How Bugs in your Gut Affect your Mood

My Notes from the Depression Sessions

An Interview with Dr. Jill Carnahan MD

Mind Altering Microorganisms: How the bugs in your gut may be affecting your mood.

I am passionate about what I do because of what I have been through, back in 2001 I was diagnosed with a very aggressive form of breast cancer and I was 25 years old. Suddenly my life changed I was a third year medical student and I always wanted to go to medical school because I was passionate about nutrition and wellness and how do we keep people well versus just give them drugs for symptoms. I had this in the background but when I was diagnosed with cancer it took on a whole new meaning because it was me dealing with a life threatening illness. I did go through chemo and radiation because at that age with this being aggressive I felt it was my best chance but, that aggressive therapy did a lot of collateral damage to my gut and my skin and all kinds of things. During that time I also saw a naturopath, I did prayer meditation and a lot of other things that allow me to be here thriving today. At that time I also realized the importance of looking beyond just the conventional treatments because I came out of that nine months later after six rounds of chemo and radiation and my body was devastated. I was down to my lowest weight since I was 14 years old, week and tired. After just a few months I started getting cyclical fevers and something else was going on a few months later I was diagnosed with Crohn’s disease. I went to functional medicine and looked for a cure and root cause to find out what was going on so I spent the last 13 years healing my gut. I realized how gut health is critical to the entire body, after I was diagnosed with Crohn’s I found out I had the high risk gene for Celiac so gluten played a big roll in all my illness as well. It was two weeks into changing my diet to no gluten, dairy or sugar and my Crohn’s symptoms just went away. Today I am thriving, healthy and happy but that never would have happened if I didn’t look deeper and ask why did this happen. There was a genetic piece, environmental I grew up on a farm with lot’s of toxic chemical exposures, put these together it’s a setup for bad things like cancer. I just spent the last 12 years looking at genetics, environment and exposure and gut health. I was in a group of 12 women under 40 and I am the only one still living because in young women this disease is a whole different ball game a lot of women in their 50-60’s survive breast cancer well, in their 20s there are not a lot of survivors.

All this had created dysbiosis in my gut which is an abnormal balance of bugs in the gut and they have everything to do with energy, mood, weight gain, weight loss and health. Basically what happens is birth is so critical if you are born naturally through the birth canal you inherit your mothers microbes and that’s why C-section babies are at a disadvantage from the day they breath their first breath because what they get is skin flora from the surgeons and hospital staff. There is evidence now that their whole entire life they could never completely overcome that disadvantage from birth, lot’s of C-section babies go on to have a healthy life but we know the microbe population can be very different compared to a vaginal delivery. From there breast feeding you are inoculated with Mom’s breast milk and natural immunoglobulins to help your immune system form and the actual natural microbes from Mom as well. Those things train your immune system so basically those things are like coaches for our immune system and when your born if you get those right bugs lactobacillus and bifidobacterium those guys are teaching your immune system at a very young age how to react to the environment.

When babies are born and they don’t have the right microbes what happens is they overreact to things or underreact to things and what were seeing is plagues of allergies, asthma and eczema and those are all related to a dysfunctional immune system. When these babies are born if they don’t get breastfed and they don’t have a vaginal delivery and then maybe they get antibiotics in the nursery those antibiotics at a very young age are extremely harmful. What we know furthermore is that the diversity of these microbes are so important so as we start from age 1 or 2 or 4 and we start to have antibiotics were starting to kill off certain species and what happens is we get overgrowth of the wrong types. Diversity is associated in study after study with good health but as we age because of antibiotics we start to loose diversity and like the C-section babies we can never completely regain that diversity throughout the rest of our life. Probiotics are helpful but to get that diversity back of the number of species, they even took from people in untouched places where they had never eaten a processed food their diversity was 10-20-30 times the diversity of you and I.

With babies food obviously breast milk is huge until the initiation of food, the other day I saw a mother giving a sip of a coke to a 1 1/2 year old and I thought come on, because sugar has such an inflammatory effect and it feeds the wrong guys and shown in studies our diet can in one day dramatically shift in the number and types of microbes. What we eat can absolutely form dysbiosis with coke, cookies, sugar and donuts or healthy fats that feed the good bifidobacteria, lean proteins and lot’s of fruits and vegetables that feed the good guys. There’s kind of a war with the good guys bad guys and who are we feeding when we put the food in.

The functions of the gut microbes besides training the immune system they aid in the digestion and absorption of nutrients so if you have the wrong microbes you may not be able to absorb vitamin K, D or E some of the fat soluble vitamins. Iron is huge if I see patients with low B12, ferritin or iron I know there is something going on with the gut because their having trouble absorbing those nutrients same with the fat soluble vitamins those microbes aid with that. They also aid in not only immune function but autoimmunity so it’s always like a seesaw you want the immune system to fight the bad things like a cold, flu or a virus but you also don’t want it to get so strong that it attacks your own body. Those TH17 versus those T-reg cells there’s this teeter-totter if you could keep that in balance and the gut microbes are responsible for that balance. Most of the time when someone gets tipped in one way or the other where their having autoimmune disease or they can’t fight infections it’s the responsibility of the gut microbes and they have gotten an imbalance that has created that disease.

Gut microbes and mood I find fascinating, it goes both directions we always knew that the brain could effect the gut but what were finding is those gut microbes are talking to our brain and our central nervous system. What happens is from our brain gut connection we have this CRF which is a corticotropin releasing hormone it’s a type of stress response. Basically when our brain gets a signal of stress it releases this hormone and this hormone has been show to effect the microbe population and dysbiosis that makes the bad microbes grow and alters permeability. We know those stress hormones are raised in people with IBS, inflammatory bowel syndrome and certain diseases of the gut. It also goes the other way too if you have the wrong microbes and there is something going on in the gut that’s inflammatory you can actually have this talk to the brain creating more stress and inflammation. A study has show that adding the right type of bacteria where they used lactobacillus rhamnosus where mice that were full of anxiety, they put them in a stressful situation half got the bacteria and they stayed calm having a modulated stress response because of that bacteria. That was the only variable and what they found was it actually effected the vagus nerve, this nerve runs along our esophagus and it’s one of the master controls of this calming response acetylcholine through the bacteria had this calming effect with an antianxiety effect like valium. The bacteria can talk to the vagus nerve which calms depression or they can create more stress hormones and make this more stressful so they can go either way. The other thing they can do is when there are bad bugs in predominance they create a situation where there is immune cytokines being released it’s like red alert, red alert. What they do is tell the immune system there is something bad happening we need to be on alert and that alert signal can actually make you feel stressed. Those cytokines will induce inflammation which makes people feel rotten.

When I learned about serotonin steel and IDO it changed the way I look at patients and ask questions, IDO is responsible for transferring tryptophan which is an amino acid precursor of serotonin. Basically the tryptophan is converted to serotonin and serotonin is converted to melatonin so if the pathway is working right we are happy we sleep well we wake up refreshed and we just love life. When the IDO enzyme is activated and things that activate this enzyme are stress, infections like parasites, fungal overgrowth in the gut or pathogenic bacteria. When it is activated the pathway is called kynurenine this means the tryptophan is going down the wrong path so instead of making serotonin it’s going down and making kynurenine and quinolinic acid. The quinolinic acid is the bad player, what happens is it effects the neurotransmitters in the brain a receptor called the N and D receptors and it is neurotoxic and can excite the cells to death. When that happens these patients are anxious, their stressed, they can’t sleep and it’s a hard pathway to reverse, what you would do for patients naturally is give them precursors to serotonin so they make more happy chemical and feel great. With these patients if you give them tryptophan or 5-HT3 which are both precursors to serotonin they feel worse instead of better you actually make that pathway go faster. These are some of my toughest patients to reverse that you have to go to the gut and ask what is causing that IDO enzyme to be up-regulated and how to reverse it. It could be a chronic infection in the gut, yeast overgrowth, clostridia, a hidden parasitic infection, and if you don’t address the root cause this guy will just go faster and faster like putting gas on the pedal and making more bad chemicals that effect the brain versus the happy chemical. It not only makes the bad guys it steels from the good guys so you have less and less serotonin. These are the patients that you give them the typical SSRI they don’t do very well because they are taking the little serotonin they have left and making quinolinic acid and they get worse.

To find the infections I do stool testing as a preliminary, I do breath testing for SIBO, we will do a full functional medicine workup to see where is this inflammation going awry and usually with the IDO enzyme it’s in the gut. I would say there is a huge amount of people out there walking around with depression that have this enzyme activated so really critical to know about. SIBO small intestinal bacterial overgrowth and it is epidemic lot’s of people have this and have no idea. If you have symptoms of gas, bloating, loose stools you might want to check for SIBO that’s a real common presentation. We are talking about the brain so what does that have to do with the brain. We have the most bacteria in the colon the majority of it should reside in the lower bowel, what happens in certain cases whether it be problems with motility or problems with wrong food, maybe it’s problems with poor digestion of food, low stomach acid or low pancreatic enzymes. What happens is those foods go down the tube and they don’t get broken down well and the bacteria go crazy they divide, they multiply and their in the wrong place so the small bowel is not meant to house that many bacteria. When that happens this plethora of bacteria in the small bowel create lot’s of garbage their partying hard, their throwing out the garbage and that part of the bowel can’t handle that amount of garbage. This damages the microvilli and now you have malabsorption of the nutrients you need to feel good and that whole toxic burden effects the liver and the cytokines. These inflammatory molecules that effect the brain and cause people to feel rotten, tired, sad, anxious and depressed are effected by that bacterial overgrowth. There are a few other tests you can do to give you a clue it might be happening but the gold standard is the breath test.

With parasite infections it’s not always from traveling to third world countries you can be in the U.S. eating sushi and get a parasite, you can be in a pool at a hotel which is not adequately chlorinated and there can be parasites there too. Most anyone anywhere can be effected by parasites and it’s amazing how many people have these parasites and have no idea. When I find a bacterial overgrowth SIBO, when I find a bacterial infection which is different from SIBO, parasitic infection all of those may require antibiotics. Now there are some wonderful herbs that can treat that but in the case of parasites there are certain one’s that are difficult to eradicate with an herbal regimen, not impossible. What I want to do if I am using medications is protect the patient with adequate probiotics and that were doing all the right things during that protocol keeping it as short as possible, not doing repeat courses if we can avoid it. There are many probiotics the ones I use are lactobacillus rhamnosus, lactobacillus casei and bifidobacter combination, the broad spectrum are still good and a good choice. What were finding now is different strains have a different effect on inflammation, histamine production and different things in the body. You can actually choose more strain specific there might be somebody with low bifidobacter that I put on just that, or someone with major histamine issues that doesn’t do well with lactobacillus casei so I’ll put them on lactobacillus rhamnosus or bifidobacter that are lower histamine producing so you can modulate for the patient. You can test for which strains you are low, the DNA probes for the bacteria in the stool so when I get the test back I see the exact strains that are there by DNA testing it’s really cool stuff.

Leaky gut could be a result of SIBO or many other things but basically the cells that line the gut their called enterocytes that are supposed to be nice and tight, what happens is the layer between the cells can get leaky or permeable. This can be caused by an overgrowth of bacteria, added chemicals in your food, glyphosate or roundup on our foods, pesticides, causing the lining between the cells to dissolve and now things that should stay in the gut cross over into the bloodstream and create an inflammatory response. Then the immune system see’s something that doesn’t belong and sends out the troops and this inflammatory response happens because the gut should be selective in what it allows. It should allow nutrients but when this permeability happens from infection, chemicals, poor diet and stress, stress does cause leaky gut allowing the wrong things to go into the bloodstream and create havoc leading to autoimmunity. This can also start the process which effects mood, of food allergies and sensitivities, if food stays in the gut it’s completely digested and never crosses over and you don’t have someone with celiac then people should never develop a food allergy or sensitivity. If someone has food allergies or sensitivities they have leaky gut it’s guaranteed, if your food is broken down into all the amino acids and all the components and fully digested and never crosses over that barrier you could never develop an antibody response to the food so you don’t have food allergies.

To determine if you have food allergies you can do an elimination diet or test for it, for those that need black and white proof we do the test but you can get the same thing through an elimination diet. Zonulin is the trap door the entry way guard that opens and closes the cells, zonulin can be triggered by inflammation, by someone who is sensitive to gluten and we now know from research that even in patients who do not have celiac disease gluten will open the door even in a totally healthy person. The difference is someone who’s healthy, doesn’t have celiac disease, doesn’t have major issues with the gut, they can have a piece of bread with diner they may have gut permeability because of that gluten effect for 3-5 hours after the meal. Because their overall healthy they don’t have autoimmune disease they don’t have anything else going on they can tolerate it. But the evidence shows that gluten even in people that are not sensitive to it increases permeability temporarily after the meal for that reason people with depression, anxiety, leaky gut, autoimmunity, any of these things the first thing I do is take them off gluten.

In another study from Ontario showed using rats that were germ free, they were born with no microbes and their stress level was off the chart. Without the microbes modulating the system they had measured increased levels of stress hormone. Then they took rats that had microbes and transplanted them into the germ free rats and all of a sudden they were cool, laid back, happy and not anxious. We have seen the same thing with mice and obesity you could take the thin mice give those microbes to the fat mice and the fat mice loose weight. This correlates in decreasing anxiety in the gut microbes and weight loss as well.

What you want to do is feed the good guys, basically sugar, artificial flavorings and colorings, gluten and dairy in most people are pretty harmful. The top three things I find people are sensitive to are gluten, egg and dairy, egg and dairy are not bad foods but because of our current state of chemicals in foods, toxicity in the environment, our poor systems are barely keeping above water. Because of that I see a lot more people with leaky gut and food sensitivities. Often soy and corn also because those are genetically modified unless their certified organic and then you get the pesticides and chemicals. Then sugar has a profoundly dramatic effect on increasing bad guys like clostridia which can cause infections and decrease good guys like bifidobacter. Then our favorite chocolate it’s very good for those bifido species I eat it with a guilt free conscious knowing I’m feeding the good guys.

Candida is huge, one of things I find with people who have candida without even testing I can usually tell because there’s a level of anxiety that’s out of the norm. I can’t explain as to the why mechanistically but I see over and over again clinically people with candida overgrowth have trouble with anxiety and when they get that candida under control the anxiety goes away. Candida is a type of yeast and there could be other species of yeast as well as mold, if someone is living in a house with mold in the walls or in the floor that contributes to weakening the immune system and often they will get fungal overgrowth as well. Anyone who has battled candida and can’t get over it they should check their house and work and make sure they don’t have any other exposures.

The nutrients to focus on with depression or anxiety vitamin D is number one and you could get that from sunshine 10-15 minutes a day with unprotected skin. You can also get that as a supplement and most people in most latitudes should do that especially in the winter. Fatty acids are key, your brain is made up of fat and those fats that we eat if their garbage trans fats it’s going to make the neurotransmission in our brain very ineffective. We want to eat cold water fish, wild salmon, nuts and seeds, vitamin D, borage, primrose, walnuts, flax, chia seed is my favorite. All of those things aid in the fat of the brain neurotransmission so we have better neurochemicals if we have good fats. I like my vitamin D to be free of corn, soy, canola oil or anything like that just a pure derivative with no additives is the best you can do a liquid or a capsule.

Other nutrients would be amino acids you should get these from protein but for some reason if your body is not breaking down proteins completely you may be lacking in the precursors to all the neurotransmitters. Dopamine requires tyrosine which is from proteins, serotonin required tryptophan and 5-HT3 which is from protein. You can take a complex like branch chain aminos and get all of them or you can selectively pick to treat brain disorders if someone has a prototype of low dopamine then we will give them precursors of that or serotonin the precursors for that. GABA we talked about you can give GABA itself or things that aid GABA like inositol. Other nutrients that are helpful for those conversions are B6 is absolutely essential, you have to have the B vitamins with this and the methyl donors so SAMe is huge, methylfolate, methyl B12, B6, riboflavin which is B2. All of these are essential and if your missing any one of those everything grinds to a halt and you can’t produce the neurotransmitters that you need.

I deal with mostly people who have gut issues and I almost always use a paleo type diet it’s not that other diets couldn’t work but I find that it’s kind of a mediteraian paleo combination. What happens is when you do a lot of processed grains and sugars your going to feed the wrong kinds of microbes, when you eat lot’s of healthy fats coconut, avocado, cold water fish and these kinds of things your feeding the bifido and lactobacillus and your feeding the vagus nerve for you to be happy and healthy. If your going to get a probiotic look for a combination anywhere from 25-100 billion per capsule you want a multi-strain there is a few available by prescription and over the counter. The jury is out on whether they need to be refrigerated or not, there are some strains that are called spore formers that were using now for SIBO patients because they tend to have too much lactobacillus which is a good guy but SIBO patients have too much of that guy so they don’t always tolerate a lactobacillus strain. They will do better with bifido by itself a bifidobacteria strain or a spore former so soil based organisms or bacillus coagulans is a popular spore former.

Remember it’s not just the bugs there is hope find purpose in life and that’s what is going to give life meaning.

Dr. Carnahan web page


Disclaimer: The information on this site is for educational purposes only and should not be used as substitute for diagnosis or treatment rendered by a licensed physician. It is essential that you discuss with your doctor any symptoms or medical problems that you may be experiencing.

M. Scherker medical researcher