The new frontiers of microbiome research

The new frontiers of microbiome research

Tuesday, April 9, 2019
/ By:
Sara Long

Research

Living on and inside our bodies is a vast array of bacteria, viruses, fungi, bacteriophage and protozoa, which makes up our bodies’ microbiomes.1 Years of research, in part funded by the National Institutes of Health (NIH) $215 million Human Microbiome Project (2007-2016), have shed light on how our lifestyle choices affect these microbial ecosystems.2 Everything from our diet, antibiotic usage, exercise, stress, occupation, sleep and social interactions can affect our microbiota.3 One of the most researched areas is how our diet changes the composition of our gut microbiome; diets high in fruits, vegetables and fiber have been shown to increase gut biodiversity, which is posited to be an indicator of a healthy gut microbiome.4,5 In contrast, newer research has shown that food additives on the US Food and Drug Administration’s Generally Regarded as Safe (GRAS) substance list and artificial sweeteners can negatively alter the composition of our gut microbiome.6-8 Although scientists are aware of multiple ways we influence our microbiota, less is known about how exactly these changes to our microbiomes impact our health. This month at the International WELL Building Institute™ (IWBI™) four leading experts in science and industry were interviewed to illuminate current trends in microbiome research and their applications on health and well-being.

Human microbiome: Emerging research trends

One of the key trends happening in human microbiome research is the investigation into which microbes influence our health and the mechanisms through which they act. Jack Gilbert, PhD, a leading researcher in this field from the University of California San Diego, argues that the goal is “to understand the explicit components of the microbiome that could be affecting everything from diabetes to neurodevelopmental disorders to depression/anxiety to immune disorders to hormonal regulation so [that] we can see correlations between changes in the microbiome and all of those components.” According to Professor Gilbert, this marks a change from past research-- until recently,  scientists have not “[been able to] pinpoint the exact compounds which bacteria produce which actually affect those [diseases].”  The importance of a more targeted approach to the microbiome is echoed by Christine McDonald, PhD, a researcher from the Cleveland Clinic, who claims that “the field of microbiome research is benefitting from technological advances that allow researchers to ask different types of questions.” These technological advances are allowing researchers like McDonald to go beyond asking “who is there” to asking “why are they there.” By exploring what components are important to our microbiome and how they influence our health, researchers hope to better understand what microbes make up a “healthy” microbiome; a task made more difficult by the fact that each person’s microbiome is unique.3

This focus on the impact of each component of the human microbiome can help link microbes to specific diseases, providing the opportunity for early intervention. This information will allow healthcare practitioners to use microbes, or the chemicals produced by these microbes, as potential disease markers – a huge accomplishment, as Gilbert points out – “if you’ve got good markers of disease then you can be better at predicting disease onset in populations.”  For example, in 2016, researchers from the University of Illinois at Chicago and the University of Chicago received a $900,000 grant to explore how the gut microbiome impacts breast cancer risk - specifically whether queuine, a compound produced by gut bacteria, could be used as a breast cancer biomarker.9 With a better understanding of the role played by each organism in our microbiome, healthcare practitioners can potentially “target the microbiome therapeutically to either adjust what [the bacteria] are making or provide health promoting metabolites to individuals as supplements,” McDonald says. This is important as research is starting to indicate that microbes in the gut are linked to depression, autism, diabetes and obesity, to name a few.3,10

Next steps for microbiome research

According to Gilbert, the future of microbiome research “is [its] translation [into] application in a way that has real efficacy.” This movement of converting research into real-world solutions can been seen in the plethora of new microbiome-oriented companies and products either hitting the market or in development, including therapeutics, skincare products, building materials and household and commercial cleaners.

Therapeutics

Microbiome research has a variety of applications in the medical field, and while there are few microbiome-targeted interventions in use currently, companies like Holobiome and AOBiome are in the process of developing therapeutics that target illnesses ranging from depression and other nervous system diseases in the case of Holobiome, to hypertension, allergies, and skin disorders in the case of AOBiome.

Skincare products

The microbiome is also a source of interest for the skincare industry, as imbalances in the skin microbiota have been linked to diseases such as eczema, acne and chronic wounds.11 Two companies putting skin microbiome health at the forefront of their product formulations are Mother Dirt and YUN Probiotherapy. Mother Dirt’s “biome-friendly” skincare products either contain live ammonia-oxidizing bacteria (AOB) or are formulated to clean and moisturize while preserving the skin’s “good” bacteria. Currently, the company is exploring new product ingredients such as essential oils which is challenging as – in the words of their founder, Jasmina Aganovic – “many are anti-bacterial (hence, they have a strong effect on the skin microbiome).” Similar to Mother Dirt, YUN Probiotherapy uses live bacteria contained in patented-microcapsules in some of their creams to reduce acne and live bacteria in their foot spray to combat athlete’s foot. The rest of YUN Probiotherapy’s skincare line is created to balance, and not disrupt, the skin’s microbiome.

Building materials

In addition to manipulating our own microbiomes, researchers are looking for ways to alter our immediate external environments’ microbiomes to keep us healthier. One such example is captured in the article by Gilbert titled, How do we make indoor environments and healthcare settings healthier?, in which he discusses the possibility of having “good” bacteria embedded in the walls of buildings.12 He articulates that these “probiotic buildings” could have applications in training children’s immune systems to prevent chronic immune disorders, inhibiting fungus growth after floods, impeding the spread of pathogenic bacteria and speeding up patient recovery in hospitals.12 However, according to the authors of the article, The microbiome of the built environment and mental health, this technology is far from being implemented in everyday life as a significant amount of research is still needed.13 For example, researchers do not currently know how different microorganisms interact with building materials and how manipulating the microbiome of the built environment impacts occupant health.13

Household and commercial cleaners

Similar to embedding bacteria into walls, probiotic cleaners utilize live bacteria to “clean” surfaces. Some of the benefits espoused by advocates of probiotic cleaners are the ability to provide a longer-lasting and more efficient cleaning, low probability of creating a superbug and environmentally-friendly and safe formulas. According to Graeme Marsh from Z BioScience, a company that develops probiotic cleaners, this class of cleaners addresses many of the issues associated with conventional cleaners such as difficulty removing biofilms (a protective coating produced by microorganisms) and maintaining long-term cleanliness.14 While probiotic cleaners sound great, their adoption has not been without resistance. Marsh highlights that using biological agents as cleaners requires a paradigm shift away from the preoccupation on purely chemical cleaners based on the flawed mindset that all bacteria are “bad.” Nevertheless, probiotic cleaners have been well integrated into the agriculture and HVAC industries and their use is currently expanding, for example, into the education and hospitality sectors. In addition, while the view that all bacteria need to be killed for health and safety purposes is particularly prevalent in hospital settings, there may be some new ideas after a recent industry-funded multi-center hospital study showed cleaners with probiotics could cut the percent of hospital-acquired infections by over half.15

Concluding thoughts

Microbiome research is illuminating new ways we can improve our health and well-being, going beyond solely exploring the influence of our internal microbiomes to include those of our external environments’ microbial ecosystem. As an emerging field of research, it promises both individual- and building-level interventions that are capable of tackling a variety of health concerns. If the research in this article is any indication, there is a lot to be excited about in regard to the future applications of microbiome research and here at IWBI, we are excited to keep following the field.

Sara is a recent Master of Public Health graduate with publications on physical activity in depressed children, gender differences in pediatric diarrhea, and nursing home emergency care. As someone who has spent her academic career studying the components of health, she is now applying her skills as a Research Intern at IWBI.

CITATIONS
  1. Yang J. The Human Microbiome Project: Extending the definition of what constitutes a human. NIH. Genome Advance of the Month Web site. https://www.genome.gov/27549400/the-human-microbiome-project-extending-the-definition-of-what-constitutes-a-human/. Published 2012. Accessed March 27, 2019.
  2. Proctor L. The NIH Human Microbiome Project: Catalyst for an emerging    field in biomedical research. National Human Genome Research Institute 2018.
  3. Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R. Current understanding of the human microbiome. Nature Medicine. 2018;24:392.
  4. Klimenko N, Tyakht A, Popenko A, et al. Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project. Nutrients. 2018;10(5):576.
  5. Larsen OFA, Claassen E. The mechanistic link between health and gut microbiota diversity. Scientific Reports. 2018;8(1):2183.
  6. Himmelman C, Rodriguez-Palacios A, Harding A, et al. The Artificial Sweetener Splenda Promotes Gut Proteobacteria, Dysbiosis, and Myeloperoxidase Reactivity in Crohn’s Disease–Like Ileitis. Inflammatory Bowel Diseases. 2018;24(5):1005-1020.
  7. Chassaing B, Koren O, Goodrich JK, et al. Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature. 2015;519:92.
  8. Zinöcker M, Lindseth I. The Western Diet-Microbiome-Host Interaction and Its Role in Metabolic Disease. Nutrients. 2018;10(3):365.
  9. Parmet S. How does the gut microbiome influence breast cancer? University of Illinois. https://today.uic.edu/how-does-the-gut-microbiome-influence-breast-cancer. Published 2016. Updated March 3, 2019. Accessed March 27, 2019.
  10. Strandwitz P, Kim KH, Terekhova D, et al. GABA-modulating bacteria of the human gut microbiota. Nature Microbiology. 2019;4(3):396-403.
  11. Byrd AL, Belkaid Y, Segre JA. The human skin microbiome. Nature Reviews Microbiology. 2018;16:143.
  12. Gilbert J. How do we make indoor environments and healthcare settings healthier? Microbial Technology. 2017;10(1):11-13.
  13. Hoisington A, Brenner L, Kinney K, Postolache T, Lowry C. The microbiome of the built environment and mental health. Microbiome. 2015;3(60).
  14. Weir W. Researchers discover how fatal biofilms form. YaleNews. October 5, 2018, 2018.
  15. Caselli E, Brusaferro SC, M, Arnoldo L, et al. Reducing healthcare-associated infections incidence by a probiotic-based sanitation system: A multicentre, prospective, intervention study. PLoS One. 2018;13(7).