Genome sequence and comparative genome analysis of Lactobacillus casei: insights into their niche-associated evolution.
Genome sequence and comparative genome analysis of Lactobacillus casei: insights into their niche-associated evolution.
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DOI：
10.1093/gbe/evp019
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发表时间：
2009-07-14
影响因子：
3.3
通讯作者：
Steele JL
中科院分区：
文献类型：
--
作者：
Cai H;Thompson R;Budinich MF;Broadbent JR;Steele JL
干酪乳杆菌对不同的生境具有显著的适应性，在食品工业中得到了广泛的应用。为了揭示其广泛的生态适应性和物种进化的基因组特征，对干酪乳杆菌ATCC 334的基因组序列进行了分析，并与其他已测序的乳杆菌进行了比较。这一分析表明，ATCC 334含有大量参与碳水化合物利用和转录调控的编码序列，反映了其应对不同环境条件的需要。比较ATCC 334和干酪乳杆菌BL23的基因组序列，分别发现12个和19个基因组岛。为了更广泛地评估干酪乳杆菌内的遗传变异，用ATCC334芯片进行比较基因组杂交，检测了从不同生境(奶酪，n=7，植物材料，n=8，人类来源，n=6)分离的21株干酪乳杆菌的基因含量。这一分析结果确定了25个高变区。其中一个区域包含与碳水化合物利用和转录调控有关的基因的过度表达，因此被认为是生活方式适应岛。干酪乳杆菌基因组清单的差异揭示了基因的获得和基因的衰退。通过获取基因组岛获得的基因，可能会在特定的栖息地带来健康益处。基因衰退，即失去不必要的祖先特征，在奶酪分离株中观察到，并可能导致乳制品生态位适合性增强。本研究首次揭示了干酪乳杆菌的稳定性和可变区，并对干酪乳杆菌的进化、生活方式适应和代谢多样性提供了有价值的见解。
Lactobacillus casei is remarkably adaptable to diverse habitats and widely used in the food industry. To reveal the genomic features that contribute to its broad ecological adaptability and examine the evolution of the species, the genome sequence of L. casei ATCC 334 is analyzed and compared with other sequenced lactobacilli. This analysis reveals that ATCC 334 contains a high number of coding sequences involved in carbohydrate utilization and transcriptional regulation, reflecting its requirement for dealing with diverse environmental conditions. A comparison of the genome sequences of ATCC 334 to L. casei BL23 reveals 12 and 19 genomic islands, respectively. For a broader assessment of the genetic variability within L. casei, gene content of 21 L. casei strains isolated from various habitats (cheeses, n = 7; plant materials, n = 8; and human sources, n = 6) was examined by comparative genome hybridization with an ATCC 334-based microarray. This analysis resulted in identification of 25 hypervariable regions. One of these regions contains an overrepresentation of genes involved in carbohydrate utilization and transcriptional regulation and was thus proposed as a lifestyle adaptation island. Differences in L. casei genome inventory reveal both gene gain and gene decay. Gene gain, via acquisition of genomic islands, likely confers a fitness benefit in specific habitats. Gene decay, that is, loss of unnecessary ancestral traits, is observed in the cheese isolates and likely results in enhanced fitness in the dairy niche. This study gives the first picture of the stable versus variable regions in L. casei and provides valuable insights into evolution, lifestyle adaptation, and metabolic diversity of L. casei.