Large Plasmid Complement Resolved: Complete Genome Sequencing of Lactobacillus plantarum MF1298, a Candidate Probiotic Strain Associated with Unfavorable Effect

Summary

Considerable attention has been given to the species Lactobacillus plantarum regarding its
probiotic potential. L. plantarum strains have shown health benefits in several studies, and even
nonstrain-specific claims are allowed in certain markets. L. plantarum strain MF1298 was considered
a candidate probiotic, demonstrating in vitro probiotic properties and the ability to survive passage
through the human intestinal tract. However, the strain showed an unfavorable effect on symptoms
in subjects with irritable bowel syndrome in a clinical trial. The properties and the genome of this
strain are thus of general interest. Obtaining the complete genome of strain MF1298 proved difficult
due to its large plasmid complement. Here, we exploit a combination of sequencing approaches to
obtain the complete chromosome and plasmid assemblies of MF1298. The Oxford Nanopore
Technologies MinION long-read sequencer was particularly useful in resolving the unusually large
number of plasmids in the strain, 14 in total. The complete genome sequence of 3,576,440 basepairs
contains 3272 protein-encoding genes, of which 315 are located on plasmids. Few unique regions
were found in comparison with other L. plantarum genomes. Notably, however, one of the plasmids
contains genes related to vitamin B12 (cobalamin) turnover and genes encoding bacterial reverse
transcriptases, features not previously reported for L. plantarum. The extensive plasmid information
will be important for future studies with this strain.

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DOI : doi.org/10.3390/microorganisms...
NVA : hdl.handle.net/11250/2640641