Microbial Ecology of the Built Environment

Urbanization and our increasingly indoor lifestyle have deeply affected how we acquire and interact with our microbiota. At the Gilbert Lab, we are working to answer fundamental questions about our microbial interaction with built environments, including what factors influence their microbial communities and how microbes are transferred throughout these environments. Much of our research relies on longitudinal surveys, including our Home Microbiome Project, which recruited citizen scientists to collect samples of their home and skin microbiota over time, as well as our Hospital Microbiome Project, which collected samples from patients, hospital staff, and surfaces of a newly constructed hospital over the course of its first year. During the COVID-19 pandemic, we followed up on this study by examining the influence of COVID-19 patient occupancy on hospital surface microbiomes over time. 

Environmental Microbial Ecology & Biogeochemistry

Microbiological water quality has broad implications for economic, health, and environmental fluctuations. It is often complicated to monitor pathogens directly as a means to assessing water quality due to their low abundance in natural river systems; in addition, they are often difficult to culture and have intermittent distributions. In conjunction with scientists at Argonne National Laboratory and the Metropolitan Wastewater Reclamation District of Greater Chicago (MWRD), we used 16S rRNA- and metagenomic-based assays in conjunction with traditional culture-based methods to assess ecosystem health in the Chicago River before and after wastewater treatment infrastructure upgrades. Additionally, biogeochemical cycling is crucial to ecosystem functioning in order to maintain a balanced influx and efflux of nutrients. Microorganisms are pivotal in nutrient transformation processes, therefore changes in microbial communities caused by pollutions or anthropological stresses may disrupt the whole ecosystem, including humans. For instance, we are monitoring the impact of the increase in greenhouse gas emissions on microbiomes in urban soil to assess the change in diversity and structure of the overall microbial community as well as the functional groups involved in biogeochemical cycling.

The Human Microbiome

The human microbiota consists of 100 trillion microorganisms and vastly outnumbers the human genetic repertoire. These microorganisms have been shown to affect a number of processes, including training the immune system to respond to infections and affecting reproductive health outcomes such as preterm births and post-partem depression. Research has suggested that bacterial probiotic therapy may prevent and reduce the symptoms of depression, possibly through both immune stimulation and the production of neuro-active compounds. Therefore, manipulating the microbial assemblages in the gut could represent a novel therapeutic for perinatal depression. The gut-brain axis mediates the interaction between bacterial communities in the intestine and neurological, immunological and endocrinological processes. Microbial immune activation and neurotransmitter metabolism (e.g. dopamine, 5-Hydroxytryptophan (5-HT), a precursor for serotonin, γ-Aminobutyric acid (GABA), noradrenalin, and acetylcholine) can directly and indirectly influence brain function, especially through the hypothalamic-pituitary-adrenal (HPA) axis. The HPA axis releases corticosteroids (i.e., cortisol) and activates downstream neurons that secrete neurotransmitters (i.e., norepinephrine), which can then modulate the gut ecosystem via immune-mediated antimicrobial peptides. Importantly, many of these interactions can be inhibited by severing the vagus nerve, thus cutting the main communication link between brain and gut. We continue to explore the intricate relationship between our microbiota and our health through our medical research in the UCSD School of Medicine and other collaborators.

Wildlife-Microbe Interactions

Diversity of microbial symbionts in wild animals is a growing area of interest. Studies of wild animal and their symbionts can yield insights into the eco-evolutionary dynamics between hosts and symbionts, provide baseline information for the health of wild populations, and address important questions linking symbionts to viral pathogenesis and transmission. The Gilbert Lab is addressing these topics in a number of wild host-symbiont systems. 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.