Complete genome sequencing and comparative genomic analysis of Lactobacillus acidophilus C5 as a potential canine probiotics
2
조회
0
다운로드
1
인용
0
참고문헌
키워드
초록
Lactobacillus acidophilus is a gram-positive, microaerophilic, and acidophilic bacterial species. L. acidophilus strains in the gastrointestinal tracts of humans and other animals have been profiled, but strains found in the canine gut have not been studied yet. Our study helps in understanding the genetic features of the L. acidophilus C5 strain found in the canine gut, determining its adaptive features evolved to survive in the canine gut environment, and in elucidating its probiotic functions. To examine the canine L. acidophilus C5 genome, we isolated the C5 strain from a Korean dog and sequenced it using PacBio SMRT sequencing technology. A comparative genomic approach was used to assess genetic relationships between C5 and six other strains and study the distinguishing features related to different hosts. We found that most genes in the C5 strain were related to carbohydrate transport and metabolism. The pan-genome of seven L. acidophilus strains contained 2,254 gene families, and the core genome contained 1,726 gene families. The phylogenetic tree of the core genes in the canine L. acidophilus C5 strain was very close to that of two strains (DSM20079 and NCFM) from humans. We identified 30 evolutionarily accelerated genes in the L. acidophilus C5 strain in the ratio of non-synonymous to synonymous substitutions (dN/dS) analysis. Five of these thirty genes were associated with carbohydrate transport and metabolism. This study provides insights into genetic features and adaptations of the L. acidophilus C5 strain to survive the canine intestinal environment. It also suggests that the evolution of the L. acidophilus genome is closely related to the host’s evolutionary adaptation process.
Abstract
Lactobacillus acidophilus is a gram-positive, microaerophilic, and acidophilic bacterial species. L. acidophilus strains in the gastrointestinal tracts of humans and other animals have been profiled, but strains found in the canine gut have not been studied yet. Our study helps in understanding the genetic features of the L. acidophilus C5 strain found in the canine gut, determining its adaptive features evolved to survive in the canine gut environment, and in elucidating its probiotic functions. To examine the canine L. acidophilus C5 genome, we isolated the C5 strain from a Korean dog and sequenced it using PacBio SMRT sequencing technology. A comparative genomic approach was used to assess genetic relationships between C5 and six other strains and study the distinguishing features related to different hosts. We found that most genes in the C5 strain were related to carbohydrate transport and metabolism. The pan-genome of seven L. acidophilus strains contained 2,254 gene families, and the core genome contained 1,726 gene families. The phylogenetic tree of the core genes in the canine L. acidophilus C5 strain was very close to that of two strains (DSM20079 and NCFM) from humans. We identified 30 evolutionarily accelerated genes in the L. acidophilus C5 strain in the ratio of non-synonymous to synonymous substitutions (dN/dS) analysis. Five of these thirty genes were associated with carbohydrate transport and metabolism. This study provides insights into genetic features and adaptations of the L. acidophilus C5 strain to survive the canine intestinal environment. It also suggests that the evolution of the L. acidophilus genome is closely related to the host’s evolutionary adaptation process.
참고문헌 (39)
- Leı̈la Bâati, "Study of the cryotolerance of Lactobacillus acidophilus: effect of culture and freezing conditions on the viability and cellular protein levels", International Journal of Food Microbiology, 59(3), pp.241~247 (2000), Elsevier BV[DOI]
- Sabina Fijan, "Microorganisms with Claimed Probiotic Properties: An Overview of Recent Literature", International Journal of Environmental Research and Public Health, 11(5), pp.4745~4767 (2014), MDPI AG[DOI]
- Ljungh A, "Lactic acid bacteria as probiotics", Curr Issues Intest Microbiol, 7, pp.73~90 (2006)
- Andrew DuPont, "Systematic review of randomized controlled trials of probiotics, prebiotics, and synbiotics in inflammatory bowel disease", Clinical and Experimental Gastroenterology, 7, pp.473~487 (2014), Informa UK Limited[DOI]
- Stefano Paolo Marelli, "Effects of probiotic Lactobacillus acidophilus D2", CSL (CECT 4529) on the nutritional and health status of boxer dogs, 2020, pp.187(4), e28~[DOI]
- P.C. Barko, "The Gastrointestinal Microbiome: A Review", Journal of Veterinary Internal Medicine, 32(1), pp.9~25 (2018), Wiley[DOI]
- Felix Sommer, "The gut microbiota — masters of host development and physiology", Nature Reviews Microbiology, 11(4), pp.227~238 (2013), Springer Science and Business Media LLC[DOI]
- Berger B, "Similarity and differences in the Lactobacillus acidophilus group identified by polyphasic analysis and comparative genomics", J Bacteriol, pp.1311~1321 (2007)[DOI]
- Matthew Bull, "The life history ofLactobacillus acidophilusas a probiotic: a tale of revisionary taxonomy, misidentification and commercial success", FEMS Microbiology Letters, 349(2), pp.77~87 (2013), Oxford University Press (OUP)[DOI]
- Laura S. Frost, "Mobile genetic elements: the agents of open source evolution", Nature Reviews Microbiology, 3(9), pp.722~732 (2005), Springer Science and Business Media LLC[DOI]
- Ryan R. Wick, "Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads", PLOS Computational Biology, 13(6), pp.e1005595~ (2017), Public Library of Science (PLoS)[DOI]
- T. Seemann, "Prokka: rapid prokaryotic genome annotation", Bioinformatics, 30(14), pp.2068~2069 (2014), Oxford University Press (OUP)[DOI]
- Jaime Huerta-Cepas, "eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses", Nucleic Acids Research, 47(D1), pp.D309~D314 (2019), Oxford University Press (OUP)[DOI]
- Michael Richter, "JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison", Bioinformatics, 32(6), pp.929~931 (2016), Oxford University Press (OUP)[DOI]
- Andrew J. Page, "Roary: rapid large-scale prokaryote pan genome analysis", Bioinformatics, 31(22), pp.3691~3693 (2015), Oxford University Press (OUP)[DOI]
- David M. Emms, "OrthoFinder: phylogenetic orthology inference for comparative genomics", Genome Biology, 20(1), pp.238~ (2019), Springer Science and Business Media LLC[DOI]
- Löytynoja A, "Multiple sequence alignment methods", pp.155~170 (2014), Humana Press
- M. Suyama, "PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments", Nucleic Acids Research, 34, pp.W609~W612 (2006), Oxford University Press (OUP)[DOI]
- J. Castresana, "Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis", Molecular Biology and Evolution, 17(4), pp.540~552 (2000), Oxford University Press (OUP)[DOI]
- Z. Yang, "PAML 4: Phylogenetic Analysis by Maximum Likelihood", Molecular Biology and Evolution, 24(8), pp.1586~1591 (2007), Oxford University Press (OUP)[DOI]
- Erika A. Pfeiler, "Characterization of a novel bile-inducible operon encoding a two-component regulatory system in Lactobacillus acidophilus", Journal of Bacteriology, 189(13), pp.4624~4634 (2007), American Society for Microbiology[DOI]
- Buffy Stahl, "Complete Genome Sequence of Probiotic Strain Lactobacillus acidophilus La-14", Genome Announcements, 1(3), pp.e00376~13 (2013), American Society for Microbiology[DOI]
- Oleg Iartchouk, "Complete Genome Sequence of Lactobacillus acidophilus FSI4, Isolated from Yogurt", Genome Announcements, 3(2), pp.e00166~15 (2015), American Society for Microbiology[DOI]
- Scott N. Dean, "Complete Genome Sequence of Lactobacillus acidophilus Strain ATCC 53544", Genome Announcements, 5(42), pp.e01138~17 (2017), American Society for Microbiology[DOI]
- Won-Hyong Chung, "Complete Genome Sequence and Genomic Characterization of Lactobacillus acidophilus LA1 (11869BP)", Frontiers in Pharmacology, 9, pp.83~ (2018), Frontiers Media SA[DOI]
- Hélène Falentin, "Draft genome sequences of five strains of Lactobacillus acidophilus, strain CIP 76.13T, isolated from humans, strains CIRM-BIA 442 and CIRM-BIA 445, isolated from dairy products, and strains DSM 20242and DSM 9126 of unknown origin", Genome Announcements, 1(4), pp.e00658~13 (2013), American Society for Microbiology[DOI]
- Seungwoo Son, "Comparative genomics of canine Lactobacillus reuteri reveals adaptation to a shared environment with humans", Genes & Genomics, 42(9), pp.1107~1116 (2020), 한국유전학회[DOI]
- 허재영, "Comparative Genome Analysis and Evaluation of Probiotic Characteristics of Lactobacillus plantarum Strain JDFM LP11", 한국축산식품학회지, 38(5), pp.878~888 (2018), 한국축산식품학회
- Yong Jun Goh, "Insights into glycogen metabolism in Lactobacillus acidophilus: impact on carbohydrate metabolism, stress tolerance and gut retention", Microbial Cell Factories, 13(1), pp.94~ (2014), Springer Science and Business Media LLC[DOI]
- Yong Jun Goh, "A functional glycogen biosynthesis pathway in Lactobacillus acidophilus: expression and analysis of the glg operon", Molecular Microbiology, 89(6), pp.1187~1200 (2013), Wiley[DOI]
- K. Makarova, "Comparative genomics of the lactic acid bacteria", Proceedings of the National Academy of Sciences, 103(42), pp.15611~15616 (2006), Proceedings of the National Academy of Sciences[DOI]
- Sergey Kryazhimskiy, "The Population Genetics of dN", dS, 2008, pp.4(12), e1000304~[DOI]
- MOTOO KIMURA, "Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution", Nature, 267(5608), pp.275~276 (1977), Springer Science and Business Media LLC[DOI]
- Ziheng Yang, "Statistical methods for detecting molecular adaptation", Trends in Ecology & Evolution, 15(12), pp.496~503 (2000), Elsevier BV[DOI]
- 장성용, "Genome Characteristics of Lactobacillus fermentum Strain JDFM216 for Application as Probiotic Bacteria", Journal of Microbiology and Biotechnology, 27(7), pp.1266~1271 (2017), 한국미생물·생명공학회[DOI]
- Jenny L. Baker, "Widespread Genetic Switches and Toxicity Resistance Proteins for Fluoride", Science, 335(6065), pp.233~235 (2012), American Association for the Advancement of Science (AAAS)[DOI]
- Bridgett M. vonHoldt, "Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication", Nature, 464(7290), pp.898~902 (2010), Springer Science and Business Media LLC[DOI]
- Erik Axelsson, "The genomic signature of dog domestication reveals adaptation to a starch-rich diet", Nature, 495(7441), pp.360~364 (2013), Springer Science and Business Media LLC[DOI]
- Luis Pedro Coelho, "Similarity of the dog and human gut microbiomes in gene content and response to diet", Microbiome, 6(1), pp.72~ (2018), Springer Science and Business Media LLC[DOI]