Towards a Genome-Based Reclassification of the Genus Lactobacillus

LETTER

Since the advent of the genomic era, it has become clear that the genus Lactobacillus is as large as a typical bacterial family (1). In addition, it has been shown several times that this genus is polyphyletic, as it encompasses at least five other genera. Attempts to define smaller genus-sized phylogroups within Lactobacillus have been undertaken, e.g., by Zheng et al. (2) and by Sun et al. (1). In a more recent paper published in this journal, Salvetti et al. (3) propose ten phylogroups and (i) assess the robust monophyly of these phylogroups, (ii) check the within-phylogroup diversity, and (iii) search for gene presence/absence signatures that are able to discriminate between the phylogroups. We believe that this effort to define phylogroups that are robustly monophyletic and of consistent diversity is an important step in the right direction toward the reclassification of the genus Lactobacillus. Nonetheless, we feel that several of the proposed phylogroups are not adequate to form new genera and believe that alternatives should first be explored.

The authors convincingly showed that their ten phylogroups are robustly monophyletic. However, four of these ten groups do not meet the commonly cited requirement that genomes of the same genus should share >50% of conserved proteins (POCP) (4). For three of those, the authors report that the POCP values without “peripheral species” are >50%, but we feel that this is somewhat arbitrary. A second point for further improvement and discussion is that these proposed phylogroups, as defined now, do not seem to be uniquely identifiable using their proposed gene signatures: several species, such as Lactobacillus floricola, Lactobacillus mellifer, and Lactobacillus brevis (see Tables 1 and 3 in reference 3), do not fully conform to the gene signature found for the phylogroup to which they belong.

We believe that some of these issues with the newly proposed phylogroups could be overcome if a less ad hoc strategy to find phylogroups is used. For example, we understand that the fourteen phylogroups that Salvetti et al. (3) used as a reference have been circulating and validated in the literature (see reference 5 for an overview). However, in the new article, some of those 14 groups were merged to form 10, while it is at present unclear why those mergers were performed and not others or, conversely, why the splitting of phylogroups was not considered. Therefore, we would like to propose that future efforts to define new phylogroups and genera follow an explorative and transparent approach—explorative in the sense that each clade within the Lactobacillus genus tree is assessed as a potential phylogroup, and transparent in the sense that explicit criteria are applied. An excellent example of a more generalized approach applicable to all bacterial genera/taxonomy is the recent proposal by Parks et al. (6), who constructed a revised bacterial taxonomy based solely on genomics. Of interest, with their approach, the Lactobacillus genus was split into sixteen smaller genera, indicating that there is still a need for further open discussion about the exact number and nature of the Lactobacillus phylogroups.

In order to form new phylogroups, we are in favor of applying three criteria, two of which are already used by Salvetti et al. (3): robust monophyly and consistent diversity. For the third criterion, we propose determining the total number of common and exclusive genes of each clade (marker genes) and selecting phylogroups that have a large common number of such genes. This final criterion ensures that phylogroups have biological meaning, even if we do not yet know the function of all these marker genes.

Thus, to conclude, bacterial taxonomy—in particular, that of the Lactobacillus genus—is under strong pressure, as evidenced by the above-mentioned publications and our recent comparative genomics work on the Lactobacillus casei group (7). As mentioned by Salvetti et al. (3), this is an important issue, since reclassification of the Lactobacillus genus could have large implications not only for the scientific community but also for legislative bodies, regulatory agencies, manufacturers of Lactobacillus-containing products, and microbial safety assessors. However, as an alternative to the polyphasic approach proposed by Salvetti et al. (3), we believe that a monophasic approach, based solely on genomics, is feasible, but only when executed in an explorative way based on explicit criteria for what constitutes a proper genus.

Ed. Note: The authors of the published article did not feel that a response was necessary.