The Microbiome Repopulation Project
The Green Team at the first Microbial Cookout Event!
The Importance of Microorganisms
When we think of humans we think of very complex organisms with incredible qualities: creativity, ingenuity, predisposition to develop systems and technologies, and collaboration. We also think of us humans as biologically complex organisms made of many specialized cells working together to insure that all of these actions can be made possible. But, we might be even more complex than we thought!
One of the surprises of the Human Genome Project was the discovery that the human genome contains only 20,000 - 25,000 protein-coding genes, about a fifth of the number of genes researchers had expected to find. To search for the missing pieces that could account for this discrepancy, researchers started looking toward other sources of genetic material that have been contributing to human functions.
The greatest source of non-human genetic material that was observed to be responsible for many human functions in our body was actually found in the human microbiome.
The human microbiome is composed of an estimated 100 trillion microbes like bacteria, fungi, and viruses that live inside and on our bodies. In fact, with the increase in understanding of the human microbiome in recent years, we have learned that there are about 10 times as many microbial cells as human cells in and on our body at all times.
Some bacteria present in our microbiome are indisputably bad for our health. But others are incredibly important for our survival, in fact, they boost our immunity, protect us from infection and produce the enzymes we need to digest our food.
These bacteria are so interconnected with us and our human functions that without them we wouldn’t survive!
Our microbiome was found to be directly linked to everything: our metabolism, immune system, central nervous system, and even some of the cognitive functions inside our brains. Understanding how these microorganisms interact inside our bodies is shifting the way the medical field views bacteria.
Problem
Unfortunately, humans in the U.S. and in other heavily industrialized countries, have lost a third of their microbial diversity, mostly on their skin and in their stomachs and digestive tracts. This is the result of a decades-long decline in microbial diversity and ancestral microbes due to the overuse of sanitizing practices, antibiotics, and urban living. These practices have become so unsustainable that many species of bacteria are actually being driven to extinction!
As stated by the Hygiene Hypothesis, the lack of a diverse human microbiota might be the root cause of several chronic inflammatory disorders affecting us today like asthma, allergies, and disorders like diabetes, anxiety, depression, and even some forms of cancer.
This extinction event is not only happening in our bodies but also in our soils, waters, as well as foods. In fact, unsustainable agricultural practices and overuse of pesticides together with the widespread use of antibiotics in farm animals—not to prevent disease, necessarily, but to increase weight gain and therefore the volume of meat available—are the main culprit in the destruction of our own microbiomes.
We are experiencing a potential health crisis in industrialized countries with exceptional long-term repercussions on our health and the health of the next generation. Upset by this statistic, our team began this project by exploring how we might make sure that these important microbes don’t become extinct in or on our bodies.
Meet the Team
Amber, Jackson, Kayden, Khaliyah, and Morgan are teens from Paul Robeson High School in Philadelphia, PA.
Robeson offered the Biodesign Challenge as an extracurricular opportunity, and these five honors students were chosen to participate, becoming one of two finalist teams for the Science Sandbox Prize for Public Engagement.
Beginnings
At the beginning of our research journey, the team was interested in understanding the origins of unhealthy behaviors, especially unhealthy behaviors that people might have against nature, other people, or themselves. Through our research, we saw that less contact with nature can have a harmful effect on your mental health by affecting one’s choices and behaviors. Additionally, the understanding that bacteria in our microbiome are actually responsible for many of the cognitive functions inside our brains prompted the students to research bacteria lacking in our system and how the discrepancy could be linked to some of the health issues we are experiencing as a society.
Some of the bacteria we found are:
Mycobacterium Vaccae
Usually Found in Soil. This Bacterium affects behavior, emotionality, and health. It has demonstrated a reduction in anxiety-related behaviors. This microbe causes cytokine levels to rise, which results in the production of higher levels of serotonin. The bacterium was tested both by injection and ingestion in rats, and the results were increased cognitive ability, lower stress, and better concentration on tasks than the control group.Firmicutes
They carry many of our disease-protective foundational flora and they are involved with raw material uptake and fermentation of fiber.Bacteroidetes
They ferment an enormous repertoire of complex plant fibers and are disease-protective.Actinobacteria
Increasing the human microbial diversity of Actinobacteria has a beneficial effect on human health and the function of the immune system.
These are some of the families of bacteria that our unsustainable and unhealthy behaviors have slowly been driving away from our microbiome. Without these, we might become a society full of health disorders with long-term repercussions.
We asked:
How might we create solutions to reintroduce important organisms and repopulate our microbiome?
Project
In response, our team conceptualized the “Microbiome Repopulation Project”!
The Microbiome Repopulation project is an initiative inspired by the “Human Microbiome Project” and created with the mission of sourcing, discovering, and supplying a variety of bacteria and microorganisms that improve our health and reintroduce them back into the microbiome of the people in our community.
With this initiative, the team plans to raise awareness about the important role that bacteria offer, strengthen the connection between people, food, nature, and microbes as well as create the opportunities to gather, research and provide a series of microbes to people with the objective of repopulating the microbiome of people living in hyper-sanitized and industrialized countries.
The way the initiative works is simple:
We collect a repository of near-extinct bacteria
The bacteria are gathered from soils, foods, water, and natural habitat of local and international origin. This is to make sure that these organisms don’t become lost or extinct in industrialized countries, not only in people’s microbiomes but also in soils and waters.We grow large quantities of these bacteria
This way the initiative could study the effect of different strains of bacteria on humans and environments and provide solutions to make them ready for human consumption and handling.We host "Microbial Cookout" events
This is the opportunity for the initiative to collaborate with local community gardens, farmers, and chefs to create bacteria-infused recipes for community outreach and education as well as create an opportunity to repopulate the microbiomes of the people of our community with important bacteria for the health of the people of our community. All the recipes use traditional food production techniques like fermentation, aging, and bacteria culture addition.
The Microbial Cookout is a monthly event that was first presented at the LAWN in Philadelphia at 37th st. on the 1st of June 2022, in collaboration with the University City Science Center and local farms that donated their products and time to make this event happen. During this event, we shared tasty bacteria-loaded recipes with our community in Philadelphia and created the opportunity for our team to share information about the important role of microbes in our human functions and the type of behaviors that would normally negatively impact our microbiomes.
The event was received with great interest from locals. The team is planning to create additional synergies with the Science Center in Philadelphia and their community outreach event called “Venture Cafè” to make sure that the Microbiome Repopulation Project and the Microbial Cookout can share their mission and create educational opportunities for the people of Philadelphia.
The first Microbial Cookout Flyer
Of course, there is much more work to be done, and the field of gut-brain research is still in its infancy. Currently, probiotics on the market are not always effective to reinstate a healthy microbiome; the gut microbiota is so unique to each human that the bacteria used and the frequency at which they should be ingested would need to be determined for each individual. But the mission of the initiative is to repopulate people’s microbiome for as many individuals as possible.
As for the team, learning about the possible extinction of some important bacteria in our microbiome and realizing how our lifestyle is endangering them, has inspired them to take care of our health and to reconnect with nature and food.
Even though the "Microbiome Repopulation project" is still young, the team has managed to raise awareness about the important role that bacteria play in our day-to-day life and managed to strengthen the connection between people, food, nature, and microbes with our community events.
There is still a lot to learn about the microbiome, the importance of healthy bacteria, and how to properly use these microorganisms in different recipes but this journey really changed the team and the people of our community to reconnect them to the microorganisms that make us the incredible organisms that we are!
Reference List
Rook, Graham A.W., and Christopher A. Lowry. “The Hygiene Hypothesis and Psychiatric Disorders.” Trends in Immunology, Elsevier Current Trends, 6 Mar. 2008, https://www.sciencedirect.com/science/article/abs/pii/S1471490608000471.
Sonnenburg, Erica D., et al. “Diet-Induced Extinctions in the Gut Microbiota Compound over Generations.” Nature News, Nature Publishing Group, 13 Jan. 2016, https://www.nature.com/articles/nature16504.
The hygiene hypothesis, the Covid pandemic, and consequences for ... - PNAS. (n.d.). Retrieved June 17, 2022, from https://www.pnas.org/doi/10.1073/pnas.2010217118
Fessl, S. (2022, May 5). What Happens to the Gut Microbiome After Taking Antibiotics? The Scientist Magazine®. https://www.the-scientist.com/news-opinion/what-happens-to-the-gut-microbiome-after-taking-antibiotics-69970?utm_campaign=TS_DAILY_NEWSLETTER_2022&utm_medium=email&_hsmi=212256288&_hsenc=p2ANqtz-_nPeUByuYNriv87OBgzkm_BXNzyFPHBBKlsTkqVisJZl-K00eVcomoGJZrHFHQqtMaVh4hVodF01USjPnusir9YsxpJFhDXniSV5AywUeKiK78Cyk&utm_content=212256288&utm_source=hs_email
https://www.genome.gov/27549400/the-human-microbiome-project-extending-the-definition-of-what-constitutes-a-human
https://futuretodayinstitute.com/trend/microbiome-extinction/
https://www.pbs.org/newshour/science/theres-extinction-happening-stomach
Veresoglou, S. D. (2015, November 23). Extinction risk of soil biota. Nature. https://www.nature.com/articles/ncomms9862?error=cookies_not_supported&code=9fbbe88e-8cc5-420b-871c-934cc522cb42
https://www.inverse.com/science/are-microbes-endangered
Tito, R. Y. (2012, December 12). Insights from Characterizing Extinct Human Gut Microbiomes. PLOS ONE. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0051146
Smith, D. G. (2019, May 22). Identification and characterization of a novel anti-inflammatory lipid isolated from Mycobacterium vaccae, a soil-derived bacterium with immunoregulatory and stress resilience properties. SpringerLink. https://link.springer.com/article/10.1007/s00213-019-05253-9?error=cookies_not_supported&code=8b0ab928-33f9-4da9-bfbb-e18de045d278
https://www.gardeningknowhow.com/garden-how-to/soil-fertilizers/antidepressant-microbes-soil.html
