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

• Published in: Microorganisms (Basel) Vol. 7; no. 8; p. 262
• Main Authors: McLeod, Anette, Fagerlund, Annette, Rud, Ida, Axelsson, Lars
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 14.08.2019; MDPI
• Subjects: Bacteria; Chromosomes; Communication; Gene sequencing; Genes; Genetic testing; Genomes; Genomics; Illumina sequencing; Irritable bowel syndrome; lactic acid bacterium; Lactobacilli; Lactobacillus plantarum; Nucleotide sequence; Oxford Nanopore MinION sequencing; PacBio sequencing; plasmid assembly; Plasmids; probiotic; Probiotics; Tuna; Vitamin B12; United Kingdom > UK; United States > US; Germany; probiotic; Lactobacillus plantarum; lactic acid bacterium; PacBio sequencing; plasmid assembly; Oxford Nanopore MinION sequencing; Illumina sequencing
• ISSN: 2076-2607; 2076-2607
• DOI: 10.3390/microorganisms7080262

Considerable attention has been given to the species Lactobacillus plantarum regarding its probiotic potential. strains have shown health benefits in several studies, and even nonstrain-specific claims are allowed in certain markets. 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 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.