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Posted 11/21/2013 2:26 PM (GMT 0)
I am beginning to think more and more that I might have picked up an internal staph infection that is lining my colon while I was in the hospital getting broad spectrum antibiotics. That's when my UC started, right there in the hospital. If that is actually indeed the case maybe I could "cure" my UC by getting rid of the staph infection, although right now I am doing better than I have ever done since my UC started 3 years ago. I hate to rock the boat until I am armed with better and more detailed information.

Tap: Did you say that you had been in touch with American Gut and they said they were sending a more detailed analysis, or are you just assuming that?
Posted 11/21/2013 2:56 PM (GMT 0)

garylouisville said...
Tap: Did you say that you had been in touch with American Gut and they said they were sending a more detailed analysis, or are you just assuming that?


Here is the response that I received on Tuesday...

American Gut Staff said...
We'll be releasing more detailed taxonomy reports in the coming weeks. If you have any bioinformatics experience, you may find it interesting to explore the data themselves. Details can be found here:

http://www.microbio.me/americangut/FAQ.psp#faq8

I'd caution you against attempting to personally diagnose yourself given the inability of the scientific community to do so at this point. I strongly recommend consulting a medical professional. In addition, it is important to realize that the American Gut Project is not a medical diagnostic, and should not be used as such.

Posted 11/21/2013 3:13 PM (GMT 0)
Hey Gary: I'm still on this bacterial infection kick and not giving in lol. Anyway here is something of interest for you to read in regards to say a Staff infection:

ac.els-cdn.com/S1931312807001667/1-s2.0-S1931312807001667-main.pdf?_tid=6b59ff36-52be-11e3-bf77-00000aacb35d&acdnat=1385046535_59f75355a6c8b2f5f746ce98539f3916

In the mice they recover and their flora goes back to normal once the infection is cleared etc... anyway, whatever you want to take from it. It does suggest that "if" this were to be the case.. a staff infection or whatever, once cleared flora may just return to normal again... I tend to believe this is the situation most of us are in. Unable to clear a bacterial infection.

I have some other studies on this as well - and of course a giant library of images of adhesive bacteria in Crohn's and UC.

EDIT: I should throw in that I honestly don't think it matters the family of bacteria or the imbalance so much as if you just happen to have the wrong "bad guys" in any family build up for one reason or aniother (antibiotics, stress, hormones).. As there are pathogenic and non-pathogenic versions of all families. And the pathogenic ones all do pretty much the same thing - adhere, break down mucus, trigger/evade/regulate immune responses to benefit them. So e-coli, staff, fragilis, etc etc.. there seem to be lot's of both good and bad of all these.

Post Edited (Canada Mark) : 11/21/2013 8:20:32 AM (GMT-7)

Posted 11/21/2013 4:36 PM (GMT 0)
Yeah, staph comes in a but load of species, but when that's all ya got it isn't good..lol

One of them of more were resistant to those abx you took and were able to get seeded.

ConquerUC
Enzymes and natural or other abx AND an antifungal. Because the gut is injured and when you unseat the staph it will try to take over. Then you move to the rest of the 4Rs.

Gary, your body might be fighting it semi successfully. That's why you are better but not well.
Posted 11/22/2013 12:29 AM (GMT 0)
Wow, phylum is a broad brush.. I wonder what is going on at the genera and species level. But gary, or anyone else, where are you getting this work done?
Posted 11/22/2013 12:32 AM (GMT 0)
I would also assume that what someone is eating, particularly heavily eating probiotic foods (or not), that the results would differ. And I assume this is all the microbiome project? Maybe even under different names.

gary or anyone, it would be interesting to get 2 samples done at the same time to see if they find the same results. I figure if you got the test done weeks later and got different results, you wouldn't know if it was because your flora changed or not.

Post Edited (freddyj) : 11/21/2013 5:35:11 PM (GMT-7)

Posted 11/22/2013 2:56 PM (GMT 0)
Great topic.

www.bouldernaturalhealth.com/comprehensive-digestive-stool-analysis/

They are just a few miles west of me in Boulder. I just had the colonoscopy so I think next year I will make it a goal to get in there too.
Posted 11/22/2013 6:33 PM (GMT 0)
Chris Kresser hosted Jeff Leach, one of the founders of the American Gut Project, on his podcast a couple of days ago. I found it interesting.

RHR: You Are What Your Bacteria Eat: The Importance of Feeding Your Microbiome – With Jeff Leach

I think it would be helpful if more of us UCers donated our poo.
Posted 11/22/2013 7:15 PM (GMT 0)
trust me tap, I've done PLENTY of donating ;-)
Posted 11/22/2013 8:50 PM (GMT 0)
Thanks soystud I needed a good chuckle.

I thought the following quote from the interview provided some useful information as well as being entertaining...

Jeff Leach said...
I tell everybody if you’re not having two to three bowel movements a day, then you need to go back and start over, and one of them should be a whopper. If you’re not having that kind of bowel activity, then you’re not fermenting enough – again, assuming you don’t have other issues – and so you need to increase the diversity and quantity of fiber. Why that’s important is when those bacteria ferment that dietary fiber – and again, get it from a lot of sources – it changes the pH of your colon. It makes it more acidic. A lot of opportunistic pathogens are pH sensitive, and so typically as those Ruminococcus and those Blautia and those Bifidobacterium and all those guys go up, you often see the other ones go down. It’s not always a one-for-one, but keeping your colon acidic through fermentation, frequent bowel habit, then all of that stuff leads to improved barrier function with regards to, you know, some people generically call it a leaky gut.


I am pretty sure that you will know it when the bacteria start getting replaced because for me I experienced a Herxheimer reaction with diarrhea for a couple of days. I also experienced this when starting fermented foods (fermented tea).
Posted 11/22/2013 9:46 PM (GMT 0)
mmmmmmm, Whopper :-)


geez, all this biodome, microzone, and florada stuff makes my head a spinning ! isn't there just a pill we can take to get better - that would be so mucher simple ;-)

the whole sinus relationship does have me curious - I've had sinus issues for years. long before uc - and also the drugs (aunties) to deal with them - definitely worth a look see at the staph thing - time to re-read some old posts -

just when I was feeling really GOOD, now I have to figure out if I can feel better - dang !

gee, thanks you guys ;-)
Posted 11/23/2013 1:17 PM (GMT 0)
Old Mike posted a study yesterday that may be useful when reviewing the American Gut Project results.

A Modular Organization of the Human Intestinal Mucosal Microbiota and Its Association with Inflammatory Bowel Disease

It said...
The IBD-associated dysbiosis of mucosal microbiota has been delineated in detail in several investigations [9,32,35]. Specifically, IBD patients have fewer Firmicutes and a concomitant increase in Proteobacteria, validated in several independent cohorts [36,37]. To determine whether previously reported alterations were also observed in our dataset, we compared the relative abundances of each phylum between disease states using analysis of variance (ANOVA). In contrast to controls, IBD patients harbored relatively more abundant Actinobacteria (FDR corrected P = 0.006 for UC, < 0.0001 for CD), accompanied with the depletion of Firmicutes (FDR corrected P = 0.056 for UC, 0.25 for CD) in these subjects (Figure 2A, Dataset S1 and S2). The increases of Proteobacteria (FDR corrected P = 0.254 for UC, 0.143 for CD) and Tenericutes (FDR corrected P = 0.115 for UC, 0.157 for CD) were also observed in IBD patients, although not statistically significant. Taken together, microbial composition represented by this study cohort, and captured by lavage sampling, reflected the changes of relative abundances of enteric microbiota in IBD subjects at phylum level observed in other datasets and sampling methods.

The reduction in bacterial diversity in IBD patients is a consistent finding across studies [32,38,39], although it is still unknown whether this alteration is causative or a secondary effect of IBD. Compared with controls, the phylogenetic diversities of UC and CD subjects at 97% OTU level were significantly lower (Figure 2B), and the difference was more evident in CD (t-test, P = 0.0003) than that in UC subjects (t-test, P = 0.0056) at the depth of 3,000 reads per sample. This data indicates that the lower microbial diversity previously observed in patients with active IBD also persists in clinically quiescent phases of disease.

Posted 11/23/2013 4:09 PM (GMT 0)
I have read in other places that UC'rs are often low on Firmicutes. I wonder how I personally fit into all this considering my Firmicutes are almost 100%.
Posted 1/16/2014 2:31 AM (GMT 0)
The American Gut folks released the detailed breakdown of our samples today.

I have not reviewed each bacteria but I find it interesting that I have no Actinobacteria or Verrucomicrobia.
Posted 1/16/2014 2:05 PM (GMT 0)
Tap: I received an email from them but after signing in to view my results, every time I click on the link with my results it repeatedly takes me back to the login page all over again.
Posted 1/16/2014 5:38 PM (GMT 0)
Anyone willing to let me see their report? I haven't seen one from this project yet.
Posted 1/16/2014 6:01 PM (GMT 0)

PathogenKiller said...
Anyone willing to let me see their report? I haven't seen one from this project yet.


I included a reference to mine in my previous post. I colored the rows to match up with the general results that they had provided before.
Posted 1/16/2014 6:14 PM (GMT 0)
sorry didnt see the blue text..

is there any breakdown on ecoli species?
Posted 1/16/2014 8:04 PM (GMT 0)
Tap: What was your UC condition at the time of the sample? Also, were you taking any probiotics at the time? I just noticed that the VSL I take is loaded with Firmicutes and could have had something to do with my sample being almost 100% Firmicutes.
Posted 1/16/2014 8:21 PM (GMT 0)
Interesting...I recall reading an article a few years back when they looked at intestinal microbiomes and saw a pattern in which there were distinct groups, and those with IBD clearly had a different gut microbiome. This: http://www.ncbi.nlm.nih.gov/pubmed/20839241 (OM probably posted this in 2011!) states that it is also genetic- and in some cases just having these genes changes the microbiome, though surely there are other influences and factors. Is Michael Pollan "the gold standard" or why is he used for comparative purposes? I am STILL waiting for my uBiome results. Would be interesting to see before and after FT, both a "successful" and "unsuccessful" FT. Thank you for sharing your data with the group...I plan to share mine as well
Posted 1/16/2014 8:53 PM (GMT 0)

garylouisville said...
Tap: What was your UC condition at the time of the sample? Also, were you taking any probiotics at the time? I just noticed that the VSL I take is loaded with Firmicutes and could have had something to do with my sample being almost 100% Firmicutes.

I did my sample on March 26th, 2013. With respect to my UC, I was having 1 to 2 stools a day and it looks like I had mostly recovered from the slice of pizza I had two and a half weeks earlier while on vacation. Six days prior to the sample I had blood in my stool.

I was having 1 cup of yogurt made from raw goat milk (I was using VSL3 for making it), 1.5 cups of kefir made from raw goat milk, and 1 cup of homemade Kombucha each day. I was also eating 1 cup of homemade sauerkraut once a week. I was not consuming any commercial probiotics.
Posted 1/17/2014 6:50 PM (GMT 0)
It would be interesting to know if those taking probiotics have any of those strains in their sample.

I was consuming yogurt that I made with VSL3 when I was sampled but none of my bacteria match up with those in the VSL3.
Posted 1/18/2014 1:38 PM (GMT 0)
Tap: That's a great comment. I have actually already started the process of looking into this very question. Since taking VSL and Prescript Assist I have been doing much better, but I wonder what that means if it turns out that none of these strains are in my sample? I noticed your sample contained zero Actinobacteria. I wonder if your immune system is attacking that and giving you your UC? By the way, American Gut finally got back to me with my results since I was having trouble accessing them. Here they are for anyone interested (I seem to have an intestinal Staph infection, going to look into this further):

#taxon relative_abundance
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus 0.390000
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Clostridiaceae; g__ 0.306000
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__ 0.048000
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__[Ruminococcus] 0.033000
k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Enterococcaceae; g__Enterococcus 0.032000
k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Streptococcaceae; g__Streptococcus 0.025000
k__Bacteria; p__Firmicutes; c__Erysipelotrichi; o__Erysipelotrichales; f__Erysipelotrichaceae; g__[Eubacterium] 0.022000
k__Bacteria; p__Firmicutes; c__Erysipelotrichi; o__Erysipelotrichales; f__Erysipelotrichaceae; g__ 0.022000
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Ruminococcus 0.020000
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Coprococcus 0.016000
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Planococcaceae; g__ 0.015000
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Dorea 0.013000
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Veillonellaceae; g__Veillonella 0.008000
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__ 0.007000
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Corynebacteriaceae; g__Corynebacterium 0.007000
k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Enterococcaceae; g__ 0.005000
k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__; g__ 0.004000
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__ 0.002000
k__Bacteria; p__Firmicutes; c__Erysipelotrichi; o__Erysipelotrichales; f__Erysipelotrichaceae; g__Coprobacillus 0.002000
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Tissierellaceae]; g__Finegoldia 0.002000
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Tissierellaceae]; g__Anaerococcus 0.002000
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__ 0.002000
k__Bacteria; p__Firmicutes; c__Bacilli; o__Gemellales; f__; g__ 0.002000
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium 0.002000
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Pseudomonadaceae; g__Pseudomonas 0.001000
k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhizobiales; f__Brucellaceae; g__Ochrobactrum 0.001000
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Tissierellaceae]; g__Peptoniphilus 0.001000
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Mogibacteriaceae]; g__ 0.001000
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira 0.001000
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Faecalibacterium 0.001000
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Peptostreptococcaceae; g__ 0.001000
k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Carnobacteriaceae; g__Granulicatella 0.001000
k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Carnobacteriaceae; g__ 0.001000
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Bacillaceae; g__Bacillus 0.001000
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__; g__ 0.001000
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__Prevotella 0.001000
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides 0.001000
Posted 1/18/2014 4:17 PM (GMT 0)
I ordered up some Prescript Assist a couple of days ago to see if I could get some Actinobacteria to populate my gut.
Posted 1/18/2014 6:31 PM (GMT 0)
Can't find any conclusive proof that anything in the probiotics I take was located in my sample results. There was a small handful that were questionable. Much of this is hard to decipher and say for sure 100%. This avenue may be a dead end. It might be more helpful to just concentrate on what is in my sample that is in overabundance and try figuring out what should have been in the sample but was not. There has been much research regarding dysbiosis in IBD patients but zero patterns. Everyone seems to have a different dysbiosis. I'm starting to believe that our problem is our immune systems have been tricked into killing off one type of our bacteria and this is what causes the inflammation and UC symptoms. Since we are probably in constant contact with this one bacteria, our immune system is always working at killing it off. If most of us had our guts analyzed it would probably show no signs of that one type of bacteria that causing our problems.
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