Microbacteriophage Babydotz was isolated in Moorhead, Minnesota in 2020 by infecting Microbacterium foliorumNRRL B-24224. Based on gene content, is is assigned to actinobacteriophage cluster EG. With no identifiable genes involved in lysogeny, it is predicted to have a lytic life cycle.
","acknowledgements":"We thank The Howard Hughes Medical Institute and the Hatfull Lab at the University of Pittsburgh for supporting this research. We would also like to thank Ethan Dotzler and Jonathan Nyandu Kanyinda and their supporting faculty from Minnesota State University Moorhead for the discovery, purification, isolation of DNA from and transmission electron microscopy of phage Babydotz.
","authors":[{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["conceptualization","project","writing_originalDraft","writing_reviewEditing","dataCuration","formalAnalysis"],"email":"hmcferri@xula.edu","firstName":"Harris","lastName":"McFerrin","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"https://orcid.org/0000-0001-7261-6320"},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["writing_originalDraft","investigation","dataCuration"],"email":"dahmed1@xula.edu","firstName":"Dahlia","lastName":"Ahmed","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"jaustin4@xula.edu","firstName":"Justice","lastName":"Austin","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"cbaker6@xula.edu","firstName":"Classie","lastName":"Baker","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"sbrown44@xula.edu","firstName":"Skyler","lastName":"Brown","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"kcoope11@xula.edu","firstName":"Kaionah","lastName":"Cooper","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"kdrake1@xula.edu","firstName":"Kennedy","lastName":"Drake","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"lgalbert@xula.edu","firstName":"Liyah","lastName":"Galbert","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"jharri60@xula.edu","firstName":"Jillian","lastName":"Harris","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"nherrera@xula.edu","firstName":"Nora","lastName":"Herrera","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"gjones13@xula.edu","firstName":"Gerald","lastName":"Jones","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"mkhalil@xula.edu","firstName":"Michael","lastName":"Khalil","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"ckimble@xula.edu","firstName":"Camerin","lastName":"Kimble","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"alewis43@xula.edu","firstName":"Alicia","lastName":"Lewis","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of 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Carmichael Endowed Professorship from the Louisiana Board of Regents and Xavier University of Louisiana.
","image":{"url":"https://portal.micropublication.org/uploads/6dc9f582dd91ee46f45134d8e39d142a.jpg"},"imageCaption":"TEM of uranyl acetate-stained microbacteriophage Babydotz shows a siphoviral morphology.
","imageTitle":"Transmission electron microscopy (TEM) of microbacteriophage Babydotz
","methods":"","reagents":"","patternDescription":"Research on bacteriophages has contributed to our understanding of viruses more broadly and in their development as therapeutics for multi-drug resistant bacterial infections (Kim et al, 2025). Here, we report the genome sequence of Babydotz, a microbacteriophage that infects Microbacterium foliorium.
Babydotz was isolated from a soil sample that was collected between two pine trees at the Minnesota State University Moorhead Campus Mall (global positioning system [GPS] 46.8673 N, 96.762 W) when the ambient temperature was -2°C. Briefly, Babydotz was extracted by washing the soil with PYCa liquid medium, filtering the wash, and plating the filtrate in top agar with M. foliorum NRRL B-24224 (Zorowik et al, 2024). After incubation at 30˚C for 24 hours, Babydotz formed clear plaques with a diameter of 0.67-0.75mm (n=5), measured using ImageJ software (Schneider, et al, 2012). Negative-staining transmission electron microscopy showed siphovirus morphology with a capsid diameter of 80-90nm (n=5) and tail length of 180-200nm (n=5) (Figure 1).
DNA was extracted from a Babydotz lysate using the Promega DNA Kit. The Pittsburgh Bacteriophage Institute generated sequencing libraries using the NEB Ultra II FS Kits and sequenced the genome on an Illumina MiSeq using 150-cycle v3 Reagent Cartridges (Russell DA, 2018). Sequencing yielded 613,595 150-base single-end reads. A single bacteriophage contig with 1387-fold coverage was assembled from the raw reads using Newbler v.2.9 and Consed v29 with default parameters (Russell DA, 2018). The resulting genome consisted of 63,076 bp, 217-bp direct terminal repeatsand 67.0% G+C nucleotides.
Auto-annotation was performed using GeneMark v.3.02 (Delcher et al., 1990) and Glimmer v.2.5p (Borodovsky et al., 2003; Besemer et al., 2005). DNA Master v5.23.6 (Pope et al., 2018), Phamerator, using Actino_draft database v578(Cresawn et al., 2011) and PECAAN (Rinehart et al., 2016) were used to manually refine the annotations. Starterator (Pacey, 2014) was used to evaluate start sites conservation. No tRNA coding genes were identified using tRNAscan-SE v2.0 (Lowe, 2016) or ARAGORN v1.2.41 (Laslett, 2004). Putative functions for 23 of 104 predicted coding ORFs were assigned using BLAST, using the Actinobacteriophage and NCBI non-redundant database (Altschul et al., 1990) and HHPRED, using the PDB_mmCIF70, Pfam- v.36, NCBI Conserved Domains databases (Zimmermann et al., 2018; Söding et al., 2005). Nine protein-coding ORFs with membrane-associated domains were determined using SOSUI (Hirokawa et al., 1998) and TMHMM v.1.0.24 (Hallgren et al., 2022). All tools were run with default parameters. AUG start codon usage was 100%. BabyDotz was assigned to cluster EG based on gene content similarity of at least 35% to phages in the Actinobacteriophage database, phagesdb (https://phageDB.org) (Pope et al., 2017; Russell and Hatfull, 2017). As with other cluster EG phages, a third of the genome encodes genes transcribed in one direction, with the remaining genes on either side of this segment transcribed in the opposite direction. An endolysin is encoded at one boundary of these divergently transcribed regions.
Other predicted genes include those encoding a putative DprA-like DNA processing chain A, three helix-turn-helix DNA binding domains, a terminase, a portal protein, a major capsid protein, a major tail protein, a phosphoesterase, a head-to-tail adaptor, a tape measure protein, three minor tail proteins, an endolysin, an exonuclease, an HNH endonuclease, a RuvC-like resolvase, a MazG-like nucleotide pyrophosphohydrolase, an SSB protein, a DNA primase/helicase and two ribbon-helix-helix DNA binding proteins. Nogenes encoding immunity repressor or integrase functions could be identified, suggesting that Babydotz is unlikely to establish lysogeny.
Nucleotide sequence accession numbers
Babydotz is available at GenBank with Accession No. 0R613478 and Sequence Read Archive (SRA) No. SRR18306109.
","references":[{"reference":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
","pubmedId":"","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33: W451-W454.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Borodovsky M, Mills R, Besemer J, Lomsadze A. 2003. Prokaryotic Gene Prediction Using GeneMark and GeneMark.hmm. Current Protocols in Bioinformatics 1: 10.1002/0471250953.bi0405s01.
","pubmedId":"","doi":"10.1002/0471250953.bi0405s01"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 10.1186/1471-2105-12-395.
","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Delcher A. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Research 27: 4636-4641.
","pubmedId":"","doi":"10.1093/nar/27.23.4636"},{"reference":"Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.
","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Hirokawa T, Boon-Chieng S, Mitaku S. 1998. SOSUI: classification and secondary structure prediction system for membrane proteins.. Bioinformatics 14: 378-379.
","pubmedId":"","doi":"10.1093/bioinformatics/14.4.378"},{"reference":"Kim MK, Suh GA, Cullen GD, Perez Rodriguez S, Dharmaraj T, Chang THW, et al., Sacher JC. 2025. Bacteriophage therapy for multidrug-resistant infections: current technologies and therapeutic approaches. J Clin Invest 135(5): 10.1172/JCI187996.
","pubmedId":"40026251","doi":""},{"reference":"Laslett D. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32: 11-16.
","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Chan PP. 2016. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Research 44: W54-W57.
","pubmedId":"","doi":" 10.1093/nar/gkw413"},{"reference":"Pacey, M. Starterator Guide. (2014) https://phagesdb.org/media/docs/Starterator_Guide_2014_2.pdf
","pubmedId":"","doi":""},{"reference":"Pope WH, Jacobs-Sera D. 2017. Annotation of Bacteriophage Genome Sequences Using DNA Master: An Overview. Methods in Molecular Biology,Bacteriophages : 217-229.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_16"},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, et al., Hatfull GF. 2017. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8(4): 10.1128/mBio.01069-17.
","pubmedId":"28811342","doi":""},{"reference":"Rinehart CA, Gaffney B, Wood JD, Smith J. PECAAN, a Phage Evidence Collection And Annotation Network. (2016) https://discover.kbrinsgd.org/login
","pubmedId":"","doi":""},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database. Bioinformatics 33: 784-786.
","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Russell DA. 2017. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Methods in Molecular Biology,Bacteriophages : 109-125.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Schneider CA, Rasband WS, Eliceiri KW. 2012. NIH Image to ImageJ: 25 years of image analysis. Nature Methods 9: 671-675.
","pubmedId":"","doi":"doi:10.1038/nmeth.2089"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 33: W244-W248.
","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, et al., Alva. 2018. A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. Journal of Molecular Biology 430: 2237-2243.
","pubmedId":"","doi":"10.1016/j.jmb.2017.12.007"},{"reference":"Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods in Molecular Biology,Phage Engineering and Analysis : 273-298.
","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Genomic Characterization of Bacteriophage Babydotz, Isolated from Microbacterium foliorum
","reviews":[],"curatorReviews":[]},{"id":"73cc729f-7541-4735-8bd9-27bc456962e9","decision":"revise","abstract":"Microbacteriophage Babydotz was isolated in Moorhead, Minnesota in 2020 by infecting Microbacterium foliorumNRRL B-24224. Based on gene content, is is assigned to actinobacteriophage cluster EG. With no identifiable genes involved in lysogeny, it is predicted to have a lytic life cycle.
","acknowledgements":"We thank The Howard Hughes Medical Institute and the Hatfull Lab at the University of Pittsburgh for supporting this research. We would also like to thank Ethan Dotzler and Jonathan Nyandu Kanyinda and their supporting faculty from Minnesota State University Moorhead for the discovery, purification, isolation of DNA from and transmission electron microscopy of phage Babydotz and Michael Khalil and Shaundessy Perry for their investigative contributions.
","authors":[{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["conceptualization","project","writing_originalDraft","writing_reviewEditing","dataCuration","formalAnalysis"],"email":"hmcferri@xula.edu","firstName":"Harris","lastName":"McFerrin","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"https://orcid.org/0000-0001-7261-6320"},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["writing_originalDraft","investigation","dataCuration"],"email":"Dahlia.Ahmed@som.umaryland.edu","firstName":"Dahlia","lastName":"Ahmed","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"jaustin4@xula.edu","firstName":"Justice","lastName":"Austin","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"cbaker6@xula.edu","firstName":"Classie","lastName":"Baker","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"bskyler202@gmail.com","firstName":"Skyler","lastName":"Brown","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"kcoope11@xula.edu","firstName":"Kaionah","lastName":"Cooper","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"kdrake1@xula.edu","firstName":"Kennedy","lastName":"Drake","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"lgalbert@xula.edu","firstName":"Liyah","lastName":"Galbert","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"jgharris26@gmail.com","firstName":"Jillian","lastName":"Harris","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"nherr1@lsuhsc.edu","firstName":"Nora","lastName":"Herrera","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"gjones13@xula.edu","firstName":"Gerald","lastName":"Jones","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"ckimble@xula.edu","firstName":"Camerin","lastName":"Kimble","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"alicia.jlewis2003@gmail.com","firstName":"Alicia","lastName":"Lewis","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"lyancey@xula.edu","firstName":"Leianna","lastName":"Yancey","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[],"conflictsOfInterest":null,"dataTable":null,"extendedData":[],"funding":"Funds supporting this research were provided by the J.W. Carmichael Endowed Professorship from the Louisiana Board of Regents and Xavier University of Louisiana.
","image":{"url":"https://portal.micropublication.org/uploads/6dc9f582dd91ee46f45134d8e39d142a.jpg"},"imageCaption":"TEM of uranyl acetate-stained microbacteriophage Babydotz shows a siphoviral morphology.
","imageTitle":"Transmission electron microscopy (TEM) of microbacteriophage Babydotz
","methods":"","reagents":"","patternDescription":"Research on bacteriophages has contributed to our understanding of viruses more broadly and in their development as therapeutics for multi-drug resistant bacterial infections (Kim et al, 2025). Here, we report the genome sequence of Babydotz, a microbacteriophage that infects Microbacterium foliorium.
Babydotz was isolated from a soil sample that was collected between two pine trees at the Minnesota State University Moorhead Campus Mall (global positioning system [GPS] 46.8673 N, 96.762 W) when the ambient temperature was -2°C. Briefly, Babydotz was extracted by washing the soil with PYCa liquid medium, filtering the wash, and plating the filtrate in top agar with M. foliorum NRRL B-24224 (Zorowik et al, 2024). After incubation at 30˚C for 24 hours, Babydotz formed clear plaques with a diameter of 0.67-0.75mm (n=5), measured using ImageJ software (Schneider, et al, 2012). Negative-staining transmission electron microscopy showed siphovirus morphology with a capsid diameter of 80-90nm (n=5) and tail length of 180-200nm (n=5) (Figure 1).
DNA was extracted from a Babydotz lysate using the Promega DNA Kit. The Pittsburgh Bacteriophage Institute generated sequencing libraries using the NEB Ultra II FS Kits and sequenced the genome on an Illumina MiSeq using 150-cycle v3 Reagent Cartridges (Russell DA, 2018). Sequencing yielded 613,595 150-base single-end reads. A single bacteriophage contig with 1387-fold coverage was assembled from the raw reads using Newbler v.2.9 and Consed v29 with default parameters (Russell DA, 2018). The resulting genome consisted of 63,076 bp, 217-bp direct terminal repeatsand 67.0% G+C nucleotides.
Auto-annotation was performed using GeneMark v.3.02 (Delcher et al., 1990) and Glimmer v.2.5p (Borodovsky et al., 2003; Besemer et al., 2005). DNA Master v5.23.6 (Pope et al., 2018), Phamerator, using Actino_draft database v578(Cresawn et al., 2011) and PECAAN (Rinehart et al., 2016) were used to manually refine the annotations. Starterator (Pacey, 2014) was used to evaluate start sites conservation. No tRNA coding genes were identified using tRNAscan-SE v2.0 (Lowe, 2016) or ARAGORN v1.2.41 (Laslett, 2004). Putative functions for 23 of 104 predicted coding ORFs were assigned using BLAST, using the Actinobacteriophage and NCBI non-redundant database (Altschul et al., 1990) and HHPRED, using the PDB_mmCIF70, Pfam- v.36, NCBI Conserved Domains databases (Zimmermann et al., 2018; Söding et al., 2005). Nine protein-coding ORFs with membrane-associated domains were determined using SOSUI (Hirokawa et al., 1998) and TMHMM v.1.0.24 (Hallgren et al., 2022). All tools were run with default parameters. AUG start codon usage was 100%. BabyDotz was assigned to cluster EG based on gene content similarity of at least 35% to phages in the Actinobacteriophage database, phagesdb (https://phageDB.org) (Pope et al., 2017; Russell and Hatfull, 2017). As with other cluster EG phages, a third of the genome encodes genes transcribed in one direction, with the remaining genes on either side of this segment transcribed in the opposite direction. An endolysin is encoded at one boundary of these divergently transcribed regions.
Other predicted genes include those encoding a putative DprA-like DNA processing chain A, three helix-turn-helix DNA binding domains, a terminase, a portal protein, a major capsid protein, a major tail protein, a phosphoesterase, a head-to-tail adaptor, a tape measure protein, three minor tail proteins, an endolysin, an exonuclease, an HNH endonuclease, a RuvC-like resolvase, a MazG-like nucleotide pyrophosphohydrolase, an SSB protein, a DNA primase/helicase and two ribbon-helix-helix DNA binding proteins. Nogenes encoding immunity repressor or integrase functions could be identified, suggesting that Babydotz is unlikely to establish lysogeny.
Nucleotide sequence accession numbers
Babydotz is available at GenBank with Accession No. 0R613478 and Sequence Read Archive (SRA) No. SRR18306109.
","references":[{"reference":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
","pubmedId":"","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33: W451-W454.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Borodovsky M, Mills R, Besemer J, Lomsadze A. 2003. Prokaryotic Gene Prediction Using GeneMark and GeneMark.hmm. Current Protocols in Bioinformatics 1: 10.1002/0471250953.bi0405s01.
","pubmedId":"","doi":"10.1002/0471250953.bi0405s01"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 10.1186/1471-2105-12-395.
","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Delcher A. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Research 27: 4636-4641.
","pubmedId":"","doi":"10.1093/nar/27.23.4636"},{"reference":"Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.
","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Hirokawa T, Boon-Chieng S, Mitaku S. 1998. SOSUI: classification and secondary structure prediction system for membrane proteins.. Bioinformatics 14: 378-379.
","pubmedId":"","doi":"10.1093/bioinformatics/14.4.378"},{"reference":"Kim MK, Suh GA, Cullen GD, Perez Rodriguez S, Dharmaraj T, Chang THW, et al., Sacher JC. 2025. Bacteriophage therapy for multidrug-resistant infections: current technologies and therapeutic approaches. J Clin Invest 135(5): 10.1172/JCI187996.
","pubmedId":"40026251","doi":""},{"reference":"Laslett D. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32: 11-16.
","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Chan PP. 2016. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Research 44: W54-W57.
","pubmedId":"","doi":" 10.1093/nar/gkw413"},{"reference":"Pacey, M. Starterator Guide. (2014) https://phagesdb.org/media/docs/Starterator_Guide_2014_2.pdf
","pubmedId":"","doi":""},{"reference":"Pope WH, Jacobs-Sera D. 2017. Annotation of Bacteriophage Genome Sequences Using DNA Master: An Overview. Methods in Molecular Biology,Bacteriophages : 217-229.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_16"},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, et al., Hatfull GF. 2017. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8(4): 10.1128/mBio.01069-17.
","pubmedId":"28811342","doi":""},{"reference":"Rinehart CA, Gaffney B, Wood JD, Smith J. PECAAN, a Phage Evidence Collection And Annotation Network. (2016) https://discover.kbrinsgd.org/login
","pubmedId":"","doi":""},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database. Bioinformatics 33: 784-786.
","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Russell DA. 2017. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Methods in Molecular Biology,Bacteriophages : 109-125.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Schneider CA, Rasband WS, Eliceiri KW. 2012. NIH Image to ImageJ: 25 years of image analysis. Nature Methods 9: 671-675.
","pubmedId":"","doi":"doi:10.1038/nmeth.2089"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 33: W244-W248.
","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, et al., Alva. 2018. A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. Journal of Molecular Biology 430: 2237-2243.
","pubmedId":"","doi":"10.1016/j.jmb.2017.12.007"},{"reference":"Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods in Molecular Biology,Phage Engineering and Analysis : 273-298.
","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Genomic Characterization of Bacteriophage Babydotz, Isolated from Microbacterium foliorum
","reviews":[{"reviewer":{"displayName":"Sarah Ball"},"openAcknowledgement":true,"status":{"submitted":true}},{"reviewer":{"displayName":"Kurt Regner"},"openAcknowledgement":true,"status":{"submitted":true}}],"curatorReviews":[]},{"id":"921b268b-93ec-4007-b7d4-7fd77d65a73d","decision":"accept","abstract":"Microbacteriophage Babydotz was isolated in Moorhead, Minnesota in 2020 by infecting Microbacterium foliorum NRRL B-24224. Based on gene content, is is assigned to actinobacteriophage cluster EG. With no identifiable genes involved in lysogeny, it is predicted to have a lytic life cycle.
","acknowledgements":"We thank The Howard Hughes Medical Institute and the Hatfull Lab at the University of Pittsburgh for supporting this research. We would also like to thank Ethan Dotzler and Jonathan Nyandu Kanyinda and their supporting faculty from Minnesota State University Moorhead for the discovery, purification, isolation of DNA from and transmission electron microscopy of phage Babydotz.
","authors":[{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["conceptualization","project","writing_originalDraft","writing_reviewEditing","dataCuration","formalAnalysis"],"email":"hmcferri@xula.edu","firstName":"Harris","lastName":"McFerrin","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"https://orcid.org/0000-0001-7261-6320"},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["writing_originalDraft","investigation","dataCuration"],"email":"Dahlia.Ahmed@som.umaryland.edu","firstName":"Dahlia","lastName":"Ahmed","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of 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States"],"departments":[""],"credit":["investigation"],"email":"michaelkhalil1001@gmail.com","firstName":"Michael","lastName":"Khalil","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"shaundessyp@gmail.com","firstName":"Shaundessy","lastName":"Perry","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"Funds supporting this research were provided by the J.W. Carmichael Endowed Professorship from the Louisiana Board of Regents and Xavier University of Louisiana.
","image":{"url":"https://portal.micropublication.org/uploads/6dc9f582dd91ee46f45134d8e39d142a.jpg"},"imageCaption":"TEM of uranyl acetate-stained microbacteriophage Babydotz shows a siphovirus morphology.
","imageTitle":"Transmission electron microscopy (TEM) of microbacteriophage Babydotz
","methods":"","reagents":"","patternDescription":"Research on bacteriophages has contributed to our understanding of viruses more broadly and in their development as therapeutics for multi-drug resistant bacterial infections (Kim et al, 2025). Here, we report the genome sequence of Babydotz, a microbacteriophage that infects Microbacterium foliorium.
Babydotz was isolated from a soil sample that was collected between two pine trees at the Minnesota State University Moorhead Campus Mall (global positioning system [GPS] 46.8673 N, 96.762 W) when the ambient temperature was -2°C. Briefly, Babydotz was extracted by washing the soil with PYCa liquid medium, filtering the wash, and plating the filtrate in top agar with M. foliorum NRRL B-24224 (Zorowik et al, 2024). After incubation at 30˚C for 24 hours, Babydotz formed clear plaques with a diameter of 0.67-0.75mm (n=5), measured using ImageJ software (Schneider, et al, 2012). Negative-staining transmission electron microscopy showed siphovirus morphology with a capsid diameter of 80-90nm (n=5) and tail length of 180-200nm (n=5) (Figure 1).
DNA was extracted from a Babydotz lysate using a Promega Wizard DNA extraction kit prior to sequencing. The Pittsburgh Bacteriophage Institute generated sequencing libraries using the NEB Ultra II FS Kits and sequenced the genome on an Illumina MiSeq using 150-cycle v3 Reagent Cartridges (Russell DA, 2018). Sequencing yielded 613,595 150-base single-end reads. A single bacteriophage contig with 1387-fold coverage was assembled from the raw reads using Newbler v.2.9 and Consed v29 with default parameters (Russell DA, 2018). The resulting genome consisted of 63,076 bp, 217-bp direct terminal repeats and 67.0% G+C nucleotides.
Auto-annotation was performed using DNA Master v5.23.6 (Pope et al., 2018) which employs GeneMark v.3.02 (Delcher et al., 1990) and Glimmer v.2.5p (Borodovsky et al., 2003; Besemer et al., 2005). DNA Master, Phamerator, using Actino_draft database v578 (Cresawn et al., 2011) and PECAAN (Rinehart et al., 2016) were used to manually refine the annotations. Starterator (Pacey, 2014) was used to further evaluate start sites conservation with Glimmer and Genemark. When there was disagreement among these software programs, BLAST results, coding potential and gene length were also used to determine the most likely start for the gene. No tRNA coding genes were identified using tRNAscan-SE v2.0 (Lowe, 2016) or ARAGORN v1.2.41 (Laslett, 2004). Putative functions for 23 of 104 predicted coding ORFs were assigned using BLASTp with an e-value cutoff of 10-4, using the Actinobacteriophage and NCBI non-redundant database (Altschul et al., 1990) and HHPRED, using the PDB_mmCIF70, Pfam- v.36, NCBI Conserved Domains databases with a probability of 90% or greater (Zimmermann et al., 2018; Söding et al., 2005). Nine protein-coding ORFs with membrane-associated domains were determined using SOSUI (Hirokawa et al., 1998) and TMHMM v.1.0.24 (Hallgren et al., 2022). All tools were run with default parameters. Following student genome annotation, the annotation underwent peer review by an experienced SEAPhage-associated faculty and passed quality control inspection. AUG start codon usage was 100%. BabyDotz was assigned to cluster EG based on gene content similarity of at least 35% to phages in the Actinobacteriophage database, phagesdb (https://phageDB.org) (Pope et al., 2017; Russell and Hatfull, 2017). Phamerator was used to compare genome architecture and gene synteny between Babydotz and other cluster EG phages. Except for several genes near the left end of the genome, Babydotz exhibits strong synteny with other peer-reviewed cluster EG phages with which there was high sequence alignment (BLASTn E value, Score) including Rowlf (0.0, .93e+04), SallieK (0.0, 1.697e+04), Tissue (0.0, 1.687e+04) and Zagie (0.0, 1.657e+04), consistent with its assignment to cluster EG. Consistent with other cluster EG phages, the central third of the Babydotz genome is transcribed in the forward direction, whereas the flanking regions are transcribed in the reverse direction. An endolysin is encoded immediately upstream of the boundary where transcription switches from the reverse to the forward direction, consistent with the genomic organization observed in other cluster EG phages including Rowlf, SallieK, Tissue and Zagie.
Other predicted genes include those encoding a putative DprA-like DNA processing chain A, three helix-turn-helix DNA binding domains, a terminase, a portal protein, a major capsid protein, a major tail protein, a phosphoesterase, a head-to-tail adaptor, a tape measure protein, three minor tail proteins, an endolysin, an exonuclease, an HNH endonuclease, a RuvC-like resolvase, a MazG-like nucleotide pyrophosphohydrolase, an SSB protein, a DNA primase/helicase and two ribbon-helix-helix DNA binding proteins. No genes encoding immunity repressor or integrase functions could be identified, suggesting that Babydotz is unlikely to establish lysogeny.
Nucleotide sequence accession numbers
Babydotz is available at GenBank with Accession No. 0R613478 and Sequence Read Archive (SRA) No. SRR18306109.
","references":[{"reference":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
","pubmedId":"","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33: W451-W454.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Borodovsky M, Mills R, Besemer J, Lomsadze A. 2003. Prokaryotic Gene Prediction Using GeneMark and GeneMark.hmm. Current Protocols in Bioinformatics 1: 10.1002/0471250953.bi0405s01.
","pubmedId":"","doi":"10.1002/0471250953.bi0405s01"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 10.1186/1471-2105-12-395.
","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Delcher A. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Research 27: 4636-4641.
","pubmedId":"","doi":"10.1093/nar/27.23.4636"},{"reference":"Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.
","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Hirokawa T, Boon-Chieng S, Mitaku S. 1998. SOSUI: classification and secondary structure prediction system for membrane proteins.. Bioinformatics 14: 378-379.
","pubmedId":"","doi":"10.1093/bioinformatics/14.4.378"},{"reference":"Kim MK, Suh GA, Cullen GD, Perez Rodriguez S, Dharmaraj T, Chang THW, et al., Sacher JC. 2025. Bacteriophage therapy for multidrug-resistant infections: current technologies and therapeutic approaches. J Clin Invest 135(5): 10.1172/JCI187996.
","pubmedId":"40026251","doi":""},{"reference":"Laslett D. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32: 11-16.
","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Chan PP. 2016. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Research 44: W54-W57.
","pubmedId":"","doi":" 10.1093/nar/gkw413"},{"reference":"Pacey, M. Starterator Guide. (2014) https://phagesdb.org/media/docs/Starterator_Guide_2014_2.pdf
","pubmedId":"","doi":""},{"reference":"Pope WH, Jacobs-Sera D. 2017. Annotation of Bacteriophage Genome Sequences Using DNA Master: An Overview. Methods in Molecular Biology,Bacteriophages : 217-229.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_16"},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, et al., Hatfull GF. 2017. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8(4): 10.1128/mBio.01069-17.
","pubmedId":"28811342","doi":""},{"reference":"Rinehart CA, Gaffney B, Wood JD, Smith J. PECAAN, a Phage Evidence Collection And Annotation Network. (2016) https://discover.kbrinsgd.org/login
","pubmedId":"","doi":""},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database. Bioinformatics 33: 784-786.
","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Russell DA. 2017. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Methods in Molecular Biology,Bacteriophages : 109-125.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Schneider CA, Rasband WS, Eliceiri KW. 2012. NIH Image to ImageJ: 25 years of image analysis. Nature Methods 9: 671-675.
","pubmedId":"","doi":"doi:10.1038/nmeth.2089"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 33: W244-W248.
","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, et al., Alva. 2018. A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. Journal of Molecular Biology 430: 2237-2243.
","pubmedId":"","doi":"10.1016/j.jmb.2017.12.007"},{"reference":"Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods in Molecular Biology,Phage Engineering and Analysis : 273-298.
","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Genomic Characterization of Bacteriophage Babydotz, Isolated from Microbacterium foliorum
","reviews":[{"reviewer":{"displayName":"Kurt Regner"},"openAcknowledgement":true,"status":{"submitted":true}}],"curatorReviews":[]},{"id":"03196033-924b-419a-a80a-5e67ec39eabf","decision":"edit","abstract":"Microbacteriophage Babydotz was isolated in Moorhead, Minnesota in 2020 by infecting Microbacterium foliorum NRRL B-24224. Based on gene content, is is assigned to actinobacteriophage cluster EG. With no identifiable genes involved in lysogeny, it is predicted to have a lytic life cycle.
","acknowledgements":"We thank The Howard Hughes Medical Institute and the Hatfull Lab at the University of Pittsburgh for supporting this research. We would also like to thank Ethan Dotzler and Jonathan Nyandu Kanyinda and their supporting faculty from Minnesota State University Moorhead for the discovery, purification, isolation of DNA from and transmission electron microscopy of phage Babydotz.
","authors":[{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["conceptualization","project","writing_originalDraft","writing_reviewEditing","dataCuration","formalAnalysis"],"email":"hmcferri@xula.edu","firstName":"Harris","lastName":"McFerrin","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"https://orcid.org/0000-0001-7261-6320"},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["writing_originalDraft","investigation","dataCuration"],"email":"Dahlia.Ahmed@som.umaryland.edu","firstName":"Dahlia","lastName":"Ahmed","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"jaustin4@xula.edu","firstName":"Justice","lastName":"Austin","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"cbaker6@xula.edu","firstName":"Classie","lastName":"Baker","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"bskyler202@gmail.com","firstName":"Skyler","lastName":"Brown","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"kcoope11@xula.edu","firstName":"Kaionah","lastName":"Cooper","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"kdrake1@xula.edu","firstName":"Kennedy","lastName":"Drake","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"lgalbert@xula.edu","firstName":"Liyah","lastName":"Galbert","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of 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","dataTable":{"url":null},"extendedData":[],"funding":"Funds supporting this research were provided by the J.W. Carmichael Endowed Professorship from the Louisiana Board of Regents and Xavier University of Louisiana.
","image":{"url":"https://portal.micropublication.org/uploads/6dc9f582dd91ee46f45134d8e39d142a.jpg"},"imageCaption":"TEM of uranyl acetate-stained microbacteriophage Babydotz shows a siphovirus morphology.
","imageTitle":"Transmission electron microscopy (TEM) of microbacteriophage Babydotz
","methods":"","reagents":"","patternDescription":"Research on bacteriophages has contributed to our understanding of viruses more broadly and in their development as therapeutics for multi-drug resistant bacterial infections (Kim et al, 2025). Here, we report the genome sequence of Babydotz, a microbacteriophage that infects Microbacterium foliorium.
Babydotz was isolated from a soil sample that was collected between two pine trees at the Minnesota State University Moorhead Campus Mall (global positioning system [GPS] 46.8673 N, 96.762 W) when the ambient temperature was -2°C. Briefly, Babydotz was extracted by washing the soil with PYCa liquid medium, filtering the wash, and plating the filtrate in top agar with M. foliorum NRRL B-24224 (Zorowik et al, 2024). After incubation at 30˚C for 24 hours, Babydotz formed clear plaques with a diameter of 0.67-0.75mm (n=5), measured using ImageJ software (Schneider, et al, 2012). Negative-staining transmission electron microscopy showed siphovirus morphology with a capsid diameter of 80-90nm (n=5) and tail length of 180-200nm (n=5) (Figure 1).
DNA was extracted from a Babydotz lysate using a Promega Wizard DNA extraction kit prior to sequencing. The Pittsburgh Bacteriophage Institute generated sequencing libraries using the NEB Ultra II FS Kits and sequenced the genome on an Illumina MiSeq using 150-cycle v3 Reagent Cartridges (Russell DA, 2018). Sequencing yielded 613,595 150-base single-end reads. A single bacteriophage contig with 1387-fold coverage was assembled from the raw reads using Newbler v.2.9 and Consed v29 with default parameters (Russell DA, 2018). The resulting genome consisted of 63,076 bp, 217-bp direct terminal repeats and 67.0% G+C nucleotides.
Auto-annotation was performed using DNA Master v5.23.6 (Pope et al., 2018) which employs GeneMark v.3.02 (Delcher et al., 1990) and Glimmer v.2.5p (Borodovsky et al., 2003; Besemer et al., 2005). DNA Master, Phamerator, using Actino_draft database v578 (Cresawn et al., 2011) and PECAAN (Rinehart et al., 2016) were used to manually refine the annotations. Starterator (Pacey, 2014) was used to further evaluate start sites conservation with Glimmer and Genemark. When there was disagreement among these software programs, BLAST results, coding potential and gene length were also used to determine the most likely start for the gene. No tRNA coding genes were identified using tRNAscan-SE v2.0 (Lowe, 2016) or ARAGORN v1.2.41 (Laslett, 2004). Putative functions for 23 of 104 predicted coding ORFs were assigned using BLASTp with an e-value cutoff of 10-4, using the Actinobacteriophage and NCBI non-redundant database (Altschul et al., 1990) and HHPRED, using the PDB_mmCIF70, Pfam- v.36, NCBI Conserved Domains databases with a probability of 90% or greater (Zimmermann et al., 2018; Söding et al., 2005). Nine protein-coding ORFs with membrane-associated domains were determined using SOSUI (Hirokawa et al., 1998) and TMHMM v.1.0.24 (Hallgren et al., 2022). All tools were run with default parameters. Following student genome annotation, the annotation underwent peer review by an experienced SEAPhage-associated faculty and passed quality control inspection. AUG start codon usage was 100%. BabyDotz was assigned to cluster EG based on gene content similarity of at least 35% to phages in the Actinobacteriophage database, phagesdb (https://phageDB.org) (Pope et al., 2017; Russell and Hatfull, 2017). Phamerator was used to compare genome architecture and gene synteny between Babydotz and other cluster EG phages. Except for several genes near the left end of the genome, Babydotz exhibits strong synteny with other peer-reviewed cluster EG phages with which there was high sequence alignment (BLASTn E value, Score) including Rowlf (0.0, .93e+04), SallieK (0.0, 1.697e+04), Tissue (0.0, 1.687e+04) and Zagie (0.0, 1.657e+04), consistent with its assignment to cluster EG. Consistent with other cluster EG phages, the central third of the Babydotz genome is transcribed in the forward direction, whereas the flanking regions are transcribed in the reverse direction. An endolysin is encoded immediately upstream of the boundary where transcription switches from the reverse to the forward direction, consistent with the genomic organization observed in other cluster EG phages including Rowlf, SallieK, Tissue and Zagie.
Other predicted genes include those encoding a putative DprA-like DNA processing chain A, three helix-turn-helix DNA binding domains, a terminase, a portal protein, a major capsid protein, a major tail protein, a phosphoesterase, a head-to-tail adaptor, a tape measure protein, three minor tail proteins, an endolysin, an exonuclease, an HNH endonuclease, a RuvC-like resolvase, a MazG-like nucleotide pyrophosphohydrolase, an SSB protein, a DNA primase/helicase and two ribbon-helix-helix DNA binding proteins. No genes encoding immunity repressor or integrase functions could be identified, suggesting that Babydotz is unlikely to establish lysogeny.
Nucleotide sequence accession numbers
Babydotz is available at GenBank with Accession No. 0R613478 and Sequence Read Archive (SRA) No. SRR18306109.
","references":[{"reference":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
","pubmedId":"","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33: W451-W454.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Borodovsky M, Mills R, Besemer J, Lomsadze A. 2003. Prokaryotic Gene Prediction Using GeneMark and GeneMark.hmm. Current Protocols in Bioinformatics 1: 10.1002/0471250953.bi0405s01.
","pubmedId":"","doi":"10.1002/0471250953.bi0405s01"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 10.1186/1471-2105-12-395.
","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Delcher A. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Research 27: 4636-4641.
","pubmedId":"","doi":"10.1093/nar/27.23.4636"},{"reference":"Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.
","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Hirokawa T, Boon-Chieng S, Mitaku S. 1998. SOSUI: classification and secondary structure prediction system for membrane proteins.. Bioinformatics 14: 378-379.
","pubmedId":"","doi":"10.1093/bioinformatics/14.4.378"},{"reference":"Kim MK, Suh GA, Cullen GD, Perez Rodriguez S, Dharmaraj T, Chang THW, et al., Sacher JC. 2025. Bacteriophage therapy for multidrug-resistant infections: current technologies and therapeutic approaches. J Clin Invest 135(5): 10.1172/JCI187996.
","pubmedId":"40026251","doi":""},{"reference":"Laslett D. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32: 11-16.
","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Chan PP. 2016. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Research 44: W54-W57.
","pubmedId":"","doi":" 10.1093/nar/gkw413"},{"reference":"Pacey, M. Starterator Guide. (2014) https://phagesdb.org/media/docs/Starterator_Guide_2014_2.pdf
","pubmedId":"","doi":""},{"reference":"Pope WH, Jacobs-Sera D. 2017. Annotation of Bacteriophage Genome Sequences Using DNA Master: An Overview. Methods in Molecular Biology,Bacteriophages : 217-229.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_16"},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, et al., Hatfull GF. 2017. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8(4): 10.1128/mBio.01069-17.
","pubmedId":"28811342","doi":""},{"reference":"Rinehart CA, Gaffney B, Wood JD, Smith J. PECAAN, a Phage Evidence Collection And Annotation Network. (2016) https://discover.kbrinsgd.org/login
","pubmedId":"","doi":""},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database. Bioinformatics 33: 784-786.
","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Russell DA. 2017. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Methods in Molecular Biology,Bacteriophages : 109-125.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Schneider CA, Rasband WS, Eliceiri KW. 2012. NIH Image to ImageJ: 25 years of image analysis. Nature Methods 9: 671-675.
","pubmedId":"","doi":"doi:10.1038/nmeth.2089"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 33: W244-W248.
","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, et al., Alva. 2018. A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. Journal of Molecular Biology 430: 2237-2243.
","pubmedId":"","doi":"10.1016/j.jmb.2017.12.007"},{"reference":"Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods in Molecular Biology,Phage Engineering and Analysis : 273-298.
","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Genomic Characterization of Bacteriophage Babydotz, Isolated from Microbacterium foliorum
","reviews":[],"curatorReviews":[]},{"id":"33f07f06-0040-41f6-8e0f-bccbaac70c0b","decision":"publish","abstract":"Microbacteriophage Babydotz was isolated in Moorhead, Minnesota in 2020 by infecting Microbacterium foliorum NRRL B-24224. Based on gene content, is is assigned to actinobacteriophage cluster EG. With no identifiable genes involved in lysogeny, it is predicted to have a lytic life cycle.
","acknowledgements":"We thank The Howard Hughes Medical Institute and the Hatfull Lab at the University of Pittsburgh for supporting this research. We would also like to thank Ethan Dotzler and Jonathan Nyandu Kanyinda and their supporting faculty from Minnesota State University Moorhead for the discovery, purification, isolation of DNA from and transmission electron microscopy of phage Babydotz.
","authors":[{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["conceptualization","project","writing_originalDraft","writing_reviewEditing","dataCuration","formalAnalysis"],"email":"hmcferri@xula.edu","firstName":"Harris","lastName":"McFerrin","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"https://orcid.org/0000-0001-7261-6320"},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["writing_originalDraft","investigation","dataCuration"],"email":"Dahlia.Ahmed@som.umaryland.edu","firstName":"Dahlia","lastName":"Ahmed","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"jaustin4@xula.edu","firstName":"Justice","lastName":"Austin","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"cbaker6@xula.edu","firstName":"Classie","lastName":"Baker","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"bskyler202@gmail.com","firstName":"Skyler","lastName":"Brown","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"kcoope11@xula.edu","firstName":"Kaionah","lastName":"Cooper","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"kdrake1@xula.edu","firstName":"Kennedy","lastName":"Drake","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"lgalbert@xula.edu","firstName":"Liyah","lastName":"Galbert","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"jgharris26@gmail.com","firstName":"Jillian","lastName":"Harris","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"nherr1@lsuhsc.edu","firstName":"Nora","lastName":"Herrera","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"gjones13@xula.edu","firstName":"Gerald","lastName":"Jones","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"ckimble@xula.edu","firstName":"Camerin","lastName":"Kimble","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"alicia.jlewis2003@gmail.com","firstName":"Alicia","lastName":"Lewis","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"lyancey@xula.edu","firstName":"Leianna","lastName":"Yancey","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"michaelkhalil1001@gmail.com","firstName":"Michael","lastName":"Khalil","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Xavier University of Louisiana, New Orleans, Louisiana, United States"],"departments":["Department of Biology"],"credit":["investigation"],"email":"shaundessyp@gmail.com","firstName":"Shaundessy","lastName":"Perry","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"Funds supporting this research were provided by the J.W. Carmichael Endowed Professorship from the Louisiana Board of Regents and Xavier University of Louisiana.
","image":{"url":"https://portal.micropublication.org/uploads/6dc9f582dd91ee46f45134d8e39d142a.jpg"},"imageCaption":"TEM of uranyl acetate-stained microbacteriophage Babydotz shows a siphovirus morphology.
","imageTitle":"Transmission electron microscopy (TEM) of microbacteriophage Babydotz
","methods":"","reagents":"","patternDescription":"Research on bacteriophages has contributed to our understanding of viruses more broadly and in their development as therapeutics for multi-drug resistant bacterial infections (Kim et al, 2025). Here, we report the genome sequence of Babydotz, a microbacteriophage that infects Microbacterium foliorium.
Babydotz was isolated from a soil sample that was collected between two pine trees at the Minnesota State University Moorhead Campus Mall (global positioning system [GPS] 46.8673 N, 96.762 W) when the ambient temperature was -2°C. Briefly, Babydotz was extracted by washing the soil with PYCa liquid medium, filtering the wash, and plating the filtrate in top agar with M. foliorum NRRL B-24224 (Zorowik et al, 2024). After incubation at 30˚C for 24 hours, Babydotz formed clear plaques with a diameter of 0.67-0.75mm (n=5), measured using ImageJ software (Schneider, et al, 2012). Negative-staining transmission electron microscopy showed siphovirus morphology with a capsid diameter of 80-90nm (n=5) and tail length of 180-200nm (n=5) (Figure 1).
DNA was extracted from a Babydotz lysate using a Promega Wizard DNA extraction kit prior to sequencing. The Pittsburgh Bacteriophage Institute generated sequencing libraries using the NEB Ultra II FS Kits and sequenced the genome on an Illumina MiSeq using 150-cycle v3 Reagent Cartridges (Russell DA, 2018). Sequencing yielded 613,595 150-base single-end reads. A single bacteriophage contig with 1387-fold coverage was assembled from the raw reads using Newbler v.2.9 and Consed v29 with default parameters (Russell DA, 2018). The resulting genome consisted of 63,076 bp, 217-bp direct terminal repeats and 67.0% G+C nucleotides.
Auto-annotation was performed using DNA Master v5.23.6 (Pope et al., 2018) which employs GeneMark v.3.02 (Delcher et al., 1990) and Glimmer v.2.5p (Borodovsky et al., 2003; Besemer et al., 2005). DNA Master, Phamerator, using Actino_draft database v578 (Cresawn et al., 2011) and PECAAN (Rinehart et al., 2016) were used to manually refine the annotations. Starterator (Pacey, 2014) was used to further evaluate start sites conservation with Glimmer and Genemark. When there was disagreement among these software programs, BLAST results, coding potential and gene length were also used to determine the most likely start for the gene. No tRNA coding genes were identified using tRNAscan-SE v2.0 (Lowe, 2016) or ARAGORN v1.2.41 (Laslett, 2004). Putative functions for 23 of 104 predicted coding ORFs were assigned using BLASTp with an e-value cutoff of 10-4, using the Actinobacteriophage and NCBI non-redundant database (Altschul et al., 1990) and HHPRED, using the PDB_mmCIF70, Pfam- v.36, NCBI Conserved Domains databases with a probability of 90% or greater (Zimmermann et al., 2018; Söding et al., 2005). Nine protein-coding ORFs with membrane-associated domains were determined using SOSUI (Hirokawa et al., 1998) and TMHMM v.1.0.24 (Hallgren et al., 2022). All tools were run with default parameters. Following student genome annotation, the annotation underwent peer review by an experienced SEAPhage-associated faculty and passed quality control inspection. AUG start codon usage was 100%. BabyDotz was assigned to cluster EG based on gene content similarity of at least 35% to phages in the Actinobacteriophage database, phagesdb (https://phageDB.org) (Pope et al., 2017; Russell and Hatfull, 2017). Phamerator was used to compare genome architecture and gene synteny between Babydotz and other cluster EG phages. Except for several genes near the left end of the genome, Babydotz exhibits strong synteny with other peer-reviewed cluster EG phages with which there was high sequence alignment (BLASTn E value, Score) including Rowlf (0.0, .93e+04), SallieK (0.0, 1.697e+04), Tissue (0.0, 1.687e+04) and Zagie (0.0, 1.657e+04), consistent with its assignment to cluster EG. Consistent with other cluster EG phages, the central third of the Babydotz genome is transcribed in the forward direction, whereas the flanking regions are transcribed in the reverse direction. An endolysin is encoded immediately upstream of the boundary where transcription switches from the reverse to the forward direction, consistent with the genomic organization observed in other cluster EG phages including Rowlf, SallieK, Tissue and Zagie.
Other predicted genes include those encoding a putative DprA-like DNA processing chain A, three helix-turn-helix DNA binding domains, a terminase, a portal protein, a major capsid protein, a major tail protein, a phosphoesterase, a head-to-tail adaptor, a tape measure protein, three minor tail proteins, an endolysin, an exonuclease, an HNH endonuclease, a RuvC-like resolvase, a MazG-like nucleotide pyrophosphohydrolase, an SSB protein, a DNA primase/helicase and two ribbon-helix-helix DNA binding proteins. No genes encoding immunity repressor or integrase functions could be identified, suggesting that Babydotz is unlikely to establish lysogeny.
Nucleotide sequence accession numbers
Babydotz is available at GenBank with Accession No. 0R613478 and Sequence Read Archive (SRA) No. SRR18306109.
","references":[{"reference":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
","pubmedId":"","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33: W451-W454.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Borodovsky M, Mills R, Besemer J, Lomsadze A. 2003. Prokaryotic Gene Prediction Using GeneMark and GeneMark.hmm. Current Protocols in Bioinformatics 1: 10.1002/0471250953.bi0405s01.
","pubmedId":"","doi":"10.1002/0471250953.bi0405s01"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 10.1186/1471-2105-12-395.
","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Delcher A. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Research 27: 4636-4641.
","pubmedId":"","doi":"10.1093/nar/27.23.4636"},{"reference":"Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.
","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Hirokawa T, Boon-Chieng S, Mitaku S. 1998. SOSUI: classification and secondary structure prediction system for membrane proteins.. Bioinformatics 14: 378-379.
","pubmedId":"","doi":"10.1093/bioinformatics/14.4.378"},{"reference":"Kim MK, Suh GA, Cullen GD, Perez Rodriguez S, Dharmaraj T, Chang THW, et al., Sacher JC. 2025. Bacteriophage therapy for multidrug-resistant infections: current technologies and therapeutic approaches. J Clin Invest 135(5): 10.1172/JCI187996.
","pubmedId":"40026251","doi":""},{"reference":"Laslett D. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32: 11-16.
","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Chan PP. 2016. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Research 44: W54-W57.
","pubmedId":"","doi":" 10.1093/nar/gkw413"},{"reference":"Pacey, M. Starterator Guide. (2014) https://phagesdb.org/media/docs/Starterator_Guide_2014_2.pdf
","pubmedId":"","doi":""},{"reference":"Pope WH, Jacobs-Sera D. 2017. Annotation of Bacteriophage Genome Sequences Using DNA Master: An Overview. Methods in Molecular Biology,Bacteriophages : 217-229.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_16"},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, et al., Hatfull GF. 2017. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8(4): 10.1128/mBio.01069-17.
","pubmedId":"28811342","doi":""},{"reference":"Rinehart CA, Gaffney B, Wood JD, Smith J. PECAAN, a Phage Evidence Collection And Annotation Network. (2016) https://discover.kbrinsgd.org/login
","pubmedId":"","doi":""},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database. Bioinformatics 33: 784-786.
","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Russell DA. 2017. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Methods in Molecular Biology,Bacteriophages : 109-125.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Schneider CA, Rasband WS, Eliceiri KW. 2012. NIH Image to ImageJ: 25 years of image analysis. Nature Methods 9: 671-675.
","pubmedId":"","doi":"doi:10.1038/nmeth.2089"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 33: W244-W248.
","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, et al., Alva. 2018. A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. Journal of Molecular Biology 430: 2237-2243.
","pubmedId":"","doi":"10.1016/j.jmb.2017.12.007"},{"reference":"Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods in Molecular Biology,Phage Engineering and Analysis : 273-298.
","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Genomic Characterization of Bacteriophage Babydotz, Isolated from Microbacterium foliorum
","reviews":[],"curatorReviews":[]}]}},"species":{"species":[{"value":"acer saccharum","label":"Acer saccharum","imageSrc":"","imageAlt":"","mod":"TreeGenes","modLink":"https://treegenesdb.org","linkVariable":""},{"value":"achillea millefolium","label":"Achillea millefolium","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"acinetobacter baylyi","label":"Acinetobacter baylyi","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"actinobacteria bacterium","label":"Actinobacteria bacterium","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"adelges tsugae","label":"Adelges tsugae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"adenocaulon chilense","label":"Adenocaulon chilense","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"aedes japonicus","label":"Aedes 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