Draft genome sequences of nine strains of brochothrix thermosphacta, carnobacterium divergens, lactobacillus algidus, lactobacillus fuchuensis, lactococcus piscium, leuconostoc gelidum subsp. gasicomitatum, pseudomonas lundensis, and weissella viridescens, a collection of psychrotrophic species involved in meat and seafood spoilage

Simon Poirier, Gwendoline Coeuret, Marie-Christine Champomier-Verges, Stephane Chaillou

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Simon Poirier, Gwendoline Coeuret, Marie-Christine Champomier-Verges, Stephane Chaillou. Draft genome sequences of nine strains of brochothrix thermosphacta, carnobacterium divergens, lactobacillus algidus, lactobacillus fuchuensis, lactococcus piscium, leuconostoc gelidum subsp. gasicomitatum, pseudomonas lundensis, and weissella viridescens, a collection of psychrotrophic species involved in meat and seafood spoilage. Microbiology Resource Announcements, 2018, 6 (24), pp.1-3. 10.1128/genomeA.00479-18 . hal-02618139

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# Draft Genome Sequences of Nine Strains of *Brochothrix thermosphacta*, *Carnobacterium divergens*, *Lactobacillus algidus*, *Lactobacillus fuchuensis*, *Lactococcus piscium*, *Leuconostoc gelidum* subsp. *gasicomitatum*, *Pseudomonas lundensis*, and *Weissella viridescens*, a Collection of Psychrotrophic Species Involved in Meat and Seafood Spoilage

Simon Poirier,ª Gwendoline Coeuret,ª Marie-Christine Champomier-Vergès,ª Stéphane Chaillouª

ªMICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France

**ABSTRACT** In this study, we present the draft genome sequences of nine strains from various psychrotrophic species identified in meat products and being recognized as important emerging food spoilers. Many of these species have only one or few strains being sequenced, and this work will contribute to the improvement of the overall genomic knowledge about them.

The bacterial communities involved in meat and seafood spoilage during storage at low temperature (0 to 8°C) include a wide range of species (1). Some of these food spoilers were characterized during the 1970s, such as *Brochothrix thermosphacta* or *Carnobacterium divergens*, but others were identified very recently, and their roles in food spoilage were only confirmed because noncultural 16S rRNA gene metagenetic analysis and/or plating on culture medium at low temperatures were performed. Most of these spoilers (old or emerging) thriving in cold environments usually share a low level of genomic identification, with only few strains being sequenced. This lack of genomic reference makes food spoilage metagenomic analysis difficult to perform. Here, we present the draft sequencing of several strains isolated from spoiled meat (2), including *Brochothrix thermosphacta* strain 160x8, representing an old spoiler isolated in 1981 from a horse steak; *Lactococcus piscium* strains CMTALT02 and CMTALT17, isolated from spoiled beef carpaccio and representing two new members from this psychrotrophic species that is ubiquitous in meat and seafood products (3); *Leuconostoc gelidum* subsp. *gasicomitatum* strain MFPA44A1401 and *Lactobacillus algidus* strain CMTALT10, representing the paradigm of emerging highly psychrotrophic spoilers that are tedious to cultivate (4–6); *Lactobacillus fuchuensis* strain MFPC41A2801, representing a poorly known member of the *Lactobacillus sakei* phylogenetic clade and which is a species that is often subdominant in meat bacterial ecosystems but whose role as a spoiler remains to be deciphered (7); *Carnobacterium divergens* strain MFPA43A1405, representing a species with high survival fitness in many meat-processing environments; *Pseudomonas lundensis* strain MFPA15A1205, representing a species closely related to another food spoiler, *Pseudomonas fragi*, but which appears to be highly prevalent in beef stored under a vacuum and which harbors strong biofilm formation capacity on meat (8); and finally, *Weissella viridescens* strain MFPC16A2805, representing the paradigm of a sporadic spoiler (9) involved in visual spoilage (green iridescence on meat slices and package swelling due to CO₂ production). This last strain also was

**Received** 30 April 2018 **Accepted** 1 May 2018 **Published** 14 June 2018

**Citation** Poirier S, Coeuret G, Champomier-Vergès M-C, Chaillou S. 2018. Draft genome sequences of nine strains of *Brochothrix thermosphacta*, *Carnobacterium divergens*, *Lactobacillus algidus*, *Lactobacillus fuchuensis*, *Lactococcus piscium*, *Leuconostoc gelidum* subsp. *gasicomitatum*, *Pseudomonas lundensis*, and *Weissella viridescens*, a collection of psychrotrophic species involved in meat and seafood spoilage. Genome Announc 6:e00479-18. https://doi.org/10.1128/genomeA.00479-18.

**Copyright** © 2018 Poirier et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

Address correspondence to Stéphane Chaillou, stephane.chaillou@inra.fr.
<table><caption>TABLE 1 Overview of the draft genome assemblies from nine strains of emerging meat spoilers</caption><thead><tr><th>Species</th><th>Source, yr</th><th>Original strain name (synonym)</th><th>Collection name</th><th>Genetic element</th><th>No. of contigs</th><th>Size (bp)</th><th>Coverage (x)</th><th>No. of CDS<sup>a</sup></th><th>BioProject no.</th><th>Assembly accession no.</th></tr></thead><tbody><tr><td>Brochothrix thermosphacta</td><td>Horse meat, 1981</td><td>J160x8 (HO01)</td><td>CIP 110942</td><td>Chromosome</td><td>32</td><td>2,443,096</td><td>70</td><td>2,473</td><td>PRJEB21917</td><td>OBMV01000001 to OBMV01000032</td></tr><tr><td rowspan="2">Carnobacterium divergens</td><td>Beef carpaccio, 2009</td><td>MFPA43A1405</td><td>CIP 110938</td><td>Plasmid pJOUY160xA1</td><td>1</td><td>44,938</td><td>85</td><td>48</td><td>PRJEB21906</td><td>OBMV01000033</td></tr><tr><td>Beef carpaccio, 2013</td><td>CMTALT10</td><td>CIP 110929</td><td>Chromosome</td><td>31</td><td>2,702,442</td><td>62</td><td>2,686</td><td>PRJEB21909</td><td>OGVA01000001 to OGVA01000031</td></tr><tr><td rowspan="2">Lactobacillus algidus</td><td>Beef carpaccio, 2009</td><td>MFPA44A1401</td><td>CIP 110936</td><td>Chromosome</td><td>20</td><td>1,624,384</td><td>56</td><td>1,582</td><td>PRJEB21909</td><td>OBKY01000001 to OBKY01000020</td></tr><tr><td>Beef carpaccio, 2013</td><td>CMTALT02</td><td>CIP 110937</td><td>Plasmid pCMTALT10B</td><td>4</td><td>13,563</td><td>302</td><td>19</td><td>PRJEB21913</td><td>OBKY01000021 to OBKY01000024</td></tr><tr><td>Lactobacillus fuchuensis</td><td>Beef carpaccio, 2009</td><td>MFPC41A2801</td><td>CIP 110928</td><td>Chromosome</td><td>51</td><td>2,045,293</td><td>65</td><td>1,977</td><td>PRJEB21913</td><td>OGVC01000001 to OGVC01000051</td></tr><tr><td>Lactococcus piscium</td><td>Beef carpaccio, 2013</td><td>CMTALT02</td><td>CIP 110936</td><td>Chromosome</td><td>35</td><td>2,154,856</td><td>63</td><td>2,177</td><td>PRJEB21910</td><td>OGVB01000001 to OGVB01000035</td></tr><tr><td>Lactococcus piscium</td><td>Beef carpaccio, 2013</td><td>CMTALT17</td><td>CIP 110937</td><td>Chromosome</td><td>68</td><td>2,271,863</td><td>63</td><td>2,307</td><td>PRJEB21911</td><td>OBKP01000001 to OBKP01000068</td></tr><tr><td>Leuconostoc gasicomitatum</td><td>Beef carpaccio, 2009</td><td>MFPA44A1401</td><td>CIP 110927</td><td>Chromosome</td><td>50</td><td>1,895,812</td><td>35</td><td>1,960</td><td>PRJEB21908</td><td>OBMW01000001 to OBMW01000050</td></tr><tr><td>Pseudomonas lundensis</td><td>Beef carpaccio, 2009</td><td>MFPA15A1205</td><td>CIP 110941</td><td>Chromosome</td><td>56</td><td>5,019,826</td><td>52</td><td>4,871</td><td>PRJEB21912</td><td>OBKZ01000001 to OBKZ01000056</td></tr><tr><td>Weissella viridescens</td><td>Beef carpaccio, 2009</td><td>MFPC16A2805</td><td>CIP 110940</td><td>Chromosome</td><td>13</td><td>1,012,612</td><td>149</td><td>1,024</td><td>PRJEB22329</td><td>OBHM01000001 to OBHM01000013</td></tr><tr><td></td><td></td><td></td><td></td><td>Plasmid pMFPC16A2805B</td><td>1</td><td>16,484</td><td>344</td><td>15</td><td></td><td>OBHM01000014</td></tr><tr><td></td><td></td><td></td><td></td><td>Plasmid pMFPC16A2805C</td><td>1</td><td>11,586</td><td>507</td><td>12</td><td></td><td>OBHM01000015</td></tr></tbody></table>

<footnote><sup>a</sup>CDS, coding sequences.</footnote>
revealed to possess one of the smallest genomes (~1 Mb) ever sequenced for a lactic acid bacterium.

Details of the draft genomes are given in Table 1. Whole-genome sequencing of these strains was carried out by Eurofins MWG Operon Laboratories (Ebersberg, Germany) using Illumina MiSeq 2 × 150-bp paired-end libraries. Reads were assembled de novo by the Velvet software (10). All contigs were aligned against a relevant complete genome of closely related strains or species using progressiveMauve (11), and annotation was performed with the MicroScope platform (12).

**Accession number(s).** The sequence data have been deposited in DDBJ/ENA/GenBank under the accession numbers cited in Table 1.

## ACKNOWLEDGMENTS

This work and S.P.'s postdoctoral fellowship were supported by the ANR RedLosses project, grant ANR-16-CE21-0006, operated by the French Agence Nationale de la Recherche.

We are grateful for the INRA MIGALE bioinformatics platform (http://migale.jouy.inra.fr) for providing computational resources and data storage. The LABGeM (CEA/IG/Genoscope & CNRS UMR8030) and the France Génomique National Infrastructure (funded as part of the Programme d'Investissements d'Avenir managed by Agence Nationale pour la Recherche, contract ANR-10-INBS-09) are acknowledged for support within the MicroScope annotation platform.

## REFERENCES

1. Chaillou S, Chaulot-Talmon A, Caekebeke H, Cardinal M, Christieans S, Denis C, Desmonts MH, Dousset X, Feurer C, Hamon E, Joffraud J-J, La Carbona S, Leroi F, Leroy S, Lorre S, Macé S, Pilet M-F, Prévost H, Rivollier M, Roux D, Talon R, Zagorec M, Champomier-Vergès M-C. 2015. Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage. ISME J 9:1105-1118. https://doi.org/10.1038/ismej.2014.202.

2. Lucquin I, Zagorec M, Champomier-Vergès M, Chaillou S. 2012. Finger-print of lactic acid bacteria population in beef carpaccio is influenced by storage process and seasonal changes. Food Microbiol 29:187-196. https://doi.org/10.1016/j.fm.2011.08.001.

3. Saraoui T, Leroi F, Björkroth J, Pilet MF. 2016. *Lactococcus piscium*: a psychrotrophic lactic acid bacterium with bioprotective or spoilage activity in food—a review. J Appl Microbiol 121:907-918. https://doi.org/10.1111/jam.13179.

4. Johansson P, Paulin L, Säde E, Salovuori N, Alatalo ER, Björkroth KJ, Auvinen P. 2011. Genome sequence of a food spoilage lactic acid bacterium, *Leuconostoc gasicomitatum* LMG 18811T, in association with specific spoilage reactions. Appl Environ Microbiol 77:4344-4351. https://doi.org/10.1128/AEM.00102-11.

5. Kato Y, Sakala RM, Hayashidani H, Kiuchi A, Kaneuchi C, Ogawa M. 2000. *Lactobacillus algidus* sp. nov., a psychrophilic lactic acid bacterium isolated from vacuum-packaged refrigerated beef. Int J Syst Evol Microbiol 50:1143-1149. https://doi.org/10.1099/00207713-50-3-1143.

6. Pothakos V, Snauwaert C, De Vos P, Huys G, Devlieghere F. 2014. Psychrotrophic members of *Leuconostoc gasicomitatum*, *Leuconostoc gelidum* and *Lactococcus piscium* dominate at the end of shelf-life in

packaged and chilled-stored food products in Belgium. Food Microbiol 39:61-67. https://doi.org/10.1016/j.fm.2013.11.005.

7. Sakala RM, Kato Y, Hayashidani H, Murakami M, Kaneuchi C, Ogawa M. 2002. *Lactobacillus fuchuensis* sp. nov., isolated from vacuum-packaged refrigerated beef. Int J Syst Evol Microbiol 52:1151-1154. https://doi.org/10.1099/00207713-52-4-1151.

8. Liu Y-J, Xie J, Zhao L-J, Qian Y-F, Zhao Y, Liu X. 2015. Biofilm formation characteristics of *Pseudomonas lundensis* isolated from meat: *Pseudomonas lundensis* biofilms. J Food Sci 80:M2904-M2910. https://doi.org/10.1111/1750-3841.13142.

9. Fusco V, Quero GM, Cho G-S, Kabisch J, Meske D, Neve H, Bockelmann W, Franz CMAP. 2015. The genus *Weissella*: taxonomy, ecology and biotechnological potential. Front Microbiol 6:155. https://doi.org/10.3389/fmicb.2015.00155.

10. Zerbino DR. 2010. Using the Velvet de novo assembler for short-read sequencing technologies. Curr Protoc Bioinformatics 11:11.5. https://doi.org/10.1002/0471250953.bi1105s31.

11. Darling AE, Mau B, Perna NT. 2010. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5:e11147. https://doi.org/10.1371/journal.pone.0011147.

12. Vallenet D, Belda E, Calteau A, Cruveiller S, Engelen S, Lajus A, Le Fèvre F, Longin C, Mornico D, Roche D, Rouy Z, Salvignol G, Scarpelli C, Thil Smith AA, Weiman M, Médigue C. 2013. MicroScope-an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Res 41:D636-D647. https://doi.org/10.1093/nar/gks1194.