AUTHOR=Moser Aline , Wüthrich Daniel , Bruggmann Rémy , Eugster-Meier Elisabeth , Meile Leo , Irmler Stefan 

TITLE=Amplicon Sequencing of the slpH Locus Permits Culture-Independent Strain Typing of Lactobacillus helveticus in Dairy Products

JOURNAL=Frontiers in Microbiology

VOLUME=8

YEAR=2017

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2017.01380

DOI=10.3389/fmicb.2017.01380

ISSN=1664-302X

ABSTRACT=<p>The advent of massive parallel sequencing technologies has opened up possibilities for the study of the bacterial diversity of ecosystems without the need for enrichment or single strain isolation. By exploiting 78 genome data-sets from <italic>Lactobacillus helveticus</italic> strains, we found that the <italic>slpH</italic> locus that encodes a putative surface layer protein displays sufficient genetic heterogeneity to be a suitable target for strain typing. Based on high-throughput <italic>slpH</italic> gene sequencing and the detection of single-base DNA sequence variations, we established a culture-independent method to assess the biodiversity of the <italic>L. helveticus</italic> strains present in fermented dairy food. When we applied the method to study the <italic>L. helveticus</italic> strain composition in 15 natural whey cultures (NWCs) that were collected at different Gruyère, a protected designation of origin (PDO) production facilities, we detected a total of 10 sequence types (STs). In addition, we monitored the development of a three-strain mix in raclette cheese for 17 weeks.</p>