I am better than I look: genome based safety assessment of the probiotic Lactiplantibacillus plantarum IS-10506
Abstract Background Safety of probiotic strains that are used in human and animal trials is a prerequisite. Genome based safety assessment of probiotics has gained popularity due its cost efficiency and speed, and even became a part of national regulation on foods containing probiotics in Indonesia....
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| Format: | Article |
| Language: | English |
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BMC
2023-09-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-023-09495-y |
| _version_ | 1797453808008167424 |
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| author | Alexander Umanets Ingrid S. Surono Koen Venema |
| author_facet | Alexander Umanets Ingrid S. Surono Koen Venema |
| author_sort | Alexander Umanets |
| collection | DOAJ |
| description | Abstract Background Safety of probiotic strains that are used in human and animal trials is a prerequisite. Genome based safety assessment of probiotics has gained popularity due its cost efficiency and speed, and even became a part of national regulation on foods containing probiotics in Indonesia. However, reliability of the safety assessment based only on a full genome sequence is not clear. Here, for the first time, we sequenced, assembled, and analysed the genome of the probiotic strain Lactiplantibacillus plantarum IS-10506, that was isolated from dadih, a traditional fermented buffalo milk. The strain has already been used as a probiotic for more than a decade, and in several clinical trials proven to be completely safe. Methods The genome of the probiotic strain L. plantarum IS-10506 was sequenced using Nanopore sequencing technology, assembled, annotated and screened for potential harmful (PH) and beneficial genomic features. The presence of the PH features was assessed from general annotation, as well as with the use of specialised tools. In addition, PH regions in the genome were compared to all other probiotic and non-probiotic L. plantarum strains available in the NCBI RefSeq database. Results For the first time, a high-quality complete genome of L. plantarum IS-10506 was obtained, and an extensive search for PH and a beneficial signature was performed. We discovered a number of PH features within the genome of L. plantarum IS-10506 based on the general annotation, including various antibiotic resistant genes (AMR); however, with a few exceptions, bioinformatics tools specifically developed for AMR detection did not confirm their presence. We further demonstrated the presence of the detected PH genes across multiple L. plantarum strains, including probiotics, and overall high genetic similarities between strains. Conclusion The genome of L. plantarum IS-10506 is predicted to have several PH features. However, the strain has been utilized as a probiotic for over a decade in several clinical trials without any adverse effects, even in immunocompromised children with HIV infection and undernourished children. This implies the presence of PH feature signatures within the probiotic genome does not necessarily indicate their manifestation during administration. Importantly, specialized tools for the search of PH features were found more robust and should be preferred over manual searches in a general annotation. |
| first_indexed | 2024-03-09T15:28:12Z |
| format | Article |
| id | doaj.art-5a13e8e2008d4c0186a5644be960edd8 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-09T15:28:12Z |
| publishDate | 2023-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-5a13e8e2008d4c0186a5644be960edd82023-11-26T12:25:03ZengBMCBMC Genomics1471-21642023-09-0124111410.1186/s12864-023-09495-yI am better than I look: genome based safety assessment of the probiotic Lactiplantibacillus plantarum IS-10506Alexander Umanets0Ingrid S. Surono1Koen Venema2Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University – campus VenloFood Technology Department, Faculty of Engineering, Bina Nusantara UniversityCentre for Healthy Eating & Food Innovation (HEFI), Maastricht University – campus VenloAbstract Background Safety of probiotic strains that are used in human and animal trials is a prerequisite. Genome based safety assessment of probiotics has gained popularity due its cost efficiency and speed, and even became a part of national regulation on foods containing probiotics in Indonesia. However, reliability of the safety assessment based only on a full genome sequence is not clear. Here, for the first time, we sequenced, assembled, and analysed the genome of the probiotic strain Lactiplantibacillus plantarum IS-10506, that was isolated from dadih, a traditional fermented buffalo milk. The strain has already been used as a probiotic for more than a decade, and in several clinical trials proven to be completely safe. Methods The genome of the probiotic strain L. plantarum IS-10506 was sequenced using Nanopore sequencing technology, assembled, annotated and screened for potential harmful (PH) and beneficial genomic features. The presence of the PH features was assessed from general annotation, as well as with the use of specialised tools. In addition, PH regions in the genome were compared to all other probiotic and non-probiotic L. plantarum strains available in the NCBI RefSeq database. Results For the first time, a high-quality complete genome of L. plantarum IS-10506 was obtained, and an extensive search for PH and a beneficial signature was performed. We discovered a number of PH features within the genome of L. plantarum IS-10506 based on the general annotation, including various antibiotic resistant genes (AMR); however, with a few exceptions, bioinformatics tools specifically developed for AMR detection did not confirm their presence. We further demonstrated the presence of the detected PH genes across multiple L. plantarum strains, including probiotics, and overall high genetic similarities between strains. Conclusion The genome of L. plantarum IS-10506 is predicted to have several PH features. However, the strain has been utilized as a probiotic for over a decade in several clinical trials without any adverse effects, even in immunocompromised children with HIV infection and undernourished children. This implies the presence of PH feature signatures within the probiotic genome does not necessarily indicate their manifestation during administration. Importantly, specialized tools for the search of PH features were found more robust and should be preferred over manual searches in a general annotation.https://doi.org/10.1186/s12864-023-09495-yLactiplantibacillus plantarumGenomeSafety assessmentComparative genomics |
| spellingShingle | Alexander Umanets Ingrid S. Surono Koen Venema I am better than I look: genome based safety assessment of the probiotic Lactiplantibacillus plantarum IS-10506 BMC Genomics Lactiplantibacillus plantarum Genome Safety assessment Comparative genomics |
| title | I am better than I look: genome based safety assessment of the probiotic Lactiplantibacillus plantarum IS-10506 |
| title_full | I am better than I look: genome based safety assessment of the probiotic Lactiplantibacillus plantarum IS-10506 |
| title_fullStr | I am better than I look: genome based safety assessment of the probiotic Lactiplantibacillus plantarum IS-10506 |
| title_full_unstemmed | I am better than I look: genome based safety assessment of the probiotic Lactiplantibacillus plantarum IS-10506 |
| title_short | I am better than I look: genome based safety assessment of the probiotic Lactiplantibacillus plantarum IS-10506 |
| title_sort | i am better than i look genome based safety assessment of the probiotic lactiplantibacillus plantarum is 10506 |
| topic | Lactiplantibacillus plantarum Genome Safety assessment Comparative genomics |
| url | https://doi.org/10.1186/s12864-023-09495-y |
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