We report the draft genome sequence of Dermacoccus nishinomiyaensis Y5 isolated from a glycerol stock prepared from a fungal culture from the gill of the lucinid bivalve, Stewartia floridana. This bacterial strain is gram-positive, coccus-shaped, and citrate-positive. Its draft genome of 3.3 Mb was assembled with 100% completeness, comprising 11 contigs and 2,937 protein-coding genes. Dermacoccus nishinomiyaensis Y5 shared 98.9% average nucleotide identity (ANI) with its closest genome relative, D. nishinomiyaensis CTOTU46710 assembled from an urban metagenome. Further investigation is needed to identify the source and pathogenicity of D. nishinomiyaensis Y5.
","acknowledgements":"We acknowledge the microbiology research support for undergraduate students provided by Michelle Green and Deborah Howard from the Department of Integrative Biology at the University of South Florida.
","authors":[{"affiliations":["University of South Florida, Tampa, FL, US","USF St. Pete, St. Petersburg, FL, US"],"departments":["","College of Marine Science"],"credit":["formalAnalysis","investigation","methodology","visualization","writing_originalDraft"],"email":"jeweliak@usf.edu","firstName":"Jewelia T","lastName":"Keller","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0009-0002-4163-9313"},{"affiliations":["USF St. Pete, St. Petersburg, FL, US","Florida International University, Miami, FL, US"],"departments":["College of Marine Science","College of Arts, Science and Education"],"credit":["conceptualization","dataCuration","formalAnalysis","investigation","methodology","software","supervision","validation","visualization","writing_originalDraft"],"email":"shlim@fiu.edu","firstName":"Shen Jean ","lastName":"Lim","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of South Florida, Tampa, FL, US"],"departments":["Department of Pediatrics, Morsani College of Medicine"],"credit":["formalAnalysis","investigation","methodology","writing_reviewEditing"],"email":"ojasn@usf.edu","firstName":"Ojas","lastName":"Natarajan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["USF St. Pete, St. Petersburg, FL, US"],"departments":["Department of Integrative Biology"],"credit":["methodology","resources"],"email":"cropper@usf.edu","firstName":"Nicholas ","lastName":"Cropper","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of South Florida, Tampa, FL, US"],"departments":["Department of Pediatrics, Morsani College of Medicine"],"credit":["conceptualization","resources","writing_reviewEditing"],"email":"ldishaw@usf.edu","firstName":"Larry J","lastName":"Dishaw","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["USF St. Pete, St. Petersburg, FL, US"],"departments":["College of Marine Science"],"credit":["fundingAcquisition","project","resources","supervision","validation","writing_reviewEditing"],"email":"mya@usf.edu","firstName":"Mya","lastName":"Breitbart","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[{"awardId":"OCE-2219547","funderName":"National Science Foundation (United States)","awardRecipient":"Mya Breitbart"}],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"Lucinid specimen collection was permitted by the Florida Fish and Wildlife Conservation Commission through a Special Activity License (SAL-22-2495B-SR) to S.J.L.
","image":{"url":"https://portal.micropublication.org/uploads/1ed5e19c92f5f6c0f447dced100c2b3d.jpeg"},"imageCaption":"Average Nucleotide Identity (ANI) comparisons between the genome of Dermacoccus nishinomiyaensis Y5 isolated in this study (annotated with black square) and other representative genomes assigned to Dermacoccus nishinomiyaensis. RefSeq accession numbers are listed in the x-axis and y-axis
","imageTitle":"Average Nucleotide Identity (ANI) comparisons across Dermacoccus nishinomiyaensis genomes
","methods":"","reagents":"","patternDescription":"Dermacoccus nishinomiyaensis is a member of the Dermococcaceae family and commonly resides in the skin microbiome, functioning as a skin commensal (Williams and MacLea, 2019). Current literature classifies D. nishinomiyaensis as a coccus-shaped, non-spore forming, aerobic, chemo-organotrophic bacterium (Stackebrandt et al., 1995). Dermacoccus nishinomiyaensis was isolated serendipitously from a glycerol stock originally prepared from a fungal culture isolated from the gill of the lucinid bivalve, Stewartia floridana. The live lucinid (specimen ID: SS1) was collected from the Terra Ceia Aquatic Preserve (GPS coordinates: 27.587404, -82.623248) on September 7, 2023 (Lim et al., 2025).
Dissection and culturing methods were as described in Lim et al., (2025). Briefly, one gill was dissected from the live lucinid specimen, rinsed, homogenized, and diluted 10X (v/v) in 0.2 μm-filtered 35 g/L Instant Ocean® solution (https://www.instantocean.com). Sterile glass plating beads were used to spread 200 μL of the homogenate on BD Difco™ Marine Agar 2216, which was then incubated in the dark at room temperature (~22°C). Fungal growth was observed on the plate after two days and re-inoculated in BD Difco™ Marine Broth 2216 under the same conditions. Upon visible growth, 500 μL of the fungal culture was added to 500 μL of 50% glycerol and stored at -80ºC. The glycerol stock was streaked on BD Difco™ Marine Agar 2216. Instead of fungal growth, yellow colonies indicative of bacterial growth were observed.
One isolated yellow colony (Y5) was randomly chosen for subculturing and maintenance on BD Difco™ Marine Agar 2216. For biochemical characterization, the subculture was inoculated in various media at 37ºC. Under the microscope, this bacterial strain was observed to be gram-positive and coccus-shaped. Based on the phenol red broth test, D. nishinomiyaensis Y5 was unable to ferment glucose, lactose or sucrose. The citrate utilization test showed that the strain was citrate-positive. The Sulfide-Indole-Motility (SIM) test indicated the bacterial strain to be non-motile and unable to produce sulfur and indole. Gelatin hydrolysis, urease and phenylalanine deaminase tests produced negative results.
For genome sequencing, three randomly chosen yellow colonies maintained on BD Difco™ Marine Agar 2216 were separately grown in BD Difco™ Marine Broth 2216. As described in Lim et al. (2025), DNA was extracted from each culture upon visible growth by centrifuging each culture at 1,700 RCF for 5 minutes and collecting the pellet. DNA extraction was performed using Qiagen’s AllPrep DNA/RNA Mini kit, followed by DNA purification using ZR’s Genomic DNA Clean & Concentrator-10 kit. The concentration and quality of each purified DNA sample was assessed using the Qubit DNA HS assay, the Nanodrop ND-1000 spectrophotometer, and electrophoresis on a 1% (w/v) agarose gel. The unsheared DNA sample with the highest concentration and quality was sent to Eurofins Genomics for library preparation using Oxford Nanopore Technologies’ (ONT) Rapid Barcoding Kit 96 V14. The library was sequenced on a GridION R10.4.1 flow cell and ONT’s Dorado v0.6.0 was used for base-calling with the dna_r10.4.1_e8.2_400bps_hac@v4.2.0 model. A total of 66,806 reads and 108,590,115 bases were sequenced with a N50 value of 2,813 bp.
Sequence data was analyzed on the KBase server (Arkin et al., 2018) using default software parameters. Quality filtering by Filtlong v0.2.1 (https://github.com/rrwick/Filtlong) retained 35,588 reads, which was assembled using Flye v2.9.4 (Kolmogorov et al., 2019). The quality of the genome assembly was assessed using Quality Assessment Tool for Genome Assemblies (QUAST) v4.4 (Gurevich et al., 2013). The assembly, totaling 3,301,037 bp, comprised 11 contigs, with 68.78% G+C content and a N50 value of 2,066,152 bp. CheckM v1.0.18 (Parks et al., 2015a) predicted the assembly to be 100% complete with 0% contamination. Using the Genome Taxonomy Database (GTDB) release R226 (Parks et al., 2022b) as reference, GTDB-Tk v2.4.0 (Chaumeil et al., 2022) assigned the genome to the species Dermacoccus nishinomiyaensis. The genome shared 98.9% average nucleotide identity (ANI) to the genome of D. nishinomiyaensis CTOTU46710 assembled from an urban metagenome (Magnúsdóttir et al., 2023), as calculated by fastANI v1.33 (Jain et al., 2018) (Figure 1). The genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline v6.10 (Li et al., 2021), which identified 2,937 protein-coding genes and three 16S rRNA genes. Sequence data, including raw reads (Sequence Read Archive accession: SRX31722345) and the genome assembly (RefSeq accession: GCF_054488915) is deposited at NCBI under the BioProject accession number PRJNA1399496.
To confirm whether the gills of lucinid bivalves contain D. nishinomiyaensis Y5, primers 79F (5’-AGCTTGCTGGTGTGGATTAG-3') and 169R (5’-GGAGATCGGTCGTATCCAGTAT-3') targeting the 16S rRNA gene of D. nishinomiyaensis Y5 were designed using the Integrated DNA Technologies (IDT) PrimerQuest™Tool (https://www.idtdna.com/pages/tools/primerquest). PCR was performed on the DNA sample extracted from the other gill of the same S. floridana specimen using Qiagen’s AllPrep DNA/RNA Mini kit, as well 13 other DNA samples extracted from clam gills dissected from other S. floridana specimens listed in Lim et al., (2025) under the following thermocycling conditions: 95ºC for 10 minutes, followed by 34 cycles 95ºC for 30 minutes, 52.5ºC for 30 minutes, 72ºC for 1 minute, and an extension period of 10 minutes at 72ºC. No amplification was observed in all DNA samples tested.
Dermacoccus nishinomiyaensis is a Gram-positive, non-spore forming bacterium commonly found as a commensal resident in the human skin microbiome (Stackebrandt et al., 1995). Outside of the skin microbiome, D. nishinomiyaensis has been isolated from human-built environments, such as wood ash (Williams and MacLea, 2019) and indoor track facilities (Klein et al., 2017). In the natural environment, D. nishinomiyaensis has been isolated from the phycosphere of red algae collected from an intertidal zone in Korea (GCF_055693885; 98.2% ANI with D. nishinomiyaensis Y5), the Ulu Slim Hot Spring in Malaysia (GCF_000725405; 98% ANI with D. nishinomiyaensis Y5), and the Styx glacier in Antarctica (GCF_ 037331475; 98.7% ANI with D. nishinomiyaensis Y5) (Kim et al., 2025). Given the negative PCR results, D. nishinomiyaensis Y5 isolated in this study is likely a rare marine bacterium, an urban contaminant, or a human skin contaminant of the glycerol stock. Species within the Dermacoccus genus do not typically exhibit pathogenic properties; however, it has been documented that D. nishinomiyaensis may cause catheter-related infections (Joron et al., 2019). Thus, the source and pathogenicity of D. nishinomiyaensis Y5 should be further investigated.
","references":[{"reference":"Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al., Yu D. 2018. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nat Biotechnol 36(7): 566-569.
","pubmedId":"29979655","doi":""},{"reference":"Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. 2022. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics 38(23): 5315-5316.
","pubmedId":"36218463","doi":""},{"reference":"Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29(8): 1072-5.
","pubmedId":"23422339","doi":""},{"reference":"Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. 2018. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 9(1): 5114.
","pubmedId":"30504855","doi":""},{"reference":"Joron C, Roméo B, Le Flèche-Matéos A, Rames C, El Samad Y, Hamdad F. 2019. Dermacoccus nishinomiyaensis as a cause of persistent paediatric catheter-related bacteraemia. Clin Microbiol Infect 25(8): 1054-1055.
","pubmedId":"30825676","doi":""},{"reference":"Kim M, Lee H, Lee S, Han Y, Kim OS. 2025. Millennial-scale depth-resolved ancient microbial diversity and pathogenic potential in Styx Glacier, Antarctica. Environ Res 285(Pt 2): 122421.
","pubmedId":"40706832","doi":""},{"reference":"Klein BA, Lemon KP, Gajare P, Jospin G, Eisen JA, Coil DA. 2017. Draft Genome Sequences of Dermacoccus nishinomiyaensis Strains UCD-KPL2534 and UCD-KPL2528 Isolated from an Indoor Track Facility. Genome Announc 5(8): 10.1128/genomeA.01652-16.
","pubmedId":"28232444","doi":""},{"reference":"Kolmogorov M, Yuan J, Lin Y, Pevzner PA. 2019. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 37(5): 540-546.
","pubmedId":"30936562","doi":""},{"reference":"Li W, O'Neill KR, Haft DH, DiCuccio M, Chetvernin V, Badretdin A, et al., Thibaud-Nissen F. 2021. RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation. Nucleic Acids Res 49(D1): D1020-D1028.
","pubmedId":"33270901","doi":""},{"reference":"Lim SJ, Natarajan O, Keller J, Dishaw LJ, Furman BT, Breitbart M. 2025. Draft genome sequence of Gracilimonas sp. strain BCB1 isolated from the gill tissue of the lucinid bivalve Stewartia floridana in Pinellas County, Florida, USA. Microbiol Resour Announc 14(11): e0059525.
","pubmedId":"41002246","doi":""},{"reference":"Magnúsdóttir S, Saraiva JP, Bartholomäus A, Soheili M, Toscan RB, Zhang J, Nunes da Rocha U, CLUE-TERRA consortium. 2023. Metagenome-assembled genomes indicate that antimicrobial resistance genes are highly prevalent among urban bacteria and multidrug and glycopeptide resistances are ubiquitous in most taxa. Front Microbiol 14: 1037845.
","pubmedId":"36760505","doi":""},{"reference":"Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25(7): 1043-55.
","pubmedId":"25977477","doi":""},{"reference":"Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil PA, Hugenholtz P. 2022. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res 50(D1): D785-D794.
","pubmedId":"34520557","doi":""},{"reference":"Stackebrandt E, Koch C, Gvozdiak O, Schumann P. 1995. Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend. Int J Syst Bacteriol 45(4): 682-92.
","pubmedId":"7547287","doi":""},{"reference":"Williams AN, MacLea KS. 2019. Draft Genome Sequence of Dermacoccus nishinomiyaensis TSA37, Isolated from Wood Ash. Microbiol Resour Announc 8(50): 10.1128/MRA.01370-19.
","pubmedId":"31831617","doi":""}],"title":"Draft genome sequence of Dermacoccus nishinomiyaensis Y5
","reviews":[{"reviewer":{"displayName":"Kyle Scott MacLea"},"openAcknowledgement":true,"status":{"submitted":true}}],"curatorReviews":[]},{"id":"14aca103-56b0-49b4-8268-a705282923b4","decision":"accept","abstract":"We report the draft genome sequence of Dermacoccus nishinomiyaensis Y5 isolated from a glycerol stock prepared from a fungal culture from the gill of the lucinid bivalve, Stewartia floridana. This bacterial strain is gram-positive, coccus-shaped, and citrate-positive. Its draft genome of 3.3 Mb was assembled with 100% completeness, comprising 11 contigs and 2,937 protein-coding genes. Dermacoccus nishinomiyaensis Y5 shared 98.9% average nucleotide identity (ANI) with its closest genome relative, D. nishinomiyaensis CTOTU46710 assembled from an urban metagenome. Further investigation is needed to identify the source and pathogenicity of D. nishinomiyaensis Y5.
","acknowledgements":"We acknowledge the microbiology research support for undergraduate students provided by Michelle Green and Deborah Howard from the Department of Integrative Biology at the University of South Florida.
","authors":[{"affiliations":["University of South Florida, Tampa, FL, US","USF St. Pete, St. Petersburg, FL, US"],"departments":["","College of Marine Science"],"credit":["formalAnalysis","investigation","methodology","visualization","writing_originalDraft"],"email":"jeweliak@usf.edu","firstName":"Jewelia T","lastName":"Keller","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0009-0002-4163-9313"},{"affiliations":["USF St. Pete, St. Petersburg, FL, US","Florida International University, Miami, FL, US"],"departments":["College of Marine Science","College of Arts, Science and Education"],"credit":["conceptualization","dataCuration","formalAnalysis","investigation","methodology","software","supervision","validation","visualization","writing_originalDraft"],"email":"shlim@fiu.edu","firstName":"Shen Jean ","lastName":"Lim","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of South Florida, Tampa, FL, US"],"departments":["Department of Pediatrics, Morsani College of Medicine"],"credit":["formalAnalysis","investigation","methodology","writing_reviewEditing"],"email":"ojasn@usf.edu","firstName":"Ojas","lastName":"Natarajan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["USF St. Pete, St. Petersburg, FL, US"],"departments":["Department of Integrative Biology"],"credit":["methodology","resources"],"email":"cropper@usf.edu","firstName":"Nicholas ","lastName":"Cropper","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of South Florida, Tampa, FL, US"],"departments":["Department of Pediatrics, Morsani College of Medicine"],"credit":["conceptualization","resources","writing_reviewEditing"],"email":"ldishaw@usf.edu","firstName":"Larry J","lastName":"Dishaw","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["USF St. Pete, St. Petersburg, FL, US"],"departments":["College of Marine Science"],"credit":["fundingAcquisition","project","resources","supervision","validation","writing_reviewEditing"],"email":"mya@usf.edu","firstName":"Mya","lastName":"Breitbart","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[{"awardId":"OCE-2219547","funderName":"National Science Foundation (United States)","awardRecipient":"Mya Breitbart"}],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"Lucinid specimen collection was permitted by the Florida Fish and Wildlife Conservation Commission through a Special Activity License (SAL-22-2495B-SR) to S.J.L.
","image":{"url":"https://portal.micropublication.org/uploads/1ed5e19c92f5f6c0f447dced100c2b3d.jpeg"},"imageCaption":"Average Nucleotide Identity (ANI) comparisons between the genome of Dermacoccus nishinomiyaensis Y5 isolated in this study (annotated with black square) and all other representative genomes at the time of analysis assigned to Dermacoccus nishinomiyaensis . RefSeq accession numbers are listed in the x-axis and y-axis.
","imageTitle":"Average Nucleotide Identity (ANI) comparisons across Dermacoccus nishinomiyaensis genomes
","methods":"","reagents":"","patternDescription":"Dermacoccus nishinomiyaensis is a member of the Dermococcaceae family and commonly resides in the skin microbiome, functioning as a skin commensal (Williams and MacLea, 2019). Current literature classifies D. nishinomiyaensis as a coccus-shaped, non-spore forming, aerobic, chemo-organotrophic bacterium (Stackebrandt et al., 1995). Dermacoccus nishinomiyaensis was isolated serendipitously from a glycerol stock originally prepared from a fungal culture isolated from the gill of the lucinid bivalve, Stewartia floridana. The live lucinid (specimen ID: SS1) was collected from the Terra Ceia Aquatic Preserve (GPS coordinates: 27.587404, -82.623248) on September 7, 2023 (Lim et al., 2025).
Dissection and culturing methods were as described in Lim et al., (2025). Briefly, one gill was dissected from the live lucinid specimen, rinsed, homogenized, and diluted 10X (v/v) in 0.2 μm-filtered 35 g/L Instant Ocean® solution (https://www.instantocean.com). Sterile glass plating beads were used to spread 200 μL of the homogenate on BD Difco™ Marine Agar 2216, which was then incubated in the dark at room temperature (~22°C). Fungal growth was observed on the plate after two days and re-inoculated in BD Difco™ Marine Broth 2216 under the same conditions. Upon visible growth, 500 μL of the fungal culture was added to 500 μL of 50% glycerol and stored at -80ºC. The glycerol stock was streaked on BD Difco™ Marine Agar 2216. Instead of fungal growth, yellow colonies indicative of bacterial growth were observed.
One isolated yellow colony (Y5) was randomly chosen for subculturing and maintenance on BD Difco™ Marine Agar 2216. For biochemical characterization, the subculture was inoculated in various media at 37ºC. Under the microscope, this bacterial strain was observed to be gram-positive and coccus-shaped. Based on the phenol red broth test, D. nishinomiyaensis Y5 was unable to ferment glucose, lactose or sucrose. The citrate utilization test showed that the strain was citrate-positive. The Sulfide-Indole-Motility (SIM) test indicated the bacterial strain to be non-motile and unable to produce sulfur and indole. Gelatin hydrolysis, urease and phenylalanine deaminase tests produced negative results.
For genome sequencing, three representative yellow colonies maintained on BD Difco™ Marine Agar 2216 were separately grown in BD Difco™ Marine Broth 2216. As described in Lim et al. (2025), DNA was extracted from each culture upon visible growth by centrifuging each culture at 1,700 RCF for 5 minutes and collecting the pellet. DNA extraction was performed using Qiagen's AllPrep DNA/RNA Mini kit, followed by DNA purification using ZR's Genomic DNA Clean & Concentrator-10 kit. The concentration and quality of each purified DNA sample was assessed using the Qubit DNA HS assay, the Nanodrop ND-1000 spectrophotometer, and electrophoresis on a 1% (w/v) agarose gel. The unsheared DNA sample with the highest concentration and quality was sent to Eurofins Genomics for library preparation using Oxford Nanopore Technologies' (ONT) Rapid Barcoding Kit 96 V14. The library was sequenced on a GridION R10.4.1 flow cell and ONT's Dorado v0.6.0 was used for base-calling with the dna_r10.4.1_e8.2_400bps_hac@v4.2.0 model. A total of 66,806 reads and 108,590,115 bases were sequenced with a N50 value of 2,813 bp.
Sequence data was analyzed on the KBase server (Arkin et al., 2018) using default software parameters. Quality filtering by Filtlong v0.2.1 (https://github.com/rrwick/Filtlong) retained 35,588 reads, which was assembled using Flye v2.9.4 (Kolmogorov et al., 2019). The quality of the genome assembly was assessed using Quality Assessment Tool for Genome Assemblies (QUAST) v4.4 (Gurevich et al., 2013). The assembly, totaling 3,301,037 bp, comprised 11 contigs, with 68.78% G+C content and a N50 value of 2,066,152 bp. CheckM v1.0.18 (Parks et al., 2015a) predicted the assembly to be 100% complete with 0% contamination. Using the Genome Taxonomy Database (GTDB) release R226 (Parks et al., 2022b) as reference, GTDB-Tk v2.4.0 (Chaumeil et al., 2022) classified the genome as Dermacoccus nishinomiyaensis. The genome shared 98.9% average nucleotide identity (ANI) with the genome of D. nishinomiyaensis CTOTU46710 assembled from an urban metagenome (Magnúsdóttir et al., 2023), as calculated by fastANI v1.33 (Jain et al., 2018) (Figure 1). The genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline v6.10 (Li et al., 2021), which identified 2,937 protein-coding genes and three copies of the 16S rRNA gene. Sequence data, including raw reads (Sequence Read Archive accession: SRX31722345) and the genome assembly (RefSeq accession: GCF_054488915) is deposited at NCBI under the BioProject accession number PRJNA1399496.
To confirm whether the gills of lucinid bivalves contain D. nishinomiyaensis Y5, primers 79F (5'-AGCTTGCTGGTGTGGATTAG-3') and 169R (5'-GGAGATCGGTCGTATCCAGTAT-3') targeting the 16S rRNA gene of D. nishinomiyaensis Y5 were designed using the Integrated DNA Technologies (IDT) PrimerQuest™Tool (https://www.idtdna.com/pages/tools/primerquest). PCR was performed on the DNA sample extracted from the other gill of the same S. floridana specimen using Qiagen's AllPrep DNA/RNA Mini kit, as well 13 other DNA samples extracted from clam gills dissected from other S. floridana specimens listed in Lim et al., (2025) under the following thermocycling conditions: 95ºC for 10 minutes, followed by 34 cycles 95ºC for 30 minutes, 52.5ºC for 30 minutes, 72ºC for 1 minute, and an extension period of 10 minutes at 72ºC. No amplification was observed in all DNA samples tested.
Dermacoccus nishinomiyaensis is a Gram-positive, non-spore forming bacterium commonly found as a commensal resident in the human skin microbiome (Stackebrandt et al., 1995). Outside of the skin microbiome, D. nishinomiyaensis has been isolated from human-built environments, such as wood ash (Williams and MacLea, 2019) and indoor track facilities (Klein et al., 2017). In the natural environment, D. nishinomiyaensis has been isolated from the phycosphere of red algae collected from an intertidal zone in Korea (GCF_055693885; 98.2% ANI with D. nishinomiyaensis Y5), the Ulu Slim Hot Spring in Malaysia (GCF_000725405; 98% ANI with D. nishinomiyaensis Y5), and the Styx glacier in Antarctica (GCF_ 037331475; 98.7% ANI with D. nishinomiyaensis Y5) (Kim et al., 2025). Although the negative PCR results suggest that D. nishinomiyaensis Y5 could be a transient contaminant during cultivation and glycerol stock preparation, the gill origin of this bacterium could not be excluded without further testing. Species within the Dermacoccus genus do not typically exhibit pathogenic properties; however, it has been documented that D. nishinomiyaensis may cause catheter-related infections (Joron et al., 2019). Further investigation is necessary to determine the ecological origin of D. nishinomiyaensis Y5 and whether it represents a transient contaminant or a rare marine bacterium.
","references":[{"reference":"Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al., Yu D. 2018. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nat Biotechnol 36(7): 566-569.
","pubmedId":"29979655","doi":""},{"reference":"Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. 2022. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics 38(23): 5315-5316.
","pubmedId":"36218463","doi":""},{"reference":"Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29(8): 1072-5.
","pubmedId":"23422339","doi":""},{"reference":"Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. 2018. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 9(1): 5114.
","pubmedId":"30504855","doi":""},{"reference":"Joron C, Roméo B, Le Flèche-Matéos A, Rames C, El Samad Y, Hamdad F. 2019. Dermacoccus nishinomiyaensis as a cause of persistent paediatric catheter-related bacteraemia. Clin Microbiol Infect 25(8): 1054-1055.
","pubmedId":"30825676","doi":""},{"reference":"Kim M, Lee H, Lee S, Han Y, Kim OS. 2025. Millennial-scale depth-resolved ancient microbial diversity and pathogenic potential in Styx Glacier, Antarctica. Environ Res 285(Pt 2): 122421.
","pubmedId":"40706832","doi":""},{"reference":"Klein BA, Lemon KP, Gajare P, Jospin G, Eisen JA, Coil DA. 2017. Draft Genome Sequences of Dermacoccus nishinomiyaensis Strains UCD-KPL2534 and UCD-KPL2528 Isolated from an Indoor Track Facility. Genome Announc 5(8): 10.1128/genomeA.01652-16.
","pubmedId":"28232444","doi":""},{"reference":"Kolmogorov M, Yuan J, Lin Y, Pevzner PA. 2019. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 37(5): 540-546.
","pubmedId":"30936562","doi":""},{"reference":"Li W, O'Neill KR, Haft DH, DiCuccio M, Chetvernin V, Badretdin A, et al., Thibaud-Nissen F. 2021. RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation. Nucleic Acids Res 49(D1): D1020-D1028.
","pubmedId":"33270901","doi":""},{"reference":"Lim SJ, Natarajan O, Keller J, Dishaw LJ, Furman BT, Breitbart M. 2025. Draft genome sequence of Gracilimonas sp. strain BCB1 isolated from the gill tissue of the lucinid bivalve Stewartia floridana in Pinellas County, Florida, USA. Microbiol Resour Announc 14(11): e0059525.
","pubmedId":"41002246","doi":""},{"reference":"Magnúsdóttir S, Saraiva JP, Bartholomäus A, Soheili M, Toscan RB, Zhang J, Nunes da Rocha U, CLUE-TERRA consortium. 2023. Metagenome-assembled genomes indicate that antimicrobial resistance genes are highly prevalent among urban bacteria and multidrug and glycopeptide resistances are ubiquitous in most taxa. Front Microbiol 14: 1037845.
","pubmedId":"36760505","doi":""},{"reference":"Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25(7): 1043-55.
","pubmedId":"25977477","doi":""},{"reference":"Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil PA, Hugenholtz P. 2022. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res 50(D1): D785-D794.
","pubmedId":"34520557","doi":""},{"reference":"Stackebrandt E, Koch C, Gvozdiak O, Schumann P. 1995. Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend. Int J Syst Bacteriol 45(4): 682-92.
","pubmedId":"7547287","doi":""},{"reference":"Williams AN, MacLea KS. 2019. Draft Genome Sequence of Dermacoccus nishinomiyaensis TSA37, Isolated from Wood Ash. Microbiol Resour Announc 8(50): 10.1128/MRA.01370-19.
","pubmedId":"31831617","doi":""}],"title":"Draft genome sequence of Dermacoccus nishinomiyaensis Y5
","reviews":[],"curatorReviews":[]},{"id":"ef11b251-7fb7-459d-ac6e-2e2e8f84c2cb","decision":"publish","abstract":"We report the draft genome sequence of Dermacoccus nishinomiyaensis Y5 isolated from a glycerol stock prepared from a fungal culture from the gill of the lucinid bivalve, Stewartia floridana. This bacterial strain is gram-positive, coccus-shaped, and citrate-positive. Its draft genome of 3.3 Mb was assembled with 100% completeness, comprising 11 contigs and 2,937 protein-coding genes. Dermacoccus nishinomiyaensis Y5 shared 98.9% average nucleotide identity (ANI) with its closest genome relative, D. nishinomiyaensis CTOTU46710 assembled from an urban metagenome. Further investigation is needed to identify the source and pathogenicity of D. nishinomiyaensis Y5.
","acknowledgements":"We acknowledge the microbiology research support for undergraduate students provided by Michelle Green and Deborah Howard from the Department of Integrative Biology at the University of South Florida.
","authors":[{"affiliations":["University of South Florida, Tampa, FL, US","University of South Florida, St. Petersburg, FL, US"],"departments":["","College of Marine Science"],"credit":["formalAnalysis","investigation","methodology","visualization","writing_originalDraft"],"email":"jeweliak@usf.edu","firstName":"Jewelia T","lastName":"Keller","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0009-0002-4163-9313"},{"affiliations":["University of South Florida, St. Petersburg, FL, US","Florida International University, Miami, FL, US"],"departments":["College of Marine Science","College of Arts, Science and Education"],"credit":["conceptualization","dataCuration","formalAnalysis","investigation","methodology","software","supervision","validation","visualization","writing_originalDraft"],"email":"shlim@fiu.edu","firstName":"Shen Jean ","lastName":"Lim","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of South Florida, Tampa, FL, US"],"departments":["Department of Pediatrics, Morsani College of Medicine"],"credit":["formalAnalysis","investigation","methodology","writing_reviewEditing"],"email":"ojasn@usf.edu","firstName":"Ojas","lastName":"Natarajan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of South Florida, St. Petersburg, FL, US"],"departments":["Department of Integrative Biology"],"credit":["methodology","resources"],"email":"cropper@usf.edu","firstName":"Nicholas ","lastName":"Cropper","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of South Florida, Tampa, FL, US"],"departments":["Department of Pediatrics, Morsani College of Medicine"],"credit":["conceptualization","resources","writing_reviewEditing"],"email":"ldishaw@usf.edu","firstName":"Larry J","lastName":"Dishaw","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of South Florida, St. Petersburg, FL, US"],"departments":["College of Marine Science"],"credit":["fundingAcquisition","project","resources","supervision","validation","writing_reviewEditing"],"email":"mya@usf.edu","firstName":"Mya","lastName":"Breitbart","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[{"awardId":"OCE-2219547","funderName":"National Science Foundation (United States)","awardRecipient":"Mya Breitbart"}],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"Lucinid specimen collection was permitted by the Florida Fish and Wildlife Conservation Commission through a Special Activity License (SAL-22-2495B-SR) to S.J.L.
","image":{"url":"https://portal.micropublication.org/uploads/1ed5e19c92f5f6c0f447dced100c2b3d.jpeg"},"imageCaption":"Average Nucleotide Identity (ANI) comparisons between the genome of Dermacoccus nishinomiyaensis Y5 isolated in this study (annotated with black square) and all other representative genomes at the time of analysis assigned to Dermacoccus nishinomiyaensis. RefSeq accession numbers are listed in the x-axis and y-axis.
","imageTitle":"Average Nucleotide Identity (ANI) comparisons across Dermacoccus nishinomiyaensis genomes
","methods":"","reagents":"","patternDescription":"Dermacoccus nishinomiyaensis is a member of the Dermococcaceae family and commonly resides in the skin microbiome, functioning as a skin commensal (Williams and MacLea, 2019). Current literature classifies D. nishinomiyaensis as a coccus-shaped, non-spore forming, aerobic, chemo-organotrophic bacterium (Stackebrandt et al., 1995). Dermacoccus nishinomiyaensis was isolated serendipitously from a glycerol stock originally prepared from a fungal culture isolated from the gill of the lucinid bivalve, Stewartia floridana. The live lucinid (specimen ID: SS1) was collected from the Terra Ceia Aquatic Preserve (GPS coordinates: 27.587404, -82.623248) on September 7, 2023 (Lim et al., 2025).
Dissection and culturing methods were as described in Lim et al., (2025). Briefly, one gill was dissected from the live lucinid specimen, rinsed, homogenized, and diluted 10X (v/v) in 0.2 μm-filtered 35 g/L Instant Ocean® solution (https://www.instantocean.com). Sterile glass plating beads were used to spread 200 μL of the homogenate on BD Difco™ Marine Agar 2216, which was then incubated in the dark at room temperature (~22°C). Fungal growth was observed on the plate after two days and re-inoculated in BD Difco™ Marine Broth 2216 under the same conditions. Upon visible growth, 500 μL of the fungal culture was added to 500 μL of 50% glycerol and stored at -80ºC. The glycerol stock was streaked on BD Difco™ Marine Agar 2216. Instead of fungal growth, yellow colonies indicative of bacterial growth were observed.
One isolated yellow colony (Y5) was randomly chosen for subculturing and maintenance on BD Difco™ Marine Agar 2216. For biochemical characterization, the subculture was inoculated in various media at 37ºC. Under the microscope, this bacterial strain was observed to be gram-positive and coccus-shaped. Based on the phenol red broth test, D. nishinomiyaensis Y5 was unable to ferment glucose, lactose or sucrose. The citrate utilization test showed that the strain was citrate-positive. The Sulfide-Indole-Motility (SIM) test indicated the bacterial strain to be non-motile and unable to produce sulfur and indole. Gelatin hydrolysis, urease and phenylalanine deaminase tests produced negative results.
For genome sequencing, three representative yellow colonies maintained on BD Difco™ Marine Agar 2216 were separately grown in BD Difco™ Marine Broth 2216. As described in Lim et al. (2025), DNA was extracted from each culture upon visible growth by centrifuging each culture at 1,700 RCF for 5 minutes and collecting the pellet. DNA extraction was performed using Qiagen's AllPrep DNA/RNA Mini kit, followed by DNA purification using ZR's Genomic DNA Clean & Concentrator-10 kit. The concentration and quality of each purified DNA sample was assessed using the Qubit DNA HS assay, the Nanodrop ND-1000 spectrophotometer, and electrophoresis on a 1% (w/v) agarose gel. The unsheared DNA sample with the highest concentration and quality was sent to Eurofins Genomics for library preparation using Oxford Nanopore Technologies' (ONT) Rapid Barcoding Kit 96 V14. The library was sequenced on a GridION R10.4.1 flow cell and ONT's Dorado v0.6.0 was used for base-calling with the dna_r10.4.1_e8.2_400bps_hac@v4.2.0 model. A total of 66,806 reads and 108,590,115 bases were sequenced with a N50 value of 2,813 bp.
Sequence data was analyzed on the KBase server (Arkin et al., 2018) using default software parameters. Quality filtering by Filtlong v0.2.1 (https://github.com/rrwick/Filtlong) retained 35,588 reads, which was assembled using Flye v2.9.4 (Kolmogorov et al., 2019). The quality of the genome assembly was assessed using Quality Assessment Tool for Genome Assemblies (QUAST) v4.4 (Gurevich et al., 2013). The assembly, totaling 3,301,037 bp, comprised 11 contigs, with 68.78% G+C content and a N50 value of 2,066,152 bp. CheckM v1.0.18 (Parks et al., 2015a) predicted the assembly to be 100% complete with 0% contamination. Using the Genome Taxonomy Database (GTDB) release R226 (Parks et al., 2022b) as reference, GTDB-Tk v2.4.0 (Chaumeil et al., 2022) classified the genome as Dermacoccus nishinomiyaensis. The genome shared 98.9% average nucleotide identity (ANI) with the genome of D. nishinomiyaensis CTOTU46710 assembled from an urban metagenome (Magnúsdóttir et al., 2023), as calculated by fastANI v1.33 (Jain et al., 2018) (Figure 1). The genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline v6.10 (Li et al., 2021), which identified 2,937 protein-coding genes and three copies of the 16S rRNA gene. Sequence data, including raw reads (Sequence Read Archive accession: SRX31722345) and the genome assembly (RefSeq accession: GCF_054488915) is deposited at NCBI under the BioProject accession number PRJNA1399496.
To confirm whether the gills of lucinid bivalves contain D. nishinomiyaensis Y5, primers 79F (5'-AGCTTGCTGGTGTGGATTAG-3') and 169R (5'-GGAGATCGGTCGTATCCAGTAT-3') targeting the 16S rRNA gene of D. nishinomiyaensis Y5 were designed using the Integrated DNA Technologies (IDT) PrimerQuest™Tool (https://www.idtdna.com/pages/tools/primerquest). PCR was performed on the DNA sample extracted from the other gill of the same S. floridana specimen using Qiagen's AllPrep DNA/RNA Mini kit, as well as 13 other DNA samples extracted from clam gills dissected from other S. floridana specimens listed in Lim et al., (2025) under the following thermocycling conditions: 95ºC for 10 minutes, followed by 34 cycles 95ºC for 30 minutes, 52.5ºC for 30 minutes, 72ºC for 1 minute, and an extension period of 10 minutes at 72ºC. No amplification was observed in all DNA samples tested.
Dermacoccus nishinomiyaensis is a Gram-positive, non-spore forming bacterium commonly found as a commensal resident in the human skin microbiome (Stackebrandt et al., 1995). Outside of the skin microbiome, D. nishinomiyaensis has been isolated from human-built environments, such as wood ash (Williams and MacLea, 2019) and indoor track facilities (Klein et al., 2017). In the natural environment, D. nishinomiyaensis has been isolated from the phycosphere of red algae collected from an intertidal zone in Korea (GCF_055693885; 98.2% ANI with D. nishinomiyaensis Y5), the Ulu Slim Hot Spring in Malaysia (GCF_000725405; 98% ANI with D. nishinomiyaensis Y5), and the Styx glacier in Antarctica (GCF_ 037331475; 98.7% ANI with D. nishinomiyaensis Y5) (Kim et al., 2025). Although the negative PCR results suggest that D. nishinomiyaensis Y5 could be a transient contaminant during cultivation and glycerol stock preparation, the gill origin of this bacterium could not be excluded without further testing. Species within the Dermacoccus genus do not typically exhibit pathogenic properties; however, it has been documented that D. nishinomiyaensis may cause catheter-related infections (Joron et al., 2019). Further investigation is necessary to determine the ecological origin of D. nishinomiyaensis Y5 and whether it represents a transient contaminant or a rare marine bacterium.
","references":[{"reference":"Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al., Yu D. 2018. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nat Biotechnol 36(7): 566-569.
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","pubmedId":"28232444","doi":""},{"reference":"Kolmogorov M, Yuan J, Lin Y, Pevzner PA. 2019. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 37(5): 540-546.
","pubmedId":"30936562","doi":""},{"reference":"Li W, O'Neill KR, Haft DH, DiCuccio M, Chetvernin V, Badretdin A, et al., Thibaud-Nissen F. 2021. RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation. Nucleic Acids Res 49(D1): D1020-D1028.
","pubmedId":"33270901","doi":""},{"reference":"Lim SJ, Natarajan O, Keller J, Dishaw LJ, Furman BT, Breitbart M. 2025. Draft genome sequence of Gracilimonas sp. strain BCB1 isolated from the gill tissue of the lucinid bivalve Stewartia floridana in Pinellas County, Florida, USA. Microbiol Resour Announc 14(11): e0059525.
","pubmedId":"41002246","doi":""},{"reference":"Magnúsdóttir S, Saraiva JP, Bartholomäus A, Soheili M, Toscan RB, Zhang J, Nunes da Rocha U, CLUE-TERRA consortium. 2023. Metagenome-assembled genomes indicate that antimicrobial resistance genes are highly prevalent among urban bacteria and multidrug and glycopeptide resistances are ubiquitous in most taxa. Front Microbiol 14: 1037845.
","pubmedId":"36760505","doi":""},{"reference":"Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25(7): 1043-55.
","pubmedId":"25977477","doi":""},{"reference":"Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil PA, Hugenholtz P. 2022. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res 50(D1): D785-D794.
","pubmedId":"34520557","doi":""},{"reference":"Stackebrandt E, Koch C, Gvozdiak O, Schumann P. 1995. Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend. Int J Syst Bacteriol 45(4): 682-92.
","pubmedId":"7547287","doi":""},{"reference":"Williams AN, MacLea KS. 2019. Draft Genome Sequence of Dermacoccus nishinomiyaensis TSA37, Isolated from Wood Ash. Microbiol Resour Announc 8(50): 10.1128/MRA.01370-19.
","pubmedId":"31831617","doi":""}],"title":"Draft genome sequence of Dermacoccus nishinomiyaensis Y5
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