Healthy Bacteria Healthy Sleep


At the same time that sleep problems have become more and more common our gut bacteria have also been changing. The four healthy bacterial species; Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria have been shown to appear spontaneously in babies by the time they’re 3 months old. How do they get there? (That baby is not taking probiotics!)  As the baby is born he passes through the birth canal and gets covered with mom’s bacteria. It is not just breast milk that helps build a healthy immune system for the baby. We now know that the right bacteria living on and in us play a very important role in protecting us from the “bad” bacteria. Because the healthy foursome of bacteria needs our vitamin D to thrive, if mom’s vitamin D level was too low during her pregnancy she only has the “wrong” bacteria. That means she only has the “wrong” bacteria to pass on to her baby and he starts his life at a disadvantage in both his digestion and his immune system. Our normal bacteria are able to dissolve certain starches in mom’s breast milk. Without those bacteria the baby is unable to break down and use those starches. That suggests that the normal bacteria help baby’s nutrition even while he’s feeding on mom’s breast milk. The normal bacteria have the same effects for adults. They help our digestion, our immune system, and also…. our sleep.

Probiotics in pill form are just purified poop bacteria.  Despite their widespread use, they have not been successful in bringing back the healthy foursome. You can supply the “right” bacteria every day but if you don’t provide what they need to flourish they will not grow to replace the bad guys. It is not the supply of bacteria that’s the problem, it is the intestinal environment. We should think of the intestinal environment as a petri dish (as pictured above). We have to provide the friendly bacteria what they need in order to flourish. If we provide the right raw materials they will grow to replace the “wrong” bacteria and we’ll have a healthy gut again. When we don’t make enough vitamin D on our skin, we don’t have “extra” to pass on, in the bile, to the intestinal bacteria. Instead we suck up every little bit of it for ourselves. If we have enough vitamin D to share with our bacteria it favors their growth over the “bad” bacteria that don’t need vitamin D. The normal foursome of bacteria also needs other vitamins that you will need to learn about to have a healthy gut and healthy sleep for the rest of your life.

Those of you who are saying to yourself, “This doesn’t apply to me, there’s nothing wrong with my gut”, if your sleep is not right, your gut is not right. Even though you have no belly symptoms now you will still benefit in the long run from understanding why I will ask you to do certain things to help you sleep normally again. So this part is still important for you to learn. Go to the blog:Yes, Your Poop Bacteria Can Affect How Well You Sleep to learn how the gut affects the sleep.


Yes, Your Poop Bacteria Can Affect How Well You Sleep

How could our intestinal bacteria affect our sleep? The bacteria actually make chemicals that we steal from them in order to sleep normally; those chemicals are called the B vitamins. (And, those of you who don’t like vitamins and are about to skip this part, you do need to understand this or you will never sleep normally, or fix your headaches, or get out of your doctor’s office.)

The B vitamins are 8 chemicals that our bodies are unable to make. They were first discovered as bacterial “growth factors”, chemicals that had to be added to the petri dish to grow bacteria. Bacteria had just been discovered and scientists were experimenting with how many different types of bugs they could find and name after themselves. Just like making beer or bread, the recipe had to be just right. They discovered that the same yeast preparation we cooked with would encourage specific bacteria to grow. There were actually bacteria already in the yeast preparation, and those bacteria were making chemicals that other bacteria liked and needed.

Eventually the scientists figured out that our human cells needed these “growth factors” too. We couldn’t live without them but we couldn’t make them ourselves. (Which a bit odd when you think about it,  every cell in our body needs this chemical to run properly but we can’t make it ourselves? Sort of bad planning!) For humans they called these chemicals “vitamins”, instead of growth factors. Once they got around to purifying the different chemicals they started naming them the “B’s” because they came after vitamin A was named.(duh!) Several chemicals were eventually grouped together as “B vitamins”, partly because some came from the same yeast broth, partly because they were all water soluble but also because they seemed to need each other to do their jobs. There were originally more than 8 (thus cyanocobalamin was named B12) but some,  B4, B8, B10 and B11 that were originally numbered eventually lost their status as “vitamins” because it turned out we could make them ourselves after all, so now there are only 8 B vitamins.  They are numbered and named, which makes the whole thing very, very confusing! Thiamine is B1, riboflavin B2, niacin B3, pantothenic acid B5 , pyridoxine B6, biotin B7, folate B9, and cyanocobalamin B12. You do not need to memorize this, you just need to know that they were meant to come together as an “eight-pack”, the 8 chemicals work together. We learned about how these chemicals work together from the study of bacteria. Bacteria need these chemicals to make energy and grow, just like we do, and there are certain bacterial species that can make some of them but not all of them. The only one we can make ourselves but is still considered a vitamin is niacin (if we have protein in our diet we can make niacin from tryptophan).

The first microbiologists (study of tiny, living things) found that there were bacterial species that could make riboflavin, B2. The bacteria made it for their own use but also released it into their surroundings. Next, they discovered that the riboflavin-producing bacteria wouldn’t grow by itself in a petri dish because it couldn’t make folate, B9. But if there was a second type of bacteria, that did make folate (but couldn’t make riboflavin), and the two were grown together, they could trade riboflavin for folate and both would be happy. Because of their shared needs the two types of bacteria appeared together and were said to have a “commensal” relationship; they each benefited from the presence of the other.

Now, back to our intestinal bacteria……The reason why the same foursome of bacterial species is found in every human with a “healthy gut” all over the world, is because each of the four makes at least one B vitamin and needs other B vitamins that the other three make and share. In other words, they need each other. They are a “commensal foursome”. And, they are secreting those vitamins into our intestine, making a sort of “B vitamin soup”. Picture all those little bacteria happily growing in their vitamin soup, which happens to be inside us!  Why did they desert us? They were so happy in there, and we needed them!  They deserted us because we stopped giving them what they needed from us, they need our vitamin D. We give them vitamin D, they give us B vitamins, everybody wins, we’re both thriving and happy! We had a commensal relationship with the bacteria in our intestine. Then, oops….. we go inside, stop making vitamin D on our skin from the sun and we can no longer provide our side of the bargain. The good guys are now slowly replaced by bacteria that don’t need vitamin D. Now we have the “wrong” bacteria and all the bad things associated with that “wrong” bacteria; irritable bowel syndrome, multiple allergies, or autoimmune diseases. The B vitamins don’t really come from the food, they come from the normal bacteria inside us. It has been that way since the first multi-celled organisms evolved with bacteria in their gastrointestinal track. There was never any reason for us to make the B vitamins because we always carried our source inside us! Read more at: Why the American Diet does not deserve all the blame

Why the American Diet does not Deserve all the Blame

The concept of a “healthy diet” was described by the early nutritionists starting in the 1930’s and 1940’s. There were two B  vitamin deficiency diseases that did come from a poor diet. Pellagra and beriberi both resulted from very limited diets, pellagra from cornmeal only, beriberi from rice only. Clearly a “diet” made up entirely of a daily serving of a single starch is not a “healthy diet” but when they added back meat and vegetables they were able to cure the disease, so from then on we’ve been taught that “the B vitamins come from food”. ( See the blog “Healthy Bacteria Healthy Sleep” to learn why the B vitamins come from the intestinal bacteria, not from the food.)

At the time that the first “healthy diets”, (the five food groups etc.) were proposed, in the 1940’s and ‘50’s, most people still lived outside and the term “irritable bowel syndrome” had not come into common use. Most of the population still had the healthy bacteria living inside them. All of the primitive diets that are described as a solution for our modern ills were also eaten by humans who lived outside and had a healthy gut! Therefore, all of us who have unsuccessfully tried to find the “right diet” really need the “right bugs” and probiotics alone are not successful. In order to live inside us the “healthy” bacteria need our vitamin D and the “B vitamin soup” that they create to support each other. When we lose them our digestion suffers, our immune system suffers and even our sleep suffers.

Though I would agree that a diet of hamburgers and donuts is not a healthy diet, I do not agree that our eating habits alone have caused the epidemic of obesity and sleep apnea. Many of my patients tried so hard to lose weight by following a healthy diet, and were unsuccessful. There is really much more to this picture! Remember what I said about hunger being involuntary, it’s run by your brain, it’s also affected by the bacteria inside you. The bacteria in our intestine are now known to have very important effects on our appetite. Certain bacteria make chemicals called short chain fatty acids that are absorbed into our blood, go up into our nose and make donuts smell very good! In the past a change in the intestinal bacteria that promoted hunger in the winter, when the D was low, would enhance our survival, it made us try harder to find high fat, high calorie foods to sustain us until the winter ended. But this change in bacteria and increased appetite was not supposed to continue through one’s whole life while abundant food was all around. After converting the intestinal bacteria back to the healthy foursome most of my patients found it easier to be successful with a healthy diet. The diet was easier to follow, their hunger was less and their weight loss was more successful. Because the bacteria that live inside us affect our diet, our sleep and our pain level most patients also found that they had enough energy to start exercising and suffered less pain afterward. Thus, even those who do not have gut complaints still need to have the right bacteria in order to live the healthy life we were meant to have.

The cells in the brain that help us sleep correctly need B vitamins too, to do their job. At least one of them, pantothenic acid (B5), is not in any of the foods we eat. I will explain in a later blog why the statement “pantothenic acid deficiency doesn’t exist because it is in every food” is not true, despite being widely accepted. And, why this one mistake produced a global change in our sleep and our health.

Why Autism is linked to Insufficient Deep Sleep.

Sleep is of two types: “light sleep”, and “deep sleep”. During the two phases of deep sleep we are paralyzed. Deep sleep can be either Slow Wave Sleep, (the brain waves that are measured from the scalp during this phase appear in a slow rhythm), or Rapid Eye Movement (REM) sleep where our eyes are moving back and forth in a regular rhythm. Based on my patient experience, those who have less deep sleep than their body needs, wake up feeling tired. This suggests that we only repair our bodies during deep sleep.

Our bodies, and all of our individual cells do different things during the day than they do while we’re sleeping. During the day we use up our chemical stores. During the night we make repairs and make and store the chemicals we will need to function properly tomorrow. Surprisingly a fat cell, taken out of the body and grown in a dish, still knows what time it is. The cells grown in the dish still make certain chemicals during the day and different chemicals at night. This has been found to be the case for many other cell types as well.

We know that growth hormone is only secreted during slow wave sleep. This means that children only grow during that specific phase. If they don’t stay in slow wave sleep long enough they don’t grow normally. All children must also develop their brain while they sleep. So if the time spent in deep sleep is shortened the brain must decide what aspect of development to abandon. Based on the astounding increase in autism that has occurred in the last 20 years, the brain appears to leave off the normal development of social interaction. What we call “autism” refers to social awkwardness, an inability to recognize social cues and interactions that are very important for normal humans. Humans, like all primates, are inherently pack animals who are very sensitive to status, we can survive without those skills but our ability to mate or interact in community is very limited without them. We have seen a significant rise in the incidence of autism during the same time that sleep disorders have become epidemic. There is also quite a bit of literature linking vitamin D deficiency to autism. Based on my patient experience the brain still remembers what it is supposed to do, therefore given back the time in deep sleep and the necessary raw materials, the brain can make up for the deep sleep it missed and develop these skills even in teen years.

“Not a Morning Person” is actually an important sleep disorder !

Most children with milder sleep disorders just have a hard time getting out of bed.  That inability to wake up means the brain has really not finished what it needs to do, biologically the brain wanted to sleep until 10:00 am to finish last night’s tasks. More severe sleep disorders present as children who can’t fall asleep or can’t stay asleep. Bed-wetting means that the child is not getting into deep sleep to make anti-diuretic hormone, a hormone that limits our urine production during sleep, so we won’t have to get up and interrupt our period of repair. That hormone is only released in deep sleep. Children who cannot get into or stay in deep sleep make too much urine and wet the bed.

Over the last 10 years there has been a significant increase in gender dysphoria. This means feeling as though one’s “gender” does not match the sexual organs one was born with. Though babies are born with male or female genitalia the sexual development of the brain is dependent on the release of sex hormones during deep sleep throughout childhood.  Sexualizing the brain to match the genitalia is a nightly, chemical event that is followed by the pubertal physical changes that make us recognizably male or female. My patient experience has shown that teen boys who still have a feminine body shape, once sleeping normally, can transition to a masculine body shape even after significant pubertal delay. So both the social interaction and the body shape are determined by having the right amount of deep sleep during childhood.

Why Blame Our Patients for Their Own Bad Sleep?

One of the most surprising things about sleep is how little we know about it. It’s almost as though we in medicine and science have purposefully ignored it. Doctors in particular, after having to stay up all night to care for patients, know that they can’t really function without the normal amount of sleep, yet there is still heated debate about what sleep is for.  We don’t even ask our lab rats how they’ve slept because, of course they can’t tell us. But we do have hundreds of patients who can tell us how they sleep and how they feel. Why haven’t we started to ask them until recently? Over time doctors have been trained to discourage their patients from taking sleep medicines, I believe for very good reasons. But that leaves the patient only two choices; the fear and stigma of addiction or the horrible feelings of being tired, grumpy and discouraged every day.

So, one of the blocks to learning about sleep is that we doctors and scientists are humans too. We have shared human assumptions like “it’s natural to sleep”, so why even think about it?The main reason to think about it is that most of the world now has sleep issues. We were wrong to assume that we would just continue on sleeping normally. Now it is more “normal” to wake tired or to have trouble sleeping. The Center for Disease Control is now recognizing this as a major health need that is not being met. . And, it is a global issue. It began in developed countries but is now showing up in undeveloped countries as well:

Unfortunately, sleep apnea was first described in obese individuals. So the general trend has been to blame the patient. We are taught that obesity is a disorder of “self-control”. That being fat is an undesirable personality trait and if one “tries harder” weight loss is easy. Although it is true that self-control helps us to lose a few pounds this is not the whole story for people who are truly obese. Both appetite, and how much fat we store are controlled by the intestinal bacteria, not by the person eating the donut. Hunger, like sleep is actually involuntary. But, since we doctors know little about how hunger is controlled we blame the patient.  Many of my patients have struggled for years to lose weight. They tell me that they eat less than other family members and still don’t lose. We don’t want to believe them because then we have to open our minds to other possibilities. Could sleeping badly tell the body that it needs to store fat? Could a low vitamin D level or some other hormone we don’t really understand yet be ruining this poor person’s life? Could their poop be wrong? I mean really, who would ever even think of that?

The “fat neck” explanation of sleep apnea has reigned for 20 years. This has had two very bad results:  we have attached “shame”, to something that is actually a brain cell malfunction AND we completely missed apnea in normal weight individuals. My headache patients didn’t look anything like what I had been trained to look for so the idea that they might have sleep apnea wouldn’t have occurred to me. It is now quite clear that apnea is not because the neck is fat. That allows us to at least wonder: “Could there be another cause and therefore a different treatment?” Once we become brainwashed by the idea of CPAP masks we stop wondering if insomnia shares anything with apnea. They are both about sleep, could they be related? See the Vitamin D Hormone page or Sleep page to see how all sleep disorders are related.

Sleep and Headache

I originally became interested in sleep when one of my headache patients with sleep apnea cured her headaches by wearing the CPAP mask. Since then I’ve learned that bad or frequent headaches are  always accompanied by abnormal sleep. And if you don’t fix the sleep you’ll never permanently fix the headaches. Most other “cures”may last for a while but they all wear off over time.

Sleep studies on over 1000 of my  headache patients all had one thing in common; not enough REM sleep. (Only a few had apnea.) All of my daily headache sufferers also  had low vitamin D ( you probably do too). Once I stumbled on the fact that vitamin D affects the brain cells that run REM sleep my headache patients and I proved that the right vitamin D blood level could fix their sleep and their headaches.

Normal sleep  (not, taking vitamins)  is what cures headache.  To get back to normal sleep and no headache, the vitamin D blood level has to be 60-80 ng/ml.  If you are taking vitamin D and you do not know what your blood level is it’s possible that you have headaches now because you are supplementing vitamin D incorrectly. Also the vitamin D effect on sleep only lasted for two years and then the sleep went bad again despite continuing vitamin  D.

So here’s the bad news: It’s not as simple as you or I would like.

Is there good news? Yes! You can still fix your headaches but it takes a little bit more work than just popping vitamin pills.

If you’re interested in getting your sleep fixed and waking without fatigue, pain or a bad mood read more. Go to the Learning section and read everything under that heading; the FAQs, sleep, sleep and vitamins,  watch the second video in the videos segment:  Why so many headaches?

If you want to know more about the “why”of how headaches are formed go to the Headache section. If you just want them to go away then spend more time learning about sleep and how you can fix your own sleep over time using a specific regimen of vitamins. No prescriptions needed, they’re cheap, they’re at your local pharmacy.  But…. you have to pay attention to what you’re doing and you have to learn what your body is trying to tell you.

The “how “of following the RightSleep®  method  is in the RightSleep® Workbook that you can download from here.  It coaches you through an entire year, telling you exactly what to do and when to do it so that you will never have a headache again. It usually only takes one or two months to get your headaches better but  if you want to  learn how to permanently fix your headaches you need to learn how to keep your sleep normal for the rest of your life.