TY - JOUR
T1 - Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation
AU - Broadbent, Jeff R.
AU - Neeno-Eckwall, Eric C.
AU - Stahl, Buffy
AU - Tandee, Kanokwan
AU - Cai, Hui
AU - Morovic, Wesley
AU - Horvath, Philippe
AU - Heidenreich, Jessie
AU - Perna, Nicole T.
AU - Barrangou, Rodolphe
AU - Steele, James L.
N1 - Funding Information:
We thank Anne-Claire Coûté-Monvoisin for technical assistance and Lars Snipen for providing a pre-release version of his R-package software. This work was supported by Danisco, Inc., the United States Department of Agriculture, the U.S. Department of Energy Great Lakes Bioenergy Research Center (DOE BER Office of Science DE-FC02-07ER64494), and the Utah Agricultural Experiment Station (UAES). This manuscript was approved by the UAES as journal paper number 8424.
PY - 2012/10/5
Y1 - 2012/10/5
N2 - Background: The broad ecological distribution of L. casei makes it an insightful subject for research on genome evolution and lifestyle adaptation. To explore evolutionary mechanisms that determine genomic diversity of L. casei, we performed comparative analysis of 17 L. casei genomes representing strains collected from dairy, plant, and human sources.Results: Differences in L. casei genome inventory revealed an open pan-genome comprised of 1,715 core and 4,220 accessory genes. Extrapolation of pan-genome data indicates L. casei has a supragenome approximately 3.2 times larger than the average genome of individual strains. Evidence suggests horizontal gene transfer from other bacterial species, particularly lactobacilli, has been important in adaptation of L. casei to new habitats and lifestyles, but evolution of dairy niche specialists also appears to involve gene decay.Conclusions: Genome diversity in L. casei has evolved through gene acquisition and decay. Acquisition of foreign genomic islands likely confers a fitness benefit in specific habitats, notably plant-associated niches. Loss of unnecessary ancestral traits in strains collected from bacterial-ripened cheeses supports the hypothesis that gene decay contributes to enhanced fitness in that niche. This study gives the first evidence for a L. casei supragenome and provides valuable insights into mechanisms for genome evolution and lifestyle adaptation of this ecologically flexible and industrially important lactic acid bacterium. Additionally, our data confirm the Distributed Genome Hypothesis extends to non-pathogenic, ecologically flexible species like L. casei.
AB - Background: The broad ecological distribution of L. casei makes it an insightful subject for research on genome evolution and lifestyle adaptation. To explore evolutionary mechanisms that determine genomic diversity of L. casei, we performed comparative analysis of 17 L. casei genomes representing strains collected from dairy, plant, and human sources.Results: Differences in L. casei genome inventory revealed an open pan-genome comprised of 1,715 core and 4,220 accessory genes. Extrapolation of pan-genome data indicates L. casei has a supragenome approximately 3.2 times larger than the average genome of individual strains. Evidence suggests horizontal gene transfer from other bacterial species, particularly lactobacilli, has been important in adaptation of L. casei to new habitats and lifestyles, but evolution of dairy niche specialists also appears to involve gene decay.Conclusions: Genome diversity in L. casei has evolved through gene acquisition and decay. Acquisition of foreign genomic islands likely confers a fitness benefit in specific habitats, notably plant-associated niches. Loss of unnecessary ancestral traits in strains collected from bacterial-ripened cheeses supports the hypothesis that gene decay contributes to enhanced fitness in that niche. This study gives the first evidence for a L. casei supragenome and provides valuable insights into mechanisms for genome evolution and lifestyle adaptation of this ecologically flexible and industrially important lactic acid bacterium. Additionally, our data confirm the Distributed Genome Hypothesis extends to non-pathogenic, ecologically flexible species like L. casei.
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U2 - 10.1186/1471-2164-13-533
DO - 10.1186/1471-2164-13-533
M3 - Article
C2 - 23035691
AN - SCOPUS:84867018919
SN - 1471-2164
VL - 13
JO - BMC genomics
JF - BMC genomics
IS - 1
M1 - 533
ER -