A Perspective Study of Koumiss Microbiome by Metagenomics Analysis Based on Single-Cell Amplification Technique

Abstract

Koumiss is a traditional fermented dairy product and a good source for isolating novel bacteria with biotechnology potential. In the present study, we applied the single-cell amplification technique in the metagenomics analysis of koumiss. This approach aimed at detecting the low-abundant bacteria in the koumiss. Briefly, each sample was first serially diluted until reaching the level of approximately 100 cells. Then, three diluted bacterial suspensions were randomly picked for further study. By analyzing 30 diluted koumiss suspensions, a total of 24 bacterial species were identified. In addition to the previously reported koumiss-associated species, such as Lactobacillus (L.) helveticus. Lactococcus lactis. L. buchneri, L. kefiranofaciens, and Acetobacter pasteurianus, we successfully detected three low-abundant taxa in the samples, namely L. otakiensis. Streptococcus macedonicus, and Ruminococcus torques. The functional koumiss metagenomes carried putative genes that relate to lactose metabolism and synthesis of typical flavor compounds. Our study would encourage the use of modern metagenomics to discover novel species of bacteria that could be useful in food industries.

Simultaneous identification of bovine and equine DNA in milks and dairy products inferred from triplex TaqMan real-time PCR technique

“…Xilingol herdsmen yield koumiss by the natural fermentation of mare milk. Koumiss has been appealing to Mongolians in Xilin Gol of Inner Mongolia, where it has been applied as a traditional Mongolian medicine to cure intestinal dyspepsia, hypertension, dyslipidemia, and so on (Rong et al, 2015;Yao et al, 2017). The above nutritional and medical properties have contributed to the prosperity of the market for mare milk and its dairy products, and consequently have attracted interest for herdsmen and producers in various regions and countries.…”

A review on selection of fermentative microorganisms for functional foods and beverages: the production and future perspectives

“…Besides these techniques, single‐cell amplification techniques for analysing the microbiome are prospective. They should futuristically showcase uncommon fermentative strains in the food substrates and thus used to control and modify food microbiomes (Yao et al ., ).…”

Raman‐activated cell sorting and metagenomic sequencing revealing carbon‐fixing bacteria in the ocean

“…It has been reported that mini-metagenomics, which starts from tens to thousands of cells and employs the single cell technology could improve amplification and help the genome assembly from the sequencing data, leading to higher hit of target gene and coverage as well as the integrity of assembled genome. In combination with advanced contig binning methods, multiple genomes can be reconstructed from mini-metagenomic data of microbiota (McLean et al, 2013;Yao et al, 2017;Yu et al, 2017). In this study, RACE isolated 30 cells for mini-metagenomic sequencing process, which can be served as blueprints for the whole genome assembly using advanced binning methods.…”

“…However, genome coverage from RACS was frequently low when sequencing one cell at a time (< 20%), which was presumably due to severe non-specific and biased amplification when starting from a very low amount of DNA template. Recently mini-metagenomics, which starts from a small number of cells rather than one single cell, has been reported to improve the genome coverage and assembly integrity (McLean et al, 2013;Yao et al, 2017;Yu et al, 2017). Moreover, deep sequencing and advanced binning algorithms can facilitate informative mining from the assembled genomic sequences (Albertsen et al, 2013;Langille et al, 2013;Nielsen et al, 2014;Magnusdottir et al, 2017).…”