The 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. We 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. B. 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.

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. 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. 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.

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.

Circular RNAs (circRNA) are associated with crucial hallmarks of tumorigenesis. Select circRNAs contain circular open reading frames (cORF) and affect tumorigenesis through encoded small peptides. However, current circRNA detection approaches bias toward using short-read RNA sequencing (RNA-seq) for detecting circRNA backsplice junctions without reliably reconstructing complete circRNA sequences, inhibiting accurate cORF prediction. To address these challenges, we performed long-read sequencing to enrich for full-length circRNAs that could serve as a guide for short-read alignment. This approach “rescued” circRNAs eluding existing tools focused on circRNA detection from short reads and enabled the development of an open-source bioinformatics workflow that characterizes and rescues circRNAs by integrating short- and long-read RNA-seq: Characterizing CircRNAs by Integrative Sequencing (CHRIS). Application of the approach to colorectal cancer cell lines and patient samples revealed 6,445 noncanonical isoforms of known circRNAs, of which, 69 were altered during cancer metastasis. Validation experiments in colorectal cancer cell lines confirmed the endogenous expression of 11 high-confidence circRNAs rescued by CHRIS. Next, proteogenomic analysis using 67,326 circRNAs detected by CHRIS and mass spectrometry data from 261 patients with colorectal cancer from the Clinical Proteomic Tumor Analysis Consortium identified 6,848 peptides encoded by circRNAs, including 994 only detectable with long-read integration and 914 potential neoantigens. Overall, this research develops an approach that can facilitate circRNA detection and provide valuable resources for future circRNA tumor biology research. Significance: A multiomic approach integrating long-read and short-read RNA sequencing enhances circRNA detection to offer biological and clinical insights into metastatic colorectal cancer. This article is part of a special series: Driving Cancer Discoveries with Computational Research, Data Science, and Machine Learning/AI .

Supplementary Table S5 from Integration of Short- and Long-Read RNA Sequencing Enables the Discovery of Circular RNAs

Supplementary Table S4 from Integration of Short- and Long-Read RNA Sequencing Enables the Discovery of Circular RNAs