Lorrie Online added some wonderful links that support the above and add additional information.

When I first started reading Mark Hyman's book on ultra simple diet - he mentioned a lot about this. It seems our eating habits and our bacteria balance or imbalance does a lot to our systems. In just googling Mark Hyman on good and bad bacteria, a number of things come up: http://www.huffingtonpost.com/dr-mark-hyman/5-simple-steps-to-cure-ib_b_576578.html#s90762&title=5_Simple_Steps

Russell Blaylock too: http://w3.newsmax.com/newsletters/blaylock/issues/probiotics/blaylock_probiotics_28.html

Yes Ronnie, I think (have been saying it for years) that absorption/metabolism issues may be contributing to autoimmune diseases. This would include gut bacteria/fungal issues, low hormone & enzymes.

I have read a couple research papers lately that have said "abnormal interstitial permeability is in multiple autoimmune diseases" such as UC, Crohns, MS, RA, etc.

me- So the GI is compromised this means that absorption/ metabolism could be impaired.

Larazotide, a zonulin protein inhibitor, has been found to reduce “intestinal barrier dysfunction” caused by gluten. It can reduce inflammation markers, GI symptoms and stopped antibodies against transglutiminase tissue. This drug is now being studied with type 1 diabetes, MS and Crohn’s disease

1,) Fasano A. Surprises from Celiac Disease. Scientific American, 2009; 301(2): 54-61

2.) Kelsall B.L. Innate and Adaptive Mechanisms to Control of Pathological Intestinal Inflammation. Journal of Pathology, 2008; 214 (4): 242-259.

'Bugs' do battle in our bodies by Liz Szabo USA TODAY 07-17-12

There's a war going on, right under our noses, and we're just too blind to see it.

Well, maybe not that blind.

We can see these tiny combatants, all 100 trillion of them, just fine under a microscope.

But they're not always under our nose. Some of them are in our nose.
And in our mouths. And our intestines. Even in our breast milk and the birth canal.

They're microbes, living on and in the human body, and they outnumber human cells 10-to-1. Collectively, the microbes and their genes have come to be called the microbiome, says Lita Proctor, who leads the National Institute of Health's Human Microbiome Project, which last month released its initial map of a "normal" microbial makeup.

It's true that no man is an island. Scientists say we're closer to a coral reef, with an estimated 10,000 species of bacteria, fungi, yeasts and assorted others making up our ecosystem.

And while a few of these microbes can make us sick if they get out of control, 99% are benign or even protect us from harm. Bacteria have evolved with humans for millennia, helping us digest our food, synthesize vitamins, regulate our immune system and more, Proctor says.

Yet our microbes are under threat -- and the enemy is us.

Modern life is changing the composition of critters that inhabit our bodies, and not always for the better, says Martin Blaser, a professor of microbiology at the New York University School of Medicine. Through a combination of clean living and industrialization, modern living could be causing our ancient microbes to become extinct.

"People think bugs are out to get us," Proctor says. "But we're the ones changing our inner ecosystem."

Although scientists can't yet prove direct cause-and-effect, researchers have linked changes in our microbial inhabitants with rising rates of obesity, allergies, autoimmune diseases and other chronic illnesses.

Scientists note that developed countries have drastically altered the environment in the past century or so. Our water is cleaner. Food is more processed, so our guts have less need for bacteria to help us digest leafy plants and whole grains. We use more antibiotics -- to treat disease, fatten livestock, even wash our hands, Blaser says.

The story of H. pylori
Scientists already have traced the steep decline of one key species of bacteria: Helicobacter pylori, or H. pylori, Blaser says.

Over the past century, the number of American children carrying H. pylori in their stomachs has dropped from nearly 90% to fewer than 10%, Blaser says. That decline may be both good and bad. H. pylori has been shown to cause ulcers and stomach cancer; as the bacteria has disappeared, so have cases of stomach cancer, once one of the nation's leading cancer killers.

But it may be too soon to celebrate, Blaser says.

Recent research suggests H. pylori also helps prevent diseases, including esophageal cancer and childhood asthma, which have become more common in recent decades. H. pylori may even help prevent obesity, Blaser says. Studies show that getting rid of H. pylori increases levels of hormones that tell the body to keep eating but suppresses hormones that tell the body it has consumed enough.

Scientists are studying links between changes in our microbial inhabitants and a variety of increasingly common ailments, such as eczema, which is now twice as common in the USA as it was 20 to 30 years ago, says Julie Segre, a scientist at the National Institutes of Health. About 15% of American children now have eczema, which causes redness and itching. About half of children with eczema go on to develop asthma or hay fever, whose rates also are rising.

Children in developing countries have far lower rates of these disorders, says James Versalovic, a professor at Baylor College of Medicine and Texas Children's Hospital in Houston.

A new field of medicine?
(me- I SURE HOPE SO it is about time for it too!)

The science of the microbiome is still relatively new, however, and complex conditions such as cancer, asthma, allergies and obesity have multiple causes, says Kjersti Aagaard, an associate professor and maternal-fetal medicine specialist also at Baylor College of Medicine.

But Blaser says the microbiome could open up a whole new sort of medicine. He envisions a future in which children might be deliberately exposed to H. pylori to reduce their risk of asthma, then treated with antibiotics as adults, to kill the bacteria before it has a chance to cause cancer.

Some of the greatest changes to the microbiome are occurring in the first moments of life.

"Babies are microbe magnets," Proctor says.

Until just a few decades ago, virtually all babies were born vaginally, a process that exposes newborns to billions of microbes in the birth canal, Proctor says. Babies are "painted" with microbes as they pass through the vagina, says J. Bruce German, a professor at the University of California-Davis. Passage through the vagina helps ensure that a baby's microbiome looks just like its mother's, which may help prepare it for the outside world.

This journey performs a number of key functions. First, this passages helps "educate" a baby's immune system, Proctor says, teaching the body's defensive cells which foreign substances are a threat and which should be ignored. Research shows that a woman's vaginal microbes actually change in the months and weeks before delivery, Proctor says. For example, microbes that digest milk begin to multiply, so they're likely to be swallowed by the baby during childbirth. "It's not an accident that the microbes that the baby needs to breastfeed tend to proliferate in the vagina," Proctor says.

Breast milk itself contains not just food for the growing baby but for the infant's microbial inhabitants, Proctor says. Babies can't digest these substances, but beneficial bacteria gobble them up. That helps ensure a plentiful supply of good guys in the baby's gut, which are essential to keeping infants healthy and crowding out more menacing microbes that could make newborns sick.

Many babies now miss out on this protection.

Though 75% of American mothers make some attempt to breastfeed, only 44% are still nursing after six months, according to the Centers for Disease Control and Prevention. Pediatricians recommend that mothers aim to nurse for one year or more.

And 30% of American babies today are born through cesarean section. Tests show their bodies become colonized not with microbes from the vagina but from the skin, Proctor says.

Doctors have long known that vaginal delivery offers a number of benefits for most mothers and babies. They're less likely to have allergies, asthma, celiac disease, type 1 diabetes (an autoimmune disease) and to be hospitalized for diarrhea and vomiting, according to a 2011 study co-written by Josef Neu, a professor of pediatrics at the University of Florida.

At least in theory, rising C-section rates -- along with other changes in ways of living, such as antibiotic use -- have the potential to cause dramatic changes to a population's microbiome. As mothers lose microbes, they lose the potential to pass those beneficial bugs on to their children, Blaser says. In the process, some microbes could be lost from a population altogether.

But mothers should not feel guilty if they've had a C-section, Aagaard says. Though an infant's microbes may be different if they're born via C-section, that's not necessarily bad.

"We as ob-gyns don't do C-sections without really good reasons," Aagaard says. "We don't have evidence that we get harmful or dangerous microbe profiles just because women get cesarean deliveries. I don't want to imply that there is a disease risk simply by virtue of having a cesarean until we have much more robust evidence."

Restoring a balance

Now that scientists have mapped the "normal" microbiome, researchers hope to get a better understanding of how things can go wrong and result in disease, Aagaard says.

Experiments in mice, for example, suggest that changes in gut microbes can alter the animal's personality, as well as the structure of its brain, Proctor says. Carefully bred "germ-free mice," raised without a microbiome, are fundamentally "abnormal" compared with other animals, Versalovic says. Instead of showing the normal amount of caution, germ-free mice are hyperactive daredevils.

"There are no microbes in the brain," Proctor says. "But the gut produces signaling molecules that travel to the brain."

In the future, doctors hope to find ways to manipulate the microbiome, perhaps restoring a balance that modern living has disturbed.

Food and supplement manufacturers are trying to come up with successful "probiotics," or compounds with active microbes -- such as those in yogurt -- to promote health, Versalovic says.

And doctors already are using healthy bacteria to "repopulate" intestinal tracts of people devastated by a sometimes deadly infection called C. difficile, which can cause severe diarrhea and a life-threatening inflammation of the colon, Versalovic says. The infections can be extremely difficult to eradicate with traditional methods.

To restore the infected intestines to health, doctors at a handful of hospitals are performing fecal transplants from patients' close relatives or loved ones, actually transplanting a stool sample from one person to another via a colonoscopy-like procedure, hoping that the healthy donor bacteria replace the destructive microbes in the sick person's gut. Although the procedures are still experimental and relatively rare, patients sometimes show dramatic recoveries in a matter of days, Versalovic says.

Studying the microbiome even could help researchers make better drugs, Proctor says. Understanding how microbes metabolize the drugs we swallow could help pharmaceutical companies develop medications that are more effective, with fewer side effects.

The microbiome could be a fertile source of new compounds, such as anti-inflammatories, as well, Proctor says.

"You don't have to go to the coral reef or the rainforest to find the next new drug," Proctor says. "Go to the gut. Nature has already made it for us."
---------------------------------------------------
Note the part about - "There are no microbes in the brain," Proctor says. "But the gut produces signaling molecules that travel to the brain."
In the future, doctors hope to find ways to manipulate the microbiome, perhaps restoring a balance that modern living has disturbed.

http://online.wsj.com/article/SB10001424052970204468004577164732944974356.html
In a study of 23 AUTISTIC children and nine typically developing kids, a bacterium unique to the intestines of those with autism called Sutterella was discovered.

The results, published online in the journal mBio by researchers at Columbia's school of public health, need to be studied further, but suggest Sutterella may be important in understanding the link between autism and digestive ailments, the authors wrote.

Dr. Gershon, professor of pathology and cell biology at Columbia, has been studying how the gut controls its behavior and that of other organs by investigating the neurotransmitter serotonin.

Low serotonin levels in the brain are known to affect mood and sleep. Several common antidepressants work by raising levels of serotonin in the brain.

Yet about 95% of the serotonin in the body is made in the gut, not in the brain, says Dr. Gershon. Serotonin and other neurotransmitters produced by gut neurons help the digestive track push food through the gut.

Work by Dr. Gershon and others has shown that serotonin is necessary for the repair of cells in the liver and lungs, and plays a role in normal heart development and bone-mass accumulation.

Me- so depression(low serotonin) and insomnia (serotonin->melatonin used to sleep) may start in your gut. I think if you have autoimmune disease it would be a good idea to rule out bacterial/fungal/parasite issues as this can up regulate immunity and inflammation.

However, you do not need to take my word for it. In the below papers they discuss abnormal interstitial permeability and inflammation in autoimmune diseases such as MS, rheumatoid arthritis (RA), Type 1 diabetes , Ulcerative Colitis (UC) and Crohn's. There is a lab in GA that does this kind of thing if you are interested.

Fasano A. Surprises from Celiac Disease. Scientific American, 2009; 301(2): 54-61

Best wishes,
EP

http://www.sciencenews.org/view/generic/id/335561/title/Gut_bacteria_linked_to_MS
Gut bacteria linked to MS: Questions remain about how autoimmune disorder is triggered
Science News December 3, 2011; Vol.180 #12 By Tina Hesman Saey
"Researchers need to figure out whether multiple sclerosis is caused by a faulty immune system that reacts inappropriately to gut bacteria, or if some specific bacterium sets off the chain reaction.

Gurumoorthy Krishnamoorthy and Hartmut Wekerle of the Max Planck Institute of Neurobiology in Martinsried, Germany, and their colleagues used the genetically engineered mice to try to figure out the series of events that might connect gut bacteria to the immune system’s attack on the brain. Something happens in the gut to stir up immune cells called T cells. The riled-up T cells then leave the gut and travel to lymph nodes in the neck where they meet up with antibody-producing immune cells called B cells. The T cells produce chemicals that help B cells mature and prepare to attack myelin. Then, both types of immune cells travel to the brain and spinal cord and begin fraying the myelin coating on nerves, the researchers propose.

It’s not clear, however, how gut bacteria prompt T cells to ramp up, or which of the hundreds of species of bacteria in the intestines might be responsible.

“I don’t personally believe that one type of bacteria will do the job,” says Krishnamoorthy. He thinks the overall mix of bacteria may be important. The researchers are beginning systematic work to try to narrow down their vast pool of suspect bacteria. Preliminary evidence suggests that some type of Clostridium may be involved, but it is still too early to say for sure, he says."

http://www.sciencenews.org/view/generic/id/335561/title/Gut_bacteria_linked_to_MS
Gut bacteria linked to MS: Questions remain about how autoimmune disorder is triggered
Science News December 3, 2011; Vol.180 #12 By Tina Hesman Saey
"Researchers need to figure out whether multiple sclerosis is caused by a faulty immune system that reacts inappropriately to gut bacteria, or if some specific bacterium sets off the chain reaction.

Gurumoorthy Krishnamoorthy and Hartmut Wekerle of the Max Planck Institute of Neurobiology in Martinsried, Germany, and their colleagues used the genetically engineered mice to try to figure out the series of events that might connect gut bacteria to the immune system’s attack on the brain. Something happens in the gut to stir up immune cells called T cells. The riled-up T cells then leave the gut and travel to lymph nodes in the neck where they meet up with antibody-producing immune cells called B cells. The T cells produce chemicals that help B cells mature and prepare to attack myelin. Then, both types of immune cells travel to the brain and spinal cord and begin fraying the myelin coating on nerves, the researchers propose.

It’s not clear, however, how gut bacteria prompt T cells to ramp up, or which of the hundreds of species of bacteria in the intestines might be responsible.

“I don’t personally believe that one type of bacteria will do the job,” says Krishnamoorthy. He thinks the overall mix of bacteria may be important. The researchers are beginning systematic work to try to narrow down their vast pool of suspect bacteria. Preliminary evidence suggests that some type of Clostridium may be involved, but it is still too early to say for sure, he says."

http://www.2ndchance.info/inflambowel-Borody2012.pdf
Fecal microbiota transplantation and emerging applications by Thomas J. Borody and Alexander Khoruts

Fecal microbiota transplantation (FMT) (me-aka poop transplant) has been utilized sporadically for over 50 years. In the past few years, Clostridium difficile infection (CDI) epidemics in the USA and Europe have resulted in the increased use of FMT, given its high efficacy in eradicating CDI and associated symptoms. As more patients request treatment and more clinics incorporate FMT into their treatment repertoire, reports of applications outside of CDI are emerging, paving the way for the use of FMT in several idiopathic conditions. Interest in this therapy has largely been driven by new research into the gut microbiota, which is now beginning to be appreciated as a microbial human organ with important roles in immunity and energy metabolism. This new paradigm raises the possibility that many diseases result, at least partially, from microbiota-related dysfunction. This understanding invites the investigation of FMT for several disorders, including IBD, IBS, the metabolic syndrome, neurodevelopmental disorders, autoimmune diseases and allergic diseases, among others. The field of microbiota-related disorders is currently in its infancy; it certainly is an exciting time in the burgeoning science of FMT and we expect to see new and previously unexpected applications in the near future. Well-designed and well-executed randomized trials are now needed to further define these microbiota-related conditions.
Borody, T. J. & Khoruts, A. Nat. Rev. Gastroenterol. Hepatol. 9, 88–96 (2012); published online 20 December 2011;

http://www.medpagetoday.com/MeetingCoverage/IDWeek/35452?utm_source=share&utm_medium=mobile&utm_campaign=medpage%2Biphone%20app

More Proof That Fecal Transplant Banishes C. Diff By Kristina Fiore, Staff Writer, MedPage Today
Published: October 19, 2012
Reviewed by Robert Jasmer, MD; Associate Clinical Professor of Medicine, University of California, San Francisco and Dorothy Caputo, MA, BSN, RN, Nurse Planner

"Evidence continues to pile up for fecal transplantation in C. difficile infection, with another single-center study reporting high "cure" rates in infected patients.

A total of 46 out of 49 patients treated with intestinal microbiota transplant, or IMT, were quickly rid of their symptoms and had no adverse effects, Mayur Ramesh, MD, of Henry Ford Hospital in Detroit, and colleagues reported at IDWeek 2012 here."

So what are Fecal Matter Transplants (FMT)?

What I understand ( I am not a medical professional) is that they give the patient enemas to clean out the intestines. Once this is done they take the fecal matter / stool / poop of a HEALTHY individual with sterile water and blend it up. Then use this to give the sick individual an enema with the donors stool. It sounds gross but the GI is meant to have poop in it either way. It is not the poop that is the main ingredient though, it is the ton of bacteria that are not in probiotics and the enema is delivered rectally. This method delivers 100's of species of LIVE bacteria to the region they are needed, namely the intestines. This versus taking maybe 1-12 bacteria orally (pill or kefir) where the vast majority are KILLED by stomach acids and enzymes.

As more research is done and controlled method of delivery is refined through clinical research there should be more answers for not only autoimmune IBD (Crohns and Ulcerative Colitis) but IBS and quite possibly other autoimmune diseases. Since they know that good bacteria can protect the gut mucosa, down regulating inflammation and immune response but key in autoimmune diseases. I will post more research as it becomes available. If you find any research on this topic please post.

Here are some doctors that are doing FMT.
Dr. Lawrence Brandt (Bronx, New York),
Jackson Siegelbaum (Harrisburg, Pennsylvania),
Bright Medicine Clinic (Portland, Oregon), and
Dr. Colleen Kelly (Providence, Rhode Island).

Research on how FMT have helped UC and MS.

1.) Borody TJ, Leis S, Campbell J et al. Fecal Microbiota Transplantation (FMT)in multiple sclerosis (MS). Am J Gastroenterol 2011; 106: S352.

2.) Borody TJ, Warren E, Leis S et al. Bacteriotherapy using fecal flora: Toying with human motions. J Clin Gastroenterol 2004; 38(6): 475-83.

3.) Borody TJ, Torres M, Campbell J et al. Reversal of inflammatory bowel disease (IBD) with recurrent fecal microbiota transplants (FMT). Am J Gastroenterol 2011; 106: S352

Wondering if FMT can affect neuro function then read how Parkinson's symptoms are being "eased" by this type of treatment.
http://www.newscientist.com/article/mg20927962.600-faecal-transplant-eases-symptoms-of-parkinsons.html
Fecal transplant eases symptoms of Parkinson's January 19, 2011 by Anil Ananthaswamy

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Here are some doctors that are doing FMT.
1.) Dr. Lawrence Brandt (Bronx, New York)
2.) Jackson Siegelbaum (Harrisburg, Pennsylvania)
3.) Bright Medicine Clinic (Portland, Oregon)
4.) Dr. Colleen Kelly (Providence, Rhode Island)

Your liver does a TON for you. It is what I liken to the mom of the body who has to juggle many tasks. If she has a problem child who constantly needs help she'll have to reduce completing her other tasks.

These are SOME of the things your liver does for you ( I have posted this many times).
* Processes medications you take orally
* Processes sugar with pancreas to break it down and store it
* makes bile to emulsify fat ( you need healthy fat for over 60% of brain, skin, sex hormones and steroids, etc)
* Makes many proteins (Albumin, etc, etc,etc)
* Processes vitamins like D
* Processes hormones
* Recycles hemoglobin off blood (RBC die every 120 days and you make over 2 million RBC every SECOND) so this is a big job
*Filters non-bacteria toxins out of blood..ie heavy metals

* Contains immune cells that filter bacteria and toxins out of the blood

SOOO if you have all these bacteria and their toxic wastes floating around like I do and confirmed through tests. Then my liver has a problem child that is taking up many resources. Then my doc gives me Asacol to take everyday which again is processed by liver and reduces function. Well then the bad bacteria and meds are taking up more of my livers time and energy. Like a mom with a problem child things are not getting done and she is getting worn out. I was told I got rid of H Pylori after second round of 3 antibitoics for a total of 4 weeks and I am hoping many of the bad bacteria. I am doing coffee enemas and taking probitoics to help.

A day before I was dx with UC I had a vitamin D check done and was 6 on a 32-100 scale this is HORRIBLY deficient. I am wondering if a weak liver was not able to make as much bile as I used to because I have had mucus poop. So I wasn't absorbing much fat and I am wondering as a consequence I had a harder time absorbing and storing fat soluble vitamin D a pro-hormone. As you need fat to absorb this vitamin and to store it.

How does this affect you? IF..IF you have bad bacteria overgrowth this could affect absorption and metabolism. Bad bacteria can negatively affect liver CENTRAL to fat and FAT SOLUBLE VITAMINs K, A, D, E.

So my question: Many of you have said you had low D levels and this is reported with many autoimmune conditions [UC, MS, etc] could this be due to impaired liver damage? This gives a plausible hypothesis as to why these people could not bring up their vitamin D levels even with high doses or why their D levels would fall so fast after stopping the high dose.

You need to see the loop made by liver and GI bacteria.
1.) Liver filters bad bacteria and their toxic byproducts zapping time and energy from liver.
2.) If liver then reduces bile factors this can impair fat breakdown (+ subsequent absorption of fat and fat sol. vitamins) of Long Fatty Acid Chains into short chains.
3.) Some good bacteria FEED on short chains so if they are deficient so will be the good bacteria.
4.) Less good bacteria to fight off bad means more bad bacteria. This goes back to the loop of more work for the liver and less time & energy to do other jobs.

So what are your thoughts on my non-medical professional pondering?

Another doc that does FMT

Dr. Peder Pedersen in Salt Lake City, Utah.

If you want to read a discussion on the main board about this topic then click the URL below:

http://www.dailystrength.org/c/Multiple_Sclerosis_MS/forum/15159707-your-thoughtsbesides-yuck

Guysgurl replied and said she had this done. She also said there is another doc that does FMT
Dr. Peder Pedersen in Salt Lake City, Utah.