Johanna B. Holm, PhD

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.

1. 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.
2. 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.
3. 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.
4. 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.