Lactobacillus fermentum strain JDFM216, isolated from a Korean infant feces sample, possesses the ability to enhance the longevity and immune response of a Caenorhabditis elegans host. To explore the characteristics of strain JDFM216 at the genetic level, we performed whole-genome sequencing using t...
Lactobacillus fermentum strain JDFM216, isolated from a Korean infant feces sample, possesses the ability to enhance the longevity and immune response of a Caenorhabditis elegans host. To explore the characteristics of strain JDFM216 at the genetic level, we performed whole-genome sequencing using the PacBio system. The circular draft genome has a total length of 2,076,427 bp and a total of 2,682 encoding sequences were identified. Five phylogenetically featured genes possibly related to the longevity and immune response of the host were identified in L. fermentum strain JDFM216. These genes encode UDP-N-acetylglucosamine 1-carboxyvinyltransferase (E.C. 2.5.1.7), ErfK/YbiS/YcfS/YnhG family protein, site-specific recombinase XerD, homocysteine S-methyltransferase (E.C. 2.1.1.10), and aspartate-ammonia ligase (E.C. 6.3.1.1), which are involved in peptidoglycan synthesis and amino acid metabolism in the gut environment. Our findings on the genetic background of L. fermentum strain JDFM216 and its potential candidate genes for host longevity and immune response provide new insight for the application of this strain in the food industry as newly isolated functional probiotic.
Lactobacillus fermentum strain JDFM216, isolated from a Korean infant feces sample, possesses the ability to enhance the longevity and immune response of a Caenorhabditis elegans host. To explore the characteristics of strain JDFM216 at the genetic level, we performed whole-genome sequencing using the PacBio system. The circular draft genome has a total length of 2,076,427 bp and a total of 2,682 encoding sequences were identified. Five phylogenetically featured genes possibly related to the longevity and immune response of the host were identified in L. fermentum strain JDFM216. These genes encode UDP-N-acetylglucosamine 1-carboxyvinyltransferase (E.C. 2.5.1.7), ErfK/YbiS/YcfS/YnhG family protein, site-specific recombinase XerD, homocysteine S-methyltransferase (E.C. 2.1.1.10), and aspartate-ammonia ligase (E.C. 6.3.1.1), which are involved in peptidoglycan synthesis and amino acid metabolism in the gut environment. Our findings on the genetic background of L. fermentum strain JDFM216 and its potential candidate genes for host longevity and immune response provide new insight for the application of this strain in the food industry as newly isolated functional probiotic.
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제안 방법
An 8–12 kb library was prepared following the Pacific Biosciences manual, and the sequencing procedure and filtration/de novo assembly of the raw sequence data was carried out on the PacBio RS II system (Pacific Biosciences, USA) using C4 chemistry on single-molecule real-time cells with a 120-min sequence capture protocol the PacBio Hierarchical Genome Assembly Process and Quiver software package, respectively.
Assembled contigs including a short length (<20,000 bp) and low coverage (<50×) were sorted for further experiment.
02% in 2,085 ORFs). Next, we constructed two ANI trees and one phylogenetic tree for a comparative tree analysis of JDFM216 and its same species. The two ANI trees were constructed by 15 available genome sequences and seven available complete genome sequences in the NCBI database, respectively (Fig.
대상 데이터
Based on the dN/dS analysis, five phylogenetically featured genes were revealed in this study (Table 2); UDP-Nacetylglucosamine 1-carboxyvinyltransferase (E.C. 2.5.1.7), ErfK/YbiS/YcfS/YnhG family protein, site-specific recombinase XerD, homocysteine S-methyltransferase (E.C. 2.1.1.10), and aspartate-ammonia ligase (E.C. 6.3.1.1).
3). Six strains, namely CECT_5716, IFO_3956, F-6, NCC2970, SNUV175, and 3872, were grouped together with JDFM216. Unexpectedly, the topological patterns of the phylogenetic tree did not completely correspond to that of the ANI tree.
이론/모형
MESTORTHO [11] and PRANK [12] methods were used for setting the orthologous gene for the eight complete genomes and for multiple sequence alignment of each orthologous gene, respectively. In addition, the construction of a phylogenetic tree with the neighbor-joining method was performed using MEGA6 [13]. Moreover, PAML4 analysis through the maximum-likelihood method [14] was used to estimate dS (synonymous substitution rate) and dN (nonsynonymous substitution rate) as well as phylogenetically featured genes investigated by the branch and branch-site model.
성능/효과
Based on our bioinformatics analysis, no plasmid could be detected in JDFM216, similar to other strains, including CECT 5716, F-6, IFO 3956, and NCC 2970, but not 3872 and SNUV175. Among the identified ORFs, 2,085 genes (77.7%) were predicted as functional genes and 597 (32.3%) were unknown or hypothetical genes. As shown in Fig.
As indicated, whole-genome sequencing results showed that JDFM216 is different from the complete genome sequences of the other strains of this species (<97% of ANI compared with others; Table 2).
2, the predicted ORFs were grouped by COG functional and SEED subsystem categorizations. First, COG functional categorization showed that 1,075 ORFs (51.56% of the COG assigned ORFs) belonged to five major COG functional categories, including amino acid transport and metabolism, carbohydrate transport and metabolism, translation, ribosomal structure and biogenesis, recombination, replication, repair, and general function prediction (Fig. 2A). In addition, SEED categorization mainly resulted in ORFs responsible for RNA metabolism, amino acids and derivatives, and DNA metabolism as well as carbohydrate, vitamins, prosthetic groups, and cofactor (54.
In conclusion, we showed that potential candidate genes of L. fermentum strain JDFM216 may be involved in enhancement of the longevity and host immune response via phylogenetically featured genes related to PG synthesis and amino acid metabolism, including methionine in the gut environments. As indicated, whole-genome sequencing results showed that JDFM216 is different from the complete genome sequences of the other strains of this species (<97% of ANI compared with others; Table 2).
참고문헌 (22)
FAO/WHO. 2002. Guidelines for the evaluation of probiotics in food. Food and Agriculture Organization of the United Nations and World Health Organization Working Group Report. Accessed July 20, 2011. http://www.who.int/foodsafety/ fs_management/en/probiotic_guidelines.pdf.
Sornplang P, Piyadeatsoontorn S. 2016. Probiotic isolates from unconventional sources: a review. J. Anim. Sci. Technol. 58: 26.
Song M, Yun B, Moon JH, Park DJ, Lim K, Oh S. 2015. Characterization of selected Lactobacillus strains for use as probiotics. Korean J. Food Sci. Anim. Resour. 35: 551-556.
Lopez-Huertas E. 2015. Safety and efficacy of human breast milk Lactobacillus fermentum CECT 5716. A mini-review of studies with infant formulae. Benef. Microbes 6: 219-224.
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9: 75.
Richter M, Rossello-Mora R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA 106: 19126-19131.
Kim KM, Sung S, Caetano-Anolles G, Han JY, Kim H. 2008. An approach of orthology detection from homologous sequences under minimum evolution. Nucleic Acids Res. 36:e110.
Wheeler R, Chevalier G, Eberl G, Gomperts Boneca I. 2014. The biology of bacterial peptidoglycans and their impact on host immunity and physiology. Cell. Microbiol. 16: 1014-1023.
Kim Y, Mylonakis E. 2012. Caenorhabditis elegans immune conditioning with the probiotic bacterium Lactobacillus acidophilus strain NCFM enhances gram-positive immune responses. Infect. Immun. 80: 2500-2508.
Obeid R. 2013. The metabolic burden of methyl donor deficiency with focus on the betaine homocysteine methyltransferase pathway. Nutrients 5: 3481-3495.
Brown-Borg HM, Buffenstein R. 2016. Cutting back on the essentials: can manipulating intake of specific amino acids modulate health and lifespan? Ageing Res. Rev. DOI:10.1016/ j.arr.2016.08.007.
Cabreiro F, Au C, Leung KY, Vergara-Irigaray N, Cocheme HM, Noori T, et al. 2013. Metformin retards aging in C. elegans by altering microbial folate and methionine metabolism. Cell 153: 228-239.
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