Distribution of Important Probiotic Genes and Identification of the Biogenic Amines Produced by Lactobacillus acidophilus PNW3

Abstract

The genome of Lactobacillus acidophilus PNW3 was assessed for probiotic and safety potentials. The genome was completely sequenced, assembled using SPAdes, and thereafter annotated with NCBI prokaryotic genome annotation pipeline (PGAP) and rapid annotation using subsystem technology (RAST). Further downstream assessment was determined using appropriate bioinformatics tools. The production of biogenic amines was confirmed through HPLC analysis and the evolutionary trend of the strain was determined through the Codon Tree pipeline. The strain was predicted as a non-human pathogen. A plethora of encoding genes for lactic acids and bioactive peptides production, adhesion molecules, resistance to the harsh gut environmental conditions, and improvement of the host metabolism, which are putative for important probiotic functionalities, were located at different loci within the genome. A bacteriocin predicted to be helveticin J was identified as one of the secondary metabolites. The maximum zone of inhibition exhibited by the crude bacteriocin against STEC E. coli O177 was 21.7 ± 0.58 mm and 24.3 ± 1.15 mm after partial purification (250 µg/mL). Three coding sequences were identified for insertion sequences and one for the CRISPR-Cas fragment. The protein-encoding sequence for Ornithine decarboxylase was found within the genome. L. acidophilus PNW3 presents important features categorizing it as a viable and safe probiotic candidate, though further safety investigations are necessary. The application of probiotics in livestock-keeping would ensure improved public health and food security.

Keywords: CRISPR-Cas; bioactive peptide; insertion sequence; ornithine decarboxylase; phylogeny.

Figure 1

Circular genome mapping with position of each contig within the L. acidophilus PNW3 genome. The mapping was generated using CGView [42].

Figure 2

Gene cluster showing the position of biosynthetic bacteriocin. The core biosynthetic (bacteriocin) genes (), other genes (), and the locations of the gene clusters were mapped by antiSMASH v5.0.0beta1.

Figure 3

Genome mapping of the L. acidophilus PNW3 showing the distribution of the roughly predicted IS family within the genome using the ISsaga v2.0.

Figure 4

Annotation diagram mapping out the location of Ornithine decarboxylase (EC 4.1.1.17) () found within the L acidophilus PNW3 genome.

Figure 5

Shared protein-based phylogeny between Lactobacillus acidophilus PNW3 and other strains.