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 will phenotypic off isolated filter systems BD177
Restrict parsimony founded and limitation opportunities phylogenetic trees utilizing the sequence that encodes to the 16S rRNA gene revealed that brand new closest variety to help you BD177 try K. michiganensis and you can K. oxytica (A lot more document 1: Fig. S1, Extra file 2: Table S1). Evolutionary divergence range off 16S rRNA gene series anywhere between BD177 and you will K kinkyads türkiye. michiganensis E718 is minimum well worth (BD177 versus K. michiganensis E718: 0.0079) certainly one of most of the sequences. Biochemical assessment was indeed performed to the BD177 by API20E to confirm their status on K. oxytoca and you may K. michiganensis. Biochemical services out of K. oxytoca ATCC13182(T)(=NCTC13727) and you may K. michiganensis W14(T)(= DSM2544) have been taken from BacDive Webservices pared which have K. oxytoca ATCC13182(T) and you can K. michiganensis W14(T), BD177 is the identical which have W14 from the ?-galactosidase enzyme positive and urease bad, exact same that have ATCC13182(T) inside arginine dihydrolase confident. not, BD177 doesn’t always have the use ability of citrate because the only carbon dioxide supply, not the same as each other types of stresses (Table 2).
Pan-genome study
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, < 500 undetermined bases per 100,000 bases, > 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 analysis off 119 genomes within this analysis. Genomes is actually labeled based on the kinds annotation on the NCBI databases (with the exception of isolate K. michiganensis BD177). an excellent GC content of all genomes was classified according to the varieties annotation regarding the NCBI database. b cake chart of the 119 analyzed Klebsiella sp. genomes. New pan-genome cake graph indicating gene content envisioned using Roary software