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Open AccessCommunication

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

1
Nofima—Norwegian Institute of Food, Fisheries and Aquaculture Research, P.O. Box 210, N-1431 Ås, Norway
2
Center for Laboratory Medicine, Østfold Hospital Trust, P.O. Box 300, N-1714 Grålum, Norway
*
Author to whom correspondence should be addressed.
Microorganisms 2019, 7(8), 262; https://doi.org/10.3390/microorganisms7080262
Received: 21 June 2019 / Revised: 8 August 2019 / Accepted: 14 August 2019 / Published: 14 August 2019
(This article belongs to the Special Issue Safety Aspects of Lactic Acid Bacteria)
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. View Full-Text
Keywords: Lactobacillus plantarum; lactic acid bacterium; probiotic; PacBio sequencing; Illumina sequencing; Oxford Nanopore MinION sequencing; plasmid assembly Lactobacillus plantarum; lactic acid bacterium; probiotic; PacBio sequencing; Illumina sequencing; Oxford Nanopore MinION sequencing; plasmid assembly
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McLeod, A.; Fagerlund, A.; Rud, I.; Axelsson, L. Large Plasmid Complement Resolved: Complete Genome Sequencing of Lactobacillus plantarum MF1298, a Candidate Probiotic Strain Associated with Unfavorable Effect. Microorganisms 2019, 7, 262.

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