Whole-genome sequencing of a novel Chryseobacterium strain isolated from poultry feather waste

Joint Event on 14^th International Conference on Microbial Interactions & Microbial Ecology & 11^th Edition of International Conference on Advances in Microbiology and Public Health

August 19-20, 2019 Vienna, Austria

Adeline Lum Nde, Charimba G, Steyn L, Newman J D and Hugo C

University of the Free State, South Africa
Cape Peninsula University of Technology, South Africa

Posters & Accepted Abstracts: J Med Microb Diagn

Abstract :

Introduction: Prokaryotic delineation has come a long way with the erstwhile methods based mainly on physiology and chemotaxonomy. Due to the limitations of these methods, genotypic methods (16S rRNA, whole-genome sequencing, DNA-DNA hybridization, average nucleotide identity and average amino acid Identity) were included to take into account the overall genome relatedness of microorganisms. The term â??polyphasic taxonomyâ?? which was introduced in 1970 has now been used for prokaryotic delineation which includes phenotypic, chemotaxonomic and genotypic parameters. The use of whole-genome sequencing has recently been recommended to be used for all prokaryotic delineations.

Aim: The aim of this study was to use whole-genome sequencing in an attempt to describe and name a new species of Chryseobacterium isolated from chicken feather waste.

Materials & Methods: Genomic DNA of Chryseobacterium sp. 1_F178T was extracted with a NucleoSpin® microbial DNA extraction kit (macherey-nagel) with the DNA quality checked with a Nanodrop ND-1000 (v3.3.0) spectrophotometer. The Nextera® XT DNA Library prep kit was used to sequence the gDNA according to manufacturerâ??s instructions. An Illumina MiSeq sequencer was used to sequence the genome and the assembly was performed with PATRIC database, with SPAdes 3.10.0 as the assembly method.

Results: The sequenced genomes were uploaded to RAST (Rapid Annotation with Subsystems Technology) database for annotation. Genome related data including gene number, genome size, G+C content, coverage, N50 value, number of contigs, full 16S rRNA sequence etc., were obtained through RAST. The whole-genome shotgun project was deposited in DDBJ/ENA/GenBank. A Venn diagram illustrating the number of shared and unique CDS among strain 1_F178T and its reference strains was constructed. The two closest relatives of strain 1_F178T as determined by 16S rRNA phylogenetic studies were C. jejuense and C. nakagawai. They both had 16S rRNA sequence similarity values (99.10 & 98.75%) above the threshold value (98.5%). Their DDH (31.4 & 32.7), ANI (86.4 & 86.6) and AAI (89.3 & 89.6) values were all less than the threshold value for species delineation. Strain 1_F178T had 2982 genes in common with its closest relatives.

Conclusions: The 16S rRNA, DDH, ANI and AAI values were not within the threshold range for species delineation hence confirming strain 1_F178T as a novel species of Chryseobacterium.

Biography :

E-mail: lumndel@ufs.ac.za