Next Article in Journal
DNA Barcoding and Analysis of Nutritional Properties as a Tool for Enhancing Traceability of Anchovies (Engraulis encrasicolus L.) Fished in the Italian Southern Adriatic Sea
Previous Article in Journal
The Complete Chloroplast Genome of Camellia tianeensis (Camellia L.) and Phylogenetic Relationships with Other Plants of the Genus Camellia
Previous Article in Special Issue
Genomic Alterations and Microbiota Crosstalk in Hepatic Cancers: The Gut–Liver Axis in Tumorigenesis and Therapy
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Genes
Volume 16
Issue 10
10.3390/genes16101218
genes-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Genomic Relationship Between Brochothrix campestris and Its Phages: A Cross-Replicon and Interspecies Perspective

by
Sabrina A. Attéré
1,2,
Laurie C. Piché
1,2 and
Antony T. Vincent
1,2,*
1
Département des Sciences Animales, Faculté des Sciences de L’agriculture et de L’alimentation, Université Laval, Quebec, QC G1V 0A6, Canada
2
Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC G1V 0A6, Canada
*
Author to whom correspondence should be addressed.
Genes 2025, 16(10), 1218; https://doi.org/10.3390/genes16101218
Submission received: 26 August 2025 / Revised: 6 October 2025 / Accepted: 14 October 2025 / Published: 15 October 2025
(This article belongs to the Special Issue Feature Papers in Microbial Genetics and Genomics)
Browse Figures
Versions Notes

Abstract

Background/Objectives: The bacterium Brochothrix campestris is closely related to Brochothrix thermosphacta, a known food spoilage agent, and Listeria monocytogenes, the causative agent of listeriosis. B. campestris garnered attention several years ago because it produces brochocin-C, a bacteriocin capable of inhibiting the growth of certain pathogens. It has been recently suggested that phages play a significant role in the evolution of B. thermosphacta, similar to the role they play for L. monocytogenes. However, understanding the role of phages in the evolution of B. campestris has been challenging because only a draft of genome sequences of a single B. campestris strain was previously available. Methods: In this study, DNA from the B. campestris type strain DSM 4712 was sequenced using Oxford Nanopore and Illumina technologies to obtain complete, high-quality genome sequences. Results: The assembly revealed the presence of a plasmid and a phage-plasmid. Additionally, chromosomal analysis identified several genomic islands, including one harboring the brochocin genes, suggesting that these genes may have undergone horizontal transfer. Conclusions: This study underscores the potential importance of phages in the evolution of B. campestris, and also highlights the need for further research into the interactions between Brochothrix species and their associated phages to better understand these complex biological relationships.

1. Introduction

The Brochothrix bacterium genus comprises two species: B. thermosphacta and B. campestris. B. thermosphacta strains are known spoilage agents and are frequently found on foods, mainly meats [1]. Currently, few strains of B. campestris are known, and they originate from soil or grass [2]. Although B. campestris may be considered an environmental bacterium, it is thought to have similar metabolic capacities to B. thermosphacta, including the ability to spoil meats [3]. B. campestris was studied from the 1990s for its ability to produce a two-peptide bacteriocin, brochocin-C, which has the capacity to inhibit pathogens such as Listeria sp. and Clostridium botulinum [4,5,6]. Consequently, this species could be of potential biotechnological interest.
Only one genomic sequence of B. campestris is currently publicly available (RefSeq: GCF_000525915.1)—the type strain (S3, DSM 4712, ATCC 43754, CIP 102920)—and no publications are associated with it. In addition, the genome of this species was initially sequenced using the IonTorrent technology; therefore, the assembly is fragmented into 128 contigs, making it difficult to study the architecture of the genome.
Recently, Nanopore sequencing of the B. thermosphacta type strain (DSM 20171) revealed variability in the chromosome sequences of this species, attributed to prophages (i.e., phage DNA integrated into the bacterial chromosome) and genomic islands [7]. Prophages are known to play an important role in the genomic diversity and adaptation of L. monocytogenes [8,9,10], which is the etiological agent of listeriosis and most closely phylogenetically related to the Brochothrix genus [11].
Mobile genetic elements are involved in the adaptation and evolution of bacteria [12]. Some of them are extra chromosomal molecules (e.g., plasmids) while others can be integrated into the chromosome (e.g., prophages). In every case, mobile genetic elements may confer multiple selective advantages to their hosts, including virulence and antibiotic resistance [13].
Phage-plasmids were first observed approximately 60 years ago in Escherichia coli and were quickly adopted as molecular tools [14,15]. However, they remain relatively obscure because they are less frequently encountered in nature and, consequently, are less well characterized. Briefly, phage-plasmids are temperate phages capable of replicating like plasmids [16]. As such, they possess viral genes responsible for functions such as lysogeny, lysis, virion structure, and DNA packaging. Additionally, like plasmids, they carry functions involved in replication and partitioning. A recent large-scale study revealed that phage-plasmids are present in several bacteria and their size distribution is bimodal, with one peak around 50 kbp and another around 100 kbp [16].
Here, we present the complete genome of the B. campestris type strain DSM 4712, sequenced using Nanopore and Illumina technologies. In addition to its chromosome, this strain harbors two circular mobile DNA elements: one plasmid (pDSM4712-1) and one phage-plasmid (ppDSM4712-2). This study underscores how mobile genetic elements, particularly those of phage origin, can shape the B. campestris genome.

2. Materials and Methods

The type strain B. campestris DSM 4712 was obtained from the DSMZ collection (Braunschweig, Germany) and was previously deposited by Talon et al. [2]. The total DNA was extracted with QIAamp PowerFecal Pro DNA Kit (QIAGEN, Toronto, ON, Canada) from a culture grown on Heart Infusion Broth agar medium and incubated for 24 h at 25 °C following the manufacturer’s instructions. The extracted DNA was quantified by fluorescence using the PicoGreen kit (Invitrogen, Waltham, MA, USA) and sequenced on an Illumina NextSeq2000 (2 × 150 bp) and a Nanopore PromethION by Plasmidsaurus (Eugene, OR, USA). The Illumina library was prepared using the SeqWell ExpressPlex 96 library prep kit (SeqWell, Beverly, MA, USA), while the Nanopore library was prepared using v14 library prep chemistry without fragmentation or size selection and sequenced on an R10.4.1 flow cell. Base calling was carried out for Nanopore reads using Dorado version 7.1.4 (https://github.com/nanoporetech/dorado accessed on 25 August 2025) on super-accurate mode. Illumina sequencing reads were filtered with Fastp version 0.23.2 [17] and those from Nanopore were filtered using Filtlong version 0.2.1 by keeping the best 90% of reads above 1000 bp or until only 500 Mbp remained (https://github.com/rrwick/Filtlong accessed on 25 August 2025). A hybrid assembly was performed with Unicycler version 0.5.0 [18]. Default parameters were used for all software unless otherwise specified.
The assembled sequences were initially annotated locally with Bakta version 1.9.1 [19]. Manual annotation with BLASTP against the NCBI nr database was also performed for the coding sequences of pDSM4712-1 and ppDSM4712-2, allowing genes to be categorized according to their possible origins. The protein sequences of ppDSM4712-2 were also functionally annotated using Pharokka version 1.7.5 [20] against the PHROG database [21]. Genomic island prediction was performed with IslandViewer 3 [22]. Maps of pDSM4712-1 and ppDSM4712-2 were constructed with SnapGene software version 7.2 (https://www.snapgene.com). Comparisons between pDSM4712-1 and ppDSM4712-2 and visualization of homologous sequences were performed with EasyFig version 2.2.2 [23]. Copy number of pDSM4712-1 and ppDSM4712-2 was inferred by mapping sequencing reads to the sequences with Bowtie version 2.5.1 [24] and SAMtools version 1.17 [25]. The sequencing depth was calculated with qualimap version 2.3 [26]. The copy number was calculated for each of the replicons by dividing its sequencing depth value by that of the chromosome sequence. CRISPR-Cas systems were detected using CRISPRCasFinder [27]. A BLASTn search was conducted for each spacer against the NCBI nucleotide database (nr/nt).
The complete chromosome sequence of B. campestris DSM 4712 has been deposited in DDBJ/ENA/GenBank under the accession number CP175511, and the sequences of pDSM4712-1 and ppDSM4712-2 were deposited under the accession numbers PQ657675 and PQ657676, respectively. Illumina and Nanopore sequencing reads were deposited in the Sequence Read Archive database under accession numbers SRR31926063 and SRR31926062, respectively.

3. Results

The aim of the project was to investigate the genome of the B. campestris type strain DSM 4712. DNA sequencing and assembly revealed three circular contigs (Table 1): a chromosome and two smaller replicons designated as pDSM4712-1 and ppDSM4712-2 (Figure 1). The adapted abbreviation (pp) before the strain name was chosen for the latter replicon to clearly distinguish phages-plasmids from plasmids, inspired by Pfeifer et al. [16]. By comparing the sequencing depth of the two smaller replicons with that of the chromosome, and assuming that the chromosome is present as a single copy per cell, pDSM4712-1 and ppDSM4712-2 were estimated to be present at 2 to 3 copies per cell.
A homology search using the BLASTN tool against the NCBI core_nt database revealed that the best match for pDSM4712-1 is the sequence of plasmid pL21564-1 (Figure 2) from B. thermosphacta strain TMW 2.1564, isolated from poultry meat (GenBank: NZ_CP016840). Except for a region that includes a gene encoding a recombinase in pDSM4712-1, both plasmid sequences are collinear, suggesting a common origin or that the plasmids may belong to the same family.
Interestingly, the homology search for ppDSM4712-2 revealed a high level of identity with two sequences (Figure 3): that of B. thermosphacta phage BtpYZU02 (GenBank: OQ863044.1) and that of B. thermosphacta TMW 2.1572 chromosome (GenBank: CP016841.1). Phage BtpYZU02 was isolated from sewage associated with retail pork stalls in China, while B. thermosphacta strain TMW 2.1572 was isolated from poultry meat [28]. All three sequences are homologous in a shared region, which primarily contains genes coding for phage structural proteins. Annotation of ppDSM4712-2 revealed that, among the 50 genes encoded by this replicon, 20 and 19 genes have phage and plasmid origins, respectively. However, when searching for homology with TBLASTN, several of the genes were also found in bacterial chromosomes (Table S1); this suggests that ppDSM4712-2 could belong to a prophage family.
Investigation of the presence of genomic islands revealed eight regions with genomic island (GEI) signatures on the chromosome (Figure S1) of B. campestris DSM 4712. These GEIs range in size from 4.7 to 56 kbp. They are uniformly distributed along the chromosome, with no preferential integration sites detected. Interestingly, one of these genomic islands (region: 1,951,597..1,977,651) includes genes producing brochocin-C (Table S2). This 26,054 bp region also contains four genes encoding transposases. It is unclear whether these transposases may have been involved in the region’s mobility or whether the region was transferred from another bacterium. A type II-A CRISPR-Cas system with 23 spacers was also discovered in the chromosome (region: 1,273,779..1,281,233). A homology search between the spacer sequences and the CRISPR-Cas++ database revealed no significant results. However, a comparative analysis between B. campestris DSM 4712 and B. thermosphacta DSM 20171 revealed that both possess a type II-A CRISPR-Cas system with identical direct repeat sequences, but with different spacers (Table S3). BLASTn analysis revealed that none of the spacers in B. campestris were linked to known phages. In contrast, spacers in B. thermosphacta DSM 20171 matched several phages, notably BtpYZU03 and A9, both of which are known to infect B. thermosphacta [29].

4. Discussion

Phages are known to play a crucial role not only in regulating bacterial populations but also in shaping bacterial genomes [30]. For instance, phages can integrate as prophages and promote gene mobility through transduction. Genomic sequences of B. thermosphacta, a known meat spoilage agent, are becoming increasingly more available, facilitating research to explore the roles and interactions of phages with this bacterium [7,31]. However, the influence of phages on the evolution of B. campestris, the only other species in the Brochothrix genus, remains largely unexplored.
Using Nanopore sequencing technology, we investigated the genome of the B. campestris DSM 4712 type strain and identified three replicons: one large replicon corresponding to the chromosome and two smaller replicons (pDSM4712-1 and ppDSM4712-2). A homology search against publicly available sequences revealed that pDSM4712-1 is homologous to plasmid pL21564-1 found in B. thermosphacta TMW 2.1564 [28]. This suggests that these two plasmids may belong to the same family and that members of this family are likely to be found in Brochothrix strains. However, the origin of the plasmids and whether they can be transferred between the two species (B. thermosphacta and B. campestris) remain unclear. Although this element has been highlighted, its activity remains uncertain. Future studies should investigate the potential mobilization capacity of this plasmid.
Characterization of ppDSM4712-2 revealed the presence of several phage-related genes in addition to typical plasmid genes. Consequently, this replicon could realistically be classified as a phage-plasmid hybrid [16]. These hybrid replicons between phages and plasmids have recently been characterized for their ability to mediate gene flow between plasmids and phages [32], as well as to transfer antibiotic resistance genes [33]. To the best of our knowledge, this is the first report of such a replicon in the Brochothrix genus. Notably, the region containing the phage genes is homologous to the sequence of phage BtpYZU02, which infects B. thermosphacta, as well as to a region of the B. thermosphacta TMW 2.1572 chromosome, likely a prophage. This further highlights a potential phage-mediated connection between B. thermosphacta and B. campestris. It remains unclear whether certain phages capable of infecting B. thermosphacta can also infect B. campestris, and vice versa. Future studies investigating these phages could provide valuable insights into the evolutionary relationships between these two species. In addition, phage–plasmids may have biotechnological applications, for example, in the development of shuttle vectors, as demonstrated in the bacterium Leptospira [34,35]. Similarly, ppDSM4712-2 could be explored as a biomolecular tool in Brochothrix species, where no such tools are currently available.
Chromosome analysis revealed that the genes responsible for producing brochocin- C, a bacteriocin with effects against Listeria sp., C. botulinum and B. thermosphacta [4,5,6], are located within a genomic island. This suggests that these genes may have an exogenous origin and were likely acquired through horizontal gene transfer. It has been suggested that the ability of certain bacteriocins to be mobilized may enhance bacterial competitiveness in complex environments, such as the microbiota [36]. Unfortunately, only a few B. campestris strains have been isolated to date. Additional strains are needed to determine whether this genomic island is consistently present across all representatives of the species—suggesting acquisition after speciation—or if it is a trait limited to a subset of strains. This investigation is especially relevant given the growing interest in bacteriocins for their antimicrobial effects, particularly in the food industry [37,38,39].
Interestingly, a type II-A CRISPR-Cas system was also identified in the B. campestris chromosome. Some strains of B. thermosphacta are also known to harbor a type II-A CRISPR-Cas system [31]. However, the number of spacers differs significantly between the system in B. campestris (23 spacers) and that in the type strain B. thermosphacta DSM 20171 (5 spacers). The search for homology between the spacer sequences and the CRISPR-Cas++ database revealed no significant results, suggesting that additional phages and mobile DNA elements remain to be discovered in B. campestris. Although the direct repeat sequences are identical in the two species, none of the spacers are shared. Thus, the presence of different spacers could reflect that the two species inhabit distinct ecological niches. It is currently unclear whether the systems were acquired independently or if they share a common origin. Additionally, the large number of spacers in the B. campestris system suggests that it is functional, despite the presence of mobile DNA elements. A study elucidating the functionality and role of the CRISPR-Cas system in B. campestris could provide insight into the regulation of mobile DNA elements and phage defense mechanisms in this bacterium.

5. Conclusions

Nanopore sequencing of the B. campestris DSM 4712 strain allowed us to obtain complete genomic sequences and analyze the replicons present in this genome. The analysis of the two secondary replicons identified a plasmid (pDSM4712-1) and a phage-plasmid (ppDSM4712-2). While pDSM4712-1 has high homology with a plasmid found in B. thermosphacta, ppDSM4712-2 is homologous to both a phage infecting B. thermosphacta and a chromosomal region, likely a prophage, from another B. thermosphacta strain. Although this study revealed a connection between the B. thermosphacta and B. campestris species, particularly in terms of their mobile genetic elements (plasmids and phages), genomic sequences from additional B. campestris strains are needed to further characterize the evolution of the Brochothrix genus. At present, only the type strain is available, underscoring the importance of isolating additional B. campestris strains in the future. Investigating the potential co-infection of both species by phages would also be of interest, as it could reveal the role of these viruses in promoting gene mobility within this bacterial genus.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/genes16101218/s1, Figure S1: Distribution of genomic islands in the B. campestris DSM 4712 chromosome; Table S1: Relative frequencies of ppDSM4712-2 coding sequences found in chromosomal, phage, and plasmid sequences; Table S2: List of genes found in the genomic islands of B. campestris DSM 4712; Table S3: List of direct repeats (DR) and spacers present in B. campestris DSM 4712 and B. thermosphacta DSM 20171.

Author Contributions

Conceptualization, S.A.A. and A.T.V.; methodology, S.A.A., L.C.P. and A.T.V.; validation, S.A.A. and A.T.V.; formal analysis, S.A.A.; investigation, S.A.A. and A.T.V.; data curation, A.T.V.; writing—original draft preparation, A.T.V.; writing—review and editing, S.A.A., L.C.P. and A.T.V.; visualization, S.A.A. and A.T.V.; supervision, A.T.V.; project administration, A.T.V.; funding acquisition, A.T.V. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) [grant number RGPIN-2022-03321].

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The complete chromosome sequence of B. campestris DSM 4712 has been deposited in DDBJ/ENA/GenBank under the accession number CP175511, and the sequences of pDSM4712-1 and ppDSM4712-2 were deposited under the accession numbers PQ657675 and PQ657676, respectively. Illumina and Nanopore sequencing reads were deposited in the Sequence Read Archive database under accession numbers SRR31926063 and SRR31926062, respectively.

Conflicts of Interest

The authors declare no conflicts of interest.

Abbreviations

The following abbreviations are used in this manuscript:
ATCCAmerican Type Culture Collection
BLASTNBasic Local Alignment Search Tool using a Nucleotide query
BLASTPBasic Local Alignment Search Tool using a Protein query
BPBase pairs
CIPCollection of the Institut Pasteur
CRISPR-CASClustered Regularly Interspaced Short Palindromic Repeats–CRISPR-associated protein
DDBJDNA DataBank of Japan
DSMZ (DSM)Deutsche Sammlung von Mikroorganismen und Zellkulturen
ENAEuropean Nucleotide Archive
GEIsGenomic islands
KbpKilo-base pairs
MbpMega-base pairs
NCBINational Center for Biotechnology Information
PPPhage-plasmid
TBLASTNTranslated Basic Local Alignment Search Tool using a Nucleotide query
TMWTreated Municipal Wastewater

References

  1. Illikoud, N.; Rossero, A.; Chauvet, R.; Courcoux, P.; Pilet, M.-F.; Charrier, T.; Jaffrès, E.; Zagorec, M. Genotypic and phenotypic characterization of the food spoilage bacterium Brochothrix thermosphacta. Food Microbiol. 2019, 81, 22–31. [Google Scholar] [CrossRef] [PubMed]
  2. Talon, R.; Grimont, P.A.D.; Grimont, F.; Gasser, F.; Boeufgras, J.M. Brochothrix campestris sp. nov. Int. J. Syst. Evol. Microbiol. 1988, 38, 99–102. [Google Scholar] [CrossRef]
  3. Gribble, A.; Brightwell, G. Spoilage characteristics of Brochothrix thermosphacta and campestris in chilled vacuum packaged lamb, and their detection and identification by real time PCR. Meat Sci. 2013, 94, 361–368. [Google Scholar] [CrossRef] [PubMed]
  4. Siragusa, G.R.; Cutter, C.N. Brochocin-C, a new bacteriocin produced by Brochothrix campestris. Appl. Environ. Microbiol. 1993, 59, 2326–2328. [Google Scholar] [CrossRef]
  5. McCormick, J.K.; Poon, A.; Sailer, M.; Gao, Y.; Roy, K.L.; McMullen, L.M.; Vederas, J.C.; Stiles, M.E.; Van Belkum, M.J. Genetic characterization and heterologous expression of brochocin-C, an antibotulinal, two-peptide bacteriocin produced by Brochothrix campestris ATCC 43754. Appl. Environ. Microbiol. 1998, 64, 4757–4766. [Google Scholar] [CrossRef]
  6. Greer, G.G.; Dilts, B.D. Control of meatborne Listeria monocytogenes and Brochothrix thermosphacta by a bacteriocinogenic Brochothrix campestris ATCC 43754. Food Microbiol. 2006, 23, 785–790. [Google Scholar] [CrossRef]
  7. Gingras, L.; Piché, L.C.; Saucier, L.; Vincent, A.T. The complete genomic sequence of the type strain Brochothrix thermosphacta DSM 20171 highlights a diversity of prophages in this species. Microbiol. Resour. Announc. 2024, 13, e00239-24. [Google Scholar] [CrossRef]
  8. Pasechnek, A.; Rabinovich, L.; Stadnyuk, O.; Azulay, G.; Mioduser, J.; Argov, T.; Borovok, I.; Sigal, N.; Herskovits, A.A. Active lysogeny in Listeria monocytogenes is a bacteria-phage adaptive response in the mammalian environment. Cell Rep. 2020, 32, 107956. [Google Scholar] [CrossRef]
  9. Vu, H.T.K.; Benjakul, S.; Vongkamjan, K. Characterization of Listeria prophages in lysogenic isolates from foods and food processing environments. PLoS ONE 2019, 14, e0214641. [Google Scholar] [CrossRef]
  10. Vu, H.T.K.; Stasiewicz, M.J.; Benjakul, S.; Vongkamjan, K. Genomic analysis of prophages recovered from Listeria monocytogenes lysogens found in seafood and seafood-related environment. Microorganisms 2021, 9, 1354. [Google Scholar] [CrossRef]
  11. Stackebrandt, E.; Jones, D. The genus Brochothrix. In The Prokaryotes: Volume 4: Bacteria: Firmicutes, Cyanobacteria; Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H., Stackebrandt, E., Eds.; Springer: New York, NY, USA, 2006; pp. 477–491. [Google Scholar]
  12. Brito, I.L. Examining horizontal gene transfer in microbial communities. Nat. Rev. Microbiol. 2021, 19, 442–453. [Google Scholar] [CrossRef]
  13. Rodríguez-Beltrán, J.; DelaFuente, J.; León-Sampedro, R.; MacLean, R.C.; San Millán, Á. Beyond horizontal gene transfer: The role of plasmids in bacterial evolution. Nat. Rev. Microbiol. 2021, 19, 347–359. [Google Scholar] [CrossRef]
  14. Bertani, G. Studies on lysogenesis I. J. Bacteriol. 1951, 62, 293–300. [Google Scholar] [CrossRef]
  15. Ravin, V.K.; Shulga, M.G. Evidence for extrachromosomal location of prophage N15. Virology 1970, 40, 800–807. [Google Scholar] [CrossRef]
  16. Pfeifer, E.; Moura de Sousa, J.A.; Touchon, M.; Rocha, E.P.C. Bacteria have numerous distinctive groups of phage–plasmids with conserved phage and variable plasmid gene repertoires. Nucleic Acids Res. 2021, 49, 2655–2673. [Google Scholar] [CrossRef] [PubMed]
  17. Chen, S.; Zhou, Y.; Chen, Y.; Gu, J. fastp: An ultra-fast all-in-one FASTQ Preprocessor. Bioinformatics 2018, 34, i884–i890. [Google Scholar] [CrossRef] [PubMed]
  18. Wick, R.R.; Judd, L.M.; Gorrie, C.L.; Holt, K.E. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol. 2017, 13, e1005595. [Google Scholar] [CrossRef] [PubMed]
  19. Schwengers, O.; Jelonek, L.; Dieckmann, M.A.; Beyvers, S.; Blom, J.; Goesmann, A. Bakta: Rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb. Genom. 2021, 7, 000685. [Google Scholar] [CrossRef]
  20. Bouras, G.; Nepal, R.; Houtak, G.; Psaltis, A.J.; Wormald, P.-J.; Vreugde, S. Pharokka: A fast scalable bacteriophage annotation tool. Bioinformatics 2023, 39, btac776. [Google Scholar] [CrossRef]
  21. Terzian, P.; Olo Ndela, E.; Galiez, C.; Lossouarn, J.; Pérez Bucio, R.E.; Mom, R.; Toussaint, A.; Petit, M.-A.; Enault, F. PHROG: Families of prokaryotic virus proteins clustered using remote homology. NAR Genom. Bioinform. 2021, 3, lqab067. [Google Scholar] [CrossRef]
  22. Dhillon, B.K.; Laird, M.R.; Shay, J.A.; Winsor, G.L.; Lo, R.; Nizam, F.; Pereira, S.K.; Waglechner, N.; McArthur, A.G.; Langille, M.G.I.; et al. IslandViewer 3: More flexible, interactive genomic island discovery, visualization and analysis. Nucleic Acids Res. 2015, 43, W104–W108. [Google Scholar] [CrossRef]
  23. Sullivan, M.J.; Petty, N.K.; Beatson, S.A. Easyfig: A genome comparison visualizer. Bioinformatics 2011, 27, 1009–1010. [Google Scholar] [CrossRef]
  24. Langmead, B.; Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 2012, 9, 357–359. [Google Scholar] [CrossRef]
  25. Li, H.; Handsaker, B.; Wysoker, A.; Fennell, T.; Ruan, J.; Homer, N.; Marth, G.; Abecasis, G.; Durbin, R.; 1000 Genome Project Data Processing Subgroup. The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25, 2078–2079. [Google Scholar] [CrossRef]
  26. García-Alcalde, F.; Okonechnikov, K.; Carbonell, J.; Cruz, L.M.; Götz, S.; Tarazona, S.; Dopazo, J.; Meyer, T.F.; Conesa, A. Qualimap: Evaluating next-generation sequencing alignment data. Bioinformatics 2012, 28, 2678–2679. [Google Scholar] [CrossRef] [PubMed]
  27. Couvin, D.; Bernheim, A.; Toffano-Nioche, C.; Touchon, M.; Michalik, J.; Néron, B.; Rocha, E.P.C.; Vergnaud, G.; Gautheret, D.; Pourcel, C. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res. 2018, 46, W246–W251. [Google Scholar] [CrossRef] [PubMed]
  28. Höll, L.; Hilgarth, M.; Geissler, A.J.; Behr, J.; Vogel, R.F. Prediction of in situ metabolism of photobacteria in modified atmosphere packaged poultry meat using metatranscriptomic data. Microbiol. Res. 2019, 222, 52–59. [Google Scholar] [CrossRef] [PubMed]
  29. Kilcher, S.; Loessner, M.J.; Klumpp, J. Brochothrix thermosphacta bacteriophages feature heterogeneous and highly mosaic genomes and utilize unique prophage insertion sites. J. Bacteriol. 2010, 192, 5441–5453. [Google Scholar] [CrossRef]
  30. Rocha, E.P.C.; Bikard, D. Microbial defenses against mobile genetic elements and viruses: Who defends whom from what? PLoS Biol. 2022, 20, e3001514. [Google Scholar] [CrossRef]
  31. Stanborough, T.; Fegan, N.; Powell, S.M.; Tamplin, M.; Chandry, P.S. Insight into the genome of Brochothrix thermosphacta, a problematic meat spoilage bacterium. Appl. Environ. Microbiol. 2017, 83, e02786-16. [Google Scholar] [CrossRef]
  32. Pfeifer, E.; Rocha, E.P.C. Phage-plasmids promote recombination and emergence of phages and plasmids. Nat. Commun. 2024, 15, 1545. [Google Scholar] [CrossRef]
  33. Pfeifer, E.; Bonnin, R.A.; Rocha, E.P.C. Phage-plasmids spread antibiotic resistance genes through infection and lysogenic conversion. mBio 2022, 13, e01851-22. [Google Scholar] [CrossRef]
  34. Girons, I.S.; Bourhy, P.; Ottone, C.; Picardeau, M.; Yelton, D.; Hendrix, R.W.; Glaser, P.; Charon, N. The LE1 bacteriophage replicates as a plasmid within Leptospira biflexa: Construction of an L. biflexa-Escherichia coli shuttle vector. J. Bacteriol. 2000, 182, 5700–5705. [Google Scholar] [CrossRef] [PubMed]
  35. Zhu, W.; Wang, J.; Zhu, Y.; Tang, B.; Zhang, Y.; He, P.; Zhang, Y.; Liu, B.; Guo, X.; Zhao, G.; et al. Identification of three extra-chromosomal replicons in Leptospira pathogenic strain and development of new shuttle vectors. BMC Genom. 2015, 16, 90. [Google Scholar] [CrossRef] [PubMed]
  36. Kommineni, S.; Bretl, D.J.; Lam, V.; Chakraborty, R.; Hayward, M.; Simpson, P.; Cao, Y.; Bousounis, P.; Kristich, C.J.; Salzman, N.H. Bacteriocin production augments niche competition by enterococci in the mammalian gastrointestinal tract. Nature 2015, 526, 719–722. [Google Scholar] [CrossRef] [PubMed]
  37. Solis-Balandra, M.A.; Sanchez-Salas, J.L. Classification and multi-functional use of bacteriocins in health, biotechnology, and food industry. Antibiotics 2024, 13, 666. [Google Scholar] [CrossRef]
  38. Sugrue, I.; Ross, R.P.; Hill, C. Bacteriocin diversity, function, discovery and application as antimicrobials. Nat. Rev. Microbiol. 2024, 22, 556–571. [Google Scholar] [CrossRef]
  39. Darbandi, A.; Asadi, A.; Mahdizade Ari, M.; Ohadi, E.; Talebi, M.; Halaj Zadeh, M.; Darb Emamie, A.; Ghanavati, R.; Kakanj, M. Bacteriocins: Properties and potential use as antimicrobials. J. Clin. Lab. Anal. 2022, 36, e24093. [Google Scholar] [CrossRef]
Genes 16 01218 g001
Figure 1. Maps of pDSM4712-1 and ppDSM4712-2. Genes encoding proteins with known functions, which are primarily found on plasmids, are shown in blue. Genes encoding hypothetical proteins are depicted in red, while genes known to be primarily found on phages are highlighted in green. tRNA genes are shown in black. In the inner circle of ppDSM4712-2, each gene is colored according to its associated function.
Figure 1. Maps of pDSM4712-1 and ppDSM4712-2. Genes encoding proteins with known functions, which are primarily found on plasmids, are shown in blue. Genes encoding hypothetical proteins are depicted in red, while genes known to be primarily found on phages are highlighted in green. tRNA genes are shown in black. In the inner circle of ppDSM4712-2, each gene is colored according to its associated function.
Genes 16 01218 g001
Genes 16 01218 g002
Figure 2. Comparison of the sequences of pDSM4712-1 and pL21564-1. Genes encoding proteins with known functions, which are primarily found on plasmids, are represented in blue. Genes encoding hypothetical proteins are depicted in red. Two tRNA genes are shown in black. Gray shading indicates the homologous regions.
Figure 2. Comparison of the sequences of pDSM4712-1 and pL21564-1. Genes encoding proteins with known functions, which are primarily found on plasmids, are represented in blue. Genes encoding hypothetical proteins are depicted in red. Two tRNA genes are shown in black. Gray shading indicates the homologous regions.
Genes 16 01218 g002
Genes 16 01218 g003
Figure 3. Comparison of the sequences of pDSM4712-1, the phage BtpYZU02, and a region of the chromosome from B. thermosphacta strain TMW 2.1572. Genes encoding proteins with known functions, primarily found on plasmids, are shown in blue. Genes encoding hypothetical proteins are depicted in red. Genes known to be primarily found on phages are highlighted in green, while those present on the chromosome are in orange. tRNA gene is shown in black. Only the functions of homologous genes are shown. Gray shading indicates the homologous regions.
Figure 3. Comparison of the sequences of pDSM4712-1, the phage BtpYZU02, and a region of the chromosome from B. thermosphacta strain TMW 2.1572. Genes encoding proteins with known functions, primarily found on plasmids, are shown in blue. Genes encoding hypothetical proteins are depicted in red. Genes known to be primarily found on phages are highlighted in green, while those present on the chromosome are in orange. tRNA gene is shown in black. Only the functions of homologous genes are shown. Gray shading indicates the homologous regions.
Genes 16 01218 g003
Table 1. General characteristics of the replicons found in B. campestris DSM 4712.
Table 1. General characteristics of the replicons found in B. campestris DSM 4712.
FeaturesChromosomepDSM4712-1ppDSM4712-2
Length (bp)2,324,17644,49338,313
GC (%)40.5435.1937.85
Number of genes21454850
tRNA8501
GenBankCP175511PQ657675PQ657676
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Attéré, S.A.; Piché, L.C.; Vincent, A.T. Genomic Relationship Between Brochothrix campestris and Its Phages: A Cross-Replicon and Interspecies Perspective. Genes 2025, 16, 1218. https://doi.org/10.3390/genes16101218

AMA Style

Attéré SA, Piché LC, Vincent AT. Genomic Relationship Between Brochothrix campestris and Its Phages: A Cross-Replicon and Interspecies Perspective. Genes. 2025; 16(10):1218. https://doi.org/10.3390/genes16101218

Chicago/Turabian Style

Attéré, Sabrina A., Laurie C. Piché, and Antony T. Vincent. 2025. "Genomic Relationship Between Brochothrix campestris and Its Phages: A Cross-Replicon and Interspecies Perspective" Genes 16, no. 10: 1218. https://doi.org/10.3390/genes16101218

APA Style

Attéré, S. A., Piché, L. C., & Vincent, A. T. (2025). Genomic Relationship Between Brochothrix campestris and Its Phages: A Cross-Replicon and Interspecies Perspective. Genes, 16(10), 1218. https://doi.org/10.3390/genes16101218

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop