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

Mcleod Mcleod,Fagerlund Fagerlund,Axelsson Axelsson,Rud Rud

doi:10.3390/microorganisms7080262

Mcleod Mcleod, Fagerlund Fagerlund + Show 2 more

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https://doi.org/10.3390/microorganisms7080262

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Journal: Microorganisms	Publication Date: Aug 14, 2019
Citations: 9	License type: CC BY 4.0

Affiliation: Nofima, Østfold Hospital Trust

Abstract

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.

Highlights

Lactobacillus plantarum is one of the most versatile species among lactic acid bacteria (LAB) [1]
The initial total genomic DNA sequencing with Pacific Biosciences (PacBio) and Illumina MiSeq strategies yielded three circular units, one large circular chromosome of 3,235,952 bp and two plasmids of 63,114 bp and 55,699 bp (Table 1)
GCA_001880185.1) contained 26 linear contigs originating from a separate Illumina assembly, in which contigs mapping to the three PacBio units were excluded, and a contig-size cutoff of 1000 bp was used

Summary

Introduction

Lactobacillus plantarum is one of the most versatile species among lactic acid bacteria (LAB) [1]. The largest successful clinical trial to date of an oral probiotic preparation was recently reported by Panigrahi et al [9]. Their findings suggest that a large proportion of neonatal sepsis in developing countries could be effectively prevented using a synbiotic containing L. plantarum ATCC 202195. Most commercially available probiotic strains are widely regarded as safe, concerns have been raised. These concerns were mainly with respect to safety in particular populations [10,11]

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