Comparative analyses of microbial community diversities of Tibetan kefir grains from three geographic regions

Bacterial diversity using metagenomics of 16s rDNA in water kefir, an innovative source of probiotics for bee nutrition

Water kefir is a sparkling, slightly acidic fermented beverage made from sugar, water, and water kefir grains, which are a mixture of yeast and bacteria. These grains produce a variety of fermentation compounds such as lactic acid, acetaldehyde, acetoin, ethanol and carbon dioxide. In this study, a high-throughput sequencing technique was used to characterize the bacterial composition of the original water kefir from which potential probiotics were obtained. We studied the bacterial diversity of both water kefir grains and beverages. DNA was extracted from three replicate samples of both grains and beverages using the Powerlyzer Microbial Kit. The hypervariable V1-V2 region of the bacterial 16S ribosomal RNA gene was amplified to prepare six DNA libraries. Between 1.4M and 2.4M base-pairs were sequenced for the library. In total, 28721971 raw reads were obtained from all the samples. Estimated species richness was higher in kefir beverage samples compared to grain samples. Moreover, a higher level of microbial alpha diversity was observed in the beverage samples. Particularly, the predominant bacteria in beverages were Anaerocolumna and Ralstonia, while in grains Liquorilactobacillus dominated, with lower levels of Leuconostoc and Oenococcus. Although the bacterial diversity in kefir grains was low because only three genera were the most represented, all of them are LAB bacteria with the potential to serve as probiotics in the artificial feeding of bees.

Long transportation duration affects nutrient composition, mycotoxins and microbial community in whole-plant corn silage

Introduction

Potential nutrient losses and mycotoxin accumulation caused by abnormal fermentation during transportation from cropland to dairy farms leads to the diseases incidence and threatens the health of dairy cows, then further causes financial losses. The aim of this study was to investigate the effects of different transportation times on the nutritional composition, mycotoxins, and microbial communities in whole-plant corn silage (WPCS).

Methods

Three groups were subjected to different transport times: DY, short (<200 min); ZY, medium time (300-500 min); and CY, long transport time (>600 min). WPCS were collected from the same field, and nutrient composition and microbial composition before and after transportation were analyzed.

Results and discussion

Our results showed that the temperature of WPCS was higher in the ZY and CY groups than in the DY group (P < 0.01). There were no significant differences in dry matter (DM), crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF), ether extract (EE) and starch contents after different transportation times (P > 0.05), whereas the starch and water-soluble carbohydrates (WSC) contents in the CY group was significantly decreased after transport (P < 0.05). Similarly, the concentration of vomitoxin in the DY and CY groups declined markedly (P < 0.05) and the zearalenone content in the DY group also significantly decreased after transportation (P < 0.05). Regarding the analysis of microorganisms in WPCS, UniFrac-distance matrices and Shannon indices showed differences in the ZY group (P < 0.05), but fungal diversities were not influenced by the transport time (P > 0.05). In the ZY group, the relative abundance of Lactiplantibacillus decreased significantly after transportation (P > 0.05), but the relative abundances of unidentified_Chloroplast, Pantoea, Gluconobacter, unidentified Acetobacter and Acinetobacter increased markedly (P < 0.05). In addition, the relative abundances of Acetobacter and Gluconobacter in the CY group increased after transport (P < 0.05). Among fungal communities, a total of three, nine, and ten different fungal flora were observed in the DY, ZY, and CY groups, respectively, although no difference was found in fungal diversity. In conclusion, increased temperature, loss of starch, and mycotoxin variation were found with increased transport time. This might be the result of competition between bacteria and fungi, and novel technologies will need to be utilized for further exploration of the mechanism.

Lactobacillus kefiranofaciens: From Isolation and Taxonomy to Probiotic Properties and Applications

One of the main lactic acid bacterial species found in the kefir grain ecosystem worldwide is Lactobacillus kefiranofaciens, exhibiting strong auto-aggregation capacity and, therefore, being involved in the mechanism of grain formation. Its occurrence and dominance in kefir grains of various types of milk and geographical origins have been verified by culture-dependent and independent approaches using multiple growth media and regions of the 16S rRNA gene, respectively, highlighting the importance of their combination for its taxonomic identification. L. kefiranofaciens comprises two subspecies, namely kefiranofaciens and kefirgranum, but only the first one is responsible for the production of kefiran, the water-soluble polysaccharide, which is a basic component of the kefir grain and famous for its technological as well as health-promoting properties. L. kefiranofaciens, although very demanding concerning its growth conditions, can be involved in mechanisms affecting intestinal health, immunomodulation, control of blood lipid levels, hypertension, antimicrobial action, and protection against diabetes and tumors. These valuable bio-functional properties place it among the most exquisite candidates for probiotic use as a starter culture in the production of health-beneficial dairy foods, such as the kefir beverage.

An updated review on bacterial community composition of traditional fermented milk products: what next-generation sequencing has revealed so far?

The emergence of next-generation sequencing (NGS) technologies has revolutionized the way to investigate the microbial diversity in traditional fermentations. In the field of food microbial ecology, different NGS platforms have been used for community analysis, including 454 pyrosequencing from Roche, Illumina's instruments and Thermo Fisher's SOLiD/Ion Torrent sequencers. These recent platforms generate information about millions of rDNA amplicons in a single running, enabling accurate phylogenetic resolution of microbial taxa. This review provides a comprehensive overview of the application of NGS for microbiome analysis of traditional fermented milk products worldwide. Fermented milk products covered in this review include kefir, buttermilk, koumiss, dahi, kurut, airag, tarag, khoormog, lait caillé, and suero costeño. Lactobacillus-mainly represented by Lb. helveticus, Lb. kefiranofaciens, and Lb. delbrueckii-is the most important and frequent genus with 51 reported species. In general, dominant species detected by culturing were also identified by NGS. However, NGS studies have revealed a more complex bacterial diversity, with estimated 400-600 operational taxonomic units, comprising uncultivable microorganisms, sub-dominant populations, and late-growing species. This review explores the importance of these discoveries and address related topics on workflow, NGS platforms, and knowledge bioinformatics devoted to fermented milk products. The knowledge that has been gained is vital in improving the monitoring, manipulation, and safety of these traditional fermented foods.

Prospects of Artificial Kefir Grains Prepared by Cheese and Encapsulated Vectors to Mimic Natural Kefir Grains

Kefir is a natural fermented dairy beverage obtained by fermenting milk with kefir starter grains. However, up to now, there is still no efficient approach to producing stable kefir grains by using the pure or cultural mixture of strains isolated from the original kefir grains. Therefore, new techniques need to be taken to promote the kefir grain production. To this purpose, an encapsulated vector produced by entrapment of the dominant strains isolated from kefir grain and the cheese vector which was produced by a traditional manufacturing method was used to mimic kefir grain forming, respectively. Then, the composition, microstructure, and microflora of the two vectors were investigated and were compared with the natural kefir grains. Results indicated that the protein and polysaccharide content of cheese vector were much higher than encapsulated vector; the distribution of microorganisms inside the cheese vector was more similar to that inside the natural kefirs. It indicated that the cheese vector would be more suitable to mimic kefir grain production. Results of the present investigations reveal the potential of the cheese vector for kefir grains production at the industrial level.

Quantification of Major Bacteria and Yeast Species in Kefir Consortia by Multiplex TaqMan qPCR

Kefir grains are complex microbial systems of several groups of microorganisms. The identification and quantification of the microbial composition of milk kefirs was described in several studies, which provided an insight into the microbial consortia in this complex ecosystem. Nevertheless, the current methods for identification and quantification are not appropriate for deeper studies on kefir consortia, e.g., population dynamics and microbial interactions in kefir grains. This requires another sensitive and reliable quantitative method. Therefore, this study aims to develop multiplexed qPCR assays to specifically detect and quantify, as an example, several microorganisms of the milk kefir microbial community. Primer-probe sets, which target species-specific genes in six bacteria and five yeasts, were designed, and their sensitivity and specificity to the target species was analyzed in simplex as well as four multiplex qPCR assays. The self-designed multiplex assays were applied for the detection of target bacteria and yeast species in milk kefirs, in both, grain and beverage fractions. Detection of all target microorganisms in simplex and multiplex qPCR was achieved by good linearity, efficiency, repeatability and reproducibility in all assays. When the designed assays were applied on six kefirs, all target microorganisms were detected in different samples, but not all in one kefir sample. The two ubiquitous lactobacilli Lactobacillus kefiranofaciens and Lb. kefiri were present in all six kefirs studied, but were associated with different other yeasts and bacteria. Especially on the yeast community a significant diversity was observed. In general, multiplex TaqMan qPCR as developed here was proven to have high potential for specific identification of target microorganisms in kefir samples and for the first time, eleven target bacteria and yeasts of kefir microbiota were rapidly detected and quantified. This study, thus, provides a fast and reliable protocol for future studies on kefir and other similar microbial ecosystems.