Bacterial microbiota of Kazakhstan cheese revealed by single molecule real time (SMRT) sequencing and its comparison with Belgian, Kalmykian and Italian artisanal cheeses

Abstract

BackgroundIn Kazakhstan, traditional artisanal cheeses have a long history and are widely consumed. The unique characteristics of local artisanal cheeses are almost completely preserved. However, their microbial communities have rarely been reported. The current study firstly generated the Single Molecule, Real-Time (SMRT) sequencing bacterial diversity profiles of 6 traditional artisanal cheese samples of Kazakhstan origin, followed by comparatively analyzed the microbiota composition between the current dataset and those from cheeses originated from Belgium, Russian Republic of Kalmykia (Kalmykia) and Italy.ResultsAcross the Kazakhstan cheese samples, a total of 238 bacterial species belonging to 14 phyla and 140 genera were identified. Lactococcus lactis (28.93%), Lactobacillus helveticus (26.43%), Streptococcus thermophilus (12.18%) and Lactobacillus delbrueckii (12.15%) were the dominant bacterial species for these samples. To further evaluate the cheese bacterial diversity of Kazakhstan cheeses in comparison with those from other geographic origins, 16S rRNA datasets of 36 artisanal cheeses from Belgium, Russian Republic of Kalmykia (Kalmykia) and Italy were retrieved from public databases. The cheese bacterial microbiota communities were largely different across sample origins. By principal coordinate analysis (PCoA) and multivariate analysis of variance (MANOVA), the structure of the Kazakhstan artisanal cheese samples was found to be different from those of the other geographic origins. Furthermore, the redundancy analysis (RDA) identified 16 bacterial OTUs as the key variables responsible for such microbiota structural difference.ConclusionOur results together suggest that the diversity of bacterial communities in different groups is stratified by geographic region. This study does not only provide novel information on the bacterial microbiota of traditional artisanal cheese of Kazakhstan at species level, but also interesting insights into the bacterial diversity of artisanal cheeses of various geographical origins.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-016-0911-4) contains supplementary material, which is available to authorized users.

Using PacBio sequencing to investigate the bacterial microbiota of traditional Buryatian cottage cheese and comparison with Italian and Kazakhstan artisanal cheeses

“…The results showed that the microbial structure varied by cheese type, animal milk source, additives used, and whether the milk was pasteurized. Other traditional cheeses have also been studied, such as Latin-style cheese, Kazakhstan cheese, Italian cheese, and Mexican cheese (Lusk et al, 2012;González-Córdova et al, 2016;Li et al, 2017;Silvetti et al, 2017). However, the microbial communities present in Buryatian cheeses have yet to be fully explored.…”

“…This method has successfully been applied to evaluate the safety of infant formula, based on the bacterial population of traditional fermented koumiss and milk products enhanced with probiotics (Gesudu et al, 2016;Zheng et al, 2016;Xu et al, 2017). However, few studies have applied the PacBio SMRT sequencing technology to study the microbiota composition of traditional cheeses, with the exception of a previous study that depicted the bacterial profiles in artisan cheese from Kazakhstan (Li et al, 2017).…”

Bacterial microbiota composition of fermented fruit and vegetable juices (jiaosu) analyzed by single-molecule, real-time (SMRT) sequencing

“…The microbiota profile of a fermented product does not only reveal its potential functions but also information regarding food safety. The application of the PacBio single-molecule, real-time (SMRT) sequencing technology in full-length 16S rRNA profiling has been applied to depict the microbiota composition in different samples, including silage (Bao et al, 2016), koji (Hui et al, 2017), infant milk powder (Zheng et al, 2016), and cheese (Li et al, 2017). This technique is advantageous over other currently available strategies in microbiota profiling because of its capacity in producing long sequence reads and thus providing high-resolution taxonomic profiles to the species level.…”

Analyses of physicochemical properties, bacterial microbiota, and lactic acid bacteria of fresh camel milk collected in Inner Mongolia

“…Therefore, studying the intrinsic microbiota composition is of high practical significance for the industrialization and promotion of camel milk. High-throughput sequencing has become a common technique to investigate microbial communities present in food products including milk (Ercolini, 2013;Li et al, 2017;Jin et al, 2018). It overcomes the limitation of isolating fastidious microbes using culture-dependent methods.…”