New Study by KDM: "...alterations of intestinal microbiota in ME/CFS patients".

[filfla4]

http://www.sciencedirect.com/science/article/pii/S1075996413000929

 

[Sushi]

High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients

Abstract

Human intestinal microbiota plays an important role in the maintenance of host health by providing energy, nutrients, and immunological protection. Intestinal dysfunction is a frequent complaint in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) patients, and previous reports suggest that dysbiosis, i.e. the overgrowth of abnormal populations of bacteria in the gut, is linked to the pathogenesis of the disease.
We used high-throughput 16S rRNA gene sequencing to investigate the presence of specific alterations in the gut microbiota of ME/CFS patients from Belgium and Norway. 43 ME/CFS patients and 36 healthy controls were included in the study. Bacterial DNA was extracted from stool samples, PCR amplification was performed on 16S rRNA gene regions, and PCR amplicons were sequenced using Roche FLX 454 sequencer.
The composition of the gut microbiota was found to differ between Belgian controls and Norwegian controls: Norwegians showed higher percentages of specific Firmicutes populations (Roseburia, Holdemania) and lower proportions of most Bacteroidetes genera. A highly significant separation could be achieved between Norwegian controls and Norwegian patients: patients presented increased proportions of Lactonifactor andAlistipes, as well as a decrease in several Firmicutes populations. In Belgian subjects the patient/control separation was less pronounced, however some abnormalities observed in Norwegian patients were also found in Belgian patients.
These results show that intestinal microbiota is altered in ME/CFS. High-throughput sequencing is a useful tool to diagnose dysbiosis in patients and could help designing treatments based on gut microbiota modulation (antibiotics, pre and probiotics supplementation).
5. Conclusions

High-throughput rRNA gene sequencing proved to be a useful tool to diagnose dysbiosis in ME/CFS patients. Our results suggest new pathogenesis mechanisms for ME/CFS, but also open new possibilities regarding the design of treatments based on gut microbiota modulation using antibiotics, pre and probiotics supplementation.

 

[natasa778]

sorry if already posted elsewhere

Anaerobe. 2013 Jun 19. pii: S1075-9964(13)00092-9. doi: 10.1016/j.anaerobe.2013.06.002. [Epub ahead of print]
High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients.

Frémont M, Coomans D, Massart S, De Meirleir K.
R.E.D Laboratories NV, Z-1 Researchpark 100, 1731 Zellik, Belgium. Electronic address: mfremont@redlabs.be.

Human intestinal microbiota plays an important role in the maintenance of host health by providing energy, nutrients, and immunological protection. Intestinal dysfunction is a frequent complaint in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) patients, and previous reports suggest that dysbiosis, i.e. the overgrowth of abnormal populations of bacteria in the gut, is linked to the pathogenesis of the disease. We used high-throughput 16S rRNA gene sequencing to investigate the presence of specific alterations in the gut microbiota of ME/CFS patients from Belgium and Norway. 43 ME/CFS patients and 36 healthy controls were included in the study. Bacterial DNA was extracted from stool samples, PCR amplification was performed on 16S rRNA gene regions, and PCR amplicons were sequenced using Roche FLX 454 sequencer. The composition of the gut microbiota was found to differ between Belgian controls and Norwegian controls: Norwegians showed higher percentages of specific Firmicutes populations (Roseburia, Holdemania) and lower proportions of most Bacteroidetes genera. A highly significant separation could be achieved between Norwegian controls and Norwegian patients: patients presented increased proportions of Lactonifactor and Alistipes, as well as a decrease in several Firmicutes populations. In Belgian subjects the patient/control separation was less pronounced, however some abnormalities observed in Norwegian patients were also found in Belgian patients. These results show that intestinal microbiota is altered in ME/CFS. High-throughput sequencing is a useful tool to diagnose dysbiosis in patients and could help designing treatments based on gut microbiota modulation (antibiotics, pre and probiotics supplementation).

 

[Enid]

Thanks natasha - it is good to see KDM's continuing research and findings.

 

[MeSci]

sorry if already posted elsewhere

Anaerobe. 2013 Jun 19. pii: S1075-9964(13)00092-9. doi: 10.1016/j.anaerobe.2013.06.002. [Epub ahead of print]
High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients.

Frémont M, Coomans D, Massart S, De Meirleir K.
R.E.D Laboratories NV, Z-1 Researchpark 100, 1731 Zellik, Belgium. Electronic address: mfremont@redlabs.be.

Human intestinal microbiota plays an important role in the maintenance of host health by providing energy, nutrients, and immunological protection. Intestinal dysfunction is a frequent complaint in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) patients, and previous reports suggest that dysbiosis, i.e. the overgrowth of abnormal populations of bacteria in the gut, is linked to the pathogenesis of the disease. We used high-throughput 16S rRNA gene sequencing to investigate the presence of specific alterations in the gut microbiota of ME/CFS patients from Belgium and Norway. 43 ME/CFS patients and 36 healthy controls were included in the study. Bacterial DNA was extracted from stool samples, PCR amplification was performed on 16S rRNA gene regions, and PCR amplicons were sequenced using Roche FLX 454 sequencer. The composition of the gut microbiota was found to differ between Belgian controls and Norwegian controls: Norwegians showed higher percentages of specific Firmicutes populations (Roseburia, Holdemania) and lower proportions of most Bacteroidetes genera. A highly significant separation could be achieved between Norwegian controls and Norwegian patients: patients presented increased proportions of Lactonifactor and Alistipes, as well as a decrease in several Firmicutes populations. In Belgian subjects the patient/control separation was less pronounced, however some abnormalities observed in Norwegian patients were also found in Belgian patients. These results show that intestinal microbiota is altered in ME/CFS. High-throughput sequencing is a useful tool to diagnose dysbiosis in patients and could help designing treatments based on gut microbiota modulation (antibiotics, pre and probiotics supplementation).

It was posted here on Tuesday:

http://forums.phoenixrising.me/inde...testinal-microbiota-in-me-cfs-patients.23935/

 

[MeSci]

Related studies:

Increased D-Lactic Acid Intestinal Bacteria
in Patients with Chronic Fatigue Syndrome

http://www.cfids-cab.org/rc/Sheedy.pdf

Normalization of leaky gut in chronic fatigue
syndrome (CFS) is accompanied by a clinical
improvement: effects of age, duration of illness
and the translocation of LPS from gram-negative bacteria

http://integrativehealthconnection....1/Leaky-gut-in-CFS-treatment-of-leaky-gut.pdf
Gut inflammation in chronic fatigue syndrome

http://www.nutritionandmetabolism.com/content/7/1/79/
Tight Junctions, Intestinal Permeability, and Autoimmunity Celiac Disease and Type 1 Diabetes Paradigms

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2886850/

Extracts from blurb accompanying Figure 2 from above paper:

"Postulated mechanism of action of gluten in T1D (Type 1 diabetes) pathogenesis. Diet affects the composition of the intestinal microflora. A hydrolyzed casein (gluten-free) diet reduces the number of Bacteroides species within the microflora, while the diabetogenic (gluten-containing) diet favors a high titer of Bacteroides [1]...The cascade of immune events eventually leads to autoimmune disease [8]."

I am sufficiently persuaded by this combined evidence to be pursuing a leaky-gut diet with suitable supplements. It's certainly effecting changes, and overall definitely positive.

 

[Firestormm]

Rather nice explanation of this paper and context provided by ME Research UK and subsequent conversations on their Facebook page:

RESEARCH UPDATE – Intestinal bacteria

Recently, scientists have begun to focus on the hidden yet extensive world of microbes that live in our bodies (the ‘microbiome’ http://bit.ly/12OineV) and, in fact, most bacterial cells are located in our gut – about 1.5 kg of bacteria per person. It’s now clear that gut bacteria can influence health in a variety of ways, such as by synthesizing nutrients, inhibiting microbial and viral pathogens, and detoxifying food. But they also contribute to the optimal functioning of the immune system; 70% of all immune cells are located in the gastrointestinal tract, for instance.

Gastrointestinal problems are very common in ME/CFS patients, so it’s at least plausible that some abnormality of gut bacteria could be linked to the development of the illness. In a full-text report http://bit.ly/14oRyuy, Belgian researchers have used high-throughput gene sequencing to search for different species of bacteria in stool samples of ME/CFS patients from Belgium (18 patients) and Norway (25 patients), and from local healthy people.

Compared with Norwegian controls, Norwegian patients had decreased percentages of some Firmicutes sub-populations (Roseburia, Syntrophococcus, Holdemania, Dialister), a strong 20-fold increase of Lactonifactor, and a 3.8-fold increase of the Bacteroidetes genus Alistipes. Belgian patients showed fewer differences compared with local controls, but Lactonifactor was again strongly increased (45-fold) while Asaccharobacter was decreased.

Scientific study of the relationship between the microbiome and human disease is still rudimentary, so all we and the authors can do is speculate about what these results might mean. Roseburia, for example, are thought to contribute to the production of energy and to protect against gut inflammation, while there is some evidence that increases in Alistipes are also related to gut inflammation (the bacteria were first identified in appendicitis tissue). So, it is certainly possible that these findings are consistent with increased intestinal inflammation. However, whether altered gut microbiota is a reproducible feature in ME/CFS populations, and whether microbiota alterations are involved in causing the illnesses or occur over time as a consequence of disease remain to be determined.

 

[MeSci]

Rather nice explanation of this paper and context provided by ME Research UK and subsequent conversations on their Facebook page:

The paper at the second link in the Facebook extract
http://bit.ly/14oRyuy
is very interesting, and I have saved it - thanks very much for this Firestormm.

I hadn't heard of Lactonifactor before.

There's also interesting stuff about Vitamin D.

I also followed a link from that one to a 2009 paper which found a significant decrease in anxiety symptoms among those taking Lactobacillus casei strain Shirota:
http://www.gutpathogens.com/content/1/1/6
I expect that one has been featured on here before, but it's all good stuff!

I have definitely reduced my anxiety levels with my gut alkalising diet and supplements, which is another way to change the gut microbiome. It's made me realise that my lifelong anxiety may have been not an innate personality trait, or even that plus life events, but that the high-carb diet I was fed and continued with through adulthood was a significant factor. (Carbohydrates tend to acidify the gut, especially in people with difficulty metabolising them, which may be hereditary.)

 

[tyson oberle]

The paper at the second link in the Facebook extract
http://bit.ly/14oRyuy
is very interesting, and I have saved it - thanks very much for this Firestormm.

I hadn't heard of Lactonifactor before.

There's also interesting stuff about Vitamin D.

I also followed a link from that one to a 2009 paper which found a significant decrease in anxiety symptoms among those taking Lactobacillus casei strain Shirota:
http://www.gutpathogens.com/content/1/1/6
I expect that one has been featured on here before, but it's all good stuff!

I have definitely reduced my anxiety levels with my gut alkalising diet and supplements, which is another way to change the gut microbiome. It's made me realise that my lifelong anxiety may have been not an innate personality trait, or even that plus life events, but that the high-carb diet I was fed and continued with through adulthood was a significant factor. (Carbohydrates tend to acidify the gut, especially in people with difficulty metabolising them, which may be hereditary.)

What type of alkalizing foods and supplements have you been eating to reduce your anxiety? How do you know that "carbohydrates tend to acidify the gut"?

 

[MeSci]

I can't remember exactly where I first read of the carb-acid connection as I've been on this regime for over a year, but there was discussion here that is of interest:

http://forums.phoenixrising.me/inde...-the-same-symptoms-as-d-lactic-acidosis.8159/

The leaky gut/alkalising diet is essentially gluten-free, low carb, dairy-free. I think the most important carbs to reduce are grains and sugar.

I list the supplements I am using here:

http://forums.phoenixrising.me/inde...ieves-full-remission.13463/page-5#post-369770

 

[tyson oberle]

I can't remember exactly where I first read of the carb-acid connection as I've been on this regime for over a year, but there was discussion here that is of interest:

http://forums.phoenixrising.me/inde...-the-same-symptoms-as-d-lactic-acidosis.8159/

The leaky gut/alkalising diet is essentially gluten-free, low carb, dairy-free. I think the most important carbs to reduce are grains and sugar.

I list the supplements I am using here:

http://forums.phoenixrising.me/inde...ieves-full-remission.13463/page-5#post-369770

What reason made you take sodium bicarbonate? How do you take it and how much and how often? I wonder if measuring your saliva ph and/or urine ph would be a good indicator of knowing whether or not you need sodium bicarbonate? Or is there a better indicator?
Also, everytime I read about acid and alkaline foods I read that many low carb foods like meat are acidifying.

 

[Sushi]

Another thing to consider is that many of us with this disease already have a gut that is too alkaline. I have had mine tested and it was so alkaline that I have to take HCL with meals.

There is a simple way to check this at home--do a google site search here for the baking soda burp test--it gives rough idea of whether your gut is too alkaline or too acid. Sorry I don't have a link handy but Rich Van Konynenburg was the one who first posted about it.

Sushi

 

[MeSci]

What reason made you take sodium bicarbonate? How do you take it and how much and how often? I wonder if measuring your saliva ph and/or urine ph would be a good indicator of knowing whether or not you need sodium bicarbonate? Or is there a better indicator?
Also, everytime I read about acid and alkaline foods I read that many low carb foods like meat are acidifying.

I can't remember the exact reason or reasons why I started but I am still taking it because it neutralises lactic acid. I don't need to worry about meat being acidifying as I am a vegan. Being vegan also probably means that I don't need as much stomach acid as omnivores, as this is primarily to break down difficult-to-digest foods such as meat, and to denature proteins. Different parts of the gut need different pH. Problems can be caused when stomach acid leaks into the next part of the gut where it should be more alkaline. It's very complicated, and quite hard to predict what will happen when you intervene. There's probably more info than most people would ever want about the human digestive system here:

http://www.britannica.com/EBchecked/topic/1081754/human-digestive-system

I pass the burp/belch test that Sushi refers to - I belch after taking bicarbonate. Also, I tried going without it a while back when I was experiencing a slight setback, and got worse, then got better when I restarted. It may not be the case for everyone.

I take about 8-10 grams a day in 4 doses taken in water about a hour after meals.

 

[end]

Related studies:

Increased D-Lactic Acid Intestinal Bacteria
in Patients with Chronic Fatigue Syndrome

http://www.cfids-cab.org/rc/Sheedy.pdf

Normalization of leaky gut in chronic fatigue
syndrome (CFS) is accompanied by a clinical
improvement: effects of age, duration of illness
and the translocation of LPS from gram-negative bacteria

http://integrativehealthconnection....1/Leaky-gut-in-CFS-treatment-of-leaky-gut.pdf
Gut inflammation in chronic fatigue syndrome

http://www.nutritionandmetabolism.com/content/7/1/79/
Tight Junctions, Intestinal Permeability, and Autoimmunity Celiac Disease and Type 1 Diabetes Paradigms

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2886850/

Extracts from blurb accompanying Figure 2 from above paper:

"Postulated mechanism of action of gluten in T1D (Type 1 diabetes) pathogenesis. Diet affects the composition of the intestinal microflora. A hydrolyzed casein (gluten-free) diet reduces the number of Bacteroides species within the microflora, while the diabetogenic (gluten-containing) diet favors a high titer of Bacteroides [1]...The cascade of immune events eventually leads to autoimmune disease [8]."

I am sufficiently persuaded by this combined evidence to be pursuing a leaky-gut diet with suitable supplements. It's certainly effecting changes, and overall definitely positive.

Apparently the "heal and seal" approach McBride outlines in her GAPS nutritional protocol forms a large part of her success. I believe Leaky Gut Syndrome forms the basis in multiple illnesses. Seeing multiple study's latterly linking LGS to ME/CFS isn't to much of a surprise. Even Dr Leo Galland mentions Leaky Gut Syndrome as a cause of Fatigue(Power Healing)15 years ago. Exact treatment however, still seems a little elusive....and not clearly defined.

 

[Leopardtail]

I can't remember the exact reason or reasons why I started but I am still taking it because it neutralises lactic acid. I don't need to worry about meat being acidifying as I am a vegan. Being vegan also probably means that I don't need as much stomach acid as omnivores, as this is primarily to break down difficult-to-digest foods such as meat, and to denature proteins. Different parts of the gut need different pH. Problems can be caused when stomach acid leaks into the next part of the gut where it should be more alkaline. It's very complicated, and quite hard to predict what will happen when you intervene. There's probably more info than most people would ever want about the human digestive system here:

http://www.britannica.com/EBchecked/topic/1081754/human-digestive-system

I pass the burp/belch test that Sushi refers to - I belch after taking bicarbonate. Also, I tried going without it a while back when I was experiencing a slight setback, and got worse, then got better when I restarted. It may not be the case for everyone.

I take about 8-10 grams a day in 4 doses taken in water about a hour after meals.

I might be telling Granny how to suck eggs here, but I went through a sort period of eating very little meat and found that eating a lot of avocado did me the world of good.

 

[Aileen]

Since the study mentioned uses 16S rRNA gene sequencing and so does the uBiome testing, I'm wondering if we can take their test and compare it to the results of the study? I'm going to do the uBiome 5 site test and am just trying to think through the best way to do this.

I was just going to do gut and nose (major sensitivity to odours). But since new revelations regarding my sensitivities see this post I've decided it might be better to have all 5 sites (gut, nose, mouth, skin, genitals) done. My thinking is that I can compare the different sites and if something unusual turns up in all places, or corresponds to the degree of problems each site is giving me, that might provide a good clue.

I am also considering asking a family member who lives in the same house to also get tested to act as a "control" sample of sorts. I'm not sure if this person should do all 5 or if just the gut would suffice. Any opinions on this would be welcome.

Also wondering if we contact uBiome if we could set something up where our samples could be entered into their data as a unique set. Perhaps we could come close to replicating the KDM study on our own? We could even provide our own control samples from friends or family.

Would anyone be interested in participating in something like this? The gut-only test is only $89US and is available to people in almost every country. I would be willing to email uBiome and perhaps send them a copy of the KDM study and tell them we'd like to do something close to it, could they help us. Maybe we could even get a discount?

 

[Aileen]

@South this is the thread I was referring to in the status update. @Sushi, do you think something like this (above post) would be possible? Maybe PR could look into it if enough people are interested?

 

[Sushi]

@South this is the thread I was referring to in the status update. @Sushi, do you think something like this (above post) would be possible? Maybe PR could look into it if enough people are interested?

I don't really know how to comment on this! Maybe give more detail on the proposal?

Best,
Sushi

 

[Aileen]

Sorry for being unclear - I blame the mystery microbe In looking at the KDM study, it looked at 4 groups - Patients (Norway), Controls (Norway), Patients (Belgium) and Controls (Belgium). All 4 groups were different. The 2 groups from Norway (patient & controls) were distinct. Same for the 2 from Belgium. Also, the 2 control groups from different countries showed different patterns as did the 2 patient groups.

The technology that the KDM study used looks the same or similar to the uBiome testing. uBiome testing is reasonably priced ($89US + int'l shipping), does not require a doctor and is available to almost any country. Those of us who are interested could get ourselves plus a local friend or relative to act as a healthy control from the same area. For large countries like Canada and USA it would probably be better to compare by state.

This way we could compare our results to the study results. A loose type of replication study. Additionally it would be expanded to include patients and controls from other countries. If you give permission, uBiome collects data to include your aggregate data in a research study. Perhaps we could have ours collected for a separate smaller study. They say they want to hear our hypothesis etc. Perhaps worth asking them about?

 

[Aileen]

Does anyone know how the results of the old Metametrix GI analysis test which used PCR compare to results from uBiome or American Gut Project? Does it test for the same stuff using the same methods? I'm so confused!