BSR LAB diversity
To better understand the genetic adaptations that separate BSR LAB from non-spoiling isolates of the same species, and their origins, we must first examine the diversity of species involved. Both Lactobacillus and Pediococcus genera are comprised of Gram-positive, catalase-negative isolates and share overlapping DNA G+C content (Lactobacillus: 32-55% mol and Pediococcus: 35-44 mol%). Although these two genera are closely related to each other and to the genus Leuconostoc, as demonstrated by 16S rRNA gene sequence analysis, they have several distinctive features (Schleifer and Ludwig, 1995). Pediococcus isolates grow under a range of facultatively aerobic to microaerophilic conditions and are homofermentative in that they do not generate CO2 when they produce lactic acid from fermentation of glucose (Holzapfel et al., 2009). Further, pediococci are not capable of reducing nitrate, while some lactobacilli isolates can (Hammes and Hertel, 2006; Hammes and Vogel, 1995). Lactobacillus species are generally anaerobic, although some are aerotolerant and may be either homofermentative like Pediococcus, or heterofermentative and produce lactic acid, CO2, and ethanol and/or acetic acid as primary end products of fermentation.
Lactobacillus spp. are currently organized into three distinct metabolic or fermentative groups, prior to further phylogenetic arrangement based on genetic relatedness (Holzapfel and Wood, 2014; Sun et al., 2014). The first fermentation group is that of the obligate homofermentative (OHO) species, which can only ferment hexoses and do so via the Embden-Meyerhof-Parnas (EMP) pathway, largely producing lactic acid as a by-product (Hammes and Vogel, 1995). Those species that are capable of homofermentation, but during starvation or glucose limitation can degrade pentoses and gluconate via the pentose phosphate pathway (PPP) to produce acetic acid, ethanol and formic acid as by-products, are referred to as facultative heterofermentative (FHE). Finally, the obligate heterofermentative (OHE) group will metabolize pentoses and hexoses solely through the first part of the PPP via the phosphogluconate pathway and produce lactic acid, CO2, and ethanol or acetic acid (Holzapfel and Wood, 2014; Sun et al., 2014; Zheng et al., 2015). In the context of brewing, common BSR LAB belong to all three groups; for example, L. brevis and L. lindneri are OHE and L. plantarum is FHE. The different metabolic capacities of these isolates therefore may influence not only the style of beer or brewery location they are able to grow in as a result of available nutrients, but also the severity and type of spoilage they cause as a result of their metabolic by-products.
To further illustrate lactobacilli diversity, Sun et al. (2014) characterized eight ‘niche type' environments where lactobacilli are commonly found, including plant or plant-associated fermentation products, sourdough, meat products, dairy products, wine products, human or animal gastrointestinal (GI) tracts, human or animal non-GI sources, and the general environment. Notably, breweries or beer products are not included likely because LAB are not necessarily an essential component of beer fermentation or production. Further, many BSR LAB species can be isolated from different environments; for example, L. brevis has been isolated from the human GI tract, and L. lindneri and L. plantarum can be recovered from plant materials and dairy products (Salvetti et al., 2012), as well as from beer. The ability of different isolates of the same species to occupy multiple niches and exhibit different fermentation types is common for Lactobacillus species (Douillard et al., 2013). Thus, it is not surprising that BSR LAB isolates occupying the same niche have different genomic features, underscoring the idea that different genetic mechanisms allow for adaptation to a given environment and/or stress (Sun et al., 2014).
As food production industries are principally concerned with LAB adaptation to their specific application (i.e. unique environment), LAB genomics and phylogenetic relationships have received considerable attention (Hammes and Vogel 1995; Salvetti et al., 2012; Zhang et al., 2011). Whole genome sequencing, phylogenomics and other bioinformatic approaches to compare LAB species have resolved questions of group diversity, evolutionary relatedness and provided a wealth of information concerning general genetic composition. Multiple LAB genomes are available publicly through the National Center for Biotechnology Information database (www.ncbi.nlm.nih.gov/ genome), with over a hundred of these being Lactobacillus isolates and a dozen being Pediococcus isolates, and an estimated 80 unreleased, ongoing projects worldwide (Sun et al., 2014). These genomic data are of great general utility, however, with respect to brewing-microbiology, only a small percentage of these genomes or projects belong to BSR isolates (Bergsveinson et al., 2015c; Kelly et al., 2012; Pittet et al., 2012a,b). The continued sequencing of LAB genomes is essential, as general analysis of genomic content will be more robust and less inclined towards bias if LAB isolates from a variety of different sources are included (Pfeiler and Klaenhammer, 2007; Sun et al., 2014). As there is assumed genetic variation between BSR isolates from beer and non-BSR isolates, and BSR LAB species isolated from any source, more data must be made available for both BSR and non-BSR LAB from multiple isolation sources in order to effectively determine the evolution and distinguishing characteristics of BSR LAB.