Age-dependent changes in gut microbiota composition and their significance for host aging
Michael Shapira, Professor
Integrative Biology
Closed. This professor is continuing with Spring 2024 apprentices on this project; no new apprentices needed for Fall 2024.
Aging involves a multi-system physiological deterioration. In addition to affected tissues, and likely as a consequence, aging also affects the gut microbiota, an extensive microbial community which contributes to diverse host functions. Imbalances in microbiota composition, or dysbiosis, are often associated with pathology, and recent reports indicate that aging-dependent dysbiosis exacerbates aging phenotypes. Potentially, microbiotas could be rebalanced to ameliorate aging; however, to achieve this, better understanding is required of the reciprocal interactions between host aging and the altered microbiota. C. elegans is a valuable model for aging research thanks to its short lifespan. We have recently established it also as a model for microbiome research, offering advantages unmatched in vertebrate models, including the ability to work with genetically homogenous populations, which average-out inter-individual variation to better discern shared patterns. We have previously shown that C. elegans harbors a characteristic and persistent gut microbiota, shaped (both structurally and functionally) by host genetics. Furthermore, we found that worms undergo extensive remodeling of their microbiota during aging, including an Enterobacteriaceae bloom, reminiscent of the overgrowth seen in aging humans. The current project will take advantage of the C. elegans model to establish causative relationships between host aging and microbiota composition, and to determine functional significance of age-altered commensals to aging, examining effects on motility, immunity, proteostasis and lifespan.
Role: The student(s) chosen for this project will work with a postdoc, or a graduate student, to examine changes in microbiota composition during worm aging. They will learn worm biology, and will work with different worm mutants. They will also learn to grow and work with various soil bacteria. They will take part in analyses that will include one or more of the following techniques: qPCR measurements of microbiota size and composition, NextGen 16S rRNA sequencing to determine community composition, analyses of fluorescent signal in worms colonized with tagged bacteria, or alternatively, in worms expressing fluorescent reporters of host gene expression and proteostasis, and survival analyses, testing host susceptibility to pathogens.
Qualifications: We seek candidates who are interested in basic science. They should have solid understanding of molecular biology (gene expression, PCR, and the like) but also an interest in evolutionary biology. pre-requisite courses are Bio1A and Bio1B, but good understanding of topics covered by these courses obtained from other sources will be fine (provided that the knowledge is there, not just the credentials). Students are also expected to be able to read from the primary scientific literature - to understand the overall gist of a scientific paper and to be able to seek (by asking, or in any other way) more information about the topic and methods.
Hours: 12 or more hours
Related website: http://ib.berkeley.edu/labs/shapira/
Biological & Health Sciences Engineering, Design & Technologies