Phylotype-level profiling of lactobacilli in highly complex environments by means of an ITS-based metagenomic approach.

Phylotype-level profiling of lactobacilli in highly complex environments by means of an ITS-based metagenomic approach. Appl Environ Microbiol. 2018 May 04;: Authors: Milani C, Duranti S, Mangifesta M, Lugli GA, Turroni F, Mancabelli L, Viappiani A, Anzalone R, Alessandri G, Ossiprandi MC, van Sinderen D, Ventura M Abstract The genus Lactobacillus is a widespread taxon, members of which are highly relevant to functional and fermented foods, while they are also commonly present in host-associated gut and vaginal microbiota. Substantial efforts have been undertaken to disclose the genetic repertoire of all members of the genus Lactobacillus, yet their species-level profiling in complex matrices is still undeveloped due to the poor phylotype resolution of profiling approaches based on the 16S rRNA gene. To overcome this limitation, an ITS-based profiling method was developed to accurately profile lactobacilli at species-level. This approach encompasses a genus-specific primer pair combined with a database of ITS sequences retrieved from all available Lactobacillus genomes and a script for the Qiime software suite that performs all required steps to reconstruct a species-level profile. This methodology was applied to several environments, i.e., human gut and vagina, cecum of free range chickens, as well as whey and fresh cheese. Interestingly, data collected confirmed a relevant role of lactobacilli present in functional and fermented fo...
Source: Applied and Environmental Microbiology - Category: Microbiology Authors: Tags: Appl Environ Microbiol Source Type: research