Hu Tong, Cui Yanhua, Zhang Yishuang, Qu Xiaojun, Zhao Chunyu
Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China.
Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, China.
Front Microbiol. 2020 Feb 28;11:184. doi: 10.3389/fmicb.2020.00184. eCollection 2020.
plays important roles in the dairy industry and is widely used as a dairy starter in the production of fermented dairy products. The genomes of strains CS5, CS9, CS18, and CS20 from fermented milk in China were sequenced and used for biodiversity analysis. In the present study, the phylogenetic analysis of all 34 genomes publicly available including these four strains reveals that the phylogenetic reconstruction does not match geographic distribution as strains isolated from the same continent are not even clustered on the nearby branches. The core and variable genes were also identified, which vary among strains from 0 to 202. CS9 strain contained 127 unique genes from a variety of distantly related species. It was speculated that CS9 had undergone horizontal gene transfer (HGT) during the long evolutionary process. The safety evaluation of these four strains indicated that none of them contains antibiotic resistance genes and that they are all sensitive to multiple antibiotics. In addition, the strains do not contain any pathogenic virulence factors or plasmids and thus can be considered safe. Furthermore, these strains were investigated in terms of their technological properties including milk acidification, exopolysaccharide (EPS) and γ-aminobutyric acid (GABA) production, and survival capacity in the gastrointestinal tract. CS9 possesses a special gene cluster containing significant traces of HGT, while the gene clusters of CS5, CS18, and CS20 are almost the same. The monosaccharide compositional analysis indicated that crude EPS-CS5, EPS-CS9, EPS-CS18, and EPS-CS20 contain similar monosaccharide compositions with different ratios. Furthermore, CS9 was one of a few GABA-producing strains that could ferment glutamate to produce GABA, which is beneficial for improving the acid tolerance of the strain. CS18 has the most potential for the production of fermented food among these four strains because of its fast growth rate, rapid acidifying capacity, and stronger acid and bile salt resistance capacity. This study focused on the genome analysis of the four new strains to investigate the diversity of strains and provides a reference for selecting excellent strains by use of the genome data.
在乳制品行业中发挥着重要作用，并且在发酵乳制品生产中被广泛用作乳制品发酵剂。对来自中国发酵乳的CS5、CS9、CS18和CS20菌株的基因组进行了测序，并用于生物多样性分析。在本研究中，对包括这四个菌株在内的所有34个公开可用基因组进行系统发育分析，结果表明系统发育重建与地理分布不匹配，因为从同一大陆分离的菌株甚至没有聚集在附近的分支上。还鉴定了核心基因和可变基因，这些基因在菌株之间的数量从0到202不等。CS9菌株包含来自多种远缘物种的127个独特基因。据推测，CS9在漫长的进化过程中经历了水平基因转移（HGT）。对这四个菌株的安全性评估表明，它们均不含有抗生素抗性基因，并且对多种抗生素均敏感。此外，这些菌株不含有任何致病毒力因子或质粒，因此可以认为是安全的。此外，还对这些菌株的技术特性进行了研究，包括乳酸酸化、胞外多糖（EPS）和γ-氨基丁酸（GABA）的产生以及在胃肠道中的存活能力。CS9拥有一个特殊的基因簇，其中含有大量水平基因转移的痕迹，而CS5、CS18和CS20的基因簇几乎相同。单糖成分分析表明，粗EPS-CS5、EPS-CS9、EPS-CS18和EPS-CS20含有相似的单糖成分，但比例不同。此外，CS9是少数能够发酵谷氨酸产生GABA的菌株之一，这有利于提高菌株的耐酸性。在这四个菌株中，CS18因其生长速度快、酸化能力强以及更强的耐酸和耐胆盐能力而在发酵食品生产方面具有最大潜力。本研究聚焦于这四个新菌株的基因组分析，以研究菌株的多样性，并为利用基因组数据选择优良菌株提供参考。
