitating discovery of novel antimicrobial agents. Here, members of the genus Bacillus are investigated as a potentially attractive source of novel antibiotics due to their broad spectrum of antimicrobial activities. We specifically focus on a computational analysis of the distinctive biosynthetic potential of Bacillus paralicheniformis strains isolated from the Red Sea, an ecosystem exposed to adverse, highly saline and hot conditions.ResultsWe report the complete circular and annotated genomes of two Red Sea strains, B. paralicheniformis Bac48 isolated from mangrove mud and B. paralicheniformis Bac84 isolated from microbial mat collected from Rabigh Harbor Lagoon in Saudi Arabia. Comparing the genomes of B. paralicheniformis Bac48 and B. paralicheniformis Bac84 with nine publicly available complete genomes of B. licheniformis and three genomes of B. paralicheniformis, revealed that all of the B. paralicheniformis strains in this study are more enriched in nonribosomal peptides (NRPs). We further report the first computationally identified trans-acyltransferase (trans-AT) nonribosomal peptide synthetase/polyketide synthase (PKS/ NRPS) cluster in strains of this species.ConclusionsB. paralicheniformis species have more genes associated with biosynthesis of antimicrobial bioactive compounds than other previously characterized species of B. licheniformis, which suggests that these species are better potential sources for novel antibiotics. Moreover, the genome of the Red Sea strain B. paralicheniformis Bac48 is more enriched in modular PKS genes compared to B. licheniformis strains and other B. paralicheniformis strains. This may be linked to adaptations that strains surviving in the Red Sea underwent to survive in the relatively hot and saline ecosystems.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4796-5) contains supplementary material, which is available to authorized users.

Recent studies show that annotated long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) encode for stable, functional peptides that contribute to human development and disease. To systematically discover lncRNAs and circRNAs encoding peptides, we performed a comprehensive integrative analysis of mass spectrometry-based proteomic and transcriptomic sequencing data from >900 patients across nine cancer types. This enabled us to identify 19,871 novel peptides derived from 8,903 lncRNAs. Further, we exploited open reading frames overlapping the backspliced region of circRNAs to identify 3,238 peptides that are uniquely derived from 2,834 circRNAs and not their corresponding linear RNAs. Collectively, our pan-cancer proteogenomic analysis will serve as a resource for evaluating the coding potential of lncRNAs and circRNAs that could aid future mechanistic studies exploring their function in cancer.

c Mycobacterium fortuitum is a member of the rapidly growing nontuberculous mycobacteria (NTM). It is ubiquitous in water and soil habitats, including hospital environments. M. fortuitum is increasingly recognized as an opportunistic nosocomial pathogen causing disseminated infection. Here we report the genome sequence of M. fortuitum subsp. fortuitum type strain DSM46621. Mycobacterium fortuitum is a nonpigmented rapidly growing Mycobacterium classified in Runyon group IV (5), first isolated from an amphibian source in 1905 and subsequently identified as the cause of a human cutaneous infection in a patient in 1938 (3). Like many other nontuberculous mycobacteria (NTM), M. fortuitum is found worldwide in natural and processed water sources, including chlorine-treated water, as well as in sewage, dirt, and hospital environments (4,8). Major types of disease caused by M. fortuitum include, in decreasing order of frequency, infections of postsurgical wounds, soft tissue, skin, and lung (3, 5, 11). Occasionally reported miscellaneous infections include keratitis, endocarditis, lymphadenitis, meningitis, hepatitis, peritonitis, catheter-related sepsis, and disseminated infections (3, 6, 11). The M. fortuitum group is attracting attention due to its increasing number of cases, its virulence, and its emerging resistance to antibiotics. However, in the genome database, there is no whole genome of this species present until now. To facilitate a more reliable genetic identification in the M. fortuitum complex, we have characterized the complete genome sequence of M. fortuitum subsp. fortuitum type strain DSM46621.To sequence the genome of M. fortuitum subsp. fortuitum type strain DSM46621, we used a shotgun sequencing method and Illumina HiSeq 2000 technology using a paired-end library, with a read length of 100 bp and an insert size of 500 bp. A total of 2.95 million Illumina sequencing reads were generated. These short sequence reads were first quality trimmed before de novo assembled using Velvet (12). The draft genome was further improved with iCORN (7) and IMAGE (10), as described in PAGIT (9), before it was scaffolded with SSPACE (2). The final assembly has 82 supercontigs and an N 50 of 159,889 bp. The genome annotation was performed using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP).The M. fortuitum subsp. fortuitum type strain DSM46621 genome sequence is 6,349,738 bp in length, with 6,241 predicted coding sequences. The overall GC content of the chromosome was 66%. There are 54 tRNA genes and four sets of rRNA operons as predicted by the PGAAP pipeline. It was possible to assign a biological function to 67.7% (4,225) of the coding sequences on the M. fortuitum subsp. fortuitum chromosome.The RAST server annotation pipeline (1) revealed that M. fortuitum subsp. fortuitum has the highest similarity with Mycobacterium smegmatis strain MC2 155, among all mycobacteria with complete genome sequences determined. The M. fortuitum subsp. fortuitum genome was found to be smaller (6.38 Mb) than the ge...

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.