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Genome sequencing of Clostridium butyricum DKU-01, isolated from infant feces.

Mo S, Kim BS, Yun SJ, Lee JJ, Yoon SH, Oh CH - Gut Pathog (2015)

Bottom Line: The extracted 16S rRNA gene from genome sequences of DKU-01 was similar to Clostridium butyricum with 99.63% pairwise similarity.Genes related to Fructooligosaccharide utilization were detected in the genome of strain DKU-01 and compared with other genera, such as Bifidobacterium and Streptococcus.We found that strain DKU-01 can metabolize a wide range of carbohydrates in comparative genome result.

View Article: PubMed Central - PubMed

Affiliation: Biosafety & Validation Center, Clinical Trial Institute, Dankook University, Choenan, 330-714 Republic of Korea.

ABSTRACT

Background: Clostridium butyricum is a butyric acid-producing anaerobic bacteriuma, and commonly present as gut microbiota in humans. This species has been used as a probiotic for the prevention of diarrhea in humans. In this study, we report the draft genome of C. butyricum DKU-01, which was isolated from infant feces, to better understand the characteristics of this strain so that it can later be used in the development of probiotic products.

Results: A total of 79 contigs generated by hybrid assembly of sequences obtained from Roche 454 and Illumina Miseq sequencing systems were investigated. The assembled genome of strain DKU-01 consisted of 4,519,722 bp (28.62% G + C content) with a N50 contig length of 108,221 bp and 4,037 predicted CDSs. The extracted 16S rRNA gene from genome sequences of DKU-01 was similar to Clostridium butyricum with 99.63% pairwise similarity. The sequence of strain DKU-01 was compared with previously reported genome sequences of C. butyricum. The value of average nucleotide identity between strains DKU-01 and C. butyricum 60E3 was 98.74%, making it the most similar strain to DKU-01.

Conclusions: We sequenced the DKU-01 strain isolated from infant feces, and compared it with the available genomes of C. butyricum on a public database. Genes related to Fructooligosaccharide utilization were detected in the genome of strain DKU-01 and compared with other genera, such as Bifidobacterium and Streptococcus. We found that strain DKU-01 can metabolize a wide range of carbohydrates in comparative genome result. Further analyses of the comparative genome and fermentation study can provide the information necessary for the development of strain DKU-01 for probiotics.

No MeSH data available.


Related in: MedlinePlus

Genome tree of strain DKU-01 withClostridium butyricumstrains obtained from NCBI database.
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Fig2: Genome tree of strain DKU-01 withClostridium butyricumstrains obtained from NCBI database.

Mentions: Extracted 16S rRNA gene of strain DKU-01 had the highest pairwise similarity with Clostridium butyricum DSM 10702T (99.63%). The genome tree of strain DKU-01 was generated by the ANI values of C. butyricum genomes, which are available on a public database (Figure 2). The results of 16S rRNA gene identification and genome tree indicated that the genome sequences of strain DKU-01 was free of contaminations. Six genome sequences of C. butyricum were compared with the genome sequences of DKU-01, and two strains of C. butyricum, 60E3 and DSM 10702T, were clustered with strain DKU-01. The ANI value of strain DKU-01 to 60E3 was 98.74% and to DSM 10702T was 98.73%. The estimated DNA-DNA hybridization values of strain DHU-01 to 60E3 (90.9 ± 2%) and to DSM 10702T (90.3 ± 2.08%) were obtained by the GGDC. The genomic features and subsystem distributions were compared among three strains (Additional file 1: Table S1). The lowest number of contigs was obtained from strain 60E3 (10), while the highest number of contigs was obtained from strain DSM 10702T (207). The abundances of gene contents in the subsystems were similar in all three genomes.Figure 2


Genome sequencing of Clostridium butyricum DKU-01, isolated from infant feces.

Mo S, Kim BS, Yun SJ, Lee JJ, Yoon SH, Oh CH - Gut Pathog (2015)

Genome tree of strain DKU-01 withClostridium butyricumstrains obtained from NCBI database.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4390090&req=5

Fig2: Genome tree of strain DKU-01 withClostridium butyricumstrains obtained from NCBI database.
Mentions: Extracted 16S rRNA gene of strain DKU-01 had the highest pairwise similarity with Clostridium butyricum DSM 10702T (99.63%). The genome tree of strain DKU-01 was generated by the ANI values of C. butyricum genomes, which are available on a public database (Figure 2). The results of 16S rRNA gene identification and genome tree indicated that the genome sequences of strain DKU-01 was free of contaminations. Six genome sequences of C. butyricum were compared with the genome sequences of DKU-01, and two strains of C. butyricum, 60E3 and DSM 10702T, were clustered with strain DKU-01. The ANI value of strain DKU-01 to 60E3 was 98.74% and to DSM 10702T was 98.73%. The estimated DNA-DNA hybridization values of strain DHU-01 to 60E3 (90.9 ± 2%) and to DSM 10702T (90.3 ± 2.08%) were obtained by the GGDC. The genomic features and subsystem distributions were compared among three strains (Additional file 1: Table S1). The lowest number of contigs was obtained from strain 60E3 (10), while the highest number of contigs was obtained from strain DSM 10702T (207). The abundances of gene contents in the subsystems were similar in all three genomes.Figure 2

Bottom Line: The extracted 16S rRNA gene from genome sequences of DKU-01 was similar to Clostridium butyricum with 99.63% pairwise similarity.Genes related to Fructooligosaccharide utilization were detected in the genome of strain DKU-01 and compared with other genera, such as Bifidobacterium and Streptococcus.We found that strain DKU-01 can metabolize a wide range of carbohydrates in comparative genome result.

View Article: PubMed Central - PubMed

Affiliation: Biosafety & Validation Center, Clinical Trial Institute, Dankook University, Choenan, 330-714 Republic of Korea.

ABSTRACT

Background: Clostridium butyricum is a butyric acid-producing anaerobic bacteriuma, and commonly present as gut microbiota in humans. This species has been used as a probiotic for the prevention of diarrhea in humans. In this study, we report the draft genome of C. butyricum DKU-01, which was isolated from infant feces, to better understand the characteristics of this strain so that it can later be used in the development of probiotic products.

Results: A total of 79 contigs generated by hybrid assembly of sequences obtained from Roche 454 and Illumina Miseq sequencing systems were investigated. The assembled genome of strain DKU-01 consisted of 4,519,722 bp (28.62% G + C content) with a N50 contig length of 108,221 bp and 4,037 predicted CDSs. The extracted 16S rRNA gene from genome sequences of DKU-01 was similar to Clostridium butyricum with 99.63% pairwise similarity. The sequence of strain DKU-01 was compared with previously reported genome sequences of C. butyricum. The value of average nucleotide identity between strains DKU-01 and C. butyricum 60E3 was 98.74%, making it the most similar strain to DKU-01.

Conclusions: We sequenced the DKU-01 strain isolated from infant feces, and compared it with the available genomes of C. butyricum on a public database. Genes related to Fructooligosaccharide utilization were detected in the genome of strain DKU-01 and compared with other genera, such as Bifidobacterium and Streptococcus. We found that strain DKU-01 can metabolize a wide range of carbohydrates in comparative genome result. Further analyses of the comparative genome and fermentation study can provide the information necessary for the development of strain DKU-01 for probiotics.

No MeSH data available.


Related in: MedlinePlus