Research and Innovation

As a microbiologist I study ‘wild’ microbial communities associated with diverse habitats: soil, insects, built environments, foods and beverages, and even textiles. I investigate these microbes by employing a panoply of technical strategies: microscopy, advanced culturing techniques, multi-locus amplicon sequencing, Sanger sequencing, biochemical analyses, bioinformatics, and through behavioral and multispecies interaction experiments. I specialized in using a systems-based approach to create microbial pipelines that have lead to new products in the diverse fields of biotechnology, agriculture technology, and food and beverage technology.


(c) Lauren Nichols/ Your Wild Life

By understanding the ecology of these microscopic creatures we find that they have solutions to many human problems.

Academic Research: I am a former Postdoctoral Research Fellow at North Carolina State University in the lab of Rob Dunn and at the University of Colorado, Boulder in the lab of Noah Fierer. There I worked on projects related to understanding how microorganisms contribute to the stink of polyester clothes, how we can use our knowledge of insect ecology to find microbes that can make better food and beer flavors, and how we can use an ecological frame work to find the world’s best sourdough. Throughout this process I work with diverse industry partners to assist with meeting their research and development needs. In the past I have studied the microbial  ecology of wasps and the crops they visit, chronically stressed wild avians, soil, and nursery schools and investigated the arthropods of homes through environmental DNA analyses.

Industry: I am a current technology cofounder and Chief Science Officer at the food and beverage tech company Lachancea LLC, which was developed to commercialize novel fermentation-related inventions. I am a former microbiologist at the biotech company Novobiotic Pharmaceuticals and Director in R&D at the world’s largest Ag tech startup, Indigo Ag.

Consulting: I privately consult for various industries who seek strategic innovation leads, or face current engagement obstacles with diverse stakeholders. Clients include academic institutions, biotechnology companies, textile firms, early stage start-ups, educators, writers, venture capital groups, and academic scientists. Produces I have created and developed for clients have gotten them media attention in National Geographic, lead to successful TEDx talks that are now showcased on, and have contributed to design projects such as MIT’s Synthetic Apiary project.

Public Speaking:  I give various types of talks and workshops centered around specific themes:

1. Innovation and industry: On developing innovative pipelines to discover wild microbes that can solve our problems. (Example: DefCon 2019, University of Nebraska Lincoln 2018, Harvard Microbial Science Initiative chalk talk 2018, North Carolina State University 2019)

2. Science Communication: On engaging different stakeholders with technically rich information to achieve results in innovative ways. Topics: Building a brand strategy, honing a mission statement, using social media for amplification, ethics in science communication, presenting information graphically, in written form, and through speaking ) (Example: Private workshops)

3. Alternative Careers in Science: On ways of finding jobs outside of academia and strategies for making yourself more attractive to these groups. (Example: Boston Bacterial Meeting Panel 2019, Independent consulting and workshops, Rowan University Commencement 2019)

4. Content Specialty Talks: On specific research or design projects I have been engaged with. (Example: Oxford Keynote 2017, Sloan Foundation Conference on Microbiology of the Built Environment 2016, TED SUMMIT 2019)

5. General Microbial Sciences: On revealing the utility and beauty of the microscopic world. (Example: My viral 2017 TED talk, TEDx Gateway (Mumbai) 2018, TED Dupont/ Techcon 2018, Indigo Ag 2018).

I give keynotes, commencement speeches, and talks at festivals, museums, corporations, and leading technology conferences across the globe.

But these are just ******a few***** of the research adventures I’m currently involved with. I’m also collaborating with groups on the microorganisms in various ant nests, the insects in the guts of certain monkey species, and other projects. For details about some of these projects, see below:

1. The Microscopic (and Macroscopic) Ecology of our Built Environments (Homes, Schools, Clothing, & Food)

How Arthropods Contribute to the Microbial Community of our Homes
We share our home with many, many species of insects. These are the roommates that crawl over our pillows, defecate in our walls, and munch on our carpets. Despite being in all of our homes, we know very little about them, or how they may be contributing to our allergies, our microbial communities, and our health. Working with Noah Fierer at the University of Colorado, Boulder, and Rob Dunn at North Carolina State University, I have developed DNA-based molecular and bioinformatic tools to determine what arthropods are in house dust. We have constructed the first continental-scale range maps for the hundreds of arthropods we have detected. We have also learned what behavioral and environmental housing factors predict the assemblages of arthropods in our homes.

This research has been featured by various news agencies, including: Newsweek, The Washington Post, Scientific American, and CBS News.

Products: Publication: Madden et al. (2017) Molecular Ecology  Tool: A molecular and bioinformatic pipeline for the identification of arthropods from dust and environmental samples. This tool was initially used by a Colorado biotech company. This work lead to the first atlas of the distributions of various arthropods in homes across the USA.

The Nursery School Microbiome
We know that human built environments–homes, offices, hospitals, schools–contain bacteria associated with the animal inhabitants, and the greater environment the building is in. Preschools are unique built environments. Preschoolers interact differently with their environment than adults do. As any parent knows, they touch and mouth more of their environment as they develop hygiene behaviors. Working with De Anna Beasley and Jianxin Hu of North Carolina State University, we are investigating the microbial communities of nursery schools and how landscape and behavioral factors correlate with the bacterial community of preschools in North Carolina.

Products: Publication: Madden et al. (In Prep). Presentation: This work was featured in a recent keynote I gave at Oxford University on Making Microbes Public and at a recent architecture and design conference.

The Microorganisms that Make Clothing Stink
Our clothing stinks after we wear it and polyester clothing seems to stink even more than other textiles. We know most of this stink comes from microorganisms, but we are just beginning to understand all the microorganisms involved in this process. Working with researchers from the Grunden lab at NCSU and with textile industry partners we’re investigating the microbes that interact with our clothes– from the manufacturing floors to our armpits. For more information on this project, visit the main project page.

Products: Company reports.

Sourdough Microbial Ecology
Sourdough is a fermented food that is the result of a dynamic microbial community of fungi (yeasts) and bacteria (particularly lactic acid and acetic acid bacteria). Though it is likely our most ancient bread, we still know relatively little about the microorganisms that make it possible including: who they are, where they come from, and how they contribute to our final breads. To answer some of these questions, I’m working with a diverse group of researchers from the Dunn lab (NCSU), the Fierer lab (CU), and the Wolfe lab (Tufts U) and using citizen science collected samples from around the globe. I’m also part of a team of researchers across academia (NCSU, CU, and Harvard) and industry (Purtatos Co.)  investigating the role of the individual baker in determining the microbial community of a sourdough starter (and dough chemistry and bread flavor). For more information, visit the main project page.

Products: Education Material: Sourdough k-12 lesson plans (available on Manuscripts: Oliverio…Madden A.A. et al. (In Prep.), Reese and Madden et al. (In Review). Media: Gastropod Podcast, The Atlantic, Civil Eats. Presentations: “On the Rise” bread industry talk and “The Year of the X” international technology conference.

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2. Innovative Pipelines for Discovering Microbial Metabolisms of Industry-Importance: Insect Yeasts for New Beer + Food Flavors and and Antimicrobial Technologies

Insect Yeasts for New Beer Flavors…and so much more
Yeasts can produce 50% of the flavors in beers, yet most beers in the world are made from only a handful of yeast species. Beyond flavor, yeast in breads can contribute to shelf-stability, crumb, freeze-tolerance, and total nutrition. Arthropods, such as various wasps, are natural reservoirs for wild yeasts. Knowing this, in collaboration with Rob Dunn, we have developed a pipeline to isolate and characterize wild yeasts for the food industry, and along with John Sheppard of North Carolina State University, for beer brewing. Using these natural yeasts from various insect sources, we have found ways of making foods and beverages with valuable flavors, such as sour and honey beers in record time. This removes the variations in quality that currently stymies the field of barrel-aged beer brewing. We’re now using this pipeline to identify new yeasts with valuable traits for various food and beverage industries (e.g. coffee, etc.).

This patent-pending brewing technology has been covered by various media outlets including The Wall Street Journal, National Geographic, Scientific American, The Daily Beast, and PBS NewsHour. It was also featured in the award-winning science documentary, “The Kingdom: How fungi made our world.”

Products: Patent: Sheppard, Dunn, Madden. 2015. Patent Application No. 62/162,379. Licensed Technology: Multiple strains were licensed to Lachancea, LLC. These have further been licensed by craft breweries throughout North Carolina in the first commercialization of primary souring yeasts. Additional yeasts have been licensed to major food companies. Tool: An isolation pipeline for cultivating and selecting wild yeast strains for brewing (Madden et al. In Prep). Company: This technology patent and seven licensed strains led to the founding of the company Lachancea, LLC. Publications: Madden et al. 2018. Proc. Royal Soc. B, Madden et al. (In Prep.). Education & Engagement: k-12 yeast activities,  a #NewYeastName citizen science yeast naming project, numerous presentations and talks (including TED, TEDxGateway, and TEDxCharlotte).

Novel Antimicrobials from Backyard Bacteria
Let’s face it, bacteria are not popular. While often referred to negatively as ‘germs,’ most of our antibiotics actually come from bacteria that live in the soil. As we currently face a dire need for new antibiotics in the era of massive antibiotic resistance, there is increasing interest in finding novel bacteria that could produce novel chemistry. I am a former microbiologist at the biotechnology company Novobiotic Pharmaceuticals, LLC. where we developed novel antibiotics from these previously uncultured bacteria. We discovered novel antibiotics that can fight VRE and MRSA, including Neocitreamicins I & II.

Products: Publication: Peoples…Madden et al. (2010) Journal of Antibiotics. Novel Antibiotics: Neocitreamicins I and II. Tools: Early testing of iChip technology.

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3. The Microbial and Arthropod Communities of non-Human Animals & Their Homes

The Microbial Jungle of Insect Bodies and Nests
Creating paper fortresses in the eaves of our houses, these insects have long been the favorite study animals of scientists interested in animal behavior. Despite such ubiquity and familiarity, we know almost nothing about the microbes they presumably carry with them and disperse throughout the environment. My doctoral research in the laboratory of Dr. Philip Starks at Tufts University explored the microbial community of paper wasps to understand how a social wasp invasion may affect the local microbial and plant community. We uncovered a diverse jungle of fungi and bacteria within the nests and bodies of these wasps, including antimicrobial producing bacteria, a new fungal species that we named Mucor nidicola and a greater understanding of the microbial communities of native and invasive insects. Working with diverse collaborators we have also investigated how Azteca ants modify the microbiomes of their Cecropia homes.

Products: Publications:  Lucas et al. (2019) Proceedings of the Royal Society B, Madden et al. (2018) Proceedings of the Royal Society B, Madden et al. (2017) PeerJ, Madden et al. (In prep), Madden et al. (2013) Environmental Entomology, Madden et al. (2012) International Journal of Systematic and Evolutionary Microbiology, Madden et al. (2010) Insectes Sociaux. New species: Mucor nidicola.

Gut Microbiomes and Arthrobiomes of Non-humans (The effect of chronic stress on the wild avian microbiome and diet differences of primate species)
The flight or fight response protects us when we are faced with a threat, but we know that chronic stress can damage our physiology as it leads to a weakened immune system. Recent evidence suggests there is a dynamic communication between the microbiome and the animal host, as the microbes respond to stress hormones by shifting their community composition, physiology, and even ability to create disease. Working with Christine Lattin and Michael Romero at Tufts University, we investigated how chronic stress affected the microbiome of wild house sparrows. Working with primate biologists we uncovered diet differences in two monkey species by investigating the arthropod DNA in their feces.

Products: Publication: Manuscript in prep. in collaboration with the lab of Ben Wolfe at Tufts University. Lyke et al. (2019) PLOS ONE. Presentations: Various

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**((The images above are various graphics produced from the research outlined above.They can only be used with explicit written permission. ))**

### CONTACT ### 

email: madden(dot)anne((at)) 
twitter @anneamadden
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