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2026
March 30, 2026
We’re pleased to share our latest paper:
“Microbial inoculation increases maize yield and root biomass across smallholder farming systems in Rwanda.”
Using a randomized field experiment across six farmer-managed sites in four agroecological zones, we found that a multi-strain microbial inoculant consistently improved maize performance under heterogeneous real-world conditions.
Across sites, treated plots showed average maize yield increases of 59–68% and root biomass increases of 61–74% compared with untreated controls. These results suggest that microbiome-based solutions could become an important complement to existing soil fertility strategies in tropical smallholder systems, with implications for productivity, resilience, and carbon sequestration.
A real team effort — and an encouraging step toward scalable microbial solutions for agriculture.
March 30, 2026
Our new paper is out in Microbiome: “Environmental microbiota transfer from forest soil into urban homes: a proof-of-principle study.” In this study, we tested whether environmental microbiota could be transferred into urban homes using a simple forest soil-on-rug intervention. We found significant post-intervention increases in forest soil-associated bacteria in house dust, with the strongest signal near the seeded rug and within two weeks of each application. The findings suggest that indoor microbial exposures may be modifiable in practical ways, opening new avenues for research into microbiome-informed prevention strategies in urban environments. Led by Martin Taubel with Megan Hill and Sarah Allard. Read more here: https://lnkd.in/gUdezti5
🌱 In the news: KPBS features UC San Diego soil health research
We’re excited to share that KPBS recently featured UC San Diego research exploring how probiotics for plants could help restore soil health, strengthen crops, and support climate resilience. The segment highlights work from the Soil Health Center at Scripps Institution of Oceanography, with contributions from Sarah Allard, Kristin Barbour, Sarah Pierce, and Adam McCurdy of Coastal Roots Farm.
Together, this work is advancing new ways to understand plant-microbe interactions and develop practical tools for healthier soils and more sustainable agriculture. 🌿🌎
Watch or listen to the full KPBS feature: (4:07 minute video)
https://www.kpbs.org/news/science-technology/2026/03/24/to-restore-soil-ucsd-scientists-are-experimenting-with-probiotics-for-plants
StartBlue Ocean Enterprise Accelerator Impact Report 2026
The Gilbert Lab is proud to be part of the StartBlue Ocean Enterprise Accelerator, supporting ocean innovation through the NOAA-funded Technology Development and Commercialization (TDC) program.
The 2025 Impact Report recently released highlights strong momentum across the Blue Economy, including $1.26M in non-dilutive funding deployed to startups, $4.75M raised by participating companies, and 12 startups supported through the accelerator.
A few of the other highlights:
📈 50+ new customers acquired or engaged
🌍 22 domestic and international conferences
🤝 Partner Highlights from TMA BlueTech™, Port of San Diego, and 1000 Ocean Startups
Read the full report here: https://lnkd.in/gcE9uUBr
We’re excited to continue contributing to this growing ecosystem advancing ocean intelligence and real-world solutions.
PRESS COVERAGE (3/18) The Austin Chronicle: SXSW Scientists Explain How They’re Trying to Save the Planet - mentions Jack Gilbert
Life at the Human Scale with Dr. Jack Gilbert and Dr. Kayce Bell | First Fridays Discussion
Life at the Human Scale with Dr. Jack Gilbert and Dr. Kayce Bell | First Fridays Discussion
Natural History Museum of Los Angeles County (NHM)
Dr. Jack Gilbert discusses several key topics related to microbes and their impact on life (5:41-5:44):
The Human Microbiome and Individuality (6:31-7:33): He explains that humans are constantly releasing bacterial cells, influencing each other's immune systems and even emotional reactions. He emphasizes that humans "don't have a beginning and an end" (6:46) when it comes to their microbial interactions, highlighting how these unseen relationships profoundly shape our physiology, health, and sense of self (7:25-7:32).
Stability and Dynamics of the Microbiome (8:57-13:03): Dr. Gilbert elaborates on how the microbiome changes dramatically throughout life, from birth, where babies acquire microbes from their mothers' gastrointestinal tracts (9:54-10:25), to adulthood. He likens the dynamic nature of the microbiome to a fluctuating ecosystem (12:57-13:03), yet one that develops a unique "fingerprint" (12:46) for each individual.
Social Sharing of Microbes in Baboons (13:19-15:05): He shares research on baboons that shows how social interactions like grooming facilitate the sharing of beneficial bacteria (13:58-14:10). This sharing helps baboons digest food and regulate their immune responses, suggesting that humans' social dynamics like kissing and hugging (14:37-14:46) may have evolved to share beneficial bacteria.
Microbes and Social Equity (22:26-26:10): Dr. Gilbert discusses his involvement in a working group examining how microbiology intersects with issues of equity and justice. He provides an example of a political decision leading to a disease outbreak due to a lack of social engagement (23:00-24:11), arguing that understanding microbes can help reduce social inequity (24:57-25:05) and even create new economic opportunities (25:47-26:10).
Microbiomes and Mental Health (Gut-Brain Axis) (29:40-32:41): He asserts that the microbiome has always been relevant to mental health, influencing brain function, memory, intellect, and emotional well-being. He highlights how certain species of gut bacteria are linked to depression (31:04-31:11) and how restoring these bacteria through "probiotic anti-depressants" (32:20-32:23) could alleviate symptoms, similar to conventional antidepressants.
Rewilding the Human Microbiome (32:46-38:27): Dr. Gilbert discusses strategies to restore microbial balance, including fecal matter transplants for infants (33:32-34:15) and "forest schools" for preschool children (34:37-35:48). He explains how exposure to natural environments and even just "healthy soil" (36:44) can profoundly impact children's immunological and neurological development, reducing inflammation, obesity risk, and improving school readiness.
https://youtu.be/zo7utY59GQo?si=yMy58QupHzVsrJ5z
PRESS COVERAGE (3/3) Orlando Sentinel: Commentary: Valuable scientific research continues despite leaders’ stance - mentions Jack Gilbert
Jack Gilbert receives the Live Long and Prosper Award from the Nimoy-Knight Foundation.
I am honored to receive the Live Long and Prosper Award from the Nimoy-Knight Foundation. Growing up, I admired Mr. Spock a someone who thought differently and often puzzled over human behavior! As a scientist, I felt caught between Spock’s logic and the bold curiosity of Captain Kirk. I suppose my personality has spent years trying to reconcile both.
To be counted alongside past recipients like Neil deGrasse Tyson, Whoopi Goldberg, and Mayim Bialik is deeply humbling.
As the father of an autistic son, this recognition also resonates personally. I’m committed to elevating neurodivergent perspectives and exploring how science, including microbiome research, can help us better understand human diversity.
Live long and prosper.
Science Friday Highlights the Role of Microbial Exposure in Children’s Health
A recent Science Friday article explores growing evidence that everyday exposure to environmental microbes — a little dirt, outdoor play, and contact with diverse natural environments — can support healthy immune development in children. The piece features insights from Jack Gilbert, who discusses how microbial diversity in early life may influence long-term health outcomes and why not all “grime” is created equal. It’s a timely look at how microbiome science is reshaping our understanding of health, development, and the environments we design for kids.
https://www.wnycstudios.org/podcasts/science-friday/articles/a-little-grime-can-boost-kids-health-but-what-kind
📢 New Publication | Microbiome Research in Practice: Priorities for Clinical Translation and Impact
Clinical Microbiology and Infection (2026)
The microbiome field is at an inflection point. We now have licensed microbiota-derived therapies, Phase 2 live biotherapeutic trials, predictive diagnostic models, and growing commercial interest. Yet clinical translation risks outpacing mechanistic understanding, regulatory readiness, and societal infrastructure.
In this Royal Society–funded interdisciplinary review, we propose a coordinated translational agenda structured around three intersecting domains:
1️⃣ Scientific Credibility
Multiomic, strain-level and functional characterisation
Robust and context-specific biomarkers
Transparent reporting and harmonised trial methodologies
2️⃣ Practical Viability
Fit-for-purpose regulatory frameworks
GMP manufacturing capacity and quality control
Sustainable public and hybrid funding models
3️⃣ Stakeholder Engagement
Embedded social science and patient involvement
Policy literacy and clinician education
Equity-focused implementation
Translation will not succeed through science alone. It requires regulatory alignment, infrastructure investment, and public trust.
Grateful to the exceptional international team who contributed to this work.
🔗 Article link:
📢 New Publication | Cell Metabolism
Ketogenic Diet Alleviates Septic Lung Injury via the Microbial Gut–Lung Axis
Sepsis remains a leading cause of mortality worldwide, with the lung being the most vulnerable organ. In this study, we demonstrate that the protective effects of the ketogenic diet (KD) in sepsis are mediated not by ketone bodies, but by microbiome-driven metabolism.
Key findings:
🔹 KD selectively enriches Limosilactobacillus reuteri and Lactiplantibacillus plantarum
🔹 These species catabolize oleic acid into azelaic acid (AZA) via a flavin-containing monooxygenase pathway
🔹 AZA translocates to the lung during sepsis
🔹 AZA activates PPAR-γ in alveolar macrophages, increasing MerTK⁺ macrophages and restoring efferocytosis
🔹 AZA also promotes neutrophil apoptosis
🔹 The overall effect improves survival and attenuates lung injury — largely independent of ketogenesis
Importantly, we translated these findings into a randomized pilot clinical trial showing that a clinically tolerable low-carbohydrate, high-fat diet combined with targeted probiotics partially recapitulates these benefits in sepsis patients.
This work highlights how dissecting the mechanisms of specialized diets can yield targeted, microbiome-based therapeutic strategies with improved safety and feasibility.
A strong example of integrative multi-omics, microbial genetics, immune phenotyping, and clinical translation working together.
The locals captivating, entertaining, and changing the face of the city right now and for years to come
Jack Gilbert
Jack Gilbert
That kombucha in your hand suggests you’ve heard about gut health, a modern craze for good reason. In San Diego, UCSD and Scripps Institution of Oceanography professor Jack Gilbert is the vanguard. He calls himself a microbial evangelist. The term’s fitting—like certain deities, those eensy-weensy organisms are everywhere and eternal. For billions of years, microbes were earth’s only resident, and bacteria remain the most abundant living thing on the planet, with trillions of them dwelling in your body alone.
Gilbert founded the American Gut Project, the world’s largest citizen science microbiome effort, analyzing samples from over 11,000 people. He’s also the UCSD PI (principal investigator, AKA head researcher) for the National Institute of Health’s $175 million program Nutrition for Precision Medicine program.
He believes deeply that microbes are the key to solving some of humanity’s greatest challenges. “You can tie [them] into food equality, health, water quality, protecting our planet from the ravages of climate change,” he says. “[The microbiome is] a universal toolkit of biological transformation of both our bodies and our world.”
Currently, he’s working on preserving microbiomes in soil, which can improve food security and reduce the impacts of climate change. He’s also putting together a list of microbes at risk of disappearing completely. “Microbes are fundamental to the function of all ecosystems,” he explains. “If we don’t understand how they work and don’t conserve how they work, the whole ecosystem will collapse.”
https://sandiegomagazine.com/features/50-san-diego-people-to-watch-2026/
🌱 Healthy soil = healthy climate = healthy crops = healthy communities!
A new interdisciplinary center at @UCSanDiego is digging into soil health research to create a more sustainable and climate-resilient food system.
Meet the UC San Diego Soil Health Center, where microbiologists, plant and soil biologists, ecologists, biochemists, growers (like the team at @CoastalRootsFarm) and community historians are coming together to shape the future of soil health and drive innovations in sustainable technology.
https://www.instagram.com/p/DT3VZ-1Eiab/?utm_source=ig_web_copy_link&igsh=NTc4MTIwNjQ2YQ==
📢 New preprint now available on bioRxiv
We report the first comprehensive characterization of the cervicovaginal mycobiome across reproductive stages and cervical disease states in Hispanic women from Puerto Rico. Our findings reveal:
• High inter-individual fungal diversity
• Reduced fungal diversity in high-grade cervical lesions
• A notable contribution of environmental fungi to vaginal microbial ecology
• Evidence that fungal–bacterial community interactions may influence cervical pathogenesis
Together, these results highlight fungi as active ecological players in women’s reproductive health and argue for interkingdom approaches to understanding HPV-associated disease.
🔗 Preprint: https://lnkd.in/gjg4uzWj
2025
Graduate student Joshua Tran received a GloCal Health Fellowship to spend a year in Hanoi, Vietnam studying gut microbiome composition along the colorectal cancer spectrum. He aims to determine whether there are shared and distinct taxonomic or functional signatures between US and Vietnamese patients. He is particularly interested in helping to expand capacity building efforts to integrate multi-omic techniques and novel approaches to investigating the microbiome’s role in cancer, in Vietnam.
Dr. Sho Kodera successfully defended his PhD, "Extracting ecological insights from microbiome time series."
Dr. Kara Wiggin successfully defended her PhD, "Plastic pollution as a vector for the human pathogen Vibrio parahaemolyticus in the marine environment.”
Project scientist Sarah Allard, director of the Research Experience and Mentoring (REM) program, and postdoctoral fellow, Kat Furtado, brought the 2024 cohort of 4 REM students to Pittsburgh, PA for the National Conference on Undergraduate Research, where they presented posters.
Undergraduate student Audrey Schneider received a 2025 Tyler Center Fellowship for International Study from UCSD to support her summer research project, "Linking Polyp-Scale Health Dynamics to Coral Microbiome Composition." She also received a summer studentship grant from Applied Microbiology International to travel to Japan for her research project.
Graduate student Kara Wiggin was featured on the podcast Sing for Science, where she discussed her research on microplastics and human health: LABS: BLOND:ISH and Kara Wiggin on Plastic and Circularity
PI Jack Gilbert was elected as a fellow into the American Academy of Microbiology.
PI Jack Gilbert's proposal with Co-PI Vanessa Scott to fund the StartBlue Ocean Enterprise Accelerator received a $13.5 million dollar award from NOAA.
2024
2024
PI Jack Gilbert was included on Clarivate's list of most highly cited researchers in the field of Microbiology for 2024.
Graduate student Vanessa Minnis joined the SIO delegation to attend COP29 in Azerbaijan. She was featured in an interview about her experience at the event: Empowering the Next Generation of Climate Leaders
Graduate student Kara Wiggin was featured in an interview in the San Diego Union Tribune, Oyster-linked norovirus case count reaches 81 in San Diego County and a segment on CBS 8, Plasticizers prove to be harmful, found in most packaged food.
The REM program had a table at the Birch Aquarium's Indigenous Ocean Day, where volunteers led hands-on microbiology activities and shared information about the internship program. Project Scientist Sarah Allard, graduate student Vanessa Minnis, undergraduate students Audrey Schneider and Jacob Hizon, and former REM interns Mayra Fonseca, Talia Quiroga, Harshika Rathod, Rebecca Mendoza, and community partner Benoni Pantoja all participated.
Graduate student Joshua Tran and Scientific Programs Coordinator Mary Buschmann traveled to Boston for the first deployment of the GutLab in the Nutrition for Precision Health study.
Graduate student Joshua Tran and Dr. Gilbert traveled to Portugal for the Seerave Foundation retreat, where Joshua presented a poster, "Determining the Impact of Dietary Intervention on Inflammation and Microbiome Composition in Patients with Recurrent Polyps Post-Colonoscopy."
Graduate student Neil Gottel successfully defended his dissertation, "Germination and Inhibitory Activity of Spore-Forming Microbes on Surface Materials Used in Healthcare Settings."
Graduate student Ryan Chung successfully defended his masters thesis, "Exploring the Interplay Between Bacteriophages and Vibrio parahaemolyticus Strains in the San Diego Bay Area."
Graduate student Emily Kunselman successfully defended her dissertation, "Microbiome Dynamics and Pathogen-Driven Impacts in Marine Mollusks: Insights from Oysters and White Abalone"
Graduate student Dottie Dothard received the Triton Student Employee of the Year and the Student Centeredness awards from UCSD. She was also featured for a student success story on UCSD's website.
Graduate student Emily Kunselman's research was featured in The Microbiologist: Oysters succumb to deadly viral outbreak - but only at higher water temperatures and on the Scripps website: Oyster Virus Detected in San Diego Bay Likely Worsened by Warmer Waters.
Project scientist Sarah Allard, director of the Research Experience and Mentoring (REM) program, brought the first cohort of 4 REM students to Washington, DC in March for the Emerging Researchers National in STEM meeting, where they presented posters on their summer research.
Postdoctoral Fellow Mariah Coley received a yearlong GloCal Health Fellowship to support her research project in Kenya, "Seasonal and landscape contributions to soil microbiome-gut microbiome relationships and child diarrheal disease burden in western Kenya."
PI Jack Gilbert became the President of Applied Microbiology International.
PI Jack Gilbert was featured in the Netflix documentary, Hack Your Health: Secrets of the Gut
PI Jack Gilbert was featured in several podcasts, including:
2025
2025
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