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Educational Information and Resources for Non-scientists

Our bodies are inhabited inside and out with trillions of micro-organisms, termed our microbiota. Our microbiota is made up of bacteria, fungi, viruses, etc. that are often difficult to culture outside of their native environment (i.e. our body sites). Luckily, technological advances in sequencing technology have enabled us to learn about these microbes by assessing their genomic content through DNA and RNA sequencing. These methods can inform us about the identity and function of the microbes, as well as potential culture conditions that will permit their growth. Bacteria have been the best studied among the microbiota.

Generally speaking, we participate in a symbiotic relationship with our microbiota. Some refer to our microbiota as our “natural flora”.  The communities of microbes differ by body site, based upon that body site’s environmental conditions and function.  For example, bacteria inhabiting the skin are usually aerobic, whereas bacteria inhabiting the gut are anaerobic. While our microbiota has evolved a mutually beneficial relationship with us, environmental disruption (antibiotics, pathogen exposure, host genetic susceptibility, etc.) can turn a good community bad. Because we harbor such complex populations of micro-organisms, it can be difficult to determine which changes are actually the cause of a particular health condition vs. which are a response.  Human studies are a powerful way of demonstrating associations between health conditions and the microbiota, but animal studies are often necessary to demonstrate a causal relationship. There are many benefits of using animal models to study the microbiota, some of which include the ability to:  Examine the microbiota over time, including before and after disease; Manipulate the microbiota by adding in or taking away select species; End an experiment at the peak of disease to study internal tissues. But how can we determine if specific microbial species or communities of microbes actually cause disease if our experimental mice already have a microbiota? How do we exclude changes to the existing microbiota?

Germ-free mice are a specialized experimental system that lacks all known types of micro-organisms. They are born and raised in tightly controlled isolation bubbles or boxes and remain sterile by using strict husbandry protocols and microbiological testing regimens.  Mice are not the only animal models that have been derived germ-free, but they currently the most abundantly used.  Germ-free mice may be examined in relation to their “conventionally” housed counterparts, or they may be colonized with defined microbes – termed gnotobiotics. Germ-free and gnotobiotic technology has been critical for scientists to demonstrate causal relationships between the native flora and health or disease states. For example, gnotobiotic techniques have helped us better understand the causes of obesity. Delores Garcia-Arocena, PhD, posted an interesting article on the Jackson Laboratory Blog on this subject.

Some applications of germ-free and gnotobiotic mice include:

  • Demonstrating a particular microbe or microbial community can cause disease
  • Testing whether patient microbiomes can recapitulate disease
  • Determining how specific microbiomes promote or protect against disease
  • Evaluating how the microbiome impacts development of host physiological systems
  • Developing and validating therapeutic regimens to target the microbiome
  • Understanding how microbiomes can impact pharmacological drug responses

General reading about the microbiota, please consider:

The Good Gut bookcover

The Good Gut: Taking Control of Your Weight, Your Mood and Your Long-term Health by Justin Sonnenburg (Author), Erica Sonnenburg (Author), Andrew Weil, MD (Forward)

Missing Microbes bookcover

Missing Microbes: How the Overuse of Anitbiotics Is Fueling Our Modern Plagues by Martin J. Blaser, MD (Author)

I Contain Multitudes - The Microbes Within Us and a Grander View of Life by Ed Yong (Author)

The Mind-Gut Connection: How the Hidden Conversation Within Our Bodies Impacts Our Mood, Our Choices, and Our Overall Health by Emeran Mayer, MD (Author)

Dirt is Good bookcover

Dirt is Good: The Advantage of Germs for Your Child's developing Immune System by Jack Gilbert (Author), Rob Knight (Author)

the Whoe-Body Microbiome bookcover

The Whole-Body Microbiome: How to Harness Microbes - Inside and Out - for Lifelong Health by B. Brett Finlay (Author), Jessica M. Finlay (Author)

Recommended reading for the younger audience:

Meet Your Microbiome bookcover

Meet Your Microbiome: Your Superheroes Within by Cheryl Corcione (Author), Chrystal Cordero (Author)

The Incredible Microbiome bookcover

The Incredible Microbiome by Sean FNP_C Davies (Author), Tori Davies (Author), Blueberry Illustrations (Illustrator)

Everyone Poops bookcover

Everyone Poops by Taro Gomi (Author)_