Comparison of Bacterial Microbiota in Raw Mare’s Milk and Koumiss Using PacBio Single Molecule Real-Time Sequencing Technology

Abstract

Koumiss is a traditional fermented raw mare's milk product. It contains high nutritional value and is well-known for its health-promoting effect as an alimentary supplement. This study aimed to investigate the bacterial diversity, especially lactic acid bacteria (LAB), in koumiss and raw mare's milk. Forty-two samples, including koumiss and raw mare's milk, were collected from the pastoral area in Yili, Kazakh Autonomous Prefecture, Xinjiang Uygur Autonomous Region in China. This work applied PacBio single-molecule real-time (SMRT) sequencing to profile full-length 16S rRNA genes, which was a powerful technology enabling bacterial taxonomic assignment to the species precision. The SMRT sequencing identified 12 phyla, 124 genera, and 227 species across 29 koumiss samples. Eighteen phyla, 286 genera, and 491 species were found across 13 raw mare's milk samples. The bacterial microbiota diversity of the raw mare's milk was more complex and diverse than the koumiss. Raw mare's milk was rich in LAB, such as Lactobacillus (L.) helveticus, L. plantarum, Lactococcus (Lc.) lactis, and L. kefiranofaciens. In addition, raw mare's milk also contained sequences representing pathogenic bacteria, such as Staphylococcus succinus, Acinetobacter lwoffii, Klebsiella (K.) oxytoca, and K. pneumoniae. The koumiss microbiota mainly comprised LAB, and sequences representing pathogenic bacteria were not detected. Meanwhile, the koumiss was enriched with secondary metabolic pathways that were potentially beneficial for health. Using a Random Forest model, the two kinds of samples could be distinguished with a high accuracy 95.2% [area under the curve (AUC) = 0.98] based on 42 species and functions. Comprehensive depiction of the microbiota in raw mare's milk and koumiss might help elucidate evolutionary and functional relationships among the bacterial communities in these dairy products. The current work suffered from the limitation of a low sample size, so further work would be required to verify our findings.

Species-Level Gut Microbiota Analysis after Antibiotic-Induced Dysbiosis in Horses

“…That suggests that either the bacteria present in the equine gut remain to be discovered or that the databases available for taxonomic classification do not contain the information required for the analysis of horse gastrointestinal samples. Other studies using PacBio to sequence the human fecal microbiota [23] and raw milk from mares [24] were able to obtain classification at the species level. This indicates that the bacteria present in the feces of the studied horses were not present in the database used for analysis (Athena).…”

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

“…kefiranofaciens occurrence and identification has also been reported in 10 samples of koumiss collected in Xinjiang Uygur Autonomous Region in China by PCR-DGGE [74]. There is one more study reporting the detection of L. kefiranofaciens in koumiss and raw mare milk collected in Xinjiang, China, using PacBio single-molecule real-time (SMRT) sequencing to profile full-length 16S rRNA genes [75]. Interestingly, the authors reported that the raw milk bacterial microbiota diversity was more complex and diverse than that of koumiss.…”

Metagenomic Exploration of Koumiss from Kazakhstan

“…One of these methods is koumiss treatment of pulmonary and gastrointestinal infections in regions with developed horse breeding. It was shown that the composition of koumiss is of great importance for the additional treatment of microbial diseases ( 4 , 5 ). In our research, the virome of koumiss (fermented dairy product made from mare’s [ Equus caballus ] milk) was studied to diagnose the presence of phages in this dairy product that can lyse pathogenic microorganisms, creating a therapeutic effect.…”