Re: NYTimes article on fecal implants and gut biology - here's it is again

[Guest guest]

Ok, here's the cut/paste version.

..In 2008, Dr. Khoruts, a gastroenterologist at the University of Minnesota, took

on a patient suffering from a vicious gut infection of Clostridium difficile.

She was crippled by constant diarrhea, which had left her in a wheelchair

wearing diapers. Dr. Khoruts treated her with an assortment of antibiotics, but

nothing could stop the bacteria. His patient was wasting away, losing 60 pounds

over the course of eight months. " She was just dwindling down the drain, and she

probably would have died, " Dr. Khoruts said.

Dr. Khoruts decided his patient needed a transplant. But he didn't give her a

piece of someone else's intestines, or a stomach, or any other organ. Instead,

he gave her some of her husband's bacteria.

Dr. Khoruts mixed a small sample of her husband's stool with saline solution and

delivered it into her colon. Writing in the Journal of Clinical Gastroenterology

last month, Dr. Khoruts and his colleagues reported that her diarrhea vanished

in a day. Her Clostridium difficile infection disappeared as well and has not

returned since.

The procedure — known as bacteriotherapy or fecal transplantation — had been

carried out a few times over the past few decades. But Dr. Khoruts and his

colleagues were able to do something previous doctors could not: they took a

genetic survey of the bacteria in her intestines before and after the

transplant.

Before the transplant, they found, her gut flora was in a desperate state. " The

normal bacteria just didn't exist in her, " said Dr. Khoruts. " She was colonized

by all sorts of misfits. "

Two weeks after the transplant, the scientists analyzed the microbes again. Her

husband's microbes had taken over. " That community was able to function and cure

her disease in a matter of days, " said Janet Jansson, a microbial ecologist at

Lawrence Berkeley National Laboratory and a co-author of the paper. " I didn't

expect it to work. The project blew me away. "

Scientists are regularly blown away by the complexity, power, and sheer number

of microbes that live in our bodies. " We have over 10 times more microbes than

human cells in our bodies, " said Weinstock of Washington University in

St. Louis. But the microbiome, as it's known, remains mostly a mystery. " It's as

if we have these other organs, and yet these are parts of our bodies we know

nothing about. "

Dr. Weinstock is part of an international effort to shed light on those puzzling

organs. He and his colleagues are cataloging thousands of new microbe species by

gathering their DNA sequences. Meanwhile, other scientists are running

experiments to figure out what those microbes are actually doing. They're

finding that the microbiome does a lot to keep us in good health. Ultimately,

researchers hope, they will learn enough about the microbiome to enlist it in

the fight against diseases.

" In just the last year, it really went from a small cottage industry to the big

time, " said Relman of Stanford University.

The microbiome first came to light in the mid-1600s, when the Dutch lens-grinder

Antonie van Leeuwenhoek scraped the scum off his teeth, placed it under a

microscope and discovered that it contained swimming creatures. Later

generations of microbiologists continued to study microbes from our bodies, but

they could only study the ones that could survive in a laboratory. For many

species, this exile meant death.

In recent years, scientists have started to survey the microbiome in a new way:

by gathering DNA. They scrape the skin or take a cheek swab and pull out the

genetic material. Getting the DNA is fairly easy. Sequencing and making sense of

it is hard, however, because a single sample may yield millions of fragments of

DNA from hundreds of different species.

A number of teams are working together to tackle this problem in a systematic

way. Dr. Weinstock is part of the biggest of these initiatives, known as the

Human Microbiome Project. The $150 million initiative was started in 2007 by the

National Institutes of Health. The project team is gathering samples from 18

different sites on the bodies of 300 volunteers.

To make sense of the genes that they're gathering, they are sequencing the

entire genomes of some 900 species that have been cultivated in the lab. Before

the project, scientists had only sequenced about 20 species in the microbiome.

In May, the scientists published details on the first 178 genomes. They

discovered 29,693 genes that are unlike any known genes. (The entire human

genome contains only around 20,000 protein-coding genes.)

" This was quite surprising to us, because these are organisms that have been

studied for a long time, " said E. of the J. Craig Venter Institute

in Rockville, Md.

The new surveys are helping scientists understand the many ecosystems our bodies

offer microbes. In the mouth alone, Dr. Relman estimates, there are between 500

and 1,000 species. " It hasn't reached a plateau yet: the more people you look

at, the more species you get, " he said. The mouth in turn is divided up into

smaller ecosystems, like the tongue, the gums, the teeth. Each tooth—and even

each side of each tooth—has a different combination of species.

Scientists are even discovering ecosystems in our bodies where they weren't

supposed to exist. Lungs have traditionally been considered to be sterile

because microbiologists have never been able to rear microbes from them. A team

of scientists at Imperial College London recently went hunting for DNA instead.

Analyzing lung samples from healthy volunteers, they discovered 128 species of

bacteria. Every square centimeter of our lungs is home to 2,000 microbes.

Some microbes can only survive in one part of the body, while others are more

cosmopolitan. And the species found in one person's body may be missing from

another's. Out of the 500 to 1,000 species of microbes identified in people's

mouths, for example, only about 100 to 200 live in any one person's mouth at any

given moment. Only 13 percent of the species on two people's hands are the same.

Only 17 percent of the species living on one person's left hand also live on the

right one.

This variation means that the total number of genes in the human microbiome must

be colossal. European and Chinese researchers recently catalogued all the

microbial genes in stool samples they collected from 124 individuals. In March,

they published a list of 3.3 million genes.

The variation in our microbiomes emerges the moment we are born.

" You have a sterile baby coming from a germ-free environment into the world, "

said Dominguez-Bello, a microbiologist at the University of Puerto Rico.

Recently, she and her colleagues studied how sterile babies get colonized in a

hospital in the Venezuelan city of Puerto Ayacucho. They took samples from the

bodies of newborns within minutes of birth. They found that babies born

vaginally were coated with microbes from their mothers' birth canals. But babies

born by Caesarean section were covered in microbes typically found on the skin

of adults.

" Our bet was that the Caesarean section babies were sterile, but it's like

they're magnets, " said Dr. Dominguez-Bello.

We continue to be colonized every day of our lives. " Surrounding us and infusing

us is this cloud of microbes, " said Gordon of Washington University. We

end up with different species, but those species generally carry out the same

essential chemistry that we need to survive. One of those tasks is breaking down

complex plant molecules. " We have a pathetic number of enzymes encoded in the

human genome, whereas microbes have a large arsenal, " said Dr. Gordon.

In addition to helping us digest, the microbiome helps us in many other ways.

The microbes in our nose, for example, make antibiotics that can kill the

dangerous pathogens we sniff. Our bodies wait for signals from microbes in order

to fully develop. When scientists rear mice without any germ in their bodies,

the mice end up with stunted intestines.

In order to co-exist with our microbiome, our immune system has to be able to

tolerate thousands of harmless species, while attacking pathogens. Scientists

are finding that the microbiome itself guides the immune system to the proper

balance.

One way the immune system fights pathogens is with inflammation. Too much

inflammation can be harmful, so we have immune cells that produce

inflammation-reducing signals. Last month, Sarkis Mazmanian and June L. Round at

Caltech reported that mice reared without a microbiome can't produce an

inflammation-reducing molecule called IL-10.

The scientists then inoculated the mice with a single species of gut bacteria,

known as Bacteroides fragilis. Once the bacteria began to breed in the guts of

the mice, they produced a signal that was taken up by certain immune cells. In

response to the signal, the cells developed the ability to produce IL-10.

Scientists are not just finding new links between the microbiome and our health.

They're also finding that many diseases are accompanied by dramatic changes in

the makeup of our inner ecosystems. The Imperial College team that discovered

microbes in the lungs, for example, also discovered that people with asthma have

a different collection of microbes than healthy people. Obese people also have a

different set of species in their guts than people of normal weight.

In some cases, new microbes may simply move into our bodies when disease alters

the landscape. In other cases, however, the microbes may help give rise to the

disease. Some surveys suggest that babies delivered by Caesarian section are

more likely to get skin infections from multiply-resistant Staphylococcus

aureus. It's possible that they lack the defensive shield of microbes from their

mother's birth canal.

Caesarean sections have also been linked to an increase in asthma and allergies

in children. So have the increased use of antibiotics in the United States and

other developed countries. Children who live on farms — where they can get a

healthy dose of microbes from the soil — are less prone to getting autoimmune

disorders than children who grow up in cities.

Some scientists argue that these studies all point to the same conclusion: when

children are deprived of their normal supply of microbes, their immune systems

get a poor education. In some people, untutored immune cells become too eager to

unleash a storm of inflammation. Instead of killing off invaders, they only

damage the host's own body.

A better understanding of the microbiome might give doctors a new way to fight

some of these diseases. For more than a century, scientists have been

investigating how to treat patients with beneficial bacteria. But probiotics, as

they're sometimes called, have only had limited success. The problem may lie in

our ignorance of precisely how most microbes in our bodies affect our health.

Dr. Khoruts and his colleagues have carried out 15 more fecal transplants, 13 of

which cured their patients. They're now analyzing the microbiome of their

patients to figure out precisely which species are wiping out the Clostridium

difficile infections. Instead of a crude transplant, Dr. Khoruts hopes that

eventually he can give his patients what he jokingly calls " God's probiotic " — a

pill containing microbes whose ability to fight infections has been

scientifically validated.

Dr. Weinstock, however, warns that a deep understanding of the microbiome is a

long way off.

" In terms of hard-boiled science, we're falling short of the mark, " he said. A

better picture of the microbiome will only emerge once scientists can use the

genetic information Dr. Weinstock and his colleagues are gathering to run many

more experiments.

" It's just old-time science. There are no short-cuts around that, " he said.

[Guest guest]

This was very interesting, thank you.

 

Ok, here's the cut/paste version.

..In 2008, Dr. Khoruts, a gastroenterologist at the University of Minnesota, took on a patient suffering from a vicious gut infection of Clostridium difficile. She was crippled by constant diarrhea, which had left her in a wheelchair wearing diapers. Dr. Khoruts treated her with an assortment of antibiotics, but nothing could stop the bacteria. His patient was wasting away, losing 60 pounds over the course of eight months. " She was just dwindling down the drain, and she probably would have died, " Dr. Khoruts said.

Dr. Khoruts decided his patient needed a transplant. But he didn't give her a piece of someone else's intestines, or a stomach, or any other organ. Instead, he gave her some of her husband's bacteria.

Dr. Khoruts mixed a small sample of her husband's stool with saline solution and delivered it into her colon. Writing in the Journal of Clinical Gastroenterology last month, Dr. Khoruts and his colleagues reported that her diarrhea vanished in a day. Her Clostridium difficile infection disappeared as well and has not returned since.

The procedure — known as bacteriotherapy or fecal transplantation — had been carried out a few times over the past few decades. But Dr. Khoruts and his colleagues were able to do something previous doctors could not: they took a genetic survey of the bacteria in her intestines before and after the transplant.

Before the transplant, they found, her gut flora was in a desperate state. " The normal bacteria just didn't exist in her, " said Dr. Khoruts. " She was colonized by all sorts of misfits. "

Two weeks after the transplant, the scientists analyzed the microbes again. Her husband's microbes had taken over. " That community was able to function and cure her disease in a matter of days, " said Janet Jansson, a microbial ecologist at Lawrence Berkeley National Laboratory and a co-author of the paper. " I didn't expect it to work. The project blew me away. "

Scientists are regularly blown away by the complexity, power, and sheer number of microbes that live in our bodies. " We have over 10 times more microbes than human cells in our bodies, " said Weinstock of Washington University in St. Louis. But the microbiome, as it's known, remains mostly a mystery. " It's as if we have these other organs, and yet these are parts of our bodies we know nothing about. "

Dr. Weinstock is part of an international effort to shed light on those puzzling organs. He and his colleagues are cataloging thousands of new microbe species by gathering their DNA sequences. Meanwhile, other scientists are running experiments to figure out what those microbes are actually doing. They're finding that the microbiome does a lot to keep us in good health. Ultimately, researchers hope, they will learn enough about the microbiome to enlist it in the fight against diseases.

" In just the last year, it really went from a small cottage industry to the big time, " said Relman of Stanford University.

The microbiome first came to light in the mid-1600s, when the Dutch lens-grinder Antonie van Leeuwenhoek scraped the scum off his teeth, placed it under a microscope and discovered that it contained swimming creatures. Later generations of microbiologists continued to study microbes from our bodies, but they could only study the ones that could survive in a laboratory. For many species, this exile meant death.

In recent years, scientists have started to survey the microbiome in a new way: by gathering DNA. They scrape the skin or take a cheek swab and pull out the genetic material. Getting the DNA is fairly easy. Sequencing and making sense of it is hard, however, because a single sample may yield millions of fragments of DNA from hundreds of different species.

A number of teams are working together to tackle this problem in a systematic way. Dr. Weinstock is part of the biggest of these initiatives, known as the Human Microbiome Project. The $150 million initiative was started in 2007 by the National Institutes of Health. The project team is gathering samples from 18 different sites on the bodies of 300 volunteers.

To make sense of the genes that they're gathering, they are sequencing the entire genomes of some 900 species that have been cultivated in the lab. Before the project, scientists had only sequenced about 20 species in the microbiome. In May, the scientists published details on the first 178 genomes. They discovered 29,693 genes that are unlike any known genes. (The entire human genome contains only around 20,000 protein-coding genes.)

" This was quite surprising to us, because these are organisms that have been studied for a long time, " said E. of the J. Craig Venter Institute in Rockville, Md.

The new surveys are helping scientists understand the many ecosystems our bodies offer microbes. In the mouth alone, Dr. Relman estimates, there are between 500 and 1,000 species. " It hasn't reached a plateau yet: the more people you look at, the more species you get, " he said. The mouth in turn is divided up into smaller ecosystems, like the tongue, the gums, the teeth. Each tooth—and even each side of each tooth—has a different combination of species.

Scientists are even discovering ecosystems in our bodies where they weren't supposed to exist. Lungs have traditionally been considered to be sterile because microbiologists have never been able to rear microbes from them. A team of scientists at Imperial College London recently went hunting for DNA instead. Analyzing lung samples from healthy volunteers, they discovered 128 species of bacteria. Every square centimeter of our lungs is home to 2,000 microbes.

Some microbes can only survive in one part of the body, while others are more cosmopolitan. And the species found in one person's body may be missing from another's. Out of the 500 to 1,000 species of microbes identified in people's mouths, for example, only about 100 to 200 live in any one person's mouth at any given moment. Only 13 percent of the species on two people's hands are the same. Only 17 percent of the species living on one person's left hand also live on the right one.

This variation means that the total number of genes in the human microbiome must be colossal. European and Chinese researchers recently catalogued all the microbial genes in stool samples they collected from 124 individuals. In March, they published a list of 3.3 million genes.

The variation in our microbiomes emerges the moment we are born.

" You have a sterile baby coming from a germ-free environment into the world, " said Dominguez-Bello, a microbiologist at the University of Puerto Rico. Recently, she and her colleagues studied how sterile babies get colonized in a hospital in the Venezuelan city of Puerto Ayacucho. They took samples from the bodies of newborns within minutes of birth. They found that babies born vaginally were coated with microbes from their mothers' birth canals. But babies born by Caesarean section were covered in microbes typically found on the skin of adults.

" Our bet was that the Caesarean section babies were sterile, but it's like they're magnets, " said Dr. Dominguez-Bello.

We continue to be colonized every day of our lives. " Surrounding us and infusing us is this cloud of microbes, " said Gordon of Washington University. We end up with different species, but those species generally carry out the same essential chemistry that we need to survive. One of those tasks is breaking down complex plant molecules. " We have a pathetic number of enzymes encoded in the human genome, whereas microbes have a large arsenal, " said Dr. Gordon.

In addition to helping us digest, the microbiome helps us in many other ways. The microbes in our nose, for example, make antibiotics that can kill the dangerous pathogens we sniff. Our bodies wait for signals from microbes in order to fully develop. When scientists rear mice without any germ in their bodies, the mice end up with stunted intestines.

In order to co-exist with our microbiome, our immune system has to be able to tolerate thousands of harmless species, while attacking pathogens. Scientists are finding that the microbiome itself guides the immune system to the proper balance.

One way the immune system fights pathogens is with inflammation. Too much inflammation can be harmful, so we have immune cells that produce inflammation-reducing signals. Last month, Sarkis Mazmanian and June L. Round at Caltech reported that mice reared without a microbiome can't produce an inflammation-reducing molecule called IL-10.

The scientists then inoculated the mice with a single species of gut bacteria, known as Bacteroides fragilis. Once the bacteria began to breed in the guts of the mice, they produced a signal that was taken up by certain immune cells. In response to the signal, the cells developed the ability to produce IL-10.

Scientists are not just finding new links between the microbiome and our health. They're also finding that many diseases are accompanied by dramatic changes in the makeup of our inner ecosystems. The Imperial College team that discovered microbes in the lungs, for example, also discovered that people with asthma have a different collection of microbes than healthy people. Obese people also have a different set of species in their guts than people of normal weight.

In some cases, new microbes may simply move into our bodies when disease alters the landscape. In other cases, however, the microbes may help give rise to the disease. Some surveys suggest that babies delivered by Caesarian section are more likely to get skin infections from multiply-resistant Staphylococcus aureus. It's possible that they lack the defensive shield of microbes from their mother's birth canal.

Caesarean sections have also been linked to an increase in asthma and allergies in children. So have the increased use of antibiotics in the United States and other developed countries. Children who live on farms — where they can get a healthy dose of microbes from the soil — are less prone to getting autoimmune disorders than children who grow up in cities.

Some scientists argue that these studies all point to the same conclusion: when children are deprived of their normal supply of microbes, their immune systems get a poor education. In some people, untutored immune cells become too eager to unleash a storm of inflammation. Instead of killing off invaders, they only damage the host's own body.

A better understanding of the microbiome might give doctors a new way to fight some of these diseases. For more than a century, scientists have been investigating how to treat patients with beneficial bacteria. But probiotics, as they're sometimes called, have only had limited success. The problem may lie in our ignorance of precisely how most microbes in our bodies affect our health.

Dr. Khoruts and his colleagues have carried out 15 more fecal transplants, 13 of which cured their patients. They're now analyzing the microbiome of their patients to figure out precisely which species are wiping out the Clostridium difficile infections. Instead of a crude transplant, Dr. Khoruts hopes that eventually he can give his patients what he jokingly calls " God's probiotic " — a pill containing microbes whose ability to fight infections has been scientifically validated.

Dr. Weinstock, however, warns that a deep understanding of the microbiome is a long way off.

" In terms of hard-boiled science, we're falling short of the mark, " he said. A better picture of the microbiome will only emerge once scientists can use the genetic information Dr. Weinstock and his colleagues are gathering to run many more experiments.

" It's just old-time science. There are no short-cuts around that, " he said.

[Guest guest]

Hey Folks,

I sent an email to Dr. Khoruts who was featured in the article. Here is his

response (my initial email is below):

Dear Sir,

Thank you for your comments and interest. I have limited experience

in doing fecal bacteriotherapy in Crohn's disease. I've done it in

three patients who had recurrent and refractory C. difficile infection

on top of their Crohn's. My impression was that although we were able

to clear the infection in 2/3 of these patients, their underlying

Crohn's disease was not altered in the long run. Obviously, the

infection wreaked havoc while it was there and needed to be treated.

I am familiar with Dr. Borody's work on ulcerative colitis. These

kinds of results are provocative and encouraging, but bigger studies

are needed. I hope to approach the question once we develop a

workable standardized formulation of bacteria.

You are correct, the colon microbiota include bacteria, Archaea,

Fungi, Protozoa, and viruses. All of those microbiomes need to be

analyzed. So far we are focusing on the bacteria, and we do measure

the relative numbers of each genus/species. However, you are quite

correct that other divisions of life and taxonomic kingdoms should

also be similarly investigated. Our focus is on patients with C.

difficile infections. Multiple other investigators are studying

microbiota in patients with IBD.

--

Khoruts, MD

Associate Professor of Medicine

University of Minnesota

Division of Gastroenterology

Center for Immunology

Microbiology, Immunology, and Cancer Biology Graduate Program

http://www.micab.umn.edu/

2101 6th St. S.E.

Medical Biosciences Building (MBB)

Room 3-184

Minneapolis, MN 55414

Campus Delivery Code 2641

Tel:

FAX:

khoru001@...

> Dear Dr. Khoruts,

>

> You are probably being inundated now with correspondence related to

> your appearance in today's New York Times article about your work in

> the area of intestinal microbiota and gastrointestinal disease.

>

> I am writing because I suffer from crohn's/colitis. While I am not

> yet in remission, my condition is fairly stable. I have been on the

> Specific Carbohydrate Diet (

http://en.wikipedia.org/wiki/Specific_Carbohydrate_Diet

> ) for the past 2.5 years and I am off all regularly prescribed

> medications. Loose stool persists, however, and I continue to try to

> assess which steps to take next.

>

> I recently became aware of fecal transplant therapy after reading

> about the work of Dr. Borody in Australia on a yahoo group to

> which I subscribe. Are you familiar with his work? He seems to have

> done extensive work with fecal transplant therapy and ulcerative

> colitis. His work can be found here:

http://www.cdd.com.au/pages/publications/publications_abstracts.html

>

> What I found exciting about your work, in addition to the fact that

> you are performing fecal transplants, is this ability you have

> developed to map the microbes of the gut. I assume this includes

> candida? I ask because, though I have not yet been tested, I have

> recently come to suspect that I have a yeast overgrowth that may be

> hampering my healing process. Does your map include existing levels

> of each microbe?

>

> I guess what I am trying to do by way of this introduction is see if

> you plan to do any work with those suffering from crohn's/colitis

> and to investigate if I would be a good candidate for mapping and

> fecal transplant if you are looking for such individuals.

>

> Thank you in advance for your time and I look forward to your

> response.

>

> Best Regards,

> Geoff

[Guest guest]

How gracious of him to write to you. It will be exciting to see research in this

field continue. Thanks for posting.

PJ

>

> > Dear Dr. Khoruts,

> >

> > You are probably being inundated now with correspondence related to

> > your appearance in today's New York Times article about your work in

> > the area of intestinal microbiota and gastrointestinal disease.

> >

> > I am writing because I suffer from crohn's/colitis. While I am not

> > yet in remission, my condition is fairly stable. I have been on the

> > Specific Carbohydrate Diet (

http://en.wikipedia.org/wiki/Specific_Carbohydrate_Diet

> > ) for the past 2.5 years and I am off all regularly prescribed

> > medications. Loose stool persists, however, and I continue to try to

> > assess which steps to take next.

> >

> > I recently became aware of fecal transplant therapy after reading

> > about the work of Dr. Borody in Australia on a yahoo group to

> > which I subscribe. Are you familiar with his work? He seems to have

> > done extensive work with fecal transplant therapy and ulcerative

> > colitis. His work can be found here:

http://www.cdd.com.au/pages/publications/publications_abstracts.html

> >

> > What I found exciting about your work, in addition to the fact that

> > you are performing fecal transplants, is this ability you have

> > developed to map the microbes of the gut. I assume this includes

> > candida? I ask because, though I have not yet been tested, I have

> > recently come to suspect that I have a yeast overgrowth that may be

> > hampering my healing process. Does your map include existing levels

> > of each microbe?

> >

> > I guess what I am trying to do by way of this introduction is see if

> > you plan to do any work with those suffering from crohn's/colitis

> > and to investigate if I would be a good candidate for mapping and

> > fecal transplant if you are looking for such individuals.

> >

> > Thank you in advance for your time and I look forward to your

> > response.

> >

> > Best Regards,

> > Geoff

>

[Guest guest]

interesting letter, geoff,

If you suspect yeast, I would start up with several

s. boulardii pills a day - but work up to it, as more than one

initially can cause bad die off. And, of course, try to

decrease sugars for a while.

Mara

> Hey Folks,

> I sent an email to Dr. Khoruts who was featured in the article. Here is his

response (my initial email is below):

>

> Dear Sir,

>

> Thank you for your comments and interest. I have limited experience

> in doing fecal bacteriotherapy in Crohn's disease. I've done it in

> three patients who had recurrent and refractory C. difficile infection

> on top of their Crohn's. My impression was that although we were able

> to clear the infection in 2/3 of these patients, their underlying

> Crohn's disease was not altered in the long run. Obviously, the

> infection wreaked havoc while it was there and needed to be treated.

>

> I am familiar with Dr. Borody's work on ulcerative colitis. These

> kinds of results are provocative and encouraging, but bigger studies

> are needed. I hope to approach the question once we develop a

> workable standardized formulation of bacteria.

>

> You are correct, the colon microbiota include bacteria, Archaea,

> Fungi, Protozoa, and viruses. All of those microbiomes need to be

> analyzed. So far we are focusing on the bacteria, and we do measure

> the relative numbers of each genus/species. However, you are quite

> correct that other divisions of life and taxonomic kingdoms should

> also be similarly investigated. Our focus is on patients with C.

> difficile infections. Multiple other investigators are studying

> microbiota in patients with IBD.

>

> --

>

>

>

> Khoruts, MD

> Associate Professor of Medicine

> University of Minnesota

> Division of Gastroenterology

>

> Center for Immunology

> Microbiology, Immunology, and Cancer Biology Graduate Program

> http://www.micab.umn.edu/

>

> 2101 6th St. S.E.

> Medical Biosciences Building (MBB)

> Room 3-184

> Minneapolis, MN 55414

> Campus Delivery Code 2641

> Tel:

> FAX:

> khoru001@...

>

>

>

>

>

>> Dear Dr. Khoruts,

>>

>> You are probably being inundated now with correspondence related to

>> your appearance in today's New York Times article about your work in

>> the area of intestinal microbiota and gastrointestinal disease.

>>

>> I am writing because I suffer from crohn's/colitis. While I am not

>> yet in remission, my condition is fairly stable. I have been on the

>> Specific Carbohydrate Diet (

http://en.wikipedia.org/wiki/Specific_Carbohydrate_Diet

>> ) for the past 2.5 years and I am off all regularly prescribed

>> medications. Loose stool persists, however, and I continue to try to

>> assess which steps to take next.

>>

>> I recently became aware of fecal transplant therapy after reading

>> about the work of Dr. Borody in Australia on a yahoo group to

>> which I subscribe. Are you familiar with his work? He seems to have

>> done extensive work with fecal transplant therapy and ulcerative

>> colitis. His work can be found here:

http://www.cdd.com.au/pages/publications/publications_abstracts.html

>>

>> What I found exciting about your work, in addition to the fact that

>> you are performing fecal transplants, is this ability you have

>> developed to map the microbes of the gut. I assume this includes

>> candida? I ask because, though I have not yet been tested, I have

>> recently come to suspect that I have a yeast overgrowth that may be

>> hampering my healing process. Does your map include existing levels

>> of each microbe?

>>

>> I guess what I am trying to do by way of this introduction is see if

>> you plan to do any work with those suffering from crohn's/colitis

>> and to investigate if I would be a good candidate for mapping and

>> fecal transplant if you are looking for such individuals.

>>

>> Thank you in advance for your time and I look forward to your

>> response.

>>

>> Best Regards,

>> Geoff

>

>

>

>

> ------------------------------------

>

>

[Guest guest]

Hi Mara,

Thanks for the advice. My yeast suspicion comes from what I believe to be a

small fungal infection on my palm in addition to a persistent dandruff that I

have had for a while. I'll be seeing a dermatologist on Friday to confirm. Also,

I am taking LDN and I haven't seen much improvement and I understand yeast

overgrowth can hamper LDN's effectiveness.

Is there a particular SCD-safe s. boulardii capsule that you like?

I have started to decrease sugars... I cut out bananas and dates starting this

past weekend as per Kim Mumbowers candida files.

peace,

Geoff

>

> interesting letter, geoff,

>

> If you suspect yeast, I would start up with several

> s. boulardii pills a day - but work up to it, as more than one

> initially can cause bad die off. And, of course, try to

> decrease sugars for a while.

>

> Mara

>

[Guest guest]

Is banana a culprit in yeast overgrowth???

I know we should aviod honey!!!

Thanks

Rani

> >

> > interesting letter, geoff,

> >

> > If you suspect yeast, I would start up with several

> > s. boulardii pills a day - but work up to it, as more than one

> > initially can cause bad die off. And, of course, try to

> > decrease sugars for a while.

> >

> > Mara

> >

>

[Guest guest]

oh yeah!! big time - stay away from all fruits and carrots/butternut squash too

eileen

> > >

> > > interesting letter, geoff,

> > >

> > > If you suspect yeast, I would start up with several

> > > s. boulardii pills a day - but work up to it, as more than one

> > > initially can cause bad die off. And, of course, try to

> > > decrease sugars for a while.

> > >

> > > Mara

> > >

> >

>

[Guest guest]

How do you know if you have yeast overgrowth? Is there a test for it? Do most general practitioners do this test or do you have to see a specialist for it?misha

 

oh yeah!! big time - stay away from all fruits and carrots/butternut squash too

eileen

> > >

> > > interesting letter, geoff,

> > >

> > > If you suspect yeast, I would start up with several

> > > s. boulardii pills a day - but work up to it, as more than one

> > > initially can cause bad die off. And, of course, try to

> > > decrease sugars for a while.

> > >

> > > Mara

> > >

> >

>

[Guest guest]

Before cutting out all fruit/sweet veggies, read this post from :

http://health.groups.yahoo.com/group/BTVC-SCD/message/46561

" This is a continuing debate about candida and fruit. I can only tell you what

I do. I eat fruit. About six months ago my doctor decided I should take a

course of Diflucan because of the high probability I had candida. I finally

agreed, but asked him if I really had to give up fruit, pointing out that my

stomach will not accept anything but fruit before 11:00 AM and I do have

hypoglycemia and need to eat something, even if just fruit isn't ideal. He said

no, not to give it up. He told me about a study he had read where the

researchers decided to do a test on people with candida, and the intent of the

study was to determine how much better they did without fruit. What they found

was not at all what they expected. As my doctor explained it, run of the mill

candida is fairly mild. That's what the people had going into the study. After

they gave up fruit, instead of getting better, the candida changed into a much

worse, more systemic form. He said it was like pussy cats changing into tigers,

and much harder to deal with. So his recommendation was that I keep the fruit

and just deal with the pussycats. That's what I did, and I did agree to take

the Diflucan for 4 months. I have to admit, I have wondered if the reason some

people insist their candida is so wicked and hard to get rid of is that they did

give up the fruit and got the tigers to deal with. "

Holly

Crohn's

SCD 12/01/08

> >

> > Is banana a culprit in yeast overgrowth???

> > I know we should aviod honey!!!

> > Thanks

> > Rani

[Guest guest]

all 3 GI's of mine say it's " controversial " -my internist tests for it BUT she

is holistic/alternative - I do ask my son's docs for it and they just write on

the slip whatever mine said - so can't hurt to ask BUT they may not know what to

do when they get a result - but we'll help you :-)

eileen

> > > > >

> > > > > interesting letter, geoff,

> > > > >

> > > > > If you suspect yeast, I would start up with several

> > > > > s. boulardii pills a day - but work up to it, as more than one

> > > > > initially can cause bad die off. And, of course, try to

> > > > > decrease sugars for a while.

> > > > >

> > > > > Mara

> > > > >

> > > >

> > >

> >

> >

> >

>

[Guest guest]

WOW can't wait to throw this by doc!!! could make sense for me at least - and

I'd be happy to have fruit back - i have cooked berries now that's it and none

for 6 months prior

eileen

> > >

> > > Is banana a culprit in yeast overgrowth???

> > > I know we should aviod honey!!!

> > > Thanks

> > > Rani

>