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The Microbiome & Its Effects on Human Health

Author Dana Schmitz covers The Microbiome & Its Effects on Human Health on BackTable OBGYN

Dana Schmitz • Aug 22, 2023 • 32 hits

The microbiome comprises all organisms outside of human cells, including bacteria, viruses, and fungi, that can both sustain health and contribute to disease states. Dr. Ian Fields, a urogynecologist, discusses the complexities of the human microbiome with a focus on clinical applications and the wide-ranging impact on human health. Altering the microbiome may impact urogynecological diseases such as urinary tract infections, and may also affect other conditions like epilepsy, heart disease, and preterm birth. This diverse impact highlights the need for ongoing exploration of this area within medicine.

This article features excerpts from the BackTable OBGYN Podcast. We’ve provided the highlight reel in this article, but you can listen to the full podcast below.

The BackTable OBGYN Brief

• The microbiome consists of all organisms outside human cells, including bacteria, viruses, and fungi. It has a role in maintaining health, but can also contribute to disease.

• The Human Microbiome Project, a pivotal NIH study launched in the early 2000s, examines the microbiome in the nose, mouth, skin, gut, and vagina to understand health.

• The Physician-Scientist Model is relevant and vital in modern healthcare; it provides opportunities to integrate scientific understanding into clinical practice. Continual research in medicine acknowledges the constant evolution in medical practices and the importance of staying up-to-date through trusted resources.

• Recurrent UTIs and genitourinary symptoms in menopause can be prevented by altering the microbiome; vaginal estrogen therapy can alter the microbiome to promote lactobacillus dominance, which creates a more acidic environment to inhibit growth of harmful pathogens.

The microbiome is significantly influenced by factors such as diet, environmental aspects, and location. Understanding these dynamics in the microbiome may have implications for personalized health strategies, emphasizing the need to consider a wide range of external influences in clinical practice.

The Microbiome & Its Effects On Human Health

Table of Contents

(1) The Microbiome in Urogynecology: Health & Homeostasis

(2) The Physician-Scientist in Modern Healthcare: Bridging Clinical Practice & Microbiome Research

(3) The Microbiome’s Role in Diverse Health Conditions

The Microbiome in Urogynecology: Health & Homeostasis

The microbiome encompasses the trillions of cells and organisms that reside outside human cells in the body, including bacteria, viruses, and fungi. It has a dual nature: the microbiome has a role not only in maintaining health but also in developing disease states. A disturbance in the symbiotic relationship between the human body and its microbiome can lead to clinical issues.

[Dr. Mark Hoffman]
The microbiome, talk to me about just for like-- Of course, I know all about it, but for our listeners who may not know everything there is to know about the microbiome, just a general overview of what it is generally. And then we'll work our way towards how that applies to what we do as OBGYNs and what you do as an urogynecologist.

[Dr. Ian Fields]
Yes. You can think about the microbiome as all of the things outside of our cells that make up our human body. There's like trillions of cells that make up the human body, but there's some studies even suggest up to three times more organisms that are living all throughout your body on your skin, in your gut, in your mouth, in your GU tract, everywhere that make up what's called the microbiome.

It's comprised of everything else aside from what makes you use cell-wise; so bacteria, viruses, fungi, all types of things that help us function. That may play a role in how we as humans maintain states of health. Also, interestingly enough, have large impacts in the pathophysiology or the development of disease states too.

There's been a lot of research done over the last 10, 20 years as it relates to the microbiome. If people are interested, I encourage them to always start with the Human Microbiome project, which was a large NIH study that really was like, how do we function in states of health? It took all these healthy individuals, looked at the microbiome in five different sites of the body. The nose, the mouth, the skin, the gut, and the vagina. It was essentially studying how do we as healthy people-- what comprises our microbiome?

[Dr. Mark Hoffman]
We will put a link to this in our show notes. When is this from, or when did this project start or is it an ongoing project? Is it like a book?

[Dr. Ian Fields]
It started, I want to say, either the early 2000s is when it all started and things have trickled out since then. It's one of a number of large microbiome studies, but yes, you can absolutely look it up. The NIH Human Microbiome Project.

[Dr. Mark Hoffman]
That's fascinating. We grew up hand-washing. We had three boys. A white kitchen, white floors, white chairs. My mom was in the kitchen with her yellow rubber gloves, everything got scrubbed, no pets in the house. Like, "Was it too clean, was there too much cleaning going on in our house?" Other people they say having a dog as a kid growing up, it allows you to know your immune system works better. It sounds like it's not just the microbiome, the bugs, but also how our immune system responds to that. It seems like it's just a constant interplay. Is that right?

[Dr. Ian Fields]
Yes. Or like in concert with it. I think it's kind of a little bit of a symbiotic relationship there too. The bacteria needs some of the things that we give it. We need some of the things that the bacteria give us. It's how we function together. This inter-play and inter-connectedness that potentially allow us to maintain this homeostasis and when things go awry, that's how we get to certain things that we as physicians may see clinically.

Listen to the Full Podcast

The Microbiome with Dr. Ian Fields on the BackTable OBGYN Podcast)
Ep 15 The Microbiome with Dr. Ian Fields
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The Physician-Scientist in Modern Healthcare: Bridging Clinical Practice & Microbiome Research

Dr. Ian Fields highlights the importance and relevance of physician-scientists in contemporary healthcare, specifically in urogynecology. Dr. Fields, who has a background in science and a particular interest in the urinary microbiome, explores the intricate balance between clinical practice and scientific research. He illustrates this with the example of vaginal estrogen therapy for recurrent UTI and genitourinary syndrome of menopause. Through firsthand research and clinical experience, he explains how vaginal estrogen promotes the dominance of "good" bacteria like lactobacillus, subsequently creating a more acidic environment that hinders the growth of Uropathogens like E. coli and Klebsiella. The physicians also discuss the evolving nature of medical knowledge, emphasizing the necessity of continuous learning, curiosity, and adaptability in an ever-changing field.

[Dr. Mark Hoffman]
I'm terrible at reading books. I was really bad at writing and so I figured I'll become an English major just to learn how to write and learn how to read more critically. I was glad I did it. I wasn't good at it but I never felt comfortable in the lab. I never felt like that was something I understood well, but for someone like you, clearly, that's your wheelhouse.
As a physician now, we always think about the physician-scientist model. I think we hear a lot about it that it's going away. It's just RVUs and clinical productivities, and academic demands. There's just not an opportunity to do that in the same way that there was. Do you feel like that's true? Do you feel like opportunities out there for physicians like you who are clearly good at doing that stuff, like to continue doing that and also be a busy surgeon?

[Dr. Ian Fields]
Oh, 100%. I think that there's absolutely room for people like that. For me, on my career trajectory, I see more in the education arena with the work that I do with the residency program and the work that I do with medical students. I think my brain is hardwired as a basic scientist to think about a lot of these things.

It's helpful sometimes in the clinical setting to be able to break it down for patients who want more answers to what they're doing. I prescribe vaginal estrogen all the time in my clinic. You can ask any medical student or resident; that's one of the things that I want them to take away from their time with me no matter how short or long they rotate in my clinic, is that vaginal estrogen is safe and it's effective, especially when we think about things like recurrent UTI and genitourinary syndrome of menopause.

It's one of those things where patients ask me, "Well, how does this work?" I'm like, "Oh well this works--" We know already that vaginal estrogen works to increase collagen production in the cells that line the vagina and it increases thickness, and that thickness increase lubrication which helps dryness and helps decrease the ability of bacteria to climb up and be mobile and get into the bladder. It also has the added effect that vaginal estrogen we know now completely changes the microbiome of the vagina and the bladder.

We talk a lot about good bacteria in the vagina like lactobacillus. I think everyone knows-- Hopefully, many people know, lactobacillus is always thought of as a good bacteria. We know based on a lot of the work that we've done that when you treat somebody that has gone through menopause with vaginal estrogen therapy, you can bring back in lactobacillus to dominate their microbiome, so they thus have a less diverse microbiome because it's dominated by lactobacillus.

We know that lactobacillus makes the environment in the vagina more acidic and therefore makes it harder for these Uropathogens we think of, like E. coli and Klebsiella to grow and therefore cause problems.

That's a frequent thing that I talk about in my clinic because my patients want to know how this is going to work. I say, "How do I know this? It's because I've studied it myself." I think it gives credence a little bit to the therapies that we're using to let people know that like, "No, I'm not just BSing you on this. I know how this works and I do think it's going to benefit you.

That's a really long-winded answer to your pretty simple question. Yes, I think there's a lot of room for physician-scientists and I think there are many in my field. I was just lucky enough to work with one of the PhDs in our department, Dr. Lisa Karstens, who's done a lot of this work here at OHSU. Her interest in the microbiome and my clinical work just linked up beautifully to be able to do that fellowship project.

If I had more time and more energy, that's always the currency that I need more of that I can't seem to find. I would love to continue to do a lot of that work here. I think there's absolutely a way for people to do that if that's really where their interest lies.

[Dr. Mark Hoffman]
Very earlier in your career and to have done that much in your career at this time is always super impressive. I'm sure you'll find an opportunity at some point to follow those things that you're curious about. Which I say again and again, I think curiosity is by far the most powerful force, at least it certainly is for me.

Passion wears out, curiosity is what keeps you up at night and gets you up in the morning to try to read something, find something out. Being curious, sounds like you're a very curious person.

The vaginal estrogen thing, again, it's funny how social media can make such an impact among providers, not even patients. That's one of the things I watch those conversations happen on Twitter and people like, "Hey, by the way, now I use it every day." There's patients across the country being treated with vaginal estrogen because of what they read on social media and the power of that particular platform to educate people and to educate physicians.

We're supposed to know it all already, that's what med school's for. Except that you and I both know that we learn a certain amount of things and things change and you got to keep learning and it's exhausting and the medicine changes

[Dr. Ian Fields]
There's only so much that stays in your noggin. Some of that stuff just leaves at some point.

[Dr. Mark Hoffman]
Also, some of the stuff that stays is no longer practiced anymore. That's why I keep certain apps on my phone with algorithms. I'm like, "They could change it tomorrow, and if I commit it to memory, I've now committed the wrong algorithm to memory, I might as well just know what resources I can trust to be up to date. The CDC website for management of STIs." They're updating that. They're the ones who will know if I need to do something differently. If I try to memorize it, it may not be--

[Dr. Ian Fields]
May not be correct.

[Dr. Mark Hoffman]
May not be right.

The Microbiome’s Role in Diverse Health Conditions

Dr. Fields highlights that the microbiome is not static; rather, it exhibits variations depending on factors like geographical location, daily life, and phases of the menstrual cycle. These insights lead to a deeper understanding that the microbiome is highly responsive and subject to influence by various external factors. Clinicians may find this information valuable as it uncovers more layers to personalized health and offers a broader perspective on patient care, incorporating the multifaceted interplay between diet, location, and individual physiological changes.

[Dr. Mark Hoffman]
What are other areas where the microbiome is-- where people looking at it in other disease processes? What are other areas where you think maybe we wouldn't expect the microbiome to be impacting our patients in a way?

[Dr. Ian Fields]
As it relates to us as OBGYN?

[Dr. Mark Hoffman]
Or just at all. Again, I'm fascinated by this idea that there's all these different populations of organisms living everywhere that we're just barely chipping into the surface of this stuff.

[Dr. Ian Fields]
I think it's just all of it. It's fascinating. Preterm birth has been linked to changes in the microbiome. Like I said, interstitial cystitis, painful bladder urinary incontinence, bacterial vaginosis, even the difference in the neonate microbiome versus when somebody is born via spontaneous vaginal birth or C-section. They're colonized immediately with different bacteria and that colonization potentially can lead to different things like asthma, allergies, things like that that you just don't think of.

Like inflammatory bowel disease, heart disease. I was at a talk the other day about links between the microbiome and childhood epilepsy because of the way that a gut bacteria can metabolize certain foods in the diet that create these byproducts that can trigger an epileptic state in the brain.

[Dr. Mark Hoffman]
That's crazy. It's overwhelming. Truthfully though, it's like, "I give up. It's too much. All right. Nature, you win." There's just too much out there. It is overwhelming I think to think about all those possible ways that it's all impacted.

I'm in eastern Kentucky, certainly an area that is underserved. I think about environmental impact. We have people we work with here looking at some of the environmental impacts of living in areas where they've done significant amounts of mining or those kinds of things. We think about the toxic potential.

[Dr. Mark Hoffman]
I imagine the microbiome is significantly impacted by diet or other environmental aspects. How does the environment impact microbiomes in a way? Is it shifting? Is it something that's changing with diet and those things?

[Dr. Ian Fields]
I think a lot of work has shown that it does. People can have different microbiomes based on where they live.

[Dr. Mark Hoffman]
Moving could change your microbiome?

[Dr. Ian Fields]
Yes. Moving could absolutely change your microbiome. That's like totally very well established that those things-- even in the day-to-day in your life can change your microbiome. Some studies have shown even women who, or I should say, people who menstruate can have different microbiomes based on the day in their menstrual cycle. I think that can come down to little things like that.

There's so much that can influence it. That absolutely like environment certainly can play a role in the establishment, maintenance disturbances in your microbiome. I think we're just beginning to scratch the surface on a lot of this.

[Dr. Mark Hoffman]
Forget who's got the best pizza. Now we have to figure out which city has the healthiest microbiome. That's, where you want to know, I'm going to move to--

[Dr. Ian Fields]
Hopefully it's a sunny place.


[Dr. Mark Hoffman]
Exactly. It is North Alaska.

[Dr. Ian Fields]
Great. It's not on a beach somewhere in Hawaii. No.

[Dr. Mark Hoffman]
You know, it won't be, it's going to be some place--

[Dr. Ian Fields]
It's going to be Alaska.

[Dr. Mark Hoffman]
It's going to be really dark and cold.

[Dr. Ian Fields]
Dark for two months of the year.

Podcast Contributors

Dr. Ian Fields discusses The Microbiome on the BackTable 15 Podcast

Dr. Ian Fields

Dr. Ian Fields is a urogeyncologist and an assistant professor with OHSU School of Medicine in Portland, Oregon.

Dr. Mark Hoffman discusses The Microbiome on the BackTable 15 Podcast

Dr. Mark Hoffman

Dr. Mark Hoffman is a minimally invasive gynecologic surgeon at the University of Kentucky.

Cite This Podcast

BackTable, LLC (Producer). (2023, February 23). Ep. 15 – The Microbiome [Audio podcast]. Retrieved from

Disclaimer: The Materials available on are for informational and educational purposes only and are not a substitute for the professional judgment of a healthcare professional in diagnosing and treating patients. The opinions expressed by participants of the BackTable Podcast belong solely to the participants, and do not necessarily reflect the views of BackTable.



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