Comparative genomics and functional analysis of a highly adhesive dairy Lactobacillus paracasei subsp. paracasei IBB3423 strain

Anna Koryszewska-Bagińska,Tamara Aleksandrzak-Piekarczyk,Adriana Nowak,Marcin Grynberg,Jan Gawor

doi:10.1007/s00253-019-10010-1

Abstract

Various Lactobacillus paracasei strains are found in diverse environments, including dairy and plant materials and the intestinal tract of humans and animals, and are also used in the food industry or as probiotics. In this study, we have isolated a new strain L. paracasei subsp. paracasei IBB3423 from samples of raw cow milk collected in a citizen science project. IBB3423 showed some desired probiotic features such as high adhesion capacity and ability to metabolize inulin. Its complete genome sequence comprising the chromosome of 3,183,386 bp and two plasmids of 5986 bp and 51,211 bp was determined. In silico analysis revealed numerous genes encoding proteins involved in carbohydrate metabolism and of extracellular localization likely supporting interaction with host tissues. In vitro tests confirmed the high adhesion capacity of IBB3423 and showed that it even exceeds that of the highly adhesive L. rhamnosus GG. Curing of the larger plasmid indicated that the adhesive properties depend on the plasmid and thus could be determined by its pilus-encoding spaCBA genes.

Highlights

Lactobacillus is the largest genus of the lactic acid bacteria (LAB) group, which currently comprises 236 species listed in the List of Prokaryotic Names (October 2018; www.bacterio. net)
The ability of L. paracasei subsp. paracasei IBB3423 to utilize certain carbohydrates was compared with the fermentation profiles of well-characterized L. casei group bacteria with fully sequenced genomes as follows: L. rhamnosus GG, L. rhamnosus LOCK 0900, L. rhamnosus LOCK 0908, and L. paracasei LOCK 0919 (Kankainen et al 2009; Aleksandrzak-Piekarczyk et al 2013; KoryszewskaBaginska et al 2013; Koryszewska-Baginska et al 2014), originally isolated from the human gastrointestinal tract
Lactobacillus casei/paracasei strains can be found in various environments and this wide range explains the broad spectrum of their applications in dairy production, biotechnological, and health-related fields (Widyastuti and Rohmatussolihat 2014; Cai et al 2009; Toh et al 2013; Douillard et al 2013; Smokvina et al 2013)

Summary

Introduction

Lactobacillus is the largest genus of the lactic acid bacteria (LAB) group, which currently comprises 236 species listed in the List of Prokaryotic Names (October 2018; www.bacterio. net). In contrast to the often well-characterized adhesive determinants of pathogens and their specific host receptors, functional understanding of the adherence of commensal bacteria is only fragmentary. These bacterial adhesive factors include exopolysaccharides (EPSs), teichoic acids (TAs), surface layer (S-layer) proteins, and some other membrane- or cell wall-associated proteins protruding from the cell (Lebeer et al 2008). Most adhesins of lactobacilli belong to a class of sortasedependent proteins (Velez et al 2007), which contain an Nterminal signal sequence for transport through the membrane and a C-terminal motif LPXTG for cell wall anchoring performed by the enzyme sortase (Navarre and Schneewind 1999). Similar structures have been identified in many lactobacilli, for example, L. rhamnosus GG and L. paracasei LOCK 0919 (Kankainen et al 2009; Aleksandrzak-Piekarczyk et al 2016)

Methods

Results

Conclusion