About

John Doe is a professor at the Baskin School of Engineering at UC Santa Cruz, a top-tier research university known for its social responsibility and diversity. The school, founded in 1997, emphasizes innovative and socially responsible engineering solutions across various disciplines, including health engineering, climate and sustainability, machine learning, artificial intelligence, and human-computer interaction. The faculty and students collaborate in a dynamic environment to create technology with a positive societal impact, leveraging the university's locations such as the main campus, Westside Research Park, and the Silicon Valley Campus. The university is recognized for its high-impact research, including cybersecurity, genomics, and health technology, with notable contributions like the UC Santa Cruz Genome Browser and advancements in genomics and AI. The institution fosters a community of problem solvers dedicated to addressing pressing global challenges such as climate change, disease prevention, and sustainable development. As a member of prestigious research associations and a Hispanic Serving Institution, UC Santa Cruz emphasizes educational equity and transformative societal change through its research and academic programs.

Research topics

• Biology
• Ecology
• Genetics
• Bioinformatics
• Physiology
• Agronomy
• Microbiology

Selected publications

• Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient

  Proceedings of the National Academy of Sciences · 2021 · 130 citations

  Senior authorCorresponding
  • Biology
  • Ecology
  • Genetics

  strain and tracked genomic mutations associated with the sites across the same climate gradient. Using a combination of genomic and metagenomic approaches, we identified a variety of nonrandom, parallel mutations associated with transplantation, including mutations in genes related to nutrient acquisition, stress response, and exopolysaccharide production. Together, the field experiments demonstrate how both demographic shifts of previously adapted ecotypes and contemporary evolution can alter the diversity of a soil microbiome on the same timescale.

  DOI

• Alpha-, beta-, and gamma-diversity of bacteria varies across habitats

  PLoS ONE · 2020 · 251 citations

  Senior authorCorresponding
  • Ecology
  • Biology

  Bacteria are essential parts of ecosystems and are the most diverse organisms on the planet. Yet, we still do not know which habitats support the highest diversity of bacteria across multiple scales. We analyzed alpha-, beta-, and gamma-diversity of bacterial assemblages using 11,680 samples compiled by the Earth Microbiome Project. We found that soils contained the highest bacterial richness within a single sample (alpha-diversity), but sediment assemblages displayed the highest gamma-diversity. Sediment, biofilms/mats, and inland water exhibited the most variation in community composition among geographic locations (beta-diversity). Within soils, agricultural lands, hot deserts, grasslands, and shrublands contained the highest richness, while forests, cold deserts, and tundra biomes consistently harbored fewer bacterial species. Surprisingly, agricultural soils encompassed similar levels of beta-diversity as other soil biomes. These patterns were robust to the alpha- and beta- diversity metrics used and the taxonomic binning approach. Overall, the results support the idea that spatial environmental heterogeneity is an important driver of bacterial diversity.

  DOI

• Drought and plant litter chemistry alter microbial gene expression and metabolite production

  The ISME Journal · 2020 · 160 citations

  • Biology
  • Ecology
  • Agronomy

  Drought represents a significant stress to microorganisms and is known to reduce microbial activity and organic matter decomposition in Mediterranean ecosystems. However, we lack a detailed understanding of the drought stress response of microbial decomposers. Here we present metatranscriptomic and metabolomic data on the physiological response of in situ microbial communities on plant litter to long-term drought in Californian grass and shrub ecosystems. We hypothesised that drought causes greater microbial allocation to stress tolerance relative to growth pathways. In grass litter, communities from the decade-long ambient and reduced precipitation treatments had distinct taxonomic and functional profiles. The most discernable physiological signatures of drought were production or uptake of compatible solutes to maintain cellular osmotic balance, and synthesis of capsular and extracellular polymeric substances as a mechanism to retain water. The results show a clear functional response to drought in grass litter communities with greater allocation to survival relative to growth that could affect decomposition under drought. In contrast, communities on chemically more diverse and complex shrub litter had smaller physiological differences in response to long-term drought but higher investment in resource acquisition traits across precipitation treatments, suggesting that the functional response to drought is constrained by substrate quality. Our findings suggest, for the first time in a field setting, a trade off between microbial drought stress tolerance, resource acquisition and growth traits in plant litter microbial communities.

  DOI

• Cervicovaginal Microbiome Composition Is Associated with Metabolic Profiles in Healthy Pregnancy

  mBio · 2020 · 56 citations

  • Biology
  • Physiology
  • Bioinformatics

  spp. Dramatic shifts in vaginal microbial communities sometimes contribute to the presence of a polymicrobial overgrowth condition called bacterial vaginosis (BV). However, many healthy women lacking BV symptoms have vaginal microbiomes dominated by microbes associated with BV, resulting in debate about the definition of a healthy vaginal microbiome. Despite substantial evidence that the reproductive health of a woman depends on the vaginal microbiota, future therapies that may improve reproductive health outcomes are stalled due to limited understanding surrounding the ecology of the vaginal microbiome. Here, we use sequencing and metabolomic techniques to show novel associations between vaginal microbes and metabolites during healthy pregnancy. We speculate these associations underlie microbiome dynamics and may contribute to a better understanding of transitions between alternative vaginal microbiome compositions.

  DOI

Frequent coauthors

• Steven D. Allison

  University of California, Irvine

  52 shared

• Adam C. Martiny

  University of California, Irvine

  46 shared

• Claudia Weihe

  University of California, Irvine

  38 shared

• Eoin Brodie

  University of California, Berkeley

  33 shared

• Alexander B. Chase

  Southern Methodist University

  23 shared

• Kathleen K. Treseder

  University of California, Irvine

  22 shared

• Gabin Piton

  Ecologie fonctionnelle & biogéochimie des sols & des agro-systèmes

  19 shared

• Philippe Jarne

  Université de Montpellier

  18 shared

Awards & honors

• Richard E. Green, Lifetime Achievement Award (2025)
• Mike Beck, Innovator of the Year (2025)
• NeuroSWARM3, developed by the Yanik Lab led by Ahmet A. Yani…
• Bud Colligan, Community Changemaker (2025)
• XR Experience Jury Award at SXSW 2026

Similar researchers at University of California, Santa Cruz

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