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Whole-genome sequence assembly of Pediococcus pentosaceus LI05 (CGMCC 7049) from the human gastrointestinal tract and comparative analysis with representative sequences from three food-borne strains.

Lv LX, Li YD, Hu XJ, Shi HY, Li LJ - Gut Pathog (2014)

Bottom Line: Additionally, P. pentosaceus LI05 genes encoded proteins associated with the biosynthesis of not only three antimicrobials, including prebacteriocin, lysin and colicin V, but also vitamins and functional amino acids, such as riboflavin, folate, biotin, thiamine and gamma-aminobutyrate.This work demonstrated the probiotic properties of P. pentosaceus LI05 from the gut and the three other food-borne P. pentosaceus strains through genomic analyses.We have revealed the major genomic differences between these strains, providing a framework for understanding the probiotic effects of strain LI05, which exhibits unique physiological and metabolic properties.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University, Hangzhou 310003, PR China ; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.

ABSTRACT

Background: Strains of Pediococcus pentosaceus from food and the human gastrointestinal tract have been widely identified, and some have been reported to reduce inflammation, encephalopathy, obesity and fatty liver in animals. In this study, we sequenced the whole genome of P. pentosaceus LI05 (CGMCC 7049), which was isolated from the fecal samples of healthy volunteers, and determined its ability to reduce acute liver injury. No other genomic information for gut-borne P. pentosaceus is currently available in the public domain.

Results: We obtained the draft genome of P. pentosaceus LI05, which was 1,751,578 bp in size and possessed a mean G + C content of 37.3%. This genome encoded an abundance of proteins that were protective against acids, bile salts, heat, oxidative stresses, enterocin A, arsenate and universal stresses. Important adhesion proteins were also encoded by the genome. Additionally, P. pentosaceus LI05 genes encoded proteins associated with the biosynthesis of not only three antimicrobials, including prebacteriocin, lysin and colicin V, but also vitamins and functional amino acids, such as riboflavin, folate, biotin, thiamine and gamma-aminobutyrate. A comparison of P. pentosaceus LI05 with all known genomes of food-borne P. pentosaceus strains (ATCC 25745, SL4 and IE-3) revealed that it possessed four novel exopolysaccharide biosynthesis proteins, additional putative environmental stress tolerance proteins and phage-related proteins.

Conclusions: This work demonstrated the probiotic properties of P. pentosaceus LI05 from the gut and the three other food-borne P. pentosaceus strains through genomic analyses. We have revealed the major genomic differences between these strains, providing a framework for understanding the probiotic effects of strain LI05, which exhibits unique physiological and metabolic properties.

No MeSH data available.


Related in: MedlinePlus

The distribution of the genes associated with the 25 general COG functional categories inP. pentosaceusLI05. The number of genes is shown in parentheses.
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Figure 2: The distribution of the genes associated with the 25 general COG functional categories inP. pentosaceusLI05. The number of genes is shown in parentheses.

Mentions: The genome of P. pentosaceus LI05 was sequenced by the Illumina method (see Methods). A total of 11.05 million 100-bp paired-end reads were generated, which provided over 500-fold coverage of the reference genome. High-quality reads with Q > 30 were assembled using de novo methods to obtain a draft genome of 1.75 Mbp with 8 contigs (the N50 of the assembled contigs was 34.3 Kb; the max length was 318 Kb). The G + C content of P. pentosaceus LI05 was 37.29%. For the main chromosome, 1,638 genes were predicted, 1,555 of which were protein-coding genes. A total of 1,321 protein-coding genes were assigned to putative functions, and the remainder were classified as hypothetical proteins. This genome contained 50 tRNAs and a complete 5S-23S-16S rRNA gene family. The properties and statistics of the genome are shown in Table 1 and Figure 2. As shown in Figure 3, the genome sequence of P. pentosaceus LI05 was highly conserved compared with those of P. pentosaceus ATCC 25745, P. pentosaceus SL4 and P. pentosaceus IE-3.


Whole-genome sequence assembly of Pediococcus pentosaceus LI05 (CGMCC 7049) from the human gastrointestinal tract and comparative analysis with representative sequences from three food-borne strains.

Lv LX, Li YD, Hu XJ, Shi HY, Li LJ - Gut Pathog (2014)

The distribution of the genes associated with the 25 general COG functional categories inP. pentosaceusLI05. The number of genes is shown in parentheses.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4209512&req=5

Figure 2: The distribution of the genes associated with the 25 general COG functional categories inP. pentosaceusLI05. The number of genes is shown in parentheses.
Mentions: The genome of P. pentosaceus LI05 was sequenced by the Illumina method (see Methods). A total of 11.05 million 100-bp paired-end reads were generated, which provided over 500-fold coverage of the reference genome. High-quality reads with Q > 30 were assembled using de novo methods to obtain a draft genome of 1.75 Mbp with 8 contigs (the N50 of the assembled contigs was 34.3 Kb; the max length was 318 Kb). The G + C content of P. pentosaceus LI05 was 37.29%. For the main chromosome, 1,638 genes were predicted, 1,555 of which were protein-coding genes. A total of 1,321 protein-coding genes were assigned to putative functions, and the remainder were classified as hypothetical proteins. This genome contained 50 tRNAs and a complete 5S-23S-16S rRNA gene family. The properties and statistics of the genome are shown in Table 1 and Figure 2. As shown in Figure 3, the genome sequence of P. pentosaceus LI05 was highly conserved compared with those of P. pentosaceus ATCC 25745, P. pentosaceus SL4 and P. pentosaceus IE-3.

Bottom Line: Additionally, P. pentosaceus LI05 genes encoded proteins associated with the biosynthesis of not only three antimicrobials, including prebacteriocin, lysin and colicin V, but also vitamins and functional amino acids, such as riboflavin, folate, biotin, thiamine and gamma-aminobutyrate.This work demonstrated the probiotic properties of P. pentosaceus LI05 from the gut and the three other food-borne P. pentosaceus strains through genomic analyses.We have revealed the major genomic differences between these strains, providing a framework for understanding the probiotic effects of strain LI05, which exhibits unique physiological and metabolic properties.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University, Hangzhou 310003, PR China ; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.

ABSTRACT

Background: Strains of Pediococcus pentosaceus from food and the human gastrointestinal tract have been widely identified, and some have been reported to reduce inflammation, encephalopathy, obesity and fatty liver in animals. In this study, we sequenced the whole genome of P. pentosaceus LI05 (CGMCC 7049), which was isolated from the fecal samples of healthy volunteers, and determined its ability to reduce acute liver injury. No other genomic information for gut-borne P. pentosaceus is currently available in the public domain.

Results: We obtained the draft genome of P. pentosaceus LI05, which was 1,751,578 bp in size and possessed a mean G + C content of 37.3%. This genome encoded an abundance of proteins that were protective against acids, bile salts, heat, oxidative stresses, enterocin A, arsenate and universal stresses. Important adhesion proteins were also encoded by the genome. Additionally, P. pentosaceus LI05 genes encoded proteins associated with the biosynthesis of not only three antimicrobials, including prebacteriocin, lysin and colicin V, but also vitamins and functional amino acids, such as riboflavin, folate, biotin, thiamine and gamma-aminobutyrate. A comparison of P. pentosaceus LI05 with all known genomes of food-borne P. pentosaceus strains (ATCC 25745, SL4 and IE-3) revealed that it possessed four novel exopolysaccharide biosynthesis proteins, additional putative environmental stress tolerance proteins and phage-related proteins.

Conclusions: This work demonstrated the probiotic properties of P. pentosaceus LI05 from the gut and the three other food-borne P. pentosaceus strains through genomic analyses. We have revealed the major genomic differences between these strains, providing a framework for understanding the probiotic effects of strain LI05, which exhibits unique physiological and metabolic properties.

No MeSH data available.


Related in: MedlinePlus