Introduction: Bacillus coagulans strain GBI-30 (ATCC Designation Number PTA-6086) is a safe strain, authorized for human consumption and it is already available in a wide choice of functional foods or as dietary supplement (Cutting, 2011). This strain is characterized by certified beneficial effects in gastrointestinal disorders, such as Irritable Bowel Syndrome, intestinal gas, rheumatoid arthritis, and in common viral infections of the respiratory tract (Jurenka, 2012). Due to its wide use, the goal of the present study is the whole genome sequencing of B. coagulans GBI-30 in order to unveil the genetic basis of its safety and probiosis. Methods Whole genome sequencing was performed using the Illumina GAIIx platform; the obtained sequences were de novo assembled using the CLC Genomic Workbench v. 7.0. with an average coverage of 840×. Finally, RAST annotation server was employed to perform annotation (Aziz et al., 2008). Results A total of 14,500,000 paired end reads of 110 bp length were assembled into 224 contigs (N50 length of 44,706 bp) with the largest assembled contig of 125,999 kb length. The draft genome consists of 3,458,655 bp with GC % content of 46.38. About 3,890 coding sequences (CDS) and a total of 90 RNAs were predicted. According to the annotation, the probiotic strain is predicted to possess 491 proteins involved in carbohydrate utilization, including glycolysis, the citrate cycle, and the pentose phosphate pathway. As expected, a total of 82 genes regarding dormancy and sporulation were annotated: seven of them are involved in spore DNA protection, while the others are associated directly to the sporulation mechanism, spore core dehydration, and spore germination. Regarding the safety of this strain, 44 CDS were included in the RAST subsystem related to virulence, disease and defense. Detailed analysis of these genes revealed that one of them is involved in adhesion (which is also a probiotic feature), while the majority are associated to copper homeostasis and cobalt-zinc-cadmium resistance. Discussion As more probiotic strains are used in the food and drug industry, more attention should be paid to confirm the safety of these strains using complete genome analysis as a tool (Zhang et al., 2012). In this perspective, the complete genome of B. coagulans GBI-30 obtained in the present study has contributed to a wider and deeper insight into the positive features of this strain. Furthermore, the comparative genomic analysis with other Bacillus strains genomes might shed new light on the molecular mechanisms at the basis of its probiotic and beneficial properties. Acknowledgements This research was funded by the Italian Ministry for Development in the framework of the project “Pass-World - pasta e salute nel mondo - Industria 2015”.
Draft genome sequence of Bacillus coagulans GBI-30, a widely used sporeforming probiotic strain
SALVETTI, Elisa;FELIS, Giovanna;Martina, Alessia;TORRIANI, Sandra
2014-01-01
Abstract
Introduction: Bacillus coagulans strain GBI-30 (ATCC Designation Number PTA-6086) is a safe strain, authorized for human consumption and it is already available in a wide choice of functional foods or as dietary supplement (Cutting, 2011). This strain is characterized by certified beneficial effects in gastrointestinal disorders, such as Irritable Bowel Syndrome, intestinal gas, rheumatoid arthritis, and in common viral infections of the respiratory tract (Jurenka, 2012). Due to its wide use, the goal of the present study is the whole genome sequencing of B. coagulans GBI-30 in order to unveil the genetic basis of its safety and probiosis. Methods Whole genome sequencing was performed using the Illumina GAIIx platform; the obtained sequences were de novo assembled using the CLC Genomic Workbench v. 7.0. with an average coverage of 840×. Finally, RAST annotation server was employed to perform annotation (Aziz et al., 2008). Results A total of 14,500,000 paired end reads of 110 bp length were assembled into 224 contigs (N50 length of 44,706 bp) with the largest assembled contig of 125,999 kb length. The draft genome consists of 3,458,655 bp with GC % content of 46.38. About 3,890 coding sequences (CDS) and a total of 90 RNAs were predicted. According to the annotation, the probiotic strain is predicted to possess 491 proteins involved in carbohydrate utilization, including glycolysis, the citrate cycle, and the pentose phosphate pathway. As expected, a total of 82 genes regarding dormancy and sporulation were annotated: seven of them are involved in spore DNA protection, while the others are associated directly to the sporulation mechanism, spore core dehydration, and spore germination. Regarding the safety of this strain, 44 CDS were included in the RAST subsystem related to virulence, disease and defense. Detailed analysis of these genes revealed that one of them is involved in adhesion (which is also a probiotic feature), while the majority are associated to copper homeostasis and cobalt-zinc-cadmium resistance. Discussion As more probiotic strains are used in the food and drug industry, more attention should be paid to confirm the safety of these strains using complete genome analysis as a tool (Zhang et al., 2012). In this perspective, the complete genome of B. coagulans GBI-30 obtained in the present study has contributed to a wider and deeper insight into the positive features of this strain. Furthermore, the comparative genomic analysis with other Bacillus strains genomes might shed new light on the molecular mechanisms at the basis of its probiotic and beneficial properties. Acknowledgements This research was funded by the Italian Ministry for Development in the framework of the project “Pass-World - pasta e salute nel mondo - Industria 2015”.
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