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  #1   ^
Old Wed, Aug-08-18, 01:59
Demi's Avatar
Demi Demi is offline
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Default Diet and Good Gut Bacteria Could Epigenetically Change Your Gene Expression

Quote:
7 August, 2018

Diet and Good Gut Bacteria Could Epigenetically Change Your Gene Expression

There are many different diets available in the nutritional world today that could dramatically adjust our gut bacteria, depending on what we consume. High-fat, low-carb diets, low-fat, high-carb diets, fasting, and cleanses are just a few examples of popular diets, and even what some may call “fads”, which might leave a person confused (and hungry).

Maintaining dietary health is one of the most important factors in ensuring a long, prosperous life. Often times we forget to prioritize healthy eating habits and as a result, we could unknowingly skew the efficiency of the healthy bacteria living in our gut that aid in digestion and may influence our epigenome.

In a recent study published in Nature Communications, a group of scientists from the Babraham Institute in Cambridge UK along with international colleagues suggest that diets high in fiber allow the good gut bacteria to prosper and potentially provide epigenetic protection against certain infections and cancers.

“Our work illuminates how short chain fatty acids contribute to the regulation of proteins that package the genome and, thus, they affect gene activity,” stated Dr. Patrick Varga-Weisz, lead researcher of the study.
Furthermore, the western diet – consisting of foods high in red meats, saturated fats, and empty carbs – has become normalized in our everyday lives, and studies show it could alter our epigenetics, potentially jeopardizing our own health and even the health of future generations. On the other hand, research has demonstrated that a ketogenic diet may be able to increase an epigenetic agent naturally produced in the body, improving memory defects in mice.

In their study, the research team investigated the bacteria in the gut that break down complex carbohydrates that we eat into nutrients to fuel the cells in our body. Specifically, they focused on the effects that gut bacteria have on gene expression in the cells that comprise the gut lining.

“Our intestine is the home of countless bacteria that help in the digestion of foods such as plant fibers. They also act as a barrier to harmful bacteria and educate our immune system,” said Dr. Varga-Weisz, highlighting the importance of keeping a healthy gut. “How these bugs affect our cells is a key part of these processes.”

The team discovered that when fiber-rich foods – particularly fruits and vegetables – ferment in the colon, the gut bacteria produce chemicals called short-chain fatty acids (SCFAs) to supply energy to the colon-lining cells. Fiber is one of the key dietary components in maintaining a healthy digestive system and foods that are high in fiber include nuts, oatmeal, apples, and blueberries.

The SCFAs produced by the gut bacteria, comprised of propionate, acetate, and butyrate, are involved in the metabolism of fats and carbs, and also hold an important role in moderating immune response. As a result, SCFAs may reduce the risk of developing hypertension, heart disease, type 2 diabetes, and obesity.

Interestingly, the researchers also discovered that SCFAs directly increase the presence of an epigenetic mark called histone crotonylation, which is a mechanism that reverses the chromatin tightening effects of histone deacetylase 2 (HDAC2). Histone deacetylases are epigenetic enzymes that remove an acetyl group, which tightens chromatin to the point where transcriptional machinery cannot access it, limiting gene expression.

Crotonylation is a process that enhances transcriptional activity by increasing the concentration of the enzyme crotonyl-CoA at the lysine, and has been implicated in the fight against HIV latency. This mechanism effectively loosens chromatin, allowing a greater amount of gene expression.

The team treated a group of mice with an antibiotic cocktail for three days in efforts to reduce bacterial presence in the gut. After the three day period, they found that the mice experienced a decrease in histone crotonylation in the colon tissue and an increase in levels of HDAC2. Increased levels of HDAC2 in the gut have been linked to the development of colon cancer, highlighting the importance that healthy gut bacteria and regulated histone crotonylation may have on overall health.

To further confirm their findings about the epigenetic effects of fiber-rich foods and short-chain fatty acids, the researchers employed cellular treatment with butyrate, which is an HDAC inhibitor, and also main component in SCFAs. They found that this treatment restored the promotion of histone crotonylation, implying that other HDAC inhibitors may be able to enhance the positive health benefits of SCFAs.

“Short chain fatty acids are a key energy source for cells in the gut but we’ve also shown they affect crotonylation of the genome,” said first author Rachel Fellows. “Crotonylation is found in many cells but it’s particularly common in the gut. Our study reveals why this is the case by identifying a new role for HDAC2. This, in turn, has been implicated in cancer and offers an interesting new drug target to be studied further.”

The results also highlight the importance of keeping a healthy diet, as it can play a crucial role in not only our overall health, but may also influence our epigenetic marks which might be inherited by our future offspring. The scientists hope that additional studies will expand upon the effects of histone crotonylation and HDAC2 on gut health in efforts to create an environment in the gut that will leave the person less-susceptible to developing digestion-related diseases.


https://www.whatisepigenetics.com/d...ene-expression/
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  #2   ^
Old Wed, Aug-08-18, 02:04
BillyHW's Avatar
BillyHW BillyHW is offline
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Okay, so how do I get all the good species of bacteria inside of me? I think I've got a bad set.
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  #3   ^
Old Wed, Aug-08-18, 07:27
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teaser teaser is online now
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I remember when complex carbohydrate was a phrase used in place of starch. Because everybody used to know excess starch was bad for you, so they needed a new term. Now it's moving over to mean fiber etc. I've even seen it used to describe fruit, as if sugars are complex...

I don't currently need much help digesting plant fibers.

I think they should continue to look for ways to make a plant based diet as healthful as possible, since so many people are likely to continue eating one.
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  #4   ^
Old Wed, Aug-08-18, 09:02
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NewRuth NewRuth is offline
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Quote:
Originally Posted by BillyHW
Okay, so how do I get all the good species of bacteria inside of me? I think I've got a bad set.


You eat them.

Dr. Pearlmutter's book, Brain Maker, is a good place to start.
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  #5   ^
Old Wed, Aug-08-18, 09:46
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doreen T doreen T is offline
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Quote:
Originally Posted by BillyHW
Okay, so how do I get all the good species of bacteria inside of me? I think I've got a bad set.

Fecal Transplant
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  #6   ^
Old Wed, Aug-08-18, 09:56
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NewRuth NewRuth is offline
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I'm re-watching the Dr. Gominak video that I linked in the other thread. She's discussing the needs of the microbiome. We're living on the cutting edge of science, so we don't know so much.

Dr. Gominak says that you need to get your Vitamin D levels above 40 so that the gut bugs can live happily. You also need to supply B-50 or B-100 for 3 months, but continuing too long or too high a dose can cause problems.

She's not a microbiome specialist, but has learned a lot from her medical practice.
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  #7   ^
Old Wed, Aug-08-18, 09:57
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NewRuth NewRuth is offline
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Quote:
Originally Posted by doreen T


It can be a lifesaving procedure if you need it. Fortunately, most of us can tolerate a slower fix.
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  #8   ^
Old Wed, Aug-08-18, 11:29
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JLx JLx is offline
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Quote:
Originally Posted by NewRuth
Dr. Gominak says that you need to get your Vitamin D levels above 40 so that the gut bugs can live happily. You also need to supply B-50 or B-100 for 3 months, but continuing too long or too high a dose can cause problems.


Thanks for the link, I'm going to watch it. Never heard that about Vit D.

(That's a dusty journal you've got there! Is your plan still "LC gut healing"? If so, how is it going?)
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  #9   ^
Old Wed, Aug-08-18, 11:50
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BillyHW BillyHW is offline
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Quote:
Originally Posted by doreen T


Question about fecal transplant: why would the small amount of transplanted donor fecal matter bacteria take over an environment that is already dominated by the recipient's bacteria?

Who's to say whether the donor's or recipient's bacteria are stronger and will come dominate?
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  #10   ^
Old Wed, Aug-08-18, 12:03
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DancinGurl DancinGurl is offline
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438885/

Weight Gain After Fecal Microbiota Transplantation
CASE REPORT
A 32-year-old female with recurrent CDI underwent FMT at our center. She had initially presented several months previously with a 2- to 3-week history of diarrhea and abdominal pain after antibiotic treatment for bacterial vaginosis and exposure to a family member who had CDI. She was treated empirically for CDI by her primary care physician with a 10-day course of oral metronidazole with only partial improvement. Her diarrhea and abdominal pain escalated after completing the metronidazole treatment, and her stool tested positive for Clostridium difficile toxin polymerase chain reaction (PCR). She was treated with a 14-day course of oral vancomycin. Testing done around the same time showed Helicobacter pylori infection (positive fecal antigen). Nausea and abdominal pain persisted after treatment of the CDI, so the H. pyloriwas treated with a course of triple therapy (amoxicillin, clarithromycin, and proton pump inhibitor). Her abdominal pain and diarrhea escalated again a few weeks later, and her stool tested positive for C. difficiletoxin PCR. She was treated with a 12-week tapering course of oral vancomycin with improvement, but diarrheal symptoms recurred again within 2 weeks of completing the course, and she was prescribed a course of rifaximin with Saccharomyces boulardii. Around this time, she underwent esophagogastroduodenoscopy, which showed persistence of H. pylori infection. She had no significant past medical history and had always been of normal weight. Review of systems was positive for diarrhea, and there was frustration over her ongoing diarrheal symptoms. Her weight before FMT was stable at 136 pounds (body mass index of [BMI] 26). Physical examination was unremarkable.
After extensive discussion, the patient elected to undergo fecal transplant. As per the patient's request, her 16-year-old daughter was chosen as the stool donor. At the time of FMT, her daughter's weight was ∼140 pounds (BMI of 26.4), but it increased later to 170 pounds. Her daughter had no other health problems, and screening for human immunodeficiency virus 1 and 2, syphilis, and viral hepatitis A, B, and C, C. difficile, Giardia lamblia, and routine stool culture for enteric pathogens were negative. The patient was retreated for H. pylori with quadruple therapy (metronidazole, tetracycline, bismuth, and proton pump inhibitor), and the FMT was performed 2 weeks later via colonoscopy. A total of 600 cc of the suspension of donor stool in sterile water was infused through the colonoscope starting in the terminal ileum. The colon and the terminal ileum appeared normal at the time of the procedure. She improved and did not suffer a further CDI recurrence after FMT.
The patient presented again 16 months after FMT, and reported an unintentional weight gain of 34 pounds. She weighed 170 pounds and had become obese (BMI of 33). She had not lost any weight over the months she was being treated for CDI. She had been unable to lose weight despite a medically supervised liquid protein diet and exercise program. Her serum cortisol and thyroid panel were normal. She has continued to gain weight despite efforts to diet and exercise, and at 36 months post-FMT her weight was 177 pounds (BMI of 34.5). She has also developed constipation and unexplained dyspeptic symptoms.
Go to:
DISCUSSION
Our patient reported unintentional rapid weight gain after FMT. There are several possible contributions to the weight gain, including the resolution of CDI (with subsequent increased appetite) and concurrent treatment of H. pylori. There is a known association between H. pylori treatment and weight gain, especially in children, thought to be due to restoration of ghrelin levels after eradication of the bacteria [1]. However, it is notable that she was never obese prior to FMT, and that the stool donor similarly experienced significant weight gain, raising the possibility that the obesity was at least in part a consequence of FMT. The hypothesis of FMT triggering or contributing to obesity is supported by animal models demonstrating that an obese microbiota can be transmitted [2]. An important limitation in our case is that the microbiome sequencing comparing the patient and the donor is not known.
With the occurrence of weight gain after FMT in this case, it is now our policy to use nonobese donors for FMT. The untoward consequences of using nonideal FMT donors are important, because patients may prefer to use a family member rather than an unrelated or unknown stool donor due to the perception that these sources are safer. However, studies have shown that FMT using a frozen inoculum from unrelated donors is effective in treating relapsing CDI [3]. In addition, most “professional” stool donors for FMT are selected on the basis of good health, including a normal BMI. This case serves as a note of caution when considering the use of nonideal donors for FMT, and we recommend selecting non-overweight donors for FMT.
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  #11   ^
Old Wed, Aug-08-18, 14:23
BillyHW's Avatar
BillyHW BillyHW is offline
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Plan: Keto + IF
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Quote:
Originally Posted by DancinGurl
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438885/

Weight Gain After Fecal Microbiota Transplantation
CASE REPORT
A 32-year-old female with recurrent CDI underwent FMT at our center. She had initially presented several months previously with a 2- to 3-week history of diarrhea and abdominal pain after antibiotic treatment for bacterial vaginosis and exposure to a family member who had CDI. She was treated empirically for CDI by her primary care physician with a 10-day course of oral metronidazole with only partial improvement. Her diarrhea and abdominal pain escalated after completing the metronidazole treatment, and her stool tested positive for Clostridium difficile toxin polymerase chain reaction (PCR). She was treated with a 14-day course of oral vancomycin. Testing done around the same time showed Helicobacter pylori infection (positive fecal antigen). Nausea and abdominal pain persisted after treatment of the CDI, so the H. pyloriwas treated with a course of triple therapy (amoxicillin, clarithromycin, and proton pump inhibitor). Her abdominal pain and diarrhea escalated again a few weeks later, and her stool tested positive for C. difficiletoxin PCR. She was treated with a 12-week tapering course of oral vancomycin with improvement, but diarrheal symptoms recurred again within 2 weeks of completing the course, and she was prescribed a course of rifaximin with Saccharomyces boulardii. Around this time, she underwent esophagogastroduodenoscopy, which showed persistence of H. pylori infection. She had no significant past medical history and had always been of normal weight. Review of systems was positive for diarrhea, and there was frustration over her ongoing diarrheal symptoms. Her weight before FMT was stable at 136 pounds (body mass index of [BMI] 26). Physical examination was unremarkable.
After extensive discussion, the patient elected to undergo fecal transplant. As per the patient's request, her 16-year-old daughter was chosen as the stool donor. At the time of FMT, her daughter's weight was ∼140 pounds (BMI of 26.4), but it increased later to 170 pounds. Her daughter had no other health problems, and screening for human immunodeficiency virus 1 and 2, syphilis, and viral hepatitis A, B, and C, C. difficile, Giardia lamblia, and routine stool culture for enteric pathogens were negative. The patient was retreated for H. pylori with quadruple therapy (metronidazole, tetracycline, bismuth, and proton pump inhibitor), and the FMT was performed 2 weeks later via colonoscopy. A total of 600 cc of the suspension of donor stool in sterile water was infused through the colonoscope starting in the terminal ileum. The colon and the terminal ileum appeared normal at the time of the procedure. She improved and did not suffer a further CDI recurrence after FMT.
The patient presented again 16 months after FMT, and reported an unintentional weight gain of 34 pounds. She weighed 170 pounds and had become obese (BMI of 33). She had not lost any weight over the months she was being treated for CDI. She had been unable to lose weight despite a medically supervised liquid protein diet and exercise program. Her serum cortisol and thyroid panel were normal. She has continued to gain weight despite efforts to diet and exercise, and at 36 months post-FMT her weight was 177 pounds (BMI of 34.5). She has also developed constipation and unexplained dyspeptic symptoms.
Go to:
DISCUSSION
Our patient reported unintentional rapid weight gain after FMT. There are several possible contributions to the weight gain, including the resolution of CDI (with subsequent increased appetite) and concurrent treatment of H. pylori. There is a known association between H. pylori treatment and weight gain, especially in children, thought to be due to restoration of ghrelin levels after eradication of the bacteria [1]. However, it is notable that she was never obese prior to FMT, and that the stool donor similarly experienced significant weight gain, raising the possibility that the obesity was at least in part a consequence of FMT. The hypothesis of FMT triggering or contributing to obesity is supported by animal models demonstrating that an obese microbiota can be transmitted [2]. An important limitation in our case is that the microbiome sequencing comparing the patient and the donor is not known.
With the occurrence of weight gain after FMT in this case, it is now our policy to use nonobese donors for FMT. The untoward consequences of using nonideal FMT donors are important, because patients may prefer to use a family member rather than an unrelated or unknown stool donor due to the perception that these sources are safer. However, studies have shown that FMT using a frozen inoculum from unrelated donors is effective in treating relapsing CDI [3]. In addition, most “professional” stool donors for FMT are selected on the basis of good health, including a normal BMI. This case serves as a note of caution when considering the use of nonideal donors for FMT, and we recommend selecting non-overweight donors for FMT.


But the donor daughter wasn't obese at the time of the donation.

And the patient underwent myriad different treatments.

It's impossoble to identify a cause here.

Maybe they both went on low fat diets after the operation.
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  #12   ^
Old Wed, Aug-08-18, 17:20
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mike_d mike_d is offline
Grease is the word!
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Quote:
Originally Posted by BillyHW
Okay, so how do I get all the good species of bacteria inside of me? I think I've got a bad set.
Kefir (homemade) the only sure way I know of, but it can take weeks or months of drinking some daily. I have the details here somewhere?
Quote:
Consumption of kefir daily can correct high blood pressure usually within 3 months. It has been shown that friendly bacteria can actually produce B vitamins in the gut which can lead to higher energy. Calcium and other essential nutrients found in milk are fully absorbed and provide better bio-availability. Any disease of the gut or colon can be benefited by drinking kefir on a regular basis.
Milk Kefir Unleashed | Fusion Teas
Quote:
Overall, the analysis showed that consumption of probiotics led to a significant decrease in both diastolic and systolic blood pressure measurements. As could be expected, larger changes were seen in those who started with high blood pressure than those who were healthy to begin with.
At the most basic level, there is no downside to starting a probiotic supplement each day. For those already taking probiotics, this is another reason to continue. Good sources of probiotics include yogurt, cheese, and fermented beverages like unsweetened kefir or kombucha. However, a high quality supplement containing at least 10 billion active cultures from 10 or more strains including lactobacillus acidophilus and bifidobacterium is the best way to ensure you meet all your probiotic needs.
-- Dr. Perlmutter author of "Grain Brain"

Last edited by mike_d : Wed, Aug-08-18 at 18:34.
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  #13   ^
Old Wed, Aug-08-18, 19:04
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Ms Arielle Ms Arielle is offline
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Fecal donation--- a good reason to bring back natural birthing.
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  #14   ^
Old Wed, Aug-08-18, 20:11
Zei Zei is offline
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If by natural you mean out the, ahem, usual exit, definitely agree. I was offered a scheduled C-section for my last child after having some really really big babies. Told doctor I didn't need that, just a scheduled induction to keep baby from getting any bigger. Nothing natural about that, but it safely got the job done plus those bacterial benefits of that style of exit. So yes, sometimes I think C-sections might be getting used when maybe they didn't need to be. On the other hand they can be life-saving at times, and it's a tough judgment call for everyone involved deciding if VBAC afterward is safe, etc. My neighbor's child got stuck sideways inside her, no way that baby was getting out on its own. VBAC worked once after that then was no longer safe for her. Bummer about the loss of bacterial opportunity plus who really is choosing C-section for convenience reasons? I wonder about that because the recovery is so much harder. Maybe some people are but not the ones I've met. Also I wonder if all those bacteria get wiped out if the child receives antibiotics in a case where they're clearly needed?
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  #15   ^
Old Wed, Aug-08-18, 20:23
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Ms Arielle Ms Arielle is offline
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There is a method of innoculating the babies after a c-section to get the same effect. Just not sure the docs are doing it. I learned of it too late--like 10 years too late after 2 c-sections for medical reasons. Doc recommended c-sections to prevent palsey issues as my babies were quite big. A nine pound bundle is nice to hold though.

The recovery time of both methods are not without issues. Each can have its comp lications.
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