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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

Statistics of annotated genes forClostridium butyricumDKU-01 based on COG (A) and SEED (B) databases.
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Fig1: Statistics of annotated genes forClostridium butyricumDKU-01 based on COG (A) and SEED (B) databases.

Mentions: A total of 79 contigs were generated by a hybrid assembly of reads from the Illumina Miseq (12,127,925 reads of 250bp paired end; ˃554-fold coverage) and Roche 454 (319,439 reads of 8kb-insert paired end; ˃13-fold coverage) systems. The genome size of strain DKU-01 was 4,519,722 bases with 28.62% G + C content and 4,037 predicted CDSs, and 59 tRNA and 17 rRNA operons. The length of the largest contig was 334,920 bp, and the N50 contig was 108,221 bp. The distributions of COG and SEED subsystems of strain DKU-01 are depicted in Figure 1. Among the COG category, R (general function prediction only; 399 ORFs) and G (carbohydrate transport and metabolism; 313 ORFs) were abundant, followed by the E category (amino acid transport and metabolism; 288 ORFs), S category (function unknown; 268 ORFs) and K category (transcription; 251 ORFs). In the subsystem distribution, the subsystems of carbohydrates (454 ORFs) and amino acids and derivatives (385 ORFs) were well-represented. The subsystems of di- and oligosaccharides (127 ORFs) and central carbohydrate metabolism (91 ORFs) were prominently detected within the carbohydrate subsystem. Beta-glucoside metabolism (40 ORFs), maltose and maltodextrin utilization (38 ORFs), lactose and galactose uptake and utilization (22 ORFs), and fructooligosaccharides and raffinose utilization (15 ORFs) were abundant categories within the subsystem of di- and oligosaccharides. Pentose phosphate pathway (20 ORFs), glycolysis and gluconeogenesis (16 ORFs), and the entner-Doudoroff pathway (13 ORFs) were prominently detected within the central carbohydrate metabolism subsystem.Figure 1


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)

Statistics of annotated genes forClostridium butyricumDKU-01 based on COG (A) and SEED (B) databases.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig1: Statistics of annotated genes forClostridium butyricumDKU-01 based on COG (A) and SEED (B) databases.
Mentions: A total of 79 contigs were generated by a hybrid assembly of reads from the Illumina Miseq (12,127,925 reads of 250bp paired end; ˃554-fold coverage) and Roche 454 (319,439 reads of 8kb-insert paired end; ˃13-fold coverage) systems. The genome size of strain DKU-01 was 4,519,722 bases with 28.62% G + C content and 4,037 predicted CDSs, and 59 tRNA and 17 rRNA operons. The length of the largest contig was 334,920 bp, and the N50 contig was 108,221 bp. The distributions of COG and SEED subsystems of strain DKU-01 are depicted in Figure 1. Among the COG category, R (general function prediction only; 399 ORFs) and G (carbohydrate transport and metabolism; 313 ORFs) were abundant, followed by the E category (amino acid transport and metabolism; 288 ORFs), S category (function unknown; 268 ORFs) and K category (transcription; 251 ORFs). In the subsystem distribution, the subsystems of carbohydrates (454 ORFs) and amino acids and derivatives (385 ORFs) were well-represented. The subsystems of di- and oligosaccharides (127 ORFs) and central carbohydrate metabolism (91 ORFs) were prominently detected within the carbohydrate subsystem. Beta-glucoside metabolism (40 ORFs), maltose and maltodextrin utilization (38 ORFs), lactose and galactose uptake and utilization (22 ORFs), and fructooligosaccharides and raffinose utilization (15 ORFs) were abundant categories within the subsystem of di- and oligosaccharides. Pentose phosphate pathway (20 ORFs), glycolysis and gluconeogenesis (16 ORFs), and the entner-Doudoroff pathway (13 ORFs) were prominently detected within the central carbohydrate metabolism subsystem.Figure 1

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