Computational protocol: Genomic Sequence of Klebsiella pneumoniae IIEMP-3, a Vitamin B12-Producing Strain from Indonesian Tempeh

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Protocol publication

[…] The presence of Klebsiella pneumoniae in Indonesian tempeh is intriguing since it produces vitamin B12 in tempeh (), while many strains of this species were known as opportunistic pathogens (). Klebsiella pneumoniae is well known for causing pneumonia, an acute infection that attacks alveoli () and causes liver abscess in human ().Previous molecular profiling employing the Enterobacterial Repetitive Intergenic Consensus PCR (ERIC-PCR) method showed that K. pneumoniae isolates from tempeh exhibited different genetic profiles from those of isolates pathogenic to humans (K. pneumoniae ATCC BAA-2146, K. pneumoniae subsp. pneumoniae ATCC 10031, K. pneumoniae ATCC 35657, and K. pneumoniae FK isolated from a patient with pneumonia) ().The nucleotide sequence of K. pneumoniae strain IIEMP-3 was determined employing a HiSeq 2000 platform (Illumina, San Diego, CA, USA) through a commercial service provider (Macrogen, Seoul, South Korea). A 350-bp paired-end library was constructed and sequenced, producing 10 million paired-end reads with read lengths of 100 bp.De novo assembly was processed using Velvet version 1.2.07 () with k-mer length 63 and no scaffolding option. A scaffolding process using SSPACE () resulted in a 350-bp insert with an error of 0.25. The scaffolding result was fixed by ICORN () with 5 times iteration and evaluated by REAPR () with aggressive breaking; as many as 51 contigs were generated from this workflow. The longest contig achieved is 827,134 bp and total bases were 5,3262,779 bp.Genome annotation was performed employing the NCBI Prokaryotic Genome Annotation Pipeline ( A total of 5,285 genes, 5,096 coding sequences (CDSs), 106 pseudogenes, 5 rRNAs, 77 tRNAs, and 1 noncoding RNA (ncRNAs) were identified. […]

Pipeline specifications

Software tools Velvet, SSPACE, iCORN, REAPR, PGAP
Application De novo sequencing analysis
Organisms Klebsiella pneumoniae
Chemicals Vitamin B 12