Academic Title:
Assistant Professor
Primary Appointment:
Microbiology and Immunology
Additional Title:
Member, Institute for Genome Sciences Member, Center for Advanced Microbiome Research and Innovation
Email:
Phone (Primary):
410-706-7905
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.
Biosketch
I am a microbial ecologist with deep expertise in characterizing the vaginal microbiome through multi-omics, bioinformatics, and experimental modeling. My research focuses on uncovering how microbial communities influence women’s reproductive health, particularly in the context of sexually transmitted infections (STIs) and bacterial vaginosis (BV). A central goal of my work is to define the microbial and molecular mechanisms by which cervicovaginal microbiota modulate host susceptibility to pathogens such as Chlamydia trachomatis, Mycoplasma genitalium, and Trichomonas vaginalis, as well as the persistent challenge of BV recurrence. Through NIH-funded training and faculty awards (F32-AI136400, K01-AI163413), I have contributed to and led the development of several widely used bioinformatic tools that enable high-resolution, taxonomic and functional analysis of vaginal microbial communities. These tools underpin my efforts to redefine clinical paradigms by replacing symptom-based diagnostics with metagenomic community state types (mgCSTs) that better predict infection risk and BV recurrence. My lab integrates taxonomic, functional, and host-response data and aims to validate mechanistic hypotheses using 3D organotypic models of the cervicovaginal epithelium.
The long-term goal of my laboratory is to uncover causal pathways linking the vaginal microbiome and host responses to infection outcomes and to translate these insights into predictive diagnostics and microbiome-informed, antibiotic-sparing interventions. By bridging computational discovery with mechanistic validation, my research aims to transform our understanding of mucosal pathogenesis and improve reproductive health outcomes globally.
Highlighted Publications
- Holm JB, France MT, Gajer P, Ma B, Brotman RM, Shardell M, Forney L, Ravel J.Integrating compositional and functional content to describe vaginal microbiomes in health and disease. Microbiome.2023 Nov 30;11(1):259.doi: 10.1186/s40168-023-01692-x.PubMed PMID: 38031142; PubMed Central PMCID: PMC10688475.
- Holm, JB, Carter, KA, Ravel, J, Brotman, RB.Lactobacillus iners and Genital Health: Molecular Clues to an Enigmatic Vaginal Species. Curr Infect Dis Rep (2023). https://doi.org/10.1007/s11908-023-00798-5. PMID: 37234911.
- 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.
Additional Publication Citations
- 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.
- 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. Ultrahigh-Throughput Multiplexing and Sequencing of >500-Base-Pair Amplicon Regions on the Illumina HiSeq 2500 Platform. mSystems. 2019 Jan-Feb;4(1). doi: 10.1128/mSystems.00029-19. eCollection 2019 Jan-Feb. PMID: 30801027; PMCID: PMC6381223.
- 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. Nat Commun. 2019 Mar 21;10(1):1305. doi: 10.1038/s41467-019-09285-9. PMID: 30899005. PMCID: PMC6428888.
- France M, Ma B, Gajer P, Brown S, Humphrys MS, Holm JB, Brotman RB, Ravel J. VALENCIA: A nearest centroid classification method for vaginal communities based on composition. 2020. Preprint. https://doi.org/10.21203/rs.2.24139/v1.
- Ma B, France MT, Crabtree J, Holm JB, Humphrys MS, Brotman RB, Ravel JR.A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina.Nat Commun11,940 (2020). https://doi.org/10.1038/s41467-020-14677-3. PMID: 32103005
- Holm JB, France MT, Ma B, et al. Comparative Metagenome-Assembled Genome Analysis of “Candidatus Lachnocurva vaginae”, Formerly Known as Bacterial Vaginosis-Associated Bacterium−1 (BVAB1). Frontiers in Cellular and Infection Microbiology 2020;10. PMID: 32296647.
- 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.
- Villette R, Autaa G, Hind S, Holm JB, Moreno-Sabater A, Larsen M.Refinement of 16S rRNA gene analysis for low biomass biospecimens.Sci Rep.2021 May 24;11(1):10741.doi: 10.1038/s41598-021-90226-2.PubMed PMID: 34031485; PubMed Central PMCID: PMC8144411.
- Brown SE, Robinson CK, Shardell MD, Holm JB, Ravel J, Ghanem KG, Brotman RM.Assessing the Concordance Between Urogenital and Vaginal Microbiota: Can Urine Specimens Be Used as a Proxy for Vaginal Samples?.Front Cell Infect Microbiol.2021;11:671413.doi: 10.3389/fcimb.2021.671413.eCollection 2021.PubMed PMID: 34268137; PubMed Central PMCID: PMC8276069.
- Ndungo E, Holm JB, Gama S, Buchwald AG, Tennant SM, Laufer MK, Pasetti MF, Rasko DA. Dynamics of the Gut Microbiome in Shigella-Infected Children during the First Two Years of Life. mSystems. 2022 Oct 26;7(5):e0044222. doi: 10.1128/msystems.00442-22. Epub 2022 Sep 19. PubMed PMID: 36121169; PubMed Central PMCID: PMC9600951.
- Holm, JB, Carter, KA, Ravel, J,Brotman, RB.Lactobacillus inersand Genital Health: Molecular Clues to an Enigmatic Vaginal Species.Curr Infect Dis Rep(2023). https://doi.org/10.1007/s11908-023-00798-5.
- Tuddenham S, Shafiq M, Mathad JS, Alexander M, Naik S, Kulkarni V, Deshpande P, Humphrys MS, Holm JB, Khan N, Yadana S, Cheedalla A, Bhosale R, Ghanem KG, Wang T, Wang S, Ma B, Ravel J, Gupta A, Shivakoti R. Association of Pregnancy and HIV Status With Molecular-Bacterial Vaginosis in Indian Women. J Acquir Immune Defic Syndr. 2023 Aug 15;93(5):422-430. doi: 10.1097/QAI.0000000000003215. PubMed PMID: 37155962; PubMed Central PMCID: PMC10524256.
- Holm JB, France MT, Gajer P, Ma B, Brotman RM, Shardell M, Forney L, Ravel J.Integrating compositional and functional content to describe vaginal microbiomes in health and disease. Microbiome.2023 Nov 30;11(1):259.doi: 10.1186/s40168-023-01692-x.PubMed PMID: 38031142; PubMed Central PMCID: PMC10688475.
In the News
The Vaginal Microbiome May Affect Health More than We Thought. Dec 2023. https://www.scientificamerican.com/article/the-vaginal-microbiome-may-affect-health-more-than-we-thought1/