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Comparative genome-scale analysis of niche-based stress-responsive genes in Lactobacillus helveticus strains

机译：瑞士乳杆菌菌株中基于小生境的胁迫响应基因的比较基因组规模分析

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摘要

Next generation sequencing technologies with advanced bioinformatic tools present a unique opportunity to compare genomes from diverse niches. The identification of niche-specific stress-responsive genes can help in characterizing robust strains for multiple applications. In this study, we attempted to compare the stress-responsive genes of a potential probiotic strain, Lactobacillus helveticus MTCC 5463, and a cheese starter strain, Lactobacillus helveticus DPC 4571, from a gut and dairy niche, respectively. Sequencing of MTCC 5463 was done using 454 GS FLX, and contigs were assembled using GS Assembler software. Genome analysis was done using BLAST hits and the prokaryotic annotation server RAST. The MTCC 5463 genome carried multiple orthologs of genes governing stress responses, whereas the DPC 4571 genome lacked in the number of major stress-response proteins. The absence of the bile salt hydrolase gene in DPC 4571 and its presence in MTCC 5463 clearly indicated niche adaptation. Further, MTCC 5463 carried higher copy numbers of genes contributing towards heat, cold, osmotic, and oxidative stress resistance as compared with DPC 4571. Through comparative genomics, we could thus identify stress-responsive gene sets required to adapt to gut and dairy niches.
机译：具有先进生物信息学工具的下一代测序技术为比较来自不同生态位的基因组提供了独特的机会。生态位特异性应激反应基因的鉴定可以帮助表征用于多种应用的稳健菌株。在这项研究中，我们试图比较潜在的益生菌菌株瑞士乳杆菌MTCC 5463和奶酪起子菌株瑞士乳杆菌DPC 4571的应激反应基因，分别来自肠道和乳制品利基市场。使用454 GS FLX进行MTCC 5463测序，并使用GS Assembler软件组装重叠群。基因组分析使用BLAST命中和原核注释服务器RAST进行。 MTCC 5463基因组带有多个控制压力反应的直系同源基因，而DPC 4571基因组缺少主要的压力反应蛋白。 DPC 4571中胆盐水解酶基因的缺失及其在MTCC 5463中的存在清楚地表明了生态位适应性。此外，与DPC 4571相比，MTCC 5463携带有助于热，冷，渗透和氧化应激抗性的基因的拷贝数更高。通过比较基因组学，我们可以鉴定出适应肠道和乳制品生态位的应激响应基因集。

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