The domestication of the probiotic bacterium Lactobacillus acidophilus

Abstract

Lactobacillus acidophilus is a Gram-positive lactic acid bacterium that has had widespread historical use in the dairy industry and more recently as a probiotic. Although L. acidophilus has been designated as safe for human consumption, increasing commercial regulation and clinical demands for probiotic validation has resulted in a need to understand its genetic diversity. By drawing on large, well-characterised collections of lactic acid bacteria, we examined L. acidophilus isolates spanning 92 years and including multiple strains in current commercial use. Analysis of the whole genome sequence data set (34 isolate genomes) demonstrated L. acidophilus was a low diversity, monophyletic species with commercial isolates essentially identical at the sequence level. Our results indicate that commercial use has domesticated L. acidophilus with genetically stable, invariant strains being consumed globally by the human population.

Figure 1. L. acidophilus lacks genomic diversity compared to other L. acidophilus group species.

A NeighborNet graph of 32 L. acidophilus (Table 1) and 108 L. acidophilus group (Table S1) genomes was generated using the sequence of 53 concatenated rMLST loci, providing a least-squares fit of 99.99%. The number of genomes from each species included in the network are given in brackets adjacent to the species name label. The scale bar indicates uncorrected P distance measured as number of nucleotide differences over 9338 parsimony informative nucleotides.

Figure 2. Whole genome MLST analysis of the infraspecies diversity of L. acidophilus.

A Neighbor Net plot was generated using wgMLST. The scale bar indicates distance measured in number of allelic differences over 1815 genomic loci conserved across all L. acidophilus genomes examined. Isolate numbers are coloured to represent their commercial (blue) or culture collection (green) history (Table 1), with other notable groups circled. High resolution analysis of the 14 commercial L. acidophilus genome sequences in the circled region of the neighbour net plot is provided in Supplementary Figure S1. The NFCM isolate genome sequenced as part of this study is indicated by an asterisk. The GenBank accession of the NCFM reference genome sequence is given brackets. Numbers given in superscript indicate CRISPR sequence types assigned in Supplementary Figure S2.

Figure 3. L. acidophilus genome sequences compared to L. acidophilus NCFM.

The black, innermost ring represents the published genome sequence of L. acidophilus NCFM (accession CP000033). Further concentric rings correspond to isolates according to the key. Co-localising isolates from Figure 2 that could be linked by alias (Table 1) are combined into a single ring. Ring presence indicates 98% sequence identity. Regions of interest are annotated.

Figure 4. Diversity of L. acidophilus MALDI-TOF profiles.

MALDI-TOF profile distance scores were plotted in two dimensions as described in the Methods. Panel A shows the profiles of L. acidophilus (isolates NCFM, LMG 9433^T, LMG 11428, LMG 11470, LMG 13550^T, Rm 344, Rm 345, CUL 21 and CUL60; Table 1) compared to 6 other lactobacillus control species. Panel B shows the profiles of commercial and culture collection L. acidophilus Distances were calculated using the Pearson correlation similarity coefficient and position tolerance optimisation was set to 2%. Coordinates were calculated using multidimensional scaling.