Probiotic characters of Bifidobacterium and Lactobacillus are a result of the ongoing gene acquisition and genome minimization evolutionary trends

- Genome decay and gene acquisition are the main evolutionary trends in probiotics genera Lactobacillus and Bifidobactrium.
- Genome decay has the major role in the evolution of the genus Lactobacillus.
- Gene acquisition (HGT) is the main trend in the evolution of the genus Bifidobacterium.
- The genus Lactobacillus harbors two groups of species: habitat specialized and habitat generalist species.
- Habitat specialized species have smaller genomes and show a higher rate of reductive evolution.
- Habitat generalist lactobacilli have larger genomes and show a very wide ecological distribution.
- Niche-specialized lactobacilli have evolved very different strategies based on their own preferred niches.

Bifidobacterium and Lactobacillus are the main probiotic genera. Collectively, these two genera harbor over 200 species among which are many strains have been introduced as probiotics. These health-promoting microbes confer health benefits upon the host and so used in food productions and as supplements. Considering the economic importance of probiotics, the biochemistry, genomics, phylogeny and physiology of such genera have been exhaustively studied. According to the genomic data, the probiotic capabilities are strain specific which may be a result of the niche-specialization of the genomes of these bacteria to certain ecological niches like gastrointestinal tract of a diverse range of animals. These microbes have a wide distribution but the culture-based studies and either genomics data suggest selective affinity of some Lactobacillus and either Bifidobacterium species to certain ecological niches. An ongoing genome degradation, which is thought to be a result of passage through an evolutionary bottleneck, is the major trend in the evolution of lactobacilli. Further, evolutionary events resulted into two categories of lactobacilli: habitat generalists and habitat specialists. In place, the main trend in the evolution of bifidobacteria tend to be the gene acquisition. However, probiotic features are the results of a co-evolutionary relationship between these bacteria and their hosts and the aforementioned evolutionary tends have driven the evolution of these probiotic genera.