question understanding fecal test results

[hmnr asg]

Hi there,
I had a recent fecal test done and I'm including the parts of it that seem salient. I was wondering if anyone could help me interpret these results? I dont really understand what they mean.
Background: 42 yo male, 13 years of cfs (6 of them borderline severe). Symptom onset was accompanied by GI issues (IBS, bloating etc).

Thank you!!

 

[LINE]

Do you have the rest of the report?

This is a panel of SCFAs as you know. For those unfamiliar, SCFAs are critical for a number of processes including repairing the gastrointestinal tract, other factors have been discovered such as involvement in immune response, inflammation etc.

There were some reports that came out recently to discover that butyrate levels are low in CFS/ME. Those levels are low but the other SCFAs are normal. There are some specific bacteria that are butyrate forming bacteria such as f. prausnitzii. The issue is that these butyrate producing bacteria are very sensitive to oxygen, and the oxygen is known as ROS which comes from the immune response.

Bottom line is that likely the problem is that you contracted a pathogenic organism that is stimulating the immune response which lowers levels of butyrate producing bacteria.

I made some videos on these reports that came out (warning: videos are boring and unprofessionally edited

https://youtube.com/playlist?list=PLA9aaXOpxIE3QBETBfDtz545PrnROUkBo

 

[hmnr asg]

Thank you for your response! I will start going through the videos.
The rest of the report was fairly unremarkable except for high cholesterol.
Also on top it should that there is no growth of enterococcus bacteria at all in my gut ! These samples were collected across three different days so the results should be more reliable. It seems strange that my gut is completely devoid of an entire family of important bacteria.

Ps I think this is the paper you are referring to:
https://pubmed.ncbi.nlm.nih.gov/36758522/

 

[LINE]

You are welcome, glad I can help. Yes, that is one paper (there were 2 released in same week). Those are anaerobes which means they are quite sensitive to oxygen. Likely, you have a pathogenic organism in the gut which the immune system is responding to thus creating high ROS thus reducing butyrate forming bacteria. Sorry for the redundancy.

Did you do any other testing that might suggest any pathogenic bacteria? If you have some identification of the offending bacteria (or possible protozoa), that could be helpful in finding a target antibiotic. I do have some other suggestions that could help.

 

[hmnr asg]

You are welcome, glad I can help. Yes, that is one paper (there were 2 released in same week). Those are anaerobes which means they are quite sensitive to oxygen. Likely, you have a pathogenic organism in the gut which the immune system is responding to thus creating high ROS thus reducing butyrate forming bacteria. Sorry for the redundancy.

Did you do any other testing that might suggest any pathogenic bacteria? If you have some identification of the offending bacteria (or possible protozoa), that could be helpful in finding a target antibiotic. I do have some other suggestions that could help.

Thank you once again for the response.
The analysis isnt so detailed. I have included the restults in pdf format (hopefully I have removed all my personal details). There doesnt seem to be anything else of interest aside from high cholestrol which i knew.

I think i should use a better lab for a followup to figure out whats going on.
Is there any way to fix this problem in the gut?
Thanks!

 

[Shanti1]

Hi @hmnr asg
I'll comment on the top part, "Bacteriology Culture". Although the sample is take across three days, the bacteriology culture is only taken from one tube. The 3 tubes are used for the microscopy parasitology portion of the test because you can sometimes miss parasites if only one stool sample is examined.

In the "Expected/Beneficial" portion of the test, Doctor's Data (DD) always lists the same 6 bacterial "families" (although they look like genera to me). DD will sometimes have comments at the end of the test related to these bacteria and the others in the culture, so make sure to check for them. Enterococcus is available as a probiotic if you wanted to give that a try.

The "Commensal (imbalanced)" section contains what DD calls Value Driven and Non-Value Driven bacteria. Value Driven bacteria are those that will move into the "Dysbiotic" category if their growth level reaches >2+. Non-Value Driven will remain in the "Commensal" category regardless of the growth level and are considered less problematic. You have only Non-Value Driven on your test. The last two are primarily found in the oral cavity that is likely their source on the culture. The Corynebacterium is generally not considered problematic.

The "Dysbiotic" bacteria section would contain any Value Driven bacteria with grown >2+ and DD will also use this section to report any of the following pathogenic bacteria: Aeromonas spp, Edwardsiella tarde, Plesiomonas shigelloides, Salmonella, Shigella, Vibrio cholerae, Vibrio spp, Yersinia spp. There is an intent to culture the aforementioned bacteria on every test and both anaerobic and anaerobic culture conditions are used.

Hope that helps

 

[Shanti1]

FYI- these are the "Value-Driven" bacteria that are checked for, so none of these cultured out in your sample:
Citrobacter farmeri/amalonaticus
Citrobacter farmer
Citrobacter freundii complex
Citrobacter koseri
Enterobacter cloacae complex
Klebsiella oxytoca
Klebsiella pneumoniae
Klebsiella pneumoniae/variicola
Klebsiella/Raoultella complex
Moellerella wisconsensis
Morganella morganii
Proteus mirabilis
Proteus penneri
Proteus vulgaris group
Providencia alcalifaciens
Providencia rettgeri
Providencia stuartii
Pseudomonas aeruginosa
Raoultella ornithinolytica

PCR is arguably more accurate than culture, but the advantage to culture is that, if something is found, you can do susceptibility testing for antibiotics/antimicrobials.

 

[Shanti1]

I think i should use a better lab for a followup to figure out whats going on.

Stool tests can't identify SIBO and if yours didn't come with a yeast culture, you could be missing candida as well.

I think stool testing provides a lot of great information, for me personally, they helped me identify a Candida kruseii overgrowth and some protozoa whose significance is debated, but clearing up both improved my brain fog. The fatty acid, inflammation markers, and digestive chemistries are also helpful

That said, I think there are some inherent challenges with stool tests. While there are a few bacteria that stand out as key pathogens an opportunist, for the most part, gut health isn't about a specific bacteria, but about how they behave as a community. I had an eye opening experience when a colleague and I both did GI-MAP tests (these provide a long list of microbes identified via PCR) one month apart and found that there was very little consistency in which bacteria where marked as high and low.

Scientists are beginning to look at the microbiome in terms of patterns instead of just single bacteria. Doctor's Data (no I am not affiliated with them) has a test called GI360 which looks at an abundance and diversity pattern across multiple bacterial phyla, classes, family, genus, and species levels to distinguish a dysbiotic microbiome from a normobiotic. What is nice about it is that the dysbiotic patterns have been verified in multiple clinical trials and verified for reproducibility, so even if some bacteria go up or down on repeat testing, the dysbiotic pattern remains. However, even though this test is probably the best out there for identification of dysbiosis, it still doesn't identify exactly which bacteria are the problem. You can see the levels of all the bacteria tested, but it is the pattern that is the issue.

 

[LINE]

@Shanti1 Blastocystis?

 

[Shanti1]

@LINE
Yes, Dientamoeba fragilis and Blastocystis hominis

 

[LINE]

@hmnr asg I would suggest getting some basic stool testing done - at least through your local doctor. Those labs will look at enteric (gastro) bugs which can spot some of the more common bugs that are known to inhabit the GI tract. They might also do a parasitology screening.

If those fail to identify, I know some other labs that might be able to find something. There are some treatment options I could suggest as well.

 

[Peyt]

Stool tests can't identify SIBO and if yours didn't come with a yeast culture, you could be missing candida as well.

I think stool testing provides a lot of great information, for me personally, they helped me identify a Candida kruseii overgrowth and some protozoa whose significance is debated, but clearing up both improved my brain fog. The fatty acid, inflammation markers, and digestive chemistries are also helpful

That said, I think there are some inherent challenges with stool tests. While there are a few bacteria that stand out as key pathogens an opportunist, for the most part, gut health isn't about a specific bacteria, but about how they behave as a community. I had an eye opening experience when a colleague and I both did GI-MAP tests (these provide a long list of microbes identified via PCR) one month apart and found that there was very little consistency in which bacteria where marked as high and low.

Scientists are beginning to look at the microbiome in terms of patterns instead of just single bacteria. Doctor's Data (no I am not affiliated with them) has a test called GI360 which looks at an abundance and diversity pattern across multiple bacterial phyla, classes, family, genus, and species levels to distinguish a dysbiotic microbiome from a normobiotic. What is nice about it is that the dysbiotic patterns have been verified in multiple clinical trials and verified for reproducibility, so even if some bacteria go up or down on repeat testing, the dysbiotic pattern remains. However, even though this test is probably the best out there for identification of dysbiosis, it still doesn't identify exactly which bacteria are the problem. You can see the levels of all the bacteria tested, but it is the pattern that is the issue.

@Shanti1
Hi,
May I ask what did you use to clear up the Protozoa? and which stool test detected it?
Thanks

 

[Shanti1]

Hi @Peyt ,

Candida and protozoa were first detected using DiagnosTech labs GI-02 panel in Feb 2015:

I retested for yeast in April 2015 using DiagnosTechs and it was clear on that test (although I am certain I still had it hiding out in biofilms or hyphae form). I have had multiple CSAs and GI360s through Doctor's Data since then, all clear for amoebas, and protozoa. I had a repeat positive candida at some point when I became lax with my diet/anti-candida supplements.

When I got the test results above, I was more focused on the candida than the parasites, but I went in full force. I took colloidal silver, grapefruit seed extract, oregano oil, garlic capsules, caprylic acid, berberine, wormwood/black walnut, enzymes to digest fungal hyphae, and probably other things too that I can't recall.

I believe I got rid of the protozoa rather quickly, the candida has been more of an ongoing battle. For the protozoa, I personally think the oregano oil and the grapefruit seed extract were most effective. Because these little buggers have a cyst form that is more difficult to kill, it is often suggested to pulse treatment, for example, 2 weeks treatment and 2 weeks off, for several cycles.