Tag Archives: Microbial Ecology Profile

Page Two

wpid-IMAG0513.jpgI had the 2100 test done to help evaluate my chronic constipation.  Neither myself nor my general surgeon really knew what in the heck we were looking at when we got the results.  So I’ve been going through each section to try to figure out what the test has to offer to help me manage my chronic constipation and just brushing up on my general knowledge.

Currently, I have been reading up on the pathogenic bacteria Metametrix reports.  Other than it’s perhaps too far-reaching of a test panel, nothing absurd jumps out at me here.  Did I need to know my H. pylori status or C. diff status?  No.  I don’t have symptoms consistent with those.  So, except for the idea that the test results offer information beyond what is necessary and which may be exceptionally confusing with regard to whether to treat or not in an asymptomatic patient, I don’t have much to say.

This is not meant to be a conclusive summary or viewpoint.  It is not meant to be a means of medical advice.  These are just some things I’ve looked up and found and thought about that I am sharing.  Consider it fodder for discussion, that’s all.


Helpful information to know:

  • GI Effects Profile= 2100
  • Microbial Ecology Profile= 2105= Only the second page of the GI Effects Profile
  • The “second page” reports pathogenic bacteria, yeast/fungi, parasites, adiposity index, and drug resistance genes.

Where to See More on the 2100/2105

Below are two Metametrix links to videos containing descriptions/case studies of the 2100 and/or the 2105 which will allow you to see more test results and how somebody on their staff interpreted them.  Sound starts as soon as you open the link.  There are outlines provided so you may speed through to specific slides and topics if you wish.

  • IBS and GI Effects:  A video with a straightforward, simple case of irritable bowel syndrome and how the GI Effects Profile was used to address the patient’s irritable bowel syndrome.
  • GI Effects test description with two case studies:   Gives an overall summary of what the test is, what it tests for, and two case studies.  Case study one is regarding gluten removal.  Case two is more of an overhaul approach; please note on the treatment slide that they forgot to put that she was also taking bifidobacter and lactobacillus probiotics, which also contributed greatly to her probiotic flora levels increasing.

SCD Lifestyles–these guys, their passion is infectious–gives an overview of the second page (also known as the Microbial Ecology) and some examples.

Metametrix selected four pathogenic bacteria to report:  Helicobacter pylori, E. coli 0157:H7, Clostridium difficile, and Campylobacter sp.

I think it is helpful to remember that even some of these pathogenic bacteria can exist normally in normal people.  They are not always pathogenic, although at times they (or particular strains of them) can be horribly pathogenic.  Escherichia coli 0127:H7 and Campylobacter jejuni you can pretty much count on being invaders intent on destruction, and they usually cause acute, more aggressive type symptoms, to let you know that.  H. pylori and C. diff’s stories are not so clear.

Metametrix uses PCR to detect these bacteria, offering high sensitivity.  No dispute about how the test is peformed, collected, validity of what they’re testing for, or if the results are misleading.  Wandering thoughts include:

  • Since H. pylori and C. diff can be present in asymptomatic carriers, and the medical field doesn’t know what to do with that information at present, will positive tests on the 2100/2105 lead to over treatment?   Over treatment can lead to encouragement of antibiotic resistance and also a huge shift in a person’s bacterial flora, perhaps predisposing the patient to other issues.
  • Should the 2100/2105 be broken apart into smaller pieces rather than offered as this huge, sweeping “shot-gun”, “let’s cover all of our bases” test?  Metametrix does broach that topic here, Which GI Test is Best?  The approach the writer advocates goes against my training as a medical doctor, which tells me to look at the patient, order tests based on my assessment, and then pursue further testing if needed based on those tests and how the patient is doing.
  • How often are Campylobacter sp. and E. coli 0157:H7 picked up on using this test?  Unlike H. pylori and C. diff, Campylobacter and E. coli 0157:H7 don’t usually transpire into indolent, low symptom disease states.  They’re usually, like, “BAM”–diarrhea, stomach cramps, and an apparent acute illness.  Just because you can test for something, does it make sense to?  I can’t see a physician ordering the GI Profile or Microbial Ecology for an acute illness, as the turn-around time isn’t rapid.  And you don’t need to know about yeast, fungi, and H. pylori when someone shows up with fevers, diarrhea, and stomach cramps.  It seems like these could have been omitted, maybe cutting costs and not changing the usefulness of the test.  But since I don’t know if it would cut cost or change resource allotment, I can’t really say much.  Sometimes adding on an element to a test does not actually require any more work, time, or money.  This may be an instance.

Helicobacter pylori (H. pylori):  H. pylori is a known gastric colonizer.  You, and about 50% of the world’s adults, are not alone if you have H. pylori in your gut.  So what’s the fuss?  Some people will live with H. pylori and be asymptomatic all of their lives, but other unlucky people may get ulcers or cancers associated with H. pylori.  A friend told me just yesterday that she’d been recently treated for H. pylori by a chiropractor.  Treatment decision was based on a stool test result and used antibiotics and proton pump inhibitors.  Her symptoms had not been GI (gastrointestinal) related, and she was questioning why he chose to treat based on what she was now reading.  And therein lies a problem.

What do you do with a positive test in an asymptomatic patient?

Gnawing abdominal pain and nausea, it’s a no-brainer.  No GI symptoms, and my friend wouldn’t even have been tested for H. pylori by most medical doctors.  But what do you do now as a practitioner with a GI asymptomatic patient with a positive H. pylori on a “shotgun” test ordered for something like fibromyalgia or fatigue?

  • Why treat an asymptomatic, positive test?  “Treatment of asymptomatic patients is somewhat controversial given the high prevalence of H. pylori–associated superficial gastritis and the relatively low incidence of clinical sequelae (ie, peptic ulcer disease). However, H. pylori is a class J carcinogen; eradication removes the cancer risk.”  (1)  H. pylori increases the risk of ulcers, gastric cancer and a certain lymphoid cancer. (2)
  • Why not treat any positive test?  Aren’t ulcers and cancer bad?  Of course they are!  However, there are always two sides to every story.  In Journal of Clinical Investigation’s article “Coadaption of Helicobacter pylori and humans:  ancient history, modern implications” (scroll down to “Absence of H. pylori as a risk factor for disease”), the evidence that H. pylori belongs in our gut for particular reasons is discussed:  “In historical terms, H. pylori is part of the normal microbiota of humans.”  The authors assert that reflux esophagitis and esophageal cancer are likely outcomes of H. pylori absence and also speculate obesity and allergic disorders may go hand in hand, as well.  In addition, the article cites many sources which are available for reading online which may interest anyone with a positive H. pylori test.

From Metametrix’s own blog comes  “What’s the H. pylori Story?”:

“Most clinicians carefully weigh the patient’s clinical presentation to determine if H. pylori needs to be treated. Treatment is only warranted if lab data, symptoms, and clinical history are consistent with H. pylori infection. Adjunctive or repeat testing should be ordered to verify the presence of H. pylori.”


“Most people infected with H. pylori are asymptomatic and never develop a complication.  Some experts have suggested that H. pylori may be a normal, commensal bacterium and should not be treated in asymptomatic individuals. In fact, non-ulcer dyspepsia and GERD have not been shown to improve with H. pylori eradication.  Patients who were seropositive for H. pylori had markedly lower risk of developing Barrett’s esophagus, suggesting that H. pylori may even have a protective effect against certain illnesses.”

E. coli 0157:H7:  E.coli 0157:H7 does not belong in your gastrointestinal tract.  It is a type of Escherichia coli that makes a special toxin (called Shiga toxin or Vero toxin) that attaches to and damages the lining of the small intestine, allowing toxin access to the blood.  This can be a terrible player.  Severe bloody diarrhea, nausea, vomiting, abdominal cramps, hemolytic anemia, kidney failure, and death are potential outcomes.  Not a good player, especially for young children and older adults.  On the flip side, a person may develop only mild diarrhea and cramping.

The source of E. coli 0157:H7 is often cattle, who can be asymptomatic carriers of it in their guts (3).  Thus, undercooked ground beef can be a source of outbreak if contamination occurs during slaughtering, but other sources include raw milk, unpasteurized juice, contact with infected animals, infected drinking water, or contaminated recreational water (lakes, swimming pools) (2, 3, 4).

Although knowing if you have this bacteria would be very important, in fact it’s a “reportable” illness to the CDC, I find it an interesting choice for inclusion on this panel.  Usually the illness is acute (lasting 5-7 days from onset of symptoms), and this 2100/2105 panel seems more geared for longer lasting, more indolent type of issues.  Doctors and hospitals wouldn’t be using the Metametrix test for E. coli 0157:H7 because they need more rapid turn-around time, and they don’t need all other information provided to evaluate bloody diarrhea (for example, yeast and H. pylori).  So, for whatever reason, they chose to put this bug on there.  Don’t know why.  I’d love to hear why or if somebody had this come back positive.  Seems like a waste.  But maybe I’m missing something.

Clostridium dificile:  C diff. has toxin producing strains and non-toxin producing strains. It’s the C. difficile that makes a toxin, toxigenic C. diff, that is the problematic strain here.  “It has been known for >25 years that nontoxigenic C. difficile strains occur naturally and, when given to hamsters during or after antibiotic treatment, are able to harmlessly colonize the gut and prevent subsequent infection challenge with toxigenic strains of C. difficile. It has also been shown in patients that natural asymptomatic colonization with C. difficile (toxigenic or nontoxigenic strains) is associated with decreased risk of CDI [C. diff infection].” (5)

Up to Date has some C. diff information if you’re interested (symptoms, diagnosis, treatment, and special considerations such as in inflammatory bowel disease):

PCR detection of C. diff with the toxigenic gene seems as good, if not better, than most of the prior tests for C. diff diagnosis. (6)  I left a question on Metametrix’s blog about their C. diff test, and it was promptly responded to.  I questioned, “Does Metametrix’s PCR for C. diff test for the toxigenic genes or just C. diff in general?”

They responded, “Our C diff detection method looks for the Toxin A gene in C diff. If that is present in sufficient numbers for a positive it will be reported as positive. In the next version of the GIfx test (and the 2105) C diff findings will reflect the Toxin B gene as well, but not currently.”  There was a bit of controversy in medicine about whether toxin A or toxin B was the problem, but the good news is Metametrix will soon test for both.  And based on this article, it should: The role of toxin A and toxin B in Clostridium difficile infection.

Dr. Peterson [MD, director of microbiology and infectious diseases research, Department of Pathology and Laboratory Medicine, Evanston (Ill.) Hospital, and associate epidemiologist, NorthShore University HealthSystem] has been emphatic about testing only patients who meet the clinical criteria for C. difficile illness, Dr. Crist [PhD, technical director/ clinical microbiologist, Department of Laboratory Services, Division of Clinical Microbiology, York (Pa.) Hospital] points out. “At this point our data support that premise,” Dr. Crist says of the chart review for one-fourth of the patients in his study. “In that subset there were no positive PCR results in patients who did not fulfill clinical criteria. All PCR-positive patients were clinically ill, not just colonized, even if they were culture negative.” (6)

  • Even if you have diarrhea, it’s possible that you’re a carrier and your diarrhea is caused by something else.  Dr. Timothy O’Leary in Sensitivity, Specificity Higher With PCR Than Conventional EIA in C Difficile-Associated Diarrhea states, “It’s [PCR] not necessarily the perfect assay because, while it is extremely sensitive, it’s possible, for example, that an individual may harbor this organism and not have the disease. You will detect that they are a carrier, which is important knowledge, but it’s not actually diagnosing the cause of their diarrhea. So, as with all laboratory tests, this has to be put into context.”  (7)

An aside–Interesting treatment for C. diff:  http://ir.viropharma.com/releasedetail.cfm?ReleaseID=758059

Campylobacter sp. Some strains from Campylobacter sp. can be part of the normal flora; however, some species/strains of species are associated with disease.  This seems pretty cut and dry.  If you have had symptoms of new acute onset diarrhea for a while and you’re testing positive, you’ve likely found a contributing culprit.  If you’re asymptomatic and positive, what do you do, since it has been found to be present in our flora?  The links below talk about some species of campylobacter.

I’m a bit curious as to why, if campylobacter and E. coli 0157:H7 were included, why bacteria like Salmonella and Shigella were not also included.

That’s it.  Will start reading about yeasts, which will be completely overwhelming.  Yeasts?  Sure, candida UTIs, candida pneumonia, thrush, etc, but not an overwhelming “candidiasis” in an immunocompetent patient.

1. http://www.merckmanuals.com/professional/gastrointestinal_disorders/gastritis_and_peptic_ulcer_disease/gastritis.html

2.  http://en.wikipedia.org/wiki/Escherichia_coli_O157:H7

3.  http://www.medicinenet.com/e_coli__0157h7/page3.htm

4.  http://legacy.jyi.org/volumes/volume6/issue5/features/hu.html

5.  http://cid.oxfordjournals.org/content/51/11/1306.full

6.  http://www.cap.org/apps/cap.portal?_nfpb=true&cntvwrPtlt_actionOverride=%2Fportlets%2FcontentViewer%2Fshow&cntvwrPtlt%7BactionForm.contentReference%7D=cap_today%2F0510%2F0510a_smart_choice.html&_pageLabel=cntvwr

7.  http://www.medscape.com/viewarticle/713134

Muddling Through the First Page of Metametrix GI Effects Profile

Today’s post is only about the Complete GI Effects Profile (2100), not Metametrix lab tests in general, and covers only the first page of the microorganism section of the test.  The Complete GI Effects Profile (2100) includes test numbers 2105, 2110, 2115, 2120.  The Microbial Ecology Profile is test number 2105 all by itself.  I may use the names Complete GI Effects Profile, 2100, GI Profile, GI Function Profile, or any mix and match of these interchangeably.  Sorry.  Please realize every post I write may be interrupted about every 3-5 minutes by little creatures just  a bit larger than the microbes I am about to discuss.

Online self-help/help-each-other-forums are really convenient, but sometimes the information is misleading and flat-out wrong.  Other times, it’s dead-on.  Sorting through the spectrum of advice is exceptionally challenging, especially if you don’t know basic microbiology, physiology, and chemistry.  Mainstream medical doctors and alternative health practitioners often seem at odds with each other, offering drastically different opinions on many issues.  As a medical doctor simply trying to address my chronic constipation issue, I have had to rethink a lot of what I learned and seek answers for myself since no answers were forthcoming from my own personal physicians.  I see both sides of the story and struggle within myself to come to terms with what I have been taught and what I am learning.  I hope I refuse to be swayed by propaganda and bad science but remain open to potentially beneficial information and strategies.  I am grateful for this time in my life to stay home with the kids, teach them school, and yet have time to reinforce a huge deficit in my medical education knowledge base.  Lately, I’ve been reading up, trying to grasp the utility of the GI Function Profile from Metametrix.

Metametrix appears to offer some dubious test options, but is the GI Function Profile 2100 one of them?  Because Metametrix offers other questionable alternative tests should the GI Function Profile be ignored?  Because the lab seems to be utilized by “alternative” health practitioners rather than medical doctors should patients be chastised and belittled for succumbing to asking for the test?  Does the test have anything to offer, or is it another moneymaking scam?  Well, with my constipation at its worst, and my doctors just saying take more Miralax, I submitted to my curiosity to “peek” into my microbial flora when it was recommended to me by someone (namely, Steve and Jordan of SCD Lifestyle, who I now realize were probably only recommending the Microbial Ecology Profile–the 2105–sure would have saved me a lot of time had I only ordered that section instead of the whole doggone thing).


We learned nothing about this particular test in medical school or residency, although there may be exceptions out there.  I laugh inside thinking of my general surgeon saying, “Metawhat?” when I asked him to order the test for me.  He ordered it, but what’s a mainstream medical doctor thinking when a patient he/she has been unable to help comes in asking for some alternative test he/she has never heard of?  Maybe things like:

  • Why do I have to “sign up” to order this test?  I don’t sign up for any other test I order, and I don’t have time now.  (A doctor has to “sign-up” to be a Metametrix test provider.)
  • What does it test for?  Probiotic flora?  Huh?
  • How is it better than my usual tests?  What’s wrong with my stool cultures?  What’s wrong with my “stool for ova and parasites”?
  • Why haven’t I heard of it?
  • Is it a “quack” test?
  • Is the testing mechanism reliable?
  • How do I interpret it? (I called to ask about the reference ranges, and I was told I had to schedule a “clinical consult” to have questions answered.)
  • What do the results imply?  Anything?
  • Should I treat something based on the test results?
  • How would I even develop a treatment strategy to address some of these things?  I don’t know what the levels of probiotics should be.  Does anyone?
  • I REALLY DO NOT HAVE TIME FOR THIS…Let me shoo this patient out the door and maybe they’ll go somewhere else next time.  Take their crazy requests elsewhere.

Metametrix GI Profile 2100 Microbiota Testing

The GI Profile is kind of a “shot-gun” test, meaning it tests for a lot of things at once.  I’m going to break it down into several posts over time by test section.  Please keep in mind this is all my opinion.  I’m not an expert on nutrition, GI issues, or actually anything for that matter.  I have no bias for or against the test.  I’m not treating you. I don’t want to treat you.  I’m simply reporting what I’ve gone through, what I’ve read, and what thoughts have passed through my head.  Please find a doctor who can help treat you.  Also, don’t blast me if I don’t get things quite right.  Educate me so I can “listen” and learn.

The first section of the 2100 GI Profile provides fecal analysis of microorganisms in your GI tract:
Predominant Bacteria (obligate anaerobes, facultative anaerobes, and obligate aerobes)–Bacteria that should be there.
Opportunistic Bacteria–Bacteria that move in when conditions are right but are not a typical house members.  Although not really pathological, they do not positively contribute to the flora, GI health, or your health.
Also tested for in the microorganism category, but to be talked about in following posts, are:
Pathogenic Bacteria–Bacteria that come in and cause disease in the right amounts and conditions.
Yeast/Fungi–Some yeast/fungus are absolutely normal and beneficial.
Parasites–I was taught that we in the United States don’t usually have problems related to parasites.  If we do, we can test for them and treat them with good success.  There seems to be a big disagreement between thoughts on parasites between mainstream medicine and alternative medicine.  Same holds true for candida/yeast/fungus/protozoa.  Sifting information and gathering my opinion on this ought to take quite a bit of forever.

The Advantage of Metametrix GI Profile 2100 Over Traditional Stool Tests for Bacteria

  • No transport or growth issues:  Upon placing the stool specimen in the Metametrix vial, the bacteria are killed by the fixative to provide a “picture in time.”  They don’t need to be alive or cultured to be found; their DNA is what’s searched for.  In traditional testing, the stool is placed in/on different vials/cultures with different mediums, hoping to grow the bacteria in an environment that MAY suit them so they’ll multiply to the point they can be identified.  Many bacteria are fussy and don’t grow well at all in the lab.  If they die in transport or while being cultured, you may get a false negative.  For Metametrix, it will not matter because the bacteria do not need cultured to be identified; only their DNA needs to be present. (1)
  • Sensitivity:  DNA probing with PCR analysis, which is used by Metametrix, allows detection of just a few genome copies in the stool, making it very sensitive.  If that piece of bacterial genome is in the mix, it will usually be found.  False negatives are minimized and better quantification of the “picture in time” is allowed.  False negatives, although rare, can happen, particularly if microorganism load is small or if there is bacterial polymorphism not allowing the probe to identify the bacteria.
  • Specificity:  DNA probing is used to identify the bacteria, and as you can imagine, this is very specific and shouldn’t give false positives of what’s not there. (1) However, false postives do occur.

My Test Results


As I look at my results, I think, “Well it’s better than I thought.”  I’m inside the 80% reference range (more below) on all Predominant Bacteria, albeit a little lower on some and higher on others.  Certainly nothing I’m in a panic about.  No lab test is an absolute, and this bacterial profile is no exception.  For example, a potassium of 6.7 in some patients has me barking orders down the hall and in other patients sitting calmly in my chair fielding pages.  A hemoglobin of 4.2 in one woman simply makes me smile in wonder, while in another patient I’m demanding to know why the blood wasn’t transfusing five minutes before they even ran the hemoglobin test in the lab.  These bacterial profiles cannot be looked at as absolutes, but more as a relative issue. 

Using both evaluation of presumed 95% range and 80% reference interval, I kind of shuffled my results along these lines:   good, okay, and could be higher or lower.  Certainly, the more of these tests a practitioner saw, the more comfortable judgement with “where most people fall”– but I’ve only seen mine and the Metametrix instructional ones–so I’m winging it.

One more thought to keep in mind:  When looking at this section, remember the words “number and type.”  Is the number good, bad, or indifferent?  Is the type of bacteria good, bad, or indifferent?  When you put it together, is the type of bacteria at that number good, bad, or indifferent?  Do we need to know a more specific type to judge good, bad, or indifference (for example, the types of Mycoplasma or the types of Clostridia)?  Type, number, and patient symptoms.  How do they fit together?  Do they fit together?

Predominant Bacteria

  • Good.  Bifidobacter and Bacteroides are “supposed to be” the bulk of the bacteria, and I’m close on that.  Should Bifidobacter be higher?  I don’t know.  Maybe.  I’m thinking probably not.  It has good, strong numbers, and it’s well within the 80% reference range (more below).  Maybe I’m just getting old. (Link to article about decreasing Bifidobacter in elderly, please note that I twisted the results to amuse myself.) Citations and supplemental reading:  Bacteroides article.  Bifidobacteria article.
  • Could be lower.  Mycoplasma is relatively high.  Well, this stumped me.  I know I had Mycoplasma pneumonia (an atypical pneumonia called “walking pneumonia” by lay people) in high school, but I fully recovered from that!  However, Mycoplasma is a NORMAL colonizer of the GI tract, a PREDOMINANT BACTERIA as Metametrix calls it.  It has also been said to be associated with rheumatoid arthritis, chronic fatigue syndrome, and Gulf War Syndrome when found in the blood. Well, I don’t have symptoms of these particular disorders and the Mycoplasma is in my stool, not my blood.  I found nothing that related the levels of Mycoplasma in stool to these conditions.  I wonder why Metametrix chose to report Mycoplasma as one of the predominant bacteria.  If you read their online test explanation brochure , it has a one-liner about Mycoplasma in relation to chronic fatigue syndrome.  There are other Predominant Bacteria Metametrix could have selected, did they cherry-pick?
    (Citation and supplemental reading:  Mycoplasma and Chronic Fatigue Syndrome and Abscence of Mycoplasma species DNA in chronic fatigue syndrome)  Bottom-line:  At this point I see no connection between Mycoplasma in my gut and in my blood.  I have no known consistent issues connected to Mycoplasma symptoms at this time.  If I did, I certainly wouldn’t be looking for the Mycoplasma in my stool.  I’d be seeking information on how to get accurate test results on my blood.  Reassuringly, Metametrix doesn’t offer Mycoplasma blood tests.  So no kick-back involved.  That’s great.  I’m just going to keep up the intensive nutrition intervention and allow my body to keep Mycoplasma where it wants it for now.
  • Good.  Lactobacillus looks good to me.  My probiotic of choice has been Lactobacillus, and whether my Lactobacillus “would live” at this nice level or not on its own, I have no idea.  But the range looks nice, and I’m feeling good with my Lactobacillus probiotic so I’ll keep on keeping on.
  • Okay.  Clostridia level seems relatively fine.  Perhaps a touch high, but I really think good nutrition and probiotics from my food and from my simple supplement will keep Clostridia in check (if it even needs to be in check).  Clostridia IS a NORMAL player, but I suppose if mine were much higher, I might go chasing recommendations to drive the value down.  However, disease seems to be due to certain known types of Clostridia (example, Clostridium difficile), but I didn’t see that disease was related to certain “levels” of Clostridia.   So I’d probably be chasing nothing.  Looking at the Predominant Bacteria doesn’t tell you “types.”  Metametrix does test for some specific bacterial types in the Pathological Bacteria section.  I read about the Clostridia and autism connection, but it is much too complex for this post.  Again, that seems more based on “types” not organism levels.
  • Okay.  Prevotella and Fusobacterium are present.  Good.  Not overgrown.  Good.  I found a couple of articles on these two players:   Click here for article on Prevotella dominance.  Here for  Fusobacterium in inflammatory bowel disease.
  • Good enough.  Streptomyces I didn’t find much on.  Mine looks good to me.
  • Good enough.  Escherichia.  I don’t have much to say on it either.  It’s a normal player, has a good role, and mine is in the ballpark.  If it gets in the wrong place, it causes problems.  Certain strains can cause problems.  But as a whole, my Escherichia looks fine to me.

Opportunistic Bacteria

Although my test results only show the results for just one microorganism, Metametrix states they test for many more (see under “clinician information”).  In the interest of space, only abnormals are reported.  Vibrio showed up as my opportunistic bacteria.  Vibrio?  For real?  As in Vibrio cholera?  Umm.  No.  Don’t have no symptoms of cholera (improper English for stress).  What is the significance of vibrio? I was about to toss it out as “normally abnormal” until I realized the exponential notation. The 95% reference range is less than 100,000 colony forming units per gram and mine is at 100,000,000 colony forming units per gram. Do I have some sort of indolent vibrio infection from all the seafood and sushi we eat? Is that even possible?  I couldn’t find much on it on the internet–except vibrio cholera—and I just don’t think that’s possible given my constipation history.  The best I’ll do is keep on my nutritional intervention and take note of any change in symptoms.  Next time I talk to an infectious disease friend (let me re-write that–The next time I talk to a friend who is an infectious disease specialist…), I’ll run it by him.  But I just can’t get too excited about the result.  Only curious.

Click article quotation below for more on vibrio:

Other vibrios may also be clinically significant in humans, and some are known to cause diseases in domestic animals. Nonpathogenic vibrios are widely distributed in the environment, particularly in estuarine waters and seafoods. For this reason, isolation of a vibrio from a patient with diarrheal disease does not necessarily indicate an etiologic relationship.

My Questions/Thoughts

I called Metametrix to ask my specific questions today.  I ran into roadblocks.  Metametrix said 1) I’d need to schedule a clinical consult and 2)  I couldn’t do that without an authorization release from the ordering physician (who in this particular case was ARUP Laboratories, although my real ordering physician is my own personal doctor here in town).  So I called ARUP Laboratories and was told I could not talk to the pathologist about my questions because I was a patient.  Some story about violating HIPAA.  Which is not true because I was not asking any questions about MY test results.  I only wanted to know some statistical questions about the test in general, in no way pertaining to my results.  However, they could not/would not answer my questions, and told me the best I could do was have my own personal doctor call and ask my questions for me.  Never mind, 1) I’m a medical doctor who COULD order this test for patients and COULD be forming judgments in my head about whether or not this test is valid and useful for my patients and 2) my medical doctor was only being nice to order the test and promptly forwarded the results on to me without a word about the results–let’s just say HE’S NOT INTERESTED in making a “clinical consult” appointment.  Runaround.

  • What population does Metametrix base its reference ranges on?
    • This may be reported somewhere.  I just couldn’t find it. ( I read somewhere online that “he said she said” that GI Profile reference ranges are based on patients who are requesting the GI Profile. People requesting the test most likely do not comprise a “normal” population.  So I hope this is not the case.)
  • How did they choose which bacteria to test for and report on the “Predominant Bacteria”?
  • Which bacteria are excluded from the Profile that are important in knowledge of gut health?  Why not report Enteroccus or Peptostreptococcus or others?  I realize it’s so complex, but I wish I knew how they decided.
  • In 2011, it seemed as if researchers had discovered the possibility that humans had one of three subtypes of bacterial predominance:  Bacteroides, Prevotella, and Ruminococcus.  (Click here for article.)  Why not report Ruminococcus?
    • Here it gets a bit confusing.  For me, a lot confusing.  The GI Profile lists the Predominant Bacteria as “sp” (example, Bifidobacter, sp), which would imply bacterial species are listed collectively as a a genus.  However, “Clostridia” is a class, and “Clostridium” is a genus (with all its subsequent species in it:  Clostridium difficile, Clostridium tetani, etc).  My microbiological knowledge is not immense, and bacteria are routinely being recategorized.  However, I found Ruminococcus as a genus of the Clostridia class on Wikipedia.  So based on this, Clostridium and Ruminococcus could have been reported separately.  Prevotella, Fusobacterium, Escherichia, Bacteroides, etc are all genuses.  Clostridia is a class with Clostridium and Ruminococcus both being genuses under the broad class Clostridia.  However, here is an article attesting to the complicated mess of the taxonomy of Ruminococcus.
    • So, I don’t know.  Could Metametrix have listed Ruminococcus apart from Clostridia?
    • Were some bacteria chosen for “fear factor”?  For example, why did they choose to list Mycoplasma?  I can find barely anything on it as flora.
  • The Bacterial Profile doesn’t tell you WHERE your bacteria are located.
    • Bacteria have their own more or less desirable locale in the GI tract.  Some reside in the distal ileum.  Some the cecum.  Some reside in the mucus layer right next to the intestinal cells whereas others like the fecal lumen.
    • If you’re having bloating and diarrhea, knowing an absolute number of each bacteria isn’t all that helpful and “abnormals” may lead you on a wild goose chase.  “Oh, my gosh.  My E. coli is in the red.”  However, simply knowing that Bifidobacterium was encroaching in increasing numbers into the small intestine, leading to your small intestinal bowel overgrowth (SIBO) problem, would be very helpful knowledge.  The Bacterial Profile won’t tell you location, which is of utmost importance in the pathology of many of these GI/GI related conditions.  This is certainly a test limitation.
  • If bacterial “dysbiosis” is present, which came first?
    • Perhaps the illness at hand lies in the RESPONSE to the bacteria, not in the levels of bacteria themselves.  Having a number won’t help you much.  Manipulating levels and rechecking may not help you much.
    • Perhaps pathology of the colon/immune response led to changes which altered bacterial strain survival and growth.  High or low Bifidobacterium just came about because of underlying conditions.  If a person has severe, chronic constipation, did slow transit of the gut lead to the bacterial changes or did the bacterial milieu/lack the of milieu cause the poor function of the gut?  If as of yet unidentified underlying pathology leads to the bacteria flora changes, you can “pump” all you want with probiotics, antibiotics, etc–but it won’t permanently change a thing until you address what caused the initial problem.  If you can even do that at all.  I think sometimes you can and probably sometimes you can’t.  Removing certain foods, adding in certain foods, etc may help.
    • Disease is related to more than just high or low bacteria or increased types of bacteria.  The test can show you numbers but not how it relates to disease.
  • If I tested today and then tested tomorrow, would the results be similar?  It should be, but is it?  Can this test really be used to measure “changes” over time?  How much variation is there from day to day, week to week, month to month, and year to year?
    • On the online self-help/help-each-other sites, people seem to “follow” these tests over time to see if they’ve “improved.”  Does “improvement” on the test prove anything?  Isn’t improvement of symptoms in these cases worth far more?  Why repeat a test?  If everything falls within the 80% percent reference interval, why would you repeat the test?

Basic Interpretation of the Report

•Results are expressed in “scientific notation”, so 4.1 is really 4.1 X 10 to the 7th power (41,000,000 colony forming units-CFU).

•After listening to the Metametrix representative on video (“How to Read Metametrix Laboratory Results:  Reference Ranges” .  Please note this opens up sound immediately, so mute it if people are sleeping), this is what I’ve come up with to interpret the reported numbers.

  • Results from the whole population have been broken into fifths (quintiles) and 80% of the people will fall between the two numbers marked on the horizontal line.  The 80% reference interval is supposed to center around the mean of the population.  (I still am unclear on who their “normal” population is.)
    • If your value is outside of these two marked numbers, you’re falling outside of where 80% of most of the population’s results are.  The video indicates that outside of the 80% reference range is considered “high” or “low”.
    • It is indicated that the colors on the horizontal lines correspond with the 80% reference interval.  Green is “normal” and red is “abnormal.”  So what do they call yellow?  I call it the “heck if anybody knows” gray area.  We don’t know “high” or “low” for microbiota at this point.  Each person has their own unique flora.  There may be three types of ecosystem.  Certainly if you’re “way high” or “way low”, that might be a consideration, but I think between there is quibbling and calling what we cannot yet call.
  • On the far right hand side of the horizontal lines, under “95% reference range”, is the listed number for the 95% “reference range” for each organism.  However, confusingly for me, there is no “range.”  I guess that 95% of the people are just greater than the number listed. I just do not wpid-IMAG0336.jpgsee an upper limit listed for the 95%.  What am I missing?
    • I’m presuming that the horizontal line (axis) is also representative of a “normal” distribution, and they just omitted listing the upper limits.  So I’m presuming that the 80% reference range sits within the 95% reference range and that the population’s distribution follows a normal distribution.  Admittedly, I am weak on statistics.  Please don’t blast me.  Educate me.

Will I Order this Again?

No.  I feel comfortable that these Predominant Bacteria are “in the ballpark.”  I will continue my committment to intense dietary nutrition because I think that’s where I’ll gain the most change that is appropriate for my body.  Currently, I’m not thrilled with antibiotics (“natural” or otherwise) for changing flora.  I may change my tune as I read more.  I prefer to take it slow and steady.  Let my body and GI tract do what they know how to do now that I’m helping out instead of piling on my favorite–another chocolate chip cookie or two or five.

Would I have ordered the test in the first place?  Yeah. I’m glad I did.  My constipation and bloating have been severe enough that I was concerned that perhaps my microbiota could use some growth or reduction.  I haven’t been particularly pleased with Metametrix’s “customer service.”  They really did a poor job guiding my local lab in submission of the test, and they clearly didn’t help me with the statistical information I wanted.

Truly wishing you the best in all the important things in life.  If this helped you at all, please drop me a line.  It was painful to write.  And as always, I don’t like typos.  So comment on those, too.


Sources are sprinkled through post as links, but also here is one cited traditionally (which takes more work):

1.  DNA Detection or Gut Microbioata:  How New Technology is Improving the Process of Stool Analysis   http://www.metametrix.com/files/learning-center/articles/GIfx_DNA-Detection-of-Gut-Microbiota.pdf