The Draft Whole-Genome Sequence of the Antibiotic Producer Empedobacter haloabium ATCC 31962 Provides Indications for Its Taxonomic Reclassification.

Henrike Miess,Friederike Hanssen,Stefan Czemmel,Patricia Arlt,Kay Nieselt,Alexander Kristian Apel,Tilmann Weber,Harald Gross,Sven Nahnsen,David Rasko

doi:10.1128/mra.01120-19

Henrike Miess, Friederike Hanssen + Show 8 more

Open Access

https://doi.org/10.1128/mra.01120-19

Copy DOI

Abstract

Strain ATCC 31962 was formerly taxonomically classified as Empedobacter haloabium and reported to be the producer of the lipopeptide antibiotic empedopeptin. Here, we report the draft genome sequence of ATCC 31962, which encodes regions that suggest a distinct biosynthetic capacity and suggests its taxonomic reclassification.

Highlights

Strain ATCC 31962 was grown in 20 ml meat medium (2% soluble starch, 1% glucose, 0.2% meat extract, 0.2% Bacto yeast extract, 0.5% N-Z-Case, 0.2% CaCO3, and double-distilled water [ddH2O] [pH 7.0]) for 2 to 3 days at 27°C on a rotary shaker (140 rpm)
For genomic DNA isolation, the Qiagen genomic DNA purification kit was used in combination with 100/G Genomic-tips according to the manufacturer’s protocol, except that for the bacterial lysis, the handled volumes were doubled, and the incubation time at 50°C was prolonged until a clear lysate was obtained
FastQC did not reveal any adapter content, and base quality was high, so all original reads were subjected to the second assembly

Summary

Introduction

Strain ATCC 31962 was grown in 20 ml meat medium (2% soluble starch, 1% glucose, 0.2% meat extract, 0.2% Bacto yeast extract, 0.5% N-Z-Case, 0.2% CaCO3, and double-distilled water [ddH2O] [pH 7.0]) for 2 to 3 days at 27°C on a rotary shaker (140 rpm). For genomic DNA isolation, the Qiagen genomic DNA purification kit was used in combination with 100/G Genomic-tips according to the manufacturer’s protocol, except that for the bacterial lysis, the handled volumes were doubled, and the incubation time at 50°C was prolonged until a clear lysate was obtained. The whole-genome sequence of ATCC 31962 was obtained using a combined strategy of paired-end sequencing (NEBNext sample preparation kit, 2 ϫ 76 bp) with an Illumina GA IIx instrument and mate pair sequencing (Nextera mate pair sample preparation kit v2, 151 bp) with an Illumina MiSeq instrument. FastQC v0.11.2 [5] was used to check both libraries for adapter content and base quality.

Results

Conclusion