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Gut Microbiome Composition
Every living organism produces RNA molecules from their DNA. By sequencing all of the RNA in the samples we receive, we can identify and quantify all of the living microorganisms in the gut (bacteria, viruses, bacteriophages, archaea, fungi, yeast, parasites, and more) at the species and strain level. The end result? A higher resolution view of your gut microbiome than has ever been available before.
Gut Microbiome Gene Expression
While identifying the microorganisms in the gut is important, we gain the most insight when we can also understand their function. This is because the microbes in the gut produce thousands of chemicals, called metabolites, that affect your overall wellness. Some of these microbial metabolites can be beneficial to our health, such as vitamin B and short chain fatty acids, while others can be detrimental, such as TMAO, which causes coronary artery disease.
By analyzing the genes that microbes express, we can identify which metabolites they produce – in other words, we can determine their role in your body’s ecosystem. By following Viome’s diet and lifestyle recommendations, a person can fine-tune the function of their gut microbiome to minimize production of harmful metabolites and maximize the production of beneficial ones.
The Viome Advantage.
What is the difference between Viome and other gut microbiome companies?
Viome is the only company whose gut microbiome test can be used to accurately make personalized diet and nutrition recommendations. The reason is our unique technology, which no other direct-to-consumer company possesses or offers. Most microbes in your gut can produce molecules that benefit you, harm you, or have no impact on your health. The only genomic tests that have the ability to see which molecules your microbes are actually producing use metatranscriptomic analysis.
The table below compares the three most common types of gut microbiome tests.
16S Sequencing 1
Metagenomic analysis 2
Viome Metatranscriptome Sequencing
|Identifies only a fraction of your gut bacteria; unable to identify nonbacterial microorganisms
|Cannot identify any RNA viruses or RNA bacteriophages
Identifies allmicroorganisms living in your gut: bacteria, viruses, archaea, yeast, fungi, parasites and bacteriophages 3
|Sequences DNA, which can come from food and dead microorganisms
|Sequences DNA, which can come from food and dead microorganisms
Sequences RNA, which comes from live microorganisms that have a great impact on our health
|Low resolution (mostly genus and lower resolution)
|High resolution (species and strain level), but does not include RNA viruses
High resolution (species and strains) of all microorganisms
|Unreliable; sequencing the same sample twice can yield very different results
Minimal variation in results, but partially biased analysis (no RNA viruses)
Minimal variation in results and unbiased analysis
|Does not measure microbial gene functions
|Does not measure microbial gene functions
Quantifies expression levels of active microbial gene functions
|Does not assess what the microbes are doing Low resolution and lack of gene expression data preclude actionable recommendations
|Does not assess what the microbes are doing Lack of gene expression data preclude actionable recommendations
Allows assessment of pathway activities that can lead to personalized health insights and recommendations with molecular-level precision based on what the microbes are doing
1Used by uBiome, American Gut Project and others.
2Used by uBiome (ExplorerPlus kit), DayTwo and others.
3We now understand that many common chronic diseases are associated with the presence of non-bacterial species in the gut.
4After sending duplicate stool samples to American Gut and uBiome, a journalist found that her results from the two companies were completely different.
How can Viome's metatranscriptome technology improve wellness?
- Increase microbial species associated with overall wellness
- Minimize microbial species associated with poor health
- Increase the diversity of your microbiome
- Stimulate production of beneficial metabolites
- Minimize production of metabolites associated with poor health
- Identify prebiotics that can induce growth of beneficial microbes and metabolites
- Identify the ideal ratio of proteins, carbohydrates and fats for your diet
- Identify foods that are most compatible with your metabolism
- Recommend a diet to help you achieve and maintain a healthy weight
- Recommend a diet that will increase your energy, focus and well-being
- Optimize your digestion and absorption
- Introduce beneficial (but missing) bacteria with probiotics
GENOVA GI Effect
When Should the GI Effects Comprehensive Stool Profile Be Considered?
The GI Effects Comprehensive Stool Profile can reveal important information about the root cause of many common gastrointestinal symptoms such as gas, bloating, indigestion, abdominal pain, diarrhea, and constipation. This stool analysis utilizes biomarkers such as Calprotectin to differentiate between Inflammatory Bowel Disease (IBD) and Irritable Bowel Syndrome (IBS) .3,4 In addition, Genova's GI Effects test can be used to evaluate patients with a clinical history that suggests a gastrointestinal infection or dysbiosis.
Gut microbes are codependent with one another and with their human host, and the health of one affects the other. A sizeable volume of research associates a dysbiotic, or imbalanced gut microbiome with multiple disease states both within and outside of the GI tract.1,2 The diverse metabolic activities of the microbiome ultimately impact the human host, and the activities of the human host ultimately affect the health of their microbiome.
What is the GI Effects Comprehensive Stool Profile?
The GI Effects® Comprehensive Stool Profile is an advanced stool test that provides immediate, actionable clinical information for the management of gastrointestinal health. Utilizing cutting-edge technologies and biomarkers, this test offers valuable insight into digestive function, intestinal inflammation, and the intestinal microbiome.
The biomarkers from the GI Effects Comprehensive Profile are reported using the DIG framework, providing key clinical information for three main gastrointestinal functional areas:
- Pancreatic Elastase-1 is a marker of exocrine pancreatic function.
- Products of Protein Breakdown are markers of undigested protein reaching the colon.
- Fecal Fat is a marker of fat breakdown and absorption.
- Calprotectin is a marker of neutrophil-driven inflammation. Produced in abundance at sites of inflammation, this biomarker has been proven clinically useful in differentiating between Inflammatory Bowel Disease (IBD) and Irritable Bowel Syndrome (IBS).3,4
- Eosinophil Protein X is a marker of eosinophil-driven inflammation and allergic response.
- Fecal Secretory IgA is a marker of gut secretory immunity and barrier function.
- Gut Microbiome:
- Metabolic indicators , including short-chain fatty acids and beta-glucuronidase, demonstrate specific and vital metabolic functions performed by the microbiota.
- Commensal Bacteria demonstrate the composition and relative abundance of gut organisms.
- More than 95% of commensal gut organisms are anaerobic and are difficult to recover by traditional (aerobic) culture techniques.
- GI Effects assesses a set of 24 genera/species that map to 7 major phyla.
- Bacterial and mycology cultures demonstrate the presence of specific beneficial and pathological organisms.
- Bacteria and mycology sensitivities are provided for pathogenic or potentially pathogenic organisms that have been cultured. The report includes effective prescriptive and natural agents.
- GI Effects provides microscopic fecal specimen examination for ova and parasites (O&P), the gold standard of diagnosis for many parasites.
- Enzyme immunoassay (EIA), widely recognized for its diagnostic utility in the detection of pathogenic antigens, is used for the identification of Cryptosporidium , Entamoeba histolytica , and Giardia lamblia .
- Selection of a one-day or three-day sample collection is based on clinician's clinical index of suspicion for parasitic infection. If there is no/low suspicion, a one-day sample will likely be adequate. For high suspicion, a three-day sample collection is optimal.
- Additional Biomarkers Available :
- Clostridium difficile
- Escherichia coli
- Fecal Lactoferrin
- Helicobacter pylori
- Macro Exam for Worms
- Zonulin Family Peptide
- KOH Preparation for Yeast
What Advantage Does the Profile Offer Compared to Other Diagnostics?
A structured fecal biomarker panel offers the advantage of assessing multiple functional areas that may be contributing to symptoms. For example, diarrhea could stem from multiple causes including pancreatic exocrine insufficiency, inflammation, food allergies, or the presence of a pathogenic or potentially pathogenic organism. A positive result on one or more fecal biomarker tests may guide therapy, either by suggesting a treatable alternative diagnosis or by eliminating a diagnosis from further consideration. The latter allows individualized targeted treatment to be redirected to more likely diagnoses.5,6
GI Effects® represents the best technical platform to assess gut health, including an anaerobic bacteria PCR molecular assay, Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) technology for cultivable species identification, as well as stool-based biomarkers for gastrointestinal diagnostics.
The test report is organized so that the clinician may move through results in a logical order that enhances clinical utility, starting with innovative Interpretation-At-A-Glance pages to synthesize the information.
What Can Clinicians and Patients Expect from GI EffectsComprehensive Profile Stool Testing?
The GI Effects Stool Profile biomarkers provide comprehensive information for the development of strategic interventions. Symptoms often improve as identified functional imbalances and inadequacies become normalized through targeted dietary, lifestyle, and supplementation therapeutics.
- Marchesi J, et. al. The gut microbiota and host health: a new clinical frontier. Gut . 2016 Feb;65(2):330-9.
- Clemente J, et. al. The impact of the gut microbiota on human health: an integrative review. Cell . 2012 Mar;148(6):1258-70.
- Menees SB, et. al. A meta-analysis of the utility of C-reactive protein, erythrocyte sedimentation rate, fecal calprotectin, and fecal lactoferrin to exclude inflammatory bowel disease in adults with IBS. Am J Gastroenterol . 2015 Mar;110(3):444-54.
- Dabritz J, Musci J, Foell D. Diagnostic utility of faecal biomarkers in patients with irritable bowel syndrome. World J Gastroenterol . 2014 Jan;20(2):363-375.
- Parsons K, et. al. Novel testing enhances irritable bowel syndrome medical management: the IMMINENT study. Glob Adv Health Med . 2014 May;3(3):25-32.
- Goepp J, et. al. Frequency of abnormal fecal biomarkers in irritable bowel syndrome. Glob Adv Health Med . 2014 May;3(3):9-15.