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There are many different microbiome tests on the market. What makes a significant difference in your test? Accuracy? Testing method like PCR or genomic sequencing? Why we need to choose your test over others?
GutID provides clinicians and patients with the highest level of resolution for identifying bacterial species. Thus, we are able to identify bacteria in a sample with high accuracy down to the strain (and even sub-strain) level. Metagenomics has the potential to reach strain level (in theory, with vast amounts of sequencing and associated costs) but we have the advantage of being database independent, and our performance has been published as superior (Gehrig, J. L., Portik, D. M., Driscoll, M. D., Jackson, E., Chakraborty, S., Gratalo, D., Ashby, M., & Valladares, R. (2022). Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data. Microbial genomics, 8(3), 000794. https://doi.org/10.1099/mgen.0.000794).
If you perform any kind of sequence analysis, whatever you can identify and “call out” must be available in some form of library. The main limitation of metagenomics is that not all microorganisms are present in a library, so even if theoretically possible to “see” them, they will not be identified in practice if they are not already included in a database. Additionally, shotgun technology currently available for metagenomics has some well-known limitations in the reassembly of genomes, affecting its accuracy. For example, pathogens and other bacteria of interest may be present at low levels, where shotgun data are very incomplete.
Having the ability to identify even rare species and their strains has proven to significantly contribute to clinical outcomes, because it gives us the ability to point out abnormal species that are often the cause of chronic illnesses (not just gastrointestinal diseases).
qPCR methods target known bacterial sequences very well, but are optimized to avoid off-target bacterial strains. It is common for these tests to contain very limited lists of strains or substrains that have been selected as significant or representative. E. coli C and E. coli 017-H7 and E.coli O1O4:H4 and E. coli K-12 are some of the thousands of E. coli that can be separately targeted using qPCR. However, as you are aware, the actual number of E. coli likely numbers in the tens of thousands or more, and any of them could disrupt the microbiome balance if out of range

I also reviewed your test through one of my patients. Im curious how you can combine different characteristics as one determinant in your test? Gut microbiome is very dynamic and one criteria can affect the other determinant.
It is not entirely clear to me which “determinant” you are talking about, but in essence, I can say that bacteria that are known for certain functions can be classified accordingly. As a result, we can determine the relative abundance of both the total and the individual bacteria that produce secondary bile acids or SCFAs (short chain fatty acids). Species may be classified differently under different sections because, for example, they may confer some protection against a certain condition, but increase risk for others. In other words, there is no single system for classifying them, such as one bacterium equals one problem. In fact, quite the opposite is true! The test report is designed in such a way that any abnormal relative abundance of ANY species/strain will be flagged so that the clinician will be made aware of potential imbalances.
As a result of a bioinformatics analysis, an overall flag will be displayed when the abundances of all bacteria related to a particular section are abnormal when compared to the general population. However, as a clinician, I examine any abnormal results under any section, even if no overall flagging is present, especially if the relative abundance is not just slightly off but very significantly out of range.

I am also curious about screening all genome in the microbiome. PCR detect the known genes in the microbiome but when you detect the other genomes in a sample, how come you know the importance of them?
A genome is not actually “screened” but rather sequenced. The difference between PCR and whole genome sequencing is that, in PCR, you are able to identify only what you want to identify, while in whole genome sequencing, you are able to provide the complete sequence of all genomes, as in metagenomics. Therefore, sequencing has nothing to do with automated clinical interpretation! It does happen for the human genome as well, so it is not necessary to know the full genome to determine what is relevant from a clinical perspective (it obviously depends on what you want to look for!)
Microbiome profiling is not merely about identifying a bacterium but rather about interpreting its abundance. For example, a low abundance of E.coli within a normal reference range may be perfectly fine and not cause any risk factors, however, a high abundance can cause a variety of problems, which may result in multiple flags in various sections.

Could you please share the articles about the group of bacteria stay stable for a long time?
In general, your microbiome, and in particular your “core” microbiome, tend to be very stable unless you introduce powerful disturbances such as antibiotics or drastic changes to your diet or supplement regime. You might, however, refer to the 2 major intestinal Phyla, Firmicutes and Bacteroidetes. In general, these two main groups represent the vast majority of an adult microbiome, and their ratio is usually very balanced (although it may not be a perfect 50:50). A significant shift in their ratio might suggest dysbiosis, sometimes of a serious nature.

Titan technology: all the bacteria in a sample identified- What is the max number you been able to detect?
First of all, a clarification: we do not have any limits in the actual number of bacteria we can identify! Whatever is in the sample, we will see it. In terms of total number of species ever observed, nobody can reach the hypothetical “maximum “ as nobody can have represented all possible bacteria. However, if the actual question is about the highest richness ever observed in an individual, I can say around 150. Most people have ~ a hundred species, and we have seen samples ranging from many to ~3 species (sepsis patient treated with long duration antibiotic therapy). We find that almost everyone contains species that are not in any database. The limit of detection is dependent on the number of reads, our assay reproducibly detects bacteria at or below 0.01% of the total population, whether known or unknown, which is sufficient for microbiome profiling. If we needed lower limits of detection, we can just turn up the dial!

So are you feeling that Gutid is the worlds best test so far? do you trust it?
Because I contributed personally to the selection of the bacteria and the development of the report, I have confidence in the results of the test. We are constantly evolving in this field and what I have learned from being exposed to literally thousands of microbiome profiles is that we are indeed collecting very significant data regarding the role of bacteria in the gut (as well as mouth, skin, vagina, etc.) and human disorders. The only suggestion I would make as a clinician is to start implementing the test in your clinical practice and see how it correlates with your patients’ symptoms. There is no substitute for practical experience!

You tell your clients to retest regularly. is there better pricing for retesting and retesting?
Yes, we have already launched a twin pack that offers a significant discount for 2 tests bought together. Please see all prices here Products – GutID

Hi Elena, while you are eliminating the pathogenic bacteria via a natural antibacterial protocol , would it be helpful to use a spore based probiotic and S Boulardii at the same time? Thanks
I quite regularly use S. boulardii when a patient experiences bad dhiarroea as I feel it is effective but at the same time “safe” while rebalancing the microbiome. Any other probiotics I noticed that they tend to either not colonise at all or even complicate the picture.

In case study 1 which antimicrobial did you use?
I usually recommend different versions of Biocidin, in dosages and form that are more suitable to patients’ symptoms and overall status

What typical traits would someone with Crohn’s have?
It’s not really a question of specific “traits” but rather a combination of factors. It also depends on the stage and severity of the diseases. During a flare-up, a patient might for instance show low abundance of protective bacteria such as the mucosa protective and the SCFAs producers, and/or an abnormally high abundance of pathogens or inflammatory bacteria. In the report, there is also a specific section that identify both beneficial and detrimental bacteria associated with IBD.

What about Saccaromyces Boulardiii as a pathogen killer?
Probiotics can facilitate, when used in the right stage of an elimination process, the antimicrobial effects of specific drugs and supplements but they do not directly”kill” pathogens. Just remember however the importance of the terrain concept! A strong, resilient microbiome will be able to fight back pathogens more efficiently while a weak one will be struggling more.

What is the price of the test?
See the prices for the public here Products – GutID