Comparative genomes study of lactobacillus species for immunosuppressive motifs (isms) in order to determine probiotic anti-allergic species
,1 Najaf allahyari fard
,2,* Zarrin minuchehr
1. Islamic azad university of science and research branch
2. National Institute for Genetic Engineering and Biotechnology
3. National Institute for Genetic Engineering and Biotechnology
The microbiota contributes to regulatory responses in the gastrointestinal (gi) tract. innate immune system plays a substantial role in immune responsiveness and homeostasis of intestine by toll-like receptors (tlrs), which identify conserved microbial structures. lactobacillus species are one of the most precious inhabitants of human gut microbiota which their immunosuppressive activity has been identified. genomic dna and cell wall components are responsible for the anti-inflammatory activity. it has been proven that the dna of live lactobacillus species have a profound role on immune responses. the existence of suppressive dna motifs was first annotated by krieg et al. in adenoviruses.
the obligation of recognizing nucleic acids is done by tlr9. in allergic disease, stimulation of tlr9 could possibly deviate immune responses towards th1 type and thus overcome the allergy-related th2-type immune response. tlr9 is a primary mediator of anti-inflammatory activity which its stimulation may increase hsp70 expression to induce the anti-inflammatory effect.
every lactobacillus dna has its own specific capacity to stimulate immune responses due to the frequency of immunosuppressive motifs (isms). these isms inhibit the activation of dendritic cells (dcs) and maintain treg cell conversion in face of inflammation.
altogether, we studied different isms in in the genomes of lactobacillus species, which indicate the anti-allergic characteristic of these bacteria.
We studied genomes of all 190 species of lactobacillus, represented in ncbi database (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/). scaffold and contig data as partial data were ignored, and then complete genome of 46 lactobacillus species with 3 assemblies as replications were downloaded. the selected genomes of annotated species were searched for a list of isms. the process of identifying these isms in the bacterial genome sequences were done by fuzznuc from the emboss (http://emboss.bioinformatics.nl/cgi-bin/emboss/fuzznuc) and mast (http://meme-suite.org/doc/mast.html).
In this study, we analyzed the frequency of 17 potent isms in genomes of 46 lactobacillus species. the most precious isms which were involved in our study are as follow: ttttgccg, ttaggg, tttcgttt and tcaagcttga. we assessed the frequency of each in the genomes of lactobacillus species. afterward, lactobacillus species were ranked based on total amount of isms and frequency of motifs per million (mpm). our results indicate that lactobacillus species with probiotic activities have more isms than non-probiotic ones.
by the way, the most effective anti-allergic species are: l. ruminis, l. rhamnosus, l. casei, l. paracasei and l. mucusae.
Lactobacillus species are potent commensal bacteria that their probiotic activity has been proved. we selected our lactobacillus species from ncbi database that their complete genome has been annotated. the frequency of isms in total genome and isms per million in genome were checked. we identified these probiotic species as the potent ones as follow: lactobacillus ruminis, l. rhamnosus, l. casei, l. paracasei and l. mucusae.
Probiotic, lactobacillus, allergy, immunosuppressive motif