Tests

VRI tests are used by Viome as part of the direct-to-consumer service, but are also excellent research tools, providing accurate and high-content data relevant to human health and chronic diseases. All VRI tests use RNA sequencing, also known as (meta)transcriptomic methods.

Why is studying RNA more powerful than DNA?

In the context of chronic diseases, RNA sequencing has major advantages over DNA sequencing, for both humans and our microbial symbionts. RNA (gene expression) is an extremely useful resource for studying health and disease, as gene expression is constantly changing throughout the course of a disease. DNA on the other hand, does not incur change and has been shown only to have a weak contribution to chronic diseases. For example, just think of a chronic disease such as IBD that goes through remission-relapse phases. The DNA will remain the same regardless of which disease phase you are in; however, the RNA will change to reflect the different disease phases. Very importantly, these changes in gene expression can be modulated, either via nutrition or microbiome functions.

Main features/advantages of VRI tests

  • They identify and quantify all microorganisms, including RNA viruses (human, plant, and phages). No other taxonomic classification method is all-inclusive.
  • All metatranscriptomic tests identify and quantify only the living microorganisms, because RNA from dead microorganisms quickly degrades. In contrast, microbial DNA remains in the sample long after a microorganism dies and can cause false positive calls.
  • They quantify the expression of all genes present in the sample, human and/or microbial.
  • Laboratory methods are automated, minimizing or eliminating batch effects. VRI tests are performed in a CLIA-licensed lab, and most of them are clinically validated. This means that:
    • All lab technicians have a B.S. in laboratory sciences
    • All lab technicians are trained and competency tested
    • Every step of every method follows SOPs that are validated and approved by the Lab Director
    • All reagents and every lot must pass strict quality control standards
    • Every instrument must have documented satisfactory performance
    • Labs are environmentally-controlled and monitored
    • Every sample and every batch of 96 samples have quality control acceptance criteria that must pass. These include positive and negative process controls, etc.
  • All tests, except for serum/plasma analysis, utilize at-home sample collection. Even our whole blood transcriptome test requires just 50 microliters of finger prick blood.
  • All samples can be shipped at ambient temperature globally. No refrigeration, freezing, or rapid and expensive shipping are needed.
  • Metatranscriptomic data are relevant to chronic diseases and actionable. That means we can develop better diagnostic tests and implement nutritional/lifestyle strategies that can modulate human gene expression and prevent/cure chronic illness.

Gut Intelligence (GI) test

Gut Intelligence (GI) test is a metatranscriptomic (RNA sequencing) stool test that identifies and quantifies all living microorganisms in the sample down to 1 part per million. This includes RNA viruses (human, plant, and phages).

  • Includes a collection kit with instructions, all necessary components, and a pre-paid return mailer
  • Can be collected anywhere and shipped at ambient temperature
  • Isolates total RNA from stool (DNA is degraded)
  • Physically removes microbial rRNAs from total RNA
  • All remaining RNAs are sequenced using full-length transcripts and a directional library preparation method
  • Produces quantitative strain-, species-, and genus-level taxonomic classification data (average number of species per stool sample is 338)
  • Produces quantitative microbial gene expression data that are clustered into KEGG orthologies (KOs). This is very different from metagenomic functional outputs, which can only tell you about the functional potential. The GI test measures the actual microbial functions. A typical gut microbiome has >1 million genes, but only 50,000 are expressed at a level of 1 part per million or above.
  • A peer-reviewed article on this test is at www.hindawi.com

GI test data provided by VRI to the grantee:

  • List of genera and their relative activity
  • List of species and their relative activity
  • List of strains and their relative activity
  • List of KOs and their relative activity

Human Gene Expression (HGE) test

Human Gene Expression (HGE) test is a transcriptomic (RNA sequencing) blood test that:

  • Includes a collection kit with instructions, all necessary components, and a pre-paid return mailer
  • Requires 50 microliters of blood from a finger prick
  • Can be collected anywhere and shipped at ambient temperature
  • Isolates total RNA from blood (DNA is degraded)
  • Physically selects polyadenylated (protein-coding) RNAs
  • Sequences the remaining (polyadenylated) RNAs using a full-length transcript, directional method
  • Produces quantitative gene expression data for human genes (average is ~14,000 per sample)
  • A pre-print of our article describing this test is at doi.org

HGE test data provided by VRI to the grantee:

  • List of human genes and their gene expression level (can be counts per million or transcripts per million)

Saliva Intelligence (SI) test

Saliva Intelligence (SI) test is a metatranscriptomic (RNA sequencing) saliva test that identifies and quantifies all living microorganisms in the sample down to 1 part per million. This includes RNA viruses (human, plant, and phages).

  • Includes a collection kit with instructions, all necessary components, and pre-paid return mailer
  • Can be collected anywhere and shipped at ambient temperature
  • Isolates total RNA from saliva (DNA is degraded)
  • Physically removes microbial and human rRNAs from total RNA
  • Sequences all remaining RNAs using a full-length transcript, directional method
  • Produces quantitative strain-, species-, and genus-level taxonomic classification data
  • Produces quantitative microbial gene expression data that are clustered into KEGG orthologies (KOs). This is very different from metagenomic functional outputs, which can only tell you about the functional potential.

Data provided by VRI to the grantee:

  • List of genera and their relative activity
  • List of species and their relative activity
  • List of strains and their relative activity
  • List of KOs and their relative activity

Vaginal Intelligence (VI) test

Vaginal Intelligence (VI) test is a metatranscriptomic (RNA sequencing) vaginal test that identifies and quantifies all living microorganisms in the sample down to 1 part per million. This includes RNA viruses (human, plant, and phages).

  • Includes a collection kit with instructions, all necessary components, and pre-paid return mailer
  • Can be collected anywhere and shipped at ambient temperature
  • Isolates total RNA from vaginal samples (DNA is degraded)
  • Physically removes microbial and human rRNAs from total RNA
  • Sequences all remaining RNAs using a full-length transcript, directional method
  • Produces quantitative strain-, species-, and genus-level taxonomic classification data
  • Produces quantitative microbial gene expression data that are clustered into KEGG orthologies (KOs). This is very different from metagenomic functional outputs, which can only tell you about the functional potential. The GI test measures the actual microbial functions.

Data provided by VRI to the grantee:

  • List of genera and their relative activity
  • List of species and their relative activity
  • List of strains and their relative activity

Plasma Intelligence (PI) test

Plasma Intelligence (PI) test is a metatranscriptomic (RNA sequencing) plasma or serum test that identifies and quantifies all living microorganisms in the sample. This includes RNA viruses (human, plant, and phages). The test can also identify cell-free RNAs.

  • The samples for this test must be collected by a phlebotomist, as it requires a venous blood draw and centrifugation
  • The phlebotomist must be trained to:
    • Use the VRI’s skin prep kit for the removal of skin contaminants
    • Properly generate and transfer plasma/serum into VRI’s sample preservation kit
    • Properly package the sample and ship at ambient temperature in a timely fashion
  • VRI includes all instructions, necessary components, and pre-paid return mailer
  • Isolates total RNA from plasma or serum (DNA is degraded)
  • Physically removes microbial and human rRNAs from total RNA
  • Sequences all remaining RNAs using a full-length transcript, directional method
  • Produces quantitative strain-, species-, and genus-level taxonomic classification data
  • Produces quantitative microbial gene expression data that are clustered into KEGG orthologies (KOs). This is very different from metagenomic functional outputs, which can only tell you about the functional potential. The GI test measures the actual microbial functions.

Data provided by VRI to the grantee:

  • List of genera and their relative activity
  • List of species and their relative activity
  • List of strains and their relative activity
  • List of KOs and their relative activity
  • List of human genes and their gene expression level (can be counts per million or transcripts per million)

FAQs

A lab claims they sequence 16S rRNA. How is that different from VRI’s RNA sequencing?

The term “16S rRNA sequencing” is inaccurate, because the method does not sequence RNA. People use this term either because they aren't familiar with its meaning, or they are misrepresenting their technology. The correct term is “16S rRNA gene sequencing”, and it refers to PCR amplification of a portion of the bacterial and archaeal 16S gene (DNA), then sequencing it. This method suffers from poor coverage (it misses a lot of microorganisms), poor resolution (genus level at best: Knight, R., et al., Nature Reviews Microbiology, 2018, 410–422), and many false positive calls (PeerJ. 2018; 6: e4652). These drawbacks can lead to false discovery, lack of discovery, or non-actionable information, since genera typically contain many species and many more strains.

How is it possible to preserve RNA at ambient temperatures for weeks?

While RNA is inherently unstable and RNases are ubiquitous, Viome’s RNA stabilizer (RPB) eliminates all these factors by denaturing enzymes and preventing RNA self cleavage. Therefore, by exposing a sample to RPB preserves the dynamic equilibrium of RNA molecules in a sample at the time of collection. RNA stability has been validated for up to 28 days at ambient temperatures and 90 days at 4C.

References

Leek, J., Scharpf, R., Bravo, H., Simcha, D., Langmead, B., Johnson, W., Geman, D., Baggerly, K., Irizarry, R. (2010). Tackling the widespread and critical impact of batch effects in high-throughput data Nature Reviews Genetics 11(10), 733-739. https://dx.doi.org/10.1038/nrg2825