Superior Diagnostics, Targeted Treatments.

Next Generation Sequencing Is Now Available To Dentists, Oral & Systemic Health Clinicians

“Based on Next-Generation Sequencing, novel microorganisms have been strongly associated with disease in addition to putative periodontal pathogens”

Colombo APV, Tanner ACR. The Role of Bacterial Biofilms in Dental Caries and Periodontal and Peri-implant Diseases: A Historical Perspective. J Dent Res. 2019 Apr;98(4):373-385. doi: 10.1177/0022034519830686. PMID: 30890060.

What is Next-Gen Sequencing?

MicroGenDX is a Molecular Laboratory that utilizes Next-Gen DNA Sequencing to accurately identify all microbes within each sample. The extracted DNA from each sample is matched to the DNA sequence codes of the National data base of over 50,000+ known microbes of bacterial and fungal species with 99.9% accuracy.

Conversely, we now know that culture methods can only grow 1% of all known microbes and have an alarming rate of negative or no growth results leaving physicians guessing what microbes are causing the infection and impacting treatment decisions.*

  • *Bjarnsholt T., “The role of bacterial biofilms in chronic infections.” US National Library of Medicine, APMIS Suppl. 2013 May;(136):1-51. doi: 10.1111/apm.12099.,, web.


To understand WHY cultures fail in correctly identifying the causitive microbes we need to understand how biofilms form and work together to survive. Microbes have switched from an acute frontal attack by planktonic cells, to a strategy of biofilm growth and chronic attack on infected tissues, and the most serious long-term effect of this tactical change is that they evade detection by the classic methods of Medical Microbiology (culture method).

Patients will be treated more effectively when the identity of any and all bacteria in their tissues can be accurately determined.

Next-Gen Sequencing (NGS)

We live in the era of precise DNA-based forensics, and of whole genome sequencing, and patients will be best served when we mobilize these resources for the prompt and accurate diagnoses of bacterial disease. ONLY Next-Gen Sequencing (NGS) can detect all of the microbes who are living at the site of the infection.

Chronic Infections, Biofilms & Next-Gen Sequencing

All planktonic or single cell microorganisms will eventually move to a biofilm state, making diagnosing the causative microbes by way of culture methods nearly impossible and leading to chronic and ongoing infections to remain.

  • “The CDC and the NIH have estimated that biofilm infections now constitute 65 – 80 % (respectively) of bacterial infection.” CDC/ NIH research shows that 80% of infections are caused by Bio-Films. Cultures fail to identify the microorganisms in a biofilm phenotype.”*
  • *Orthopaedic biofilm infections – Paul Stoodley,a Garth D. Ehrlich,b Parish P. Sedghizadeh,c Luanne Hall-Stoodley,d Mark E. Baratz,e Daniel T. Altman,e Nicholas G. Sotereanos,e John William Costerton,e and Patrick DeMeoe

Molecular Diagnostic Versus & My Microlab

There are many reasons NGS is a far superior tool in identifying microbes, NOT having to grow anything is just one reason why. Reasons the MicroLab did not find or grow microbes that we detect with DNA sequencing:


  1. Science has proven that less than 1% of all microbes can be detected by traditional culture.
  2. Pradeep Singh, MD has recently shown (Singh P Copenhagen biofilm meeting 2011-site this) “that cells of Pseudomonas aeruginosa undergo a structural change in the lipopolysaccharide (LPS) of their outer membranes that makes them unable to grow on the surface of agar plates, even if the medium is otherwise ideal.
  3. There are National Guidelines for Microbiology (cultures). These guidelines are established by the IDSA and ASM. They require your sample for culture to be at the microlab in 2 hours and kept at room temperature. Why does the IDSA and ASM have strict sample management criteria ? They know that in order for the sample to “grow” it has to be at the lab in a condition that allows the lab to have a chance to successfully grow the specimen on the plate. Look at the lab boxes sitting outside medical offices and ask yourself, “Is that swab or urine specimen going to be at the lab in 2 hours?”
  4. PCR and NGS do not have the same limitations of time and temperature as culture!
  5. The microbes were part of a biofilm and have changed their genotype and phenotype and “refuse” to grow.
    1. The microbes created a team to successfully fool traditional and archaic testing methods.
  6. Wrong media was used: If the microbes are anaerobes, they are extremely difficult to grow in desired conditions and will not grow in “normal” agar environments.
  7. Fungi takes weeks to grow, if at all.
  8. MicroGenDX laboratory uses Molecular Diagnostics of PCR and NGS to identify the microbes by extracting the microbial DNA within each sample. In the PCR Test Level I we detect a precise number of microbes typically known to cause the specific infection. We also identify Antibiotic resistance gene markers and deliver the overall bacteria load within 24 hours. We then take the extracted DNA and use this on our NGS Test or Level II and match the DNA sequence codes to a national data base of 50,000 known microbes to accurately deliver the microbial data of what is really inside the sample collected from the infection site.

Yes, there may be contaminants listed on your report. How could contaminants appear on my lab report?


Contamination could happen during the sampling process. For example, if proper skin prep is not done correctly, normal flora on the skin may attach itself to the needle while penetrating the skin for an aspiration sample of say a knee or shoulder. For example, this should be considered if Staph Epi or P Acne are listed on your lab report. Also we know that lactobacillus is a normal flora in the vaginal area. Normal flora may be on the list but not part of the problem.


Remember, these microbes are there for a reason and if balanced, live in harmony with the host. The area of the sample collection needs to be considered when reviewing your report to determine which microbes are to be treated.

What do I do with all the information on my lab report?

Part 1 Is the PCR test result

qPCR Rapid Screening will detect 8-16+ microbes traditionally found or determined to cause a certain type of infection. Within 24hrs qPCR will identify the “usual suspects” at the scene of the infection but can not tell you if any other species are there.

We also detect and deliver Antibiotic Resistance Genes to identify what antibiotics may not work to treat detected microbes.

But the limitation of PCR stops at those 8-16+ identified microbes. Within all chronic infections the story doesn’t stop with 16 or even 45 species of microbes. In human samples alone our NGS technology has detected over 6,500 species of microorganisms! This is why NGS is so crucial to provide a comprehensive analysis of exactly which microbial species are at the site of the infection.

Part 2 Is Next-gen sequencing

To date, we have found over 6,500 microbial species in human samples. This level of detail is crucial in assisting physicians treat the actual cause of the infection. 

This is not magic or a miracle. This is the most comprehensive diagnostic tool you will ever need to assist with delivering you accurate data on the microbes causing the infection.

Interpreting Your Patients PerioDX® Report

How To Read Your PerioDX® Report