Abilities

1.3 Gbp) were processed to remove SMRT bell adapters, short and low-quality reads (< 80% accuracy) using SMRT Analysis version 2.3 ( A total of 155,828 filtered reads (average length, 8.9 Kb) were used for de novo assembly using Celera Assembler , with self-correction of the PacBio reads. A total of 1091 Mb paired-end Illumina reads screened from a 500-bp genomic library were mapped using SOAP to the bacterial plasmid database for tracing the presence of any plasmid and filling the gaps. The de novo assembly resulted in five contigs, representing the K. michiganensis BD177 complete genome of 6,812,698 bp with GC content % in a single chromosome and four plasmids. The annotated genome contains 6714 genes, 25rRNA genes, and 86 tRNA genes (Table 1).

16S rRNA phylogenetic study and you can phenotypic of isolated strain BD177

Maximum parsimony dependent and you can maximum probability phylogenetic trees using the succession you to definitely encodes with the 16S rRNA gene showed that the fresh new closest types so you can BD177 are K. michiganensis and you will K. oxytica (Extra file step 1: Fig. S1, Most document dos: Dining table S1). Evolutionary divergence distance out-of 16S rRNA gene sequence anywhere between BD177 and K. michiganensis E718 are minimum worthy of (BD177 versus K. michiganensis E718: 0.0079) certainly every sequences. Biochemical testing was basically performed on BD177 by API20E to confirm their condition regarding K. oxytoca and you will K. michiganensis. Biochemical features off K. oxytoca ATCC13182(T)(=NCTC13727) and you may K. michiganensis W14(T)(= DSM2544) was in fact taken from BacDive Webservices pared that have K. oxytoca ATCC13182(T) and you will K. michiganensis W14(T), BD177 is the same that have W14 on ?-galactosidase chemical confident and you can urease https://datingranking.net/tr/farmers-dating-site-inceleme negative, exact same having ATCC13182(T) when you look at the arginine dihydrolase confident. However, BD177 does not have the use feature out of citrate as only carbon provider, distinct from both method of challenges (Desk dos).

Pan-genome analysis

In this study, we considered the 128 publicly available genome assemblies for the Klebsiella sp. (Additional file 3: Table S2). Of these genomes, 26 were originally annotated as K. aerogenes, 13 were K. michiganensis, 27 were K. oxytoca, and 15 were K. pneumoniae. 25 were K. quasipneumoniae, 1 was K. quasivariicola, 21 were K. variicola. The type strain genome of each species is included in these genomes. These genome assemblies were passed strict quality control (N75 values of > 10,000 bp, 90% completeness and < 5% contamination) by quast and checkm (Additional file 4: Table S3). This resulted in a total of 118 Klebsiella sp. strains studied, where ten low-quality genome assemblies were discarded. The GC contents of the species K. michiganensis, K. oxytoca, K. pneumoniae, K. variicola, and K. quasipneumoniae showed low intraspecies variation, with respective average values of , , , and % (Fig. 1a), whereas larger interspecies diversity was observed. In contrast, K. aerogenes genomes can be divided into two groups, a large group showing a GC content in the range of that of Klebsiella aerogenes ( to %) and a small group of two genomes ( and %) showing a much greater GC content, similar to that of the K. pneumoniae, K.variicola and K. quasipneumoniae genomes (respective average values about 57%). Based on GC content of the genome, K. pneumoniae, K.variicola, K. quasivariicola, and K. quasipneumoniae were considered as a high GC group content, and K. michiganensis and K. oxytoca were considered as a low GC content group. The genome sequence of our new isolate, which we designated K. michiganensis BD177 with % GC content (Table 1), shows a similar to that of the low GC content Klebsiella sp. group (Fig. 1a).

Pan-genome investigation from 119 genomes contained in this study. Genomes was grouped predicated on the species annotation in the NCBI databases (apart from split K. michiganensis BD177). an effective GC posts of all genomes is actually categorized centered on its species annotation throughout the NCBI databases. b cake chart of 119 analyzed Klebsiella sp. genomes. The latest bowl-genome pie graph appearing gene blogs envisioned with the use of Roary application