A comparative pan-genome perspective of niche-adaptable cell-surface protein phenotypes in Lactobacillus rhamnosus

Abstract

Lactobacillus rhamnosus is a ubiquitously adaptable Gram-positive bacterium and as a typical commensal can be recovered from various microbe-accessible bodily orifices and cavities. Then again, other isolates are food-borne, with some of these having been long associated with naturally fermented cheeses and yogurts. Additionally, because of perceived health benefits to humans and animals, numerous L. rhamnosus strains have been selected for use as so-called probiotics and are often taken in the form of dietary supplements and functional foods. At the genome level, it is anticipated that certain genetic variances will have provided the niche-related phenotypes that augment the flexible adaptiveness of this species, thus enabling its strains to grow and survive in their respective host environments. For this present study, we considered it functionally informative to examine and catalogue the genotype-phenotype variation existing at the cell surface between different L. rhamnosus strains, with the presumption that this might be relatable to habitat preferences and ecological adaptability. Here, we conducted a pan-genomic study involving 13 genomes from L. rhamnosus isolates with various origins. In using a benchmark strain (gut-adapted L. rhamnosus GG) for our pan-genome comparison, we had focused our efforts on a detailed examination and description of gene products for certain functionally relevant surface-exposed proteins, each of which in effect might also play a part in niche adaptability among the other strains. Perhaps most significantly of the surface protein loci we had analyzed, it would appear that the spaCBA operon (known to encode SpaCBA-called pili having a mucoadhesive phenotype) is a genomic rarity and an uncommon occurrence in L. rhamnosus. However, for any of the so-piliated L. rhamnosus strains, they will likely possess an increased niche-specific fitness, which functionally might presumably be manifested by a protracted transient colonization of the gut mucosa or some similar microhabitat.

Figure 1. Phylogenomic tree of L. rhamnosus.

For establishing the evolutionary relationships among the L. rhamnosus genomes, unrooted genome phylogenies based on aligned gene content were generated using the neighbor-joining method as described in Materials and Methods. Identities of the L. rhamnosus genomes (strains) are indicated. Origin and source of strains are grouped by color as follows: gut (blue), mouth (green), lungs (magenta), and dairy (red).

Figure 2. The pan-genome of L. rhamnosus.

A flower-plot schematic representation illustrates the number of predicted core (2,095) and dispensable (2,798) genes that together make up the L. rhamnosus pan-genome (4,893 loci). Shown in the flower petals are the numbers of loci per genome that are predicted to be either unique or ORFan-like (parenthesized). Names of the L. rhamnosus genomes (strains) are indicated. All annotated genes are listed in Table S1.

Figure 3. The pan-genome development plot of L. rhamnosus.

Shown is the progression of the L. rhamnosus pan-genome as additional strain-genomes are included. Pan-genome development was calculated with R statistical programming language and using Heap’s Law (see Materials and Methods).

Figure 4. The “classical” pan-secretome of L. rhamnosus.

A flower-plot schematic representation depicts the main components of the SignalP-predicted L. rhamnosus pan-secretome (230 proteins). Shown are the number of core (103) and dispensable (127) proteins and the total numbers of classically secreted proteins per each genome (flower petals). Names of the L. rhamnosus genomes (strains) are indicated. All annotated secreted proteins are listed in Table S2.