Microbiome

Videos

Katherine Pollard: "Massive Data Sheds Light on Your Microbiome"

William Davis - Germs, Muscle, and Pac-Man: Exciting New Concepts

Your microbiome is influenced by the people you hang out with

The Brave New World of Microbiome-based Therapies

“The shift in our perception of bacteria from pathogen and enemy to our most important health ally represents the greatest turnaround in science and medicine in 150 years.” - Dr. Raphel Kellman

"We believe that germs and microbes should be looked upon as beneficent workers instead of enemies to human health." - Dr. Benedict Lust (founder of Naturopathic Medicine in 1907)

“It is reasonable to propose that the composition of the microbiome and its activities are involved in most, if not all, of the biological processes that constitute human health and disease.” – Martin J. Blaser, PhD

The microbiome has been called "the software of the body", "the forgotten organ" (not really forgotten since we never knew about it).

It can directly speak to the genes, genes that code for inflammation for example.

Life did not take over the globe by combat, but by networking.

Mayo Clinic: “It is likely that in a short time, understanding the basic concepts about the interactions between humans and their microbiomes will be as important to clinicians as understanding concepts of genetics or germ theory.”

Bacteria rule the world, having a profound effect on every facet of life.

By the time we finished the Human Genome Project, we realized that genetically speaking, we are the most rudimentary being on the face of the earth. With only 25,000 genes we’re at the very bottom of hierarchy in terms of sophistication. The worms used to go fishing, for example, have 75,000 genes. Wheat has 150,000 genes. What makes us most unique is our ability to attach and lose attachments.

However, it would be inappropriate to describe the human body without considering the 300,000,000,000 bacteria (microbiome) gladly living inside us and that have over 100 fold more genes than the human genome.

If you have genes known to cause a disease, it doesn't mean you will. This is modified by the microbiome and the microbiome is highly influenced by lifestyle; the way that you eat, infections, antibiotic abuse, exposure to chemicals and radiation --- all of this impinges on how the microbiome is composed. Our genes are modified by the genes of the microbiome (epigenetics). Its not a chemical that changes our genes...(it happens only rarely). Its through the way a chemical or radiation changes the microbiome. Most important is the food we eat. If we eat junk, the microbiome will be belligerent.

Think about your microbes as a landscape you want to nurture rather than as a battle ground you want to destroy. Bacteria are most of them but there are also Archaea (more closely related to us than they are to bacteria), also Eukaryota like yeast, amoeba. We don't see a lot of Eukaryota in the Western world but in other countries we see a lot more diversity. The vast majority cannot be cultured as we've done classically with infectious diseases in the petri dish. 95% are not visible to us because we don't have the methodology to grow them, so we've only been aware of the tip of the iceberg. The microbiome is the set of genes they all have.

It's turned out to be very difficult to find any disease that isn't linked to our microbiome. And it's also difficult to intervene in the microbiome when we don't have any idea what's in it, which species are necessary for health and the required balance. The only thing we know now is that the microbial species need to be very diversified. If a species takes over and robs the others of resources, there's a problem. We don't yet know what to do about it, but its a start. We know that most diseases are associated with the microbiome but we don't yet know what to do about it, we're still learning.

We thought we were sterile in the womb, but we're not. The microbiome starts to colonize the intestines when we are still in the womb. During the last trimester (why its important to be born at term) very specialized immune cells of the mother enter the gut and send out "periscopes" to sample the good bacteria which they take into their own cell and travel through the bloodstream and placenta, to deliver it to the baby.

The microbiome is influenced not only by diet and environment, but by the host genotype.

Stress is the most powerful stimulus to put us in a situation of loss of microbiome and loss of its function. When we're stressed it affects gut motility and that affects the microbiota.

In addition to disease-related factors, there are profound shifts in an individual’s microbiota across months, weeks, and even days [R, R]. Small changes, such as diet alterations, can lead to rapid and pronounced shifts in the intestinal microbiome. The composition of the vaginal microbiota varies with menses [R]. Even seasonal variation or time of day can affect microbial balance. For example, the nasopharyngeal microbiota in young children changes depending on the time of year [R]. After using microarray analysis to sample the ileal microbiome of patients with Crohn’s disease, Booijink reported that in

one asymptomatic patient the fluctuations in the gut microbiome composition over the course of a single day exceeded those from samples taken at the same

time over several days [R]. Thus, our focus should not only be on detecting and naming species but understanding what their genomes do to drive disease

dysfunction.

More recently we've discovered another part of the overall microbiome, the Virome.

The Integrative Human Microbiome Project

Microbiome is the term for the ecosystems consisting of bacteria, viruses, fungi and parasites that live in our bodies. 90% of our genetic material derive from the microbiome with only 10% being human genetic code. There are such ecosystems living throughout the entire body, not just in the gut. They contribute to both our health and to disease.

Many aspects of modern living cause a shift towards dysbiosis, including immunosuppressive drugs (per Amy Proal). What we eat changes the microbiome over time. The greatest impact comes from how many different kinds of plants we eat and the balance between carbohydrates and fats (especially animal fats).

Our microbes originate at birth, babies born vaginally have the protective microbiome of the mother. Babies born by C-section have a microbiome that looks like skin only and this may account for differences in health associated with cesarean birth such as more asthma, allergies, and obesity.

If the outer ecology is being affected, the inner ecology is being affected as well. The more we understand the outer ecology and why it becomes dysfunctional, the more we'll understand what hurts the inner ecology.

"We all understand how there are differences between different humans, there is that kind of granularity between microbial species too. "

Microbes are at the interface between our own genetic material and our genetic environment. Inflammatory autoimmune diseases may have to do with the human/microbiome interaction. Some of what we're doing with changes in lifestyle and antibiotic use could be altering microbial communities.

Microbes live in us because they can find the nutrients they need.

(Julie Sege, PhD, National Human Genome Research Institute, NIH)

Microbes, bacteria in biofilms can communicate using potassium ion channel electrical signals. The same kind of signaling our neurons use and they are coordinating their behaviors together. they can even send a signal from a biofilm in one area of the body to one in a distant area. Bacteria also use a chemical language called Quorum Sensing, that can travel to other communities and change their behavior.

What we're finding in research studies still needs to be applied to better care of patients.

As adults, our microbial community is quite stable so even if we're living with others, our individual microbial identify remains intact over a period of weeks, months, even years.

Diseases now associated with our microbiome: IBD, heart disease, colon cancer, asthma, allergies and especially obesity. Today, scientists can look at your gut microbiome and tell with 95% accuracy whether you're lean or obese.

Recent discoveries show that microbes can cure disease, for example, using fecal transplants.

The future - Omics: With the host genotype you'll have a certain microbiome. We've got to take full DNA sequencing to predict what the microbiome could be to optimize your host genome to minimize disease risk and maximize longevity. Then you can add which specific type of diet, how much exercise or supplements to add to those effects, based on your genotype. Without this kind of "big data" crunched together we're just guessing.

The studies yet to be done look at the whole microbiome ecosystem (bacteria, virus, bacteriophage, fungi) and how it's all working together. If you take a probiotic, how does it affect the whole ecosystem?

VIDEOS

Debbie Cotton - The Microbiome: CNM Specialist Podcast

How much of you is microbial? With Seth Bordenstein

Are We More Microbial than Human?

The Microorganisms in Our Body That Keep Us Alive – Naveen Jain

Updates on Gut Microbiome in Health and Disease - Christine Rosche (June 2018) -

Microbiome, We Are What They Eat

Me and My Microbes: What's My Microbiome and How Does It Affect My Health?

Our Toxic World And It's Effect On Microbiome

How Your City Has Its Own Unique Microbiome

Center for Individualized Medicine Microbiome, Mayo Clinic

Microbiome Clinical Study Part 2

Assessing and Supporting the Microbiome with Jessica Cox

The Microbiome -Bidding Farewell to Medications

The Vital Cells of Existence

Activated Immune Cells and the Human Microbiome

Renowned Gastroenterologist Evaluates Microbial Discord

Microbiomes & Aging

Mitochondria and Microbiome and Q&A

Activated Immune Cells & the Microbiome

Are High Fat Diets Bad for the Microbiome?

How Microbes Rule our Health

The Microbiome and Darwin's Mystery of Mysteries

Short Course in the Microbiome: Microbiome & Cancer Therapy

Short Course in the Microbiome: The Systems Biology Approach

Hungary Microbiome; Starch Fermentation

A person in a state of health doesn't need to be overly concerned about their microbiome. In disease the microbiome can shift towards a state of dysbiosis. In dysbiosis, pathogens can begin to drive chronic symptoms. See theVDR nuclear receptor for an example of how they can disregulate the immune system. There are many aspects of our modern way of living that shift our microbiome away from a state of balance.

It determines how attractive we are to mosquitoes.

It may even affect our behavior.

The skin is more variable on a daily basis than the mouth and gut…the mouth is the most stable. We retain our individual microbiome even when living with others.

We share some microbes with our pets and researchers can match you up to your pet by the microbes you share. However, our pets’ microbiome does remain separate from ours and they have their own individual microbes.

Our microbes depend mostly on how we are born. Babies born by c-section lack the microbes from the mother’s vaginal canal and we think the lack of that community may explain some differences in health from vaginally delivered vs caesarian delivered. There’s a higher risk of atopic dermatitis, food allergies and obesity in c-section children. Researchers are developing a procedure to restore the infant microbial community by applying vaginal microbes from the mother to the skin of the newborn and so far, it is promising, but procedures for large clinical studies are in the works.

90% of the identifiable chemicals on the body were found to be from beauty/skin products.

While pathogens persist on the mucosal surfaces, they are also present in tissue and blood. There is growing evidence that signature/unique blood microbiomes

may be associated with one or more chronic inflammatory diseases.