Probiotic Strain Specificity

A study by Ghattargi et al. (2018) highlights the potential for strains from a single species to range from probiotic to pathogenic, with some being cultivated in traditional fermentation while others exhibit a neutrality that is neither probiotic nor pathogenic.  This study compared the genomes of ten different strains of Enterococcus faecium.  While these different strains are all considered to be members of the same species, each had at least 10 and as many as 87 genes that were unique to itself and not found in any of the others, while there were 1,935 genes that were found consistently in every strain.  One example of how these genetic differences determine whether a strain can be considered a probiotic or not is the fact that the probiotic strains were able to synthesize essential amino acids and vitamins that could be taken up by the host, whereas the pathogenic strains lacked this activity.  They also found that the probiotic strains produced antibiotic compounds against the pathogen Listeria, while the other strains did not.  The authors suggest that being able to identify genes involved in various beneficial as well as pathogenic mechanisms is a useful tool that could be used to comb through vast numbers of different strains in order to identify ones that could be marketed as probiotics.

Lactobacillus crispatus genes coding for antibiotic compounds were studied by Fontana et al. (2021), who found that the Lactobacillus crispatus strains of human origin in their study had a set of these genes in common, thought to be antagonistic against streptococci; while strains collected from poultry did not exhibit these genes.  If this particular antibiotic compound is desirable in a probiotic intended to protect against bacterial vaginosis, the strains derived from poultry that were included in this study may not have the same effect as other strains.  They found six different sets of genes coding for antibiotic compounds, with different ones being found in different strains, and only three strains exhibiting all six.  Out of the 97 strains they studied, they identified three that they felt had potential as probiotics since they appeared to possess a good ability to antagonize pathogens and also had characteristics making them better suited for establishing themselves in the microbiome.  While this type of genetic analysis has the ability to catalog strains of interest according to characteristics that would make them suitable as probiotics, human trials are then needed to determine whether the strain does indeed have the desired effect. 

References:

Fontana, F., Alessandri, G., Lugli, G. A., Mancabelli, L., Longhi, G., Anzalone, R., Viappiani, A., Ventura, M., Turroni, F., & Milani, C. (2021). Probiogenomics Analysis of 97 Lactobacillus crispatus Strains as a Tool for the Identification of Promising Next-Generation Probiotics. Microorganisms, 9(1), 73. 

Ghattargi, V. C., Gaikwad, M. A., Meti, B. S., Nimonkar, Y. S., Dixit, K., Prakash, O., Shouche, Y. S., Pawar, S. P., & Dhotre, D. P. (2018). Comparative genome analysis reveals key genetic factors associated with probiotic property in Enterococcus faecium strains. BMC Genomics, 19(1), 652.