Microbiology and Immunology
Education and Training
I received my Ph.D. from the University of Southern California, with specialized training in marine microbiome analyses. I pursued postdoctoral training in the laboratory of Dr. Jacques Ravel and then joined the faculty at the Institute for Genome Sciences and Department of Microbiology and Immunology at the University of Maryland School of Medicine.
For the past six years, I have been performing bioinformatic characterization of the vaginal microbiome in the context of clinically relevant outcomes including incident sexually transmitted infections (STIs), spontaneous pre-term birth, and bacterial vaginosis. My long-term goal is to improve clinical outcomes related to women’s reproductive health through the application of high-throughput sequencing technologies. I have pursued this research through the support of a postdoctoral NIH National Research Service Award (F32-AI136400) and currently through an NIH Mentored Research Scientist Development Award (K01-AI163413). With colleagues I have produced circularized genomes for clinically relevant, uncultivable bacteria, a non-redundant gene catalog for the vaginal microbiome, and a taxonomic classifier for amplicon sequencing for vaginal microbiota. Recently, I led the effort developing methods to produce metagenomic community state types (mgCSTs) which are categories of functional and compositional components of the vaginal microbiome using metagenomic sequence data (>800,000 genes) from 1,868 samples, detailed in a manuscript in late-stage preparation. Already, I have used mgCSTs to measure associations of the vaginal microbiome with incident STIs, a late-stage manuscript.
- Elovitz MA, Gajer P, Riis V, Brown AG, Humphrys MS, Holm JB, Ravel J. Cervicovaginal microbiota and local immune response modulate the risk of spontaneous preterm delivery. Nature Communications. 10(1):1305. PMID: 30899005.
- Holm JB, Humphrys MS, Robinson CK, Settles ML, Ott S, Fu L, Yang H, Gajer P, He X, McComb E, Gravitt PE, Ghanem KG, Brotman RM, Ravel J. 2019. Ultrahigh-Throughput Multiplexing and Sequencing of >500-Base-Pair Amplicon Regions on the Illumina HiSeq 2500 Platform. mSystems 2019;4. PMID: 30801027.
- Ma B, France MT, Crabtree J, Holm JB, Humphrys MS, Brotman RM, Ravel J. A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina. Nat Communications. 2020 Feb 26;11(1):940. PMID: 32103005.
- Holm JB, France M, Ma B, McComb E, Robinson CK, Mehta A, Tallon LJ, Brotman RM, Ravel J. Comparative genome analysis of “Candidatus Lachnocurva vaginae”, formerly known as Bacterial Vaginosis Associated Bacteria – 1 (BVAB1), Frontiers Cellular and Infection Microbiology, 2020 Mar 31;10:117. PMID: 32296647, PMCID: PMC7136613.
- Hvorecny LM, Grudowski JL, Blakeslee CJ, Simmons TL, Roy PR, Brooks JA, Hanner RM, Beigel ME, Karson MA, Nichols RH, Holm JB, Boal JG. Octopuses (Octopus bimaculoides) and cuttlefishes (Sepia pharaonis, S. officinalis) can conditionally discriminate. Anim Cogn. 2007 Oct;10(4):449-59. doi: 10.1007/s10071-007-0085-4. Epub 2007 Apr 17. PMID: 17437139.
- Boal JG, Prosser KN, Holm JB, Simmons TL, Haas RE, Nagle GT. Sexually mature cuttlefish are attracted to the eggs of conspecifics. J Chem Ecol. 2010 Aug;36(8):834-6. doi: 10.1007/s10886-010-9816-0. Epub 2010 Jul 1. PMID: 20593225.
- Cummins SF, Boal JG, Buresch KC, Kuanpradit C, Sobhon P, Holm JB, Degnan BM, Nagle GT, Hanlon RT. Extreme aggression in male squid induced by a β-MSP-like pheromone. Curr Biol. 2011 Feb 22;21(4):322-7. doi: 10.1016/j.cub.2011.01.038. PMID: 21315594.
- Xu X, Lee YJ, Holm JB, Terry MD, Oswald RE, Horne WA. The Ca2+ channel beta4c subunit interacts with heterochromatin protein 1 via a PXVXL binding motif. J Biol Chem. 2011 Mar 18;286(11):9677-87. doi: 10.1074/jbc.M110.187864. Epub 2011 Jan 10. PMID: 21220418; PMID: 21220418.
- Walderon MD, Nolt KJ, Haas RE, Prosser KN, Holm JB, Nagle GT, Boal JG. Distance chemoreception and the detection of conspecifics in Octopus bimaculoides. The Journal of Molluscan Studies. 2011 June; PMID: N/A
- Heidelberg KB, Nelson WC, Holm JB, Eisenkolb N, Andrade K, Emerson JB Characterization of eukaryotic microbial diversity in hypersaline Lake Tyrrell, Australia. Front Microbiol. 2013;4:115. doi: 10.3389/fmicb.2013.00115. eCollection 2013. PMID: 23717306; PMCID: PMC3651956.
- Holm JB, Heidelberg KB. Microbiomes of Muricea californica and M. fruticosa: Comparative Analyses of Two Co-occurring Eastern Pacific Octocorals. Front Microbiol. 2016;7:917. doi: 10.3389/fmicb.2016.00917. eCollection 2016. PMID: 27445997; PMCID: PMC4914490.
- Girard L, Birse K, Holm JB, Gajer P, Humphrys MS, Garber D, Guenthner P, Noël-Romas L, Abou M, McCorrister S, Westmacott G, Wang L, Rohan LC, Matoba N, McNicholl J, Palmer KE, Ravel J, Burgener AD. Impact of the griffithsin anti-HIV microbicide and placebo gels on the rectal mucosal proteome and microbiome in non-human primates. Sci Rep. 2018 May 23;8(1):8059. doi: 10.1038/s41598-018-26313-8. PMID: 29795295; PMCID: PMC5966460.
- McComb E, Holm J, Ma B, Ravel J. Complete Genome Sequence of Lactobacillus crispatus CO3MRSI1. Microbiol Resour Announc. 2019 Jan;8(5). doi: 10.1128/MRA.01538-18. eCollection 2019 Jan. PMID: 30714033; PMCID: PMC6357639.
- Moreno-Sabater A, Autaa G, Sterlin D, Jerbi A, Villette R, Holm JB, Parizot C, Selim S, Senghor Y, Ghillani-Dalbin P, Bachmeyer C, Hennequin C, Gorochov G, Larsen M. Systemic anti-commensal response to fungi analyzed by flow cytometry is related to gut mycobiome ecology. Microbiome.2020 Nov 15;8(1):159. doi: 10.1186/s40168-020-00924-8. PubMed PMID: 33190643; PubMed Central PMCID: PMC7667786.