Complete Genome Sequence of the Dairy Isolate Lactobacillus acidipiscis ACA-DC 1533

Introduction: Lactic acid bacteria constitute a significant group of microorganisms for the food industry, as they play a key role in food fermentation and consequently in human health. Lactobacillus acidipiscis is a recently described species and L. acidipiscis ACA-DC 1533 is a strain isolated from traditional Greek Kopanisti cheese.

Purpose: The in silico analysis of the first complete genome sequence of L. acidipiscis ACA-DC 1533.

Methods: The genomic DNA was extracted as described previously. Sequencing of L. acidipiscis genome was performed using the HiSeq 2000 and PacBio RSII sequencing platform technologies. SOAPdenovo software was used to assemble the reads after filtering, while SOAPsnp and SOAPindel were applied for error correction. Furthermore, the genome assembly was validated against an NheI optical map of the L. acidipiscis genome. Protein-coding sequences were predicted by Glimmer, rRNA genes by RNAmmer, tRNA genes by the tRNAscan-SE server, tandem repeats by Tandem Repeat Finder and the reconstruction of metabolic pathways was performed using the KEGG pathway database.

Results: The sequencing analysis resulted in one continuous genomic scaffold of 2,678,726 bp with a G+C content of 39.75% and two plasmids of 3,554 (37.65% G+C content) and 13,512 (34.99% G+C content) bp. The genome contains 2,525 protein-coding genes on the chromosome covering up to 82.09% of the genome sequence. We also found 63 tRNA, 18 rRNA and 14 tandem repeat sequences. Finally, the reconstruction of metabolic pathways provided interesting information about the basic biological functions of the genome.

Significance: The in silico analysis of the first complete genome sequence of L. acidipiscis.