For thirty years, the lab has studied the border where the visible life ends and the microbiological world begins. Biology has long taught for centuries to see a plant or an animal as a solitary actor, a lonely island of its own cells and DNA. Yet when we look closer, that island reveals itself to be a metropolis. From the evolutionary gears that turn within an insect’s reproductive tract to the gut microbial conversations that dictate human health, our lab’s work has helped lead a new reality of the natural world: there is no such thing as a solitary organism. Visible life forms are holobionts – communities where the host and invisible microbes connect into a structural and functional unit of life that determines biological form, function, and fitness.

Through our science education program, Sarah Bordenstein directs the awarded and discovery-based lab series Discover the Microbes Within! The Wolbachia Project that engages pre-college and college students worldwide in nature and real-world research of their own on biodiversity, biotechnology, and bioinformatics. Seth Bordenstein directs the internationally recognized One Health Microbiome Center – one of the largest and most active microbiome centers housed in the Huck Institutes at Penn State University.

Key questions that drive the science and translational outcomes:

• What is the molecular basis of a global symbiotic adaptation that underpins the most common animal-associated bacteria (Wolbachia) and a major vector control strategy?
• What are the rules of human microbiome, virome, and mycobiome variation, and how do they intersect with health disparities across self-identity groups?
• How do microbes drive the origin of new host species? What are the rules of microbiome and virome variation between host species? What is the functional basis of  phylosymbiosis?
• How can science education rethink student achievement for high schools, colleges, and citizen scientists? How can students infuse themselves in discovery-based research to learn scientific concepts, make new discoveries, and apply hands-on biotechnology?

Summary of Illustrative Findings: Our collective work exemplifies transformative science that solves longstanding mysteries and opens entirely new research directions. The discoveries provide mechanistic understanding where only phenomenology existed, demonstrate cross-system generality where only isolated observations were known, and deliver translational applications from fundamental insights. We study two broad forms of symbiotic interactions: intimate and facultative.

In intimate symbioses between inherited, parasitic bacteria (Wolbachia) and arthropods, we discovered the long-sought genes in Wolbachia endosymbionts that selfishly kill male embryos (wmk gene) and control sperm-egg compatibility in a process termed cytoplasmic incompatibility (cifA and cifB genes). These three genes occur in a novel, genetic module of prophage WO of Wolbachia that contains an unprecedented menagerie of genes with eukaryotic-like DNA and annotated functions in eukaryotic cell biology. We discovered that the cytoplasmic incompatibility factor proteins invade animal gametic nuclei and wreak havoc on gametic epigenetic processes involved in sexual reproduction, including regulatory long non-coding RNA and the histone-to-protamine transition fundamental to sperm maturation. Some of the genes in this prophage module have also transferred across the tree of life into animal genomes and Archaea where they function as thermotolerant, antibacterial peptides.

By studying facultative interactions between animals and their microbiomes, we established the investigative framework for one of the rare, cross-system trends in the microbiome field that host phylogenetic relationships frequently mirror their microbiome relationships. We termed this new pattern “phylosymbiosis” in 2013, and experimental transplants of microbiomes between related species specify that phylosymbiosis arises due to selection pressures. Furthermore, our human microbiome analyses reveal the influences of human genetics on the microbiome and disease; and our dietary intervention trial reinforces our discovery that self-identified social groups such as ethnicity and race have a persistent association with gut/oral microbiome and virome variation in the United States. Finally, we evaluated and elevated the fungal kingdom – the mycobiome – to a new appreciation in human gut biology. We recently uncovered the first ternary relationships between human genetic variation, gut fungi, and chronic disease.