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Posted 11/19/2013 3:17 PM (GMT 0)
At the beginning of the year I submitted a stool sample to American Gut to analyze. Here are the results:

The average person has roughly 45% Bacteroidetes, 42% Firmicutes, and 10% Proteobacteria along with some smaller percentages of other types populated in their guts. These percentages vary somewhat from person to person due to age, diet, etc..

My stool sample showed 99% Firmicutes. Of these Firmicutes 41% were from the Genus Staphylococcus and 32% were from the family Clostridiaceae. My sample also included the following rare Taxa: Unclassified order Gemellales, Unclassified family Carnobacteriaceae, Genus Thiothrix.

I know this is Greek to most, including me, but the big question is what happened to my share of Bacteroidetes and Proteobacteria?

Is this as simple as repopulating my gut with these kinds of bacteria or has my immune system attacked and killed off these types and if I tried reintroducing more of these kinds would my immune system merely kill them off as well?

Has my intestinal wall been taken over by the Firmicutes and it would be next to impossible to repopulate my gut with Bacteroidetes because the Firmicutes have taken over and would not allow colonization by anything else?

Are other UC'rs similar to me or is our gut population different in every one of us? Maybe some of us have 99% Bacteroidetes.

Do the probiotics I take have anything to do with this 99%? I did read that VSL seems to increase Bacteroidetes and decrease Firmicutes so how does that relate to me having 99% Firmicutes and very little anything else? I also take Prescript Assist probiotic.

Did the broad spectrum antibiotics I took while in the hospital which I believe caused my UC kill off everything but the Firmicutes? If so, can I just repopulate or did the antibiotics permanently reprogram my immune system to kill off the Bacteroidetes and others?

Since I have been doing much better recently than when the sample was taken is my population different now than what the results show?

Questions. Questions. Questions. Now I need answers, answers, answers.

 

Posted 11/19/2013 3:38 PM (GMT 0)
Very interesting.. Where did you get the percentages of the healthy gut bacterial make up? is this provided with your analysis? What's the process to getting this analysis done? I'm interested.
Posted 11/19/2013 3:49 PM (GMT 0)
I know it will take a while, but can you "order" another sample kit and send it in? That way you will have an idea of what is happening now that you are better.
I sent in my UBiome sample a month ago but I expect it will take a while to get results. I will post them when they come in.
Posted 11/19/2013 3:54 PM (GMT 0)
Interesting.
From the early onset ibd study we are not dysbiotic at the start of UC.
Still leaves me to believe the immune system is doing the killing,possibly along with meds/antibiotics.
Seems also you now have established niches,and nothing else will grow well.
Perhaps a way is radical diet change,but even then the bacteria can feed on mucus and byproducts
of other bacteria.
Then again these are stool samples,hard to tell what is controlling stool populations vs mucosal populations. Does the mucosal population control what goes on in the stool,or are other factors involved.
Did they supply graphs of population distributions.

I guess a retest might be inorder,now that you are feeling better.
OM

Post Edited (Old Mike) : 11/19/2013 8:57:04 AM (GMT-7)

Posted 11/19/2013 4:30 PM (GMT 0)
I see that UBiome and American Gut are different companies right? Is their reporting of results similar? It would be interesting to see what results they would report of the same sample from the same individual.
Posted 11/19/2013 5:44 PM (GMT 0)
I don't know if American Gut is doing this anymore or not. Anyone interested could try googling. It cost me about one hundred dollars and took about 10 months from the time I got the kit to get these results and it took probably 3-4 months to get the kit from the time I ordered it. There are different companies which do this. Don't know if their reporting is similar or not.

Kickboxer: Somewhere I recently read what those ratios were but could not find them again when I made this post. My analysis does have a graph of what they called "average" and I used this graph as best as I could to estimate the ratios. The graph also showed several other comparisons but all of them did not differeniate by that much to the average. The graphs do not show different populations distributions, although they did get samples returned from all over the world. In searches I made it appears that obese people have more Firmicutes than Bacteroidetes. I don't know what those ratios are but I highly doubt that the most obese person in the world has 99%. I am about 20 pounds overweight. Very far from being labeled obese.

Some other questions I thought of:

1. As Old Mike asked, "What did the ratio look like in the very beginning of my UC diagnosis compared to the time of the sample, compared to how it looks now"?

2. Do UC meds influence our gut bacteria ratios, or are they pretty much a non-factor? Related question: If we take a particular med and it helps, does this this alter our gut population or merely act in a different way, not related to gut bacteria population at all?

3. Does the fecal sample accurately represent what is lining my intestinal walls or does it merely reflect what is actually coming out? Maybe I have the exact opposite problem in that the Bacteroidetes are actually lining my intestinal wall 99%, causing all of my Firmicutes to be excreted and leading to my particular analysis.
Posted 11/19/2013 6:04 PM (GMT 0)
I am pretty sure the American gut project is still accepting samples. They were on NPR a couple of weeks ago.
Posted 11/19/2013 6:12 PM (GMT 0)
Do you mind sharing the excel sheet that you got. I may be able to help you, or just share screenshots of important stuff removing any identifiable details.


To answer your questions,
1. Nobody will be able to tell you this. It so much depends on the person, their diet, the environment they are in. There are just too many variables to count. You can get a generalized opinion if this company or the other company samples really a ton of people from different ends of the world, with different socio-economic backgrounds.
The average present in your graph is probably the sample size that they must have used in the beginning. It 'may' represent US population but I do not consider it as a 'true' average, may be 'working' average. In all ideal case, I would like to see an 'average' from the population that has least incidence of IBD.
I wonder, do you have brother? Similar lifestyle, food habits. That is the closest you can get. If not, your son but still he is ~50% different than you are.

2. UC meds will alter the gut population, because although they may not act directly on the bugs, the environment that they create in there allows/denies access to some bugs. I don't have any proof to back this statement.

3. If you ask me, it represents whats in there right from your sphincter at the end of stomach to last end of the rectum. The population changes according to ghettos. The pH of your gut is different that makes certain bugs to stay and certain bugs to go live somewhere else. Whatever passes through this area would collect a representative sample of flora and carry it out. This will not tell you, which bug resides where but this is generalized idea. Unless you are dead and autopsy is performed or you are undergoing surgery, I don't think it is that easy to get sample of small intestine and region above that.


Is UBiome sending out kits? Last time I asked them, they told me that I can purchase it now and will start shipping 'when they are ready'.
Plus, one thing that bothers me with UBiome is their policy with use of the data is rather unclear. 23andMe is at least clear, although I do not trust them either.
Posted 11/19/2013 6:42 PM (GMT 0)
Delta:

I did not get an Excel sheet. They sent me some kind of a small size poster, which is larger than a regular sheet of paper (didn't measure). I did scan part of it into my computer as a jpeg. The portion I scanned is 8 1/2 X 11. I don't remember there being anything on the poster, other than my full name, that I would object to being made public. I was trying to figure out how to post it here but hadn't come up with any ideas yet. Most of it would involve picture graphs. If you have any suggestions of how I could post it that would be fine with me. If that won't work you can email me at the address in my profile and I can foward you what I have scanned. I might also be able to scan both halves of the poster if necessary.

By the way, I do have a brother one year yonger than myself but his lifestyle and living location are completely different than mine. I have no sons but two very young daughters. I don't believe any of these people would be of any help at this time.

Posted 11/19/2013 7:26 PM (GMT 0)
Multiple options to post

postimage.org/
Google drive, click on share and copy that link here.
If you use Dropbox, put it in public folder, right click and you will see copy public link, paste the link here.

It is VERY surprising that they did not send you excel sheet, then how the heck are you suppose to know which strain is in there and what % of it?
Posted 11/19/2013 7:41 PM (GMT 0)
I will look into this later when I get home.
Posted 11/19/2013 11:47 PM (GMT 0)
American Gut Result Images:

http://www.postimg.org/gallery/amuyb9gk/

Not quite sure how to make the images larger.

Posted 11/20/2013 3:33 AM (GMT 0)
Do you clot alot? Kill the staph then take a well rounded probiotic.

I posted about sinus infections and UC many times as well as the role of staph
www.biomedcentral.com/1471-230X/5/6/
Posted 11/20/2013 3:40 AM (GMT 0)
Basically you can't get well till you kill the staph and free up some real estate for good bacteria. It's like your gut is populated by the yakuza gang now. You can send in a billion folks to clean crap up (probiotics) but the resident dysbiosis will just attack it.

Staph means biofilm. Attack the bacteria and the biofilm simultaneously.
Posted 11/20/2013 1:32 PM (GMT 0)

garylouisville said...
American Gut Result Images:

http://www.postimg.org/gallery/amuyb9gk/
Not quite sure how to make the images larger.

Gary,
I am sorry to say this is not at all useful. It just tells the family of the species but no genus and species. If there are abundant staph, which staph is it? Is it S. aureus which is pathogenic or other ones? In Clostradiceae, again this is huge umbrella and there are ton of species and strains, very few of them actually useful, so again you need details.

It only tells you clearly that your bacterial flora is messed up, which you also knew otherwise.

Can you contact them and ask them for a species information. If they don't know strains, fine but species would be the ultimate information you need.
Posted 11/20/2013 2:00 PM (GMT 0)
Patho: Thanks for the link. I will need some time to digest all of this. I'm not sure what you mean by "clot a lot". I think the answer is no. In fact, I used to have ITP, which made me not clot a lot. I haven't had any problems with that in years and believe my platelet count to currently be in the normal range and clotting to be normal. I'm not sure about probiotics as I already take two now, VSL and prescript Assist. The VSL is supposed to increase Bacteroidetes and decrease Firmicutes but according to this graph it has obviously not done that. I have gotten better since being on the VSL and at one time was on a much higher dose than I am now taking. The prescript assist is designed to repopulate the gut with the kind of good bacteria that gets killed off due to antibiotics, which I believe is what caused my UC. I used to get chronic sinus infections a long long time ago, way before UC but since getting allergy shots starting over 10 years ago and continuing through today I rarely get a sinus infection. Not sure what that means regarding what you are talking about. I've only had UC for three years.


Delta: I realize that these results are nothing but the very tip of the iceberg. I believe I can email American Gut but don't believe I will get any further information than what they have provided. I'll give it a try. I was disappointed that the results weren't more detailed but the results are enough to possibly start going down the correct road. That's part of the problem in finding a "cure" in the first place. You can't get to that pot of gold at the end of the rainbow until you have turned down the correct road in the first place. This at least gives me a starting point.

Posted 11/20/2013 2:05 PM (GMT 0)
I got mine in the mail yesterday but I downloaded the pdf from my American Gut account and converted it to a jpg (tap's Stool Sample).

My sample is different than the normal noted with some bacteria missing and many more than expected of others. I asked the American Gut staff if a full breakdown of all bacteria will be made available and I got a message back this morning noting that a more thorough data set will be made available in the coming weeks.

I found this document (Microbial Communities in IBD) this morning while searching for information on actinobacteria.

The document said...
IBD is associated with:
• Increased prevalence of Proteobacteria (e.g. E. coli) and Actinobacteria.
• Decreased prevalence of “normal” microbiota:
- Bacteroides
- Butryate-producing bacteria (e.g. Lachnospiraceae group)

Posted 11/20/2013 2:12 PM (GMT 0)
tap: My sample indicated 99% firmicutes. Was your's similar to mine at all or completely different?
Posted 11/20/2013 3:06 PM (GMT 0)

garylouisville said...
tap: My sample indicated 99% firmicutes. Was your's similar to mine at all or completely different?

Completely different. My sample results jpg is accessible from the link in my previous entry.

If I was you I would take it with me to my GP and discuss it. As others have noted you seem to be overrun by one bacteria.
Posted 11/20/2013 3:44 PM (GMT 0)
Fascinating. Yours seems to have come back fairly normal and yet you have UC. What was your UC like at the time of submitting your sample and what treatments were you on?
Posted 11/20/2013 5:01 PM (GMT 0)

garylouisville said...
Fascinating. Yours seems to have come back fairly normal and yet you have UC. What was your UC like at the time of submitting your sample and what treatments were you on?


Strange. I look at mine and I see that it looks significantly different than average. I think that the devil in the details and until I get a thorough detailed list of my bacteria by percentages then I won't be able to draw any conclusions.

I find it unusual that it appears that I have few if any Actinobacteria but there should be a significant percentage based on what I have been able to research.

Here a another document, Introduction to intestinal microbiota, that describes the microbiota at an introductory level.

It said...
Is there a core microbiome?
• Firmicutes (65%)
• Bacteroidetes (16%)
• Proteobacteria (9%)
• Actinobacteria (5%)


My UC has been well controlled for the past couple of years as long as I stay away from wheat and a couple of other items although Lyme's Disease this past summer kicked off some bleeding which enemas quickly addressed. I was on Asacol (2x400x3 times per day) at the time of my sample collection and had been on the Perfect Health Diet for about six months.

<mod: changed normal to average>

Post Edited (tap) : 11/20/2013 10:39:06 AM (GMT-7)

Posted 11/20/2013 5:06 PM (GMT 0)
Hindsight is 20/20. We should have all gotten together and as many of us as we could all send in samples at roughly the same time and compared notes when the results came in.
Posted 11/21/2013 2:35 AM (GMT 0)
Gary: i think that since you don't have bouts of the ITP anymore then maybe you are 'clotting more' as PathogenKiller said. Hence why your ITP is not flaring up bc something else is keeping it in balance.

So PK: how do you recommend he attacke the biofilm and the staph? (What to take supplement/med wise?)
Posted 11/21/2013 2:45 AM (GMT 0)
I have looked up the staph and it comes with 40 different species and a few subspecies, not all of them necessarily bad and we don't know yet which ones I actually have. I was wondering the same question but I also have to take into account that I am doing better right now than I have ever been and the stool sample I provided is several months in the past.
Posted 11/21/2013 12:58 PM (GMT 0)
I examined my results more closely and I determined that my breakdown is as follows:

Me______Average
46.0%___43.3% Firmicutes
48.3%___42.3% Bacteroidetes
02.5%__08.5% Proteobacteria
00.0%__02.2% Actinobacteria
00.0%___02.9% Verrucomicrobia
03.0%___00.6% Tenericutes
00.2%___<0.1% Cyanobacteria
00.0%___>0.0% Fusobacteria
00.0%___<0.1% Other

Based on the documents I referenced above, typical UC patients have significantly more Proteobacteria and Actinobacteria then an average person. So I would infer that I'm not a typical UC patient or I have a disease other than what a typical UC patient has.

I read the article written by Michael Pollan (Some of My Best Friends Are Germs) and clearly he had more detailed information than what we have received so far so I expect a more detailed breakdown of the data to arrive in the coming weeks.
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