# Draft Genome Sequence of Herminiimonas contaminans Strain CCM 7991 T, a Biopharmaceutical Contaminant

Luis Johnson Kangale, Rita Zgheib, Eric Ghigo, Didier Raoult,

Pierre-Edouard Fournier

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Luis Johnson Kangale, Rita Zgheib, Eric Ghigo, Didier Raoult, Pierre-Edouard Fournier. Draft Genome Sequence of Herminiimonas contaminans Strain CCM 7991 T, a Biopharmaceutical Contaminant. Microbiology Resource Announcements, 2021, 10 (7), 10.1128/mra.01432-20. http://dx.doi.org/10.1128/mra.01432-20

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# Draft Genome Sequence of *Herminiimonas contaminans* Strain CCM 7991<sup>T</sup>, a Biopharmaceutical Contaminant

Luis Johnson Kangale,ª,ᵇ Rita Zgheib,ª,ᵇ Eric Ghigo,ᵇ,ᶜ Didier Raoult,ᵇ,ᶜ,ᵈ Pierre-Edouard Fournierª,ᵇ

**ABSTRACT** *Herminiimonas contaminans* was described as a new bacterial species, a contaminant isolated from a biopharmaceutical production process in Sweden. Since the genome sequence was not available, we performed draft genome sequencing. The genome of strain CCM 7991T (=CCUG 53591T = DSM 28178T = Marseille-Q4544T) was 4,038,814 bp long, with a G+C content of 53.9%; a total of 3,860 genes were identified, along with 3 rRNAs, 44 tRNAs, and 4 noncoding RNAs (ncRNAs).

The genus *Herminiimonas* was first described by Fernandes et al. in 2005, with *Herminiimonas fonticola* as the type species (1). Strain CCM 7991 is a contaminant isolated from a biopharmaceutical production process in Sweden and was described as the type strain of *Herminiimonas contaminans* (2). Working on the planarian microbiota, we identified a new bacterial species. The characterization of this species required a comparison with *H. contaminans*, but no genome sequence was available for *H. contaminans* at the time. We acquired *H. contaminans* DSM 28178T (=CCM 7991T) from the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ). *H. contaminans* DSM 28178T was then deposited in the Collection des Souches de l'Unité des Rickettsies (CSUR) culture collection under the number Marseille-Q4544T. However, because no genome sequence was available for *H. contaminans*, we performed whole-genome sequencing for this species. In our laboratory, strain Marseille-Q4544T was grown on Columbia agar supplemented with 5% sheep blood (bioMérieux, Marcy l'Etoile, France), at 28°C for 24 h. To extract bacterial genomic DNA (gDNA) from strain Marseille-Q4544T, a mechanical treatment was first performed on a single colony by glass beads acid washed (Sigma-Aldrich Chimie, Saint-Quentin-Fallavier, France) using a FastPrep-24 5G grinder (MP Biomedicals, Illkirch, France) at maximum speed (6.5) for 90 sec. Then, after a 30-min lysozyme incubation at 37°C, DNA was extracted on an EZ1 BioRobot system with the EZ1 DNA tissue kit (Qiagen, Hilden, Germany). The gDNA was sequenced using MiSeq technology (Illumina, Inc., San Diego, CA, USA) (3) with the Nextera XT DNA sample prep kit (Illumina) and mate pair strategy. The gDNA was fragmented and then amplified by 12 cycles of PCR, followed by the addition of tag adapters and the introduction of dual-index barcodes. The libraries were purified using AMPure XP beads (Beckman Coulter, Inc., Fullerton, CA, USA), normalized using specific beads following the Nextera XT protocol, and pooled into a single library for sequencing. After 39 h, automated cluster generation and paired-end sequencing with dual-index reads were performed in a single run in 2 × 250-bp format. Total information of 5.51 Gb was obtained from a 578,000/mm² cluster density with clusters passing quality control filters at 93.8%. Within this run, the index representation

**Citation** Kangale LJ, Zgheib R, Ghigo E, Raoult D, Fournier P-E. 2021. Draft genome sequence of *Herminiimonas contaminans* strain CCM 7991T, a biopharmaceutical contaminant. *Microbiol Resour Announc* 10:e01432-20. https://doi.org/10.1128/MRA.01432-20.

**Editor** J. Cameron Thrash, University of Southern California

**Copyright** © 2021 Kangale et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

Address correspondence to Eric Ghigo, eric.ghigo@gmail.com, or Pierre-Edouard Fournier, pierre-edouard.fournier@univ-amu.fr.

**Received** 14 December 2020

**Accepted** 27 January 2021

**Published** 18 February 2021

<footnote>ªAix-Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France</footnote>

<footnote>ᵇIHU Méditerranée Infection, Marseille, France</footnote>

<footnote>ᶜAix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France</footnote>

<footnote>ᵈSpecial Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia</footnote>

<footnote>ᵉTechno-Jouvence, Marseille, France</footnote>
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for strain Marseille-Q4544<sup>T</sup> was determined to be 6.2%. The 11,232,685 paired-end reads of the MiSeq run were quality checked using FastQC version 0.11.8 with default parameters (4). We used Shovill on the Galaxy Australia server (www.usegalaxy.org.au) (Galaxy version 1.0.4+galaxy0) with the following options: Trimmomatic version 0.39 for trimming the reads and SPAdes version 3.14 for genomic assembly, with default parameters (5, 6). Strain Marseille-Q4544<sup>T</sup> was assembled into 56 contigs (N<sub>50</sub>, 201,954 bp; L<sub>50</sub>, 6; coverage, 46.95×) for a total size of 4,038,814 bp, with a G+C content of 53.9%. Genomic annotation was obtained using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) version 4.13 (7). A total of 3,860 genes were identified, along with 3 rRNAs, 44 tRNAs, and 4 noncoding RNAs (ncRNAs). A BLASTN search of complete 16S rRNA gene sequences on NCBI showed 100% identity with *Herminiimonas contaminans* (16S rRNA GenBank accession number NR_108871.1).

**Data availability.** The genome and read sequences of *Herminiimonas contaminans* strain Marseille-Q4544<sup>T</sup> (BioProject PRJNA677876 and BioSample SAMN16775933) were deposited in GenBank under the accession numbers JADOEL010000001 through JADOEL010000056 and SRR13040143, respectively. *Herminiimonas contaminans* strain Marseille-Q4544<sup>T</sup> is available in the CSUR, CCM, CCUG, and DSMZ culture collections under the accession numbers CSUR Q4544<sup>T</sup>, CCM 7991<sup>T</sup>, CCUG 53591<sup>T</sup>, and DSM 28178<sup>T</sup>, respectively.

## ACKNOWLEDGMENTS

The study was funded by the Méditerranée-Infection Foundation, National Research Agency, under the program Investissements d'avenir, reference number ANR-10-IAHU-03, and by Région Provence Alpes Côte d'Azur and European funding number FEDER IHUBIOTK. L.J.K. is a fellow of the Méditerranée-Infection Foundation.

We thank Aurelia Caputo for submitting the genomic sequences to GenBank.

L.J.K. conceived the experiments, realized the experiments, analyzed the data, prepared the figures, and wrote the manuscript. R.Z. submitted the genome and read sequences to NCBI. E.G. and P.-E.F. designed the experiments, conceived the experiments, and analyzed the data.

We have no conflicts of interest to declare. The funding sources had no role in the study design, data collection and analysis, decision to publish, or manuscript preparation.

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