The Human Microbiome in Nutrition, Disease, and Mental Health 

The human microbiota consists of approximately 40 trillion microorganisms, and the genes of these taxa vastly outnumber those found in the human genome. These microbes influence our health in a variety of ways, including training the immune system to respond to infection and affecting reproductive health outcomes (such as those associated with preterm birth and postpartum depression). These outcomes can be moderated by lifestyle and individual factors, such as diet and physiology. Diet can influence the diversity and metabolic behavior of the microbiome, as dietary components act as substrates for microbial metabolism, and the gut-brain axis further mediates the interaction between bacterial communities in the intestine and neurological, immunological and endocrinological processes. We continue to explore the intricate relationship between our microbiota and our health through clinical-based research at the UCSD School of Medicine and with collaborators around the world.  

Recent and ongoing projects: 

Microbial Ecology of the Built Environment 

Urbanization and our indoor lifestyle have deeply affected how we acquire and interact with our microbiota. In the Gilbert Lab, we are working to answer fundamental questions about how built environments shape our microbial interactions, including what factors influence their assemblage, persistence, selection for genetic traits, and transmission throughout these spaces. Much of our research relies on longitudinal surveys. This includes our Home Microbiome Project, in which we recruited public scientists to collect microbes from their home and skin over time. Additionally, our Hospital Microbiome Project characterized microbes from hospital patients, staff, and surfaces over the course of its first year, post-opening. During the COVID-19 pandemic, we followed up on this study to examine the influence of COVID-19 patient occupancy on hospital surface microbiomes, and we continue to explore ways in which we can manipulate microbial communities to reduce infection risk indoors, such as in hospitals, in homes, and on the International Space Station.  

Recent and ongoing projects: 

Marine Microbial Ecology in Human and Environmental Health 

The links between ocean and human health are of great interest to our group, and we are particularly interested in understanding how host-microbe interactions present opportunities to ameliorate anthropogenic impacts and how host-associated microbiomes influence disease ecology. At Scripps Institution of Oceanography, we have a diverse set of research objectives designed to address urgent issues in environmental and human health linked to our oceans.

Microbial ecology, evolution, and biogeography over time: 

  • DDT pollution and microbial bioremediation: DDT and associated chemicals such as DDMU, DDNU, DDE, DDT, etc. (DDT+) are absorbed onto marine sediment and accumulate in invertebrates, which threatens the marine food web, human and environmental health. Our objective is to determine how DDT biodegradation by defined bacterial consortia could influence DDT and associated breakdown product accumulation in model invertebrates. We are working with a team of SIO scientists to investigate these dynamics at an offshore dumpsite in southern California. 
  • Time series investigation of human impacts on riverine communities: In conjunction with scientists at Argonne National Laboratory and the Metropolitan Wastewater Reclamation District of Greater Chicago (MWRD), we assessed the response of microbial communities in an urban waterway before and after wastewater treatment infrastructure upgrades. Publication: Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades 
  • Review: Conceptual strategies for characterizing interactions in microbial communities 

Host-microbe-environment interactions: 

Disease ecology in a changing climate: