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. 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.

Evaluation of Safety and Probiotic Traits from a Comprehensive Genome-Based In Silico Analysis of Ligilactobacillus salivarius P1CEA3, Isolated from Pigs and Producer of Nisin S

“…They are either released into the food matrix or stay affixed to the cell surface, forming capsular polysaccharides. EPSs have been proposed to yield several beneficial health effects, including lowering cholesterol, regulating intestinal immunity, anti-tumor and anti-inflammatory properties, and inhibiting pathogens by disrupting biofilms and suppressing adhesion [ 77 ]. As in L. salivarius UCC118 [ 78 ], the L. salivarius P1CEA3 genome shows two putative operons encoding the production of EPS.…”

Illuminating the Genomic Landscape of Lactiplantibacillus plantarum PU3—A Novel Probiotic Strain Isolated from Human Breast Milk, Explored through Nanopore Sequencing

“…Furthermore, the development of software-based calling algorithms has contributed significantly to the refinement of ONT sequencing data. All these factors will slowly but surely contribute to the independent use of ONT technology without the need for additional Illumina data [47].…”

“…oorganisms 2023, 11, x FOR PEER REVIEW 6 of 24 contribute to the independent use of ONT technology without the need for additional Illumina data [47].…”

“…Furthermore, KEGG annotation by BlastKOALA assigned functional information to 1291 genes. Most notably, the protein families were associated with carbohydrate metabolism (162), signaling and cellular processes (154), environmental information processing (105), genetic information processing Microorganisms 2023, 11, 2440 9 of 23 (138), amino acid metabolism (74), nucleotide metabolism (57), metabolism of cofactors and vitamins (47), etc.…”

The Description and Analysis of the Complete Genome of Dermacoccus barathri FBCC-B549 Strain

“…Potential virulence prediction and toxin factor analysis were performed against the VFDB [ 27 ] using the DIAMOND v2.1.8 tool [ 28 ]. Toxicity factors were filtered under relaxed conditions with an identity above 70% and query coverage above 60% [ 29 ].…”