Investigation of bacterial and fungal diversity in tarag using high-throughput sequencing

Sun, Zhihong; Chen, Li; Bao, Qiuhua; Zhang, Jiachao; Hou, Qiangchuan; Kwok, Lai‐Yu; Sun, Tiansong; Zhang, Heping

doi:10.3168/jds.2014-8360

Cited by 68 publications

(62 citation statements)

References 54 publications

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“…Proteobacteria was the major phylum across all samples, with 99.79%, 99.7%, and 99.55% in Samples 1 to 3, respectively. This result was rather different with other studies describing the microbiota composition of traditional fermented foods, such as homemade yoghurts (Xu and others ), tarag (Sun and others ), Korean traditional food kochujang (Nam and others ), and Brazilian kefir grains (Leite and others ), which were dominated by Firmicutes. The Firmicutes phylum is consisted of low G+C content Gram‐positive bacteria, including many LAB.…”

Section: Resultscontrasting

confidence: 97%

“…Ascomycota was the predominant phylum, with an average of 99.26% of the total fungal sequences. This phylum was also prevalent in different types of fermented products, including dairy‐based products like homemade yoghurt from Xinjiang (Xu and others ), tarag (Sun and others ), an Tibetan naturally fermented yak milk (Liu and others ), Therefore, the phylum Ascomycota may be considered as major members involving in food fermentation. The minor phylum, Basidiomycota, contributed to only an average of 0.06% (Table ).…”

Section: Resultsmentioning

confidence: 99%

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Identification of Microbial Profile of Koji Using Single Molecule, Real‐Time Sequencing Technology

Hui

Hou

Cao

et al. 2017

Journal of Food Science

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Koji is a kind of Japanese traditional fermented starter that has been used for centuries. Many fermented foods are made from koji, such as sake, miso, and soy sauce. This study used the single molecule real-time sequencing technology (SMRT) to investigate the bacterial and fungal microbiota of 3 Japanese koji samples. After SMRT analysis, a total of 39121 high-quality sequences were generated, including 14354 bacterial and 24767 fungal sequence reads. The high-quality gene sequences were assigned to 5 bacterial and 2 fungal plyla, dominated by Proteobacteria and Ascomycota, respectively. At the genus level, Ochrobactrum and Wickerhamomyces were the most abundant bacterial and fungal genera, respectively. The predominant bacterial and fungal species were Ochrobactrum lupini and Wickerhamomyces anomalus, respectively. Our study profiled the microbiota composition of 3 Japanese koji samples to the species level precision. The results may be useful for further development of traditional fermented products, especially optimization of koji preparation. Meanwhile, this study has demonstrated that SMRT is a robust tool for analyzing the microbial composition in food samples.

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Section: Resultscontrasting

confidence: 97%

Section: Resultsmentioning

confidence: 99%

Identification of Microbial Profile of Koji Using Single Molecule, Real‐Time Sequencing Technology

Hui

Hou

Cao

et al. 2017

Journal of Food Science

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“…There were apparent differences in the microbiota communities between cheeses of different groups, as revealed by PCoA and MANOVA, suggesting that the geographic location may play a role in shaping the sample microbiota. Similar geographical-based variations were reported in traditional fermented vegetables [59] and home-made fermented milks [39, 44, 60]. By comparing with the cheese production methods, the four kinds of cheese varied greatly in their ripening stage (Table 1).…”

Section: Discussionsupporting

confidence: 59%

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

Zheng

et al. 2017

BMC Microbiol

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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.

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“…The above comparative alpha indicators illustrated that koumiss from Inner Mongolia had more bacterial phylotypes than fungus. In contrast, in tarag, a bacteria-and fungi-containing dairy product produced by traditional fermentation of cow milk in Inner Mongolia, the bacterial diversity was significantly lower than the diversity of fungi (Sun et al, 2014). We speculated that the difference in nutritional profile between mare and cow milks (e.g., high lactose content of mare milk) may arouse the predominance of bacteria or fungi in traditional fermented dairy products.…”

Section: Bacterial and Fungal Sequence Abundance And Diversitymentioning

confidence: 96%

Study of bacterial and fungal community structures in traditional koumiss from Inner Mongolia

Guo¹,

Ya²,

Guo³

et al. 2019

Journal of Dairy Science

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Koumiss is notable for its nutritional functions, and microorganisms in koumiss determine its versatility. In this study, the bacterial and fungal community structures in traditional koumiss from Inner Mongolia, China, were investigated. Our results demonstrated that 6 bacterial phyla represented by 126 genera and 49 species and 3 fungal phyla represented by 59 genera and 57 species were detected in 11 samples of artisanal koumiss. Among them, Lactobacillus was the predominant genus of bacterium, and Kluyveromyces and Saccharomyces dominated at the fungal genus level. In addition, there were no differences in the bacterial and fungal richness and diversity of koumiss from 3 neighboring administrative divisions in Inner Mongolia, and the bacterial and fungal community structures (the varieties and relative abundance of bacterial and fungal genera and species) were clearly distinct in individual samples. This study provides a comprehensive understanding of the bacterial and fungal population profiles and the predominant genus and species, which would be beneficial for screening, isolation, and culture of potential probiotics to simulate traditional fermentation of koumiss for industrial and standardized production in the future.

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Investigation of bacterial and fungal diversity in tarag using high-throughput sequencing

Cited by 68 publications

References 54 publications

Identification of Microbial Profile of Koji Using Single Molecule, Real‐Time Sequencing Technology

Identification of Microbial Profile of Koji Using Single Molecule, Real‐Time Sequencing Technology

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

Study of bacterial and fungal community structures in traditional koumiss from Inner Mongolia

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