Aug 11, 2026
This guide is for you whether you have a report in hand or are considering if NGS testing is right for you. Either way, you’ll walk away knowing what you get from a MicroGenDX NGS test.
A MicroGenDX report shows the bacteria, fungi, and drug resistance genes that DNA testing uncovered in your sample, giving you and your provider a comprehensive view of the microbial landscape, along with antimicrobials for your provider’s consideration.
We get that reading a report can feel like reading something in an unfamiliar language, and we’re here to help.
This guide walks through each section of the report, from the list of microbes and how abundantly each was present, to what the resistance markers and treatment options mean, so you can arrive at your next appointment ready to have a productive conversation.
Free support is available for both patients and providers if you have questions along the way.
If you’re looking for details on the assistance we offer, jump to the “Help is available” section below. Are you a provider? Read the physician’s guide to MicroGenDX testing.
If you’ve ever had a lab result that says everything is fine when you feel otherwise, you’re not alone.
Standard cultures grow a small slice of the bacteria and fungi that live in the human body, catching about 2% of known bacteria species. The other 98% don’t thrive on a lab dish and a fungal culture can take weeks to process.
These gaps are part of why so many patients with chronic or complex infections can spend months or years without clear answers.
MicroGenDX closes these gaps, using Next-Generation DNA Sequencing (NGS) to identify infection-causing organisms against a curated database of more than 60,000 bacteria, mycobacteria, and fungi. With 99.2% accurate results in as soon as 24 hours after your sample arrives at our lab, patients receive faster, more reliable answers for targeted care.
The catch: a MicroGenDX report doesn’t look like a typical lab result. There’s no single “positive” or “negative” stamped across the top.
Keep these four ideas in mind as you read through the sections below.
Your MicroGenDX test combines two different tools.
qPCR works like a security guard checking IDs at a door. It’s fast and very precise.
But it can only recognize the specific microbes and resistance genes it already has on its guest list (its “panel”). It’s especially useful in spotting these drug resistance genes, helping providers know what drugs may be ineffective.
NGS works more like a security camera system that records everything happening in the building, giving a complete picture of what’s happening. It reads all the genetic material of microbes in your sample and compares it against our library of 60,000+ organisms, so it can catch a wide variety of bacteria and fungi, including rare or mutated ones.
This explainer goes through your report the same way your doctor would read it, evaluating your infection as they plan treatment.
This list of the bacteria and fungi found in your sample is the heart of your NGS results. It’s generated by reading and matching your sample’s microbial DNA material against the PCR panel and MicroGenDX’s NGS database of over 60,000 bacteria, fungi, and mycobacteria.
The organism names here may look unfamiliar as they follow scientific naming conventions, a genus name followed by the species. It’s similar to how “golden retriever” is more specific than just “dog.”
That species-level naming gives helpful clinical clarity to your provider, as microbes of the same genus can behave very differently and respond to different medications.
You can tell if a microbe was found via PCR or NGS. If it sits next to a number like 6.43 x 10³ then it was found by PCR, otherwise it was detected by NGS.
The microbes are listed by relative abundance, or how much each one makes up of the total microbial DNA, shown as a percentage. Picture a pie chart of your sample: if one microbe makes up 54% of the total, it’s the dominant one, while others in smaller slices are present but less abundant.
Seeing this distribution can help your provider judge which ones are most likely contributing to your infection.
For quality control, MicroGenDX doesn’t report organisms that make up less than 2% of the total microbial abundance in a sample to keep the focus on the most impactful findings.
You can expect that your result list will be longer than what a culture test would report. This is the benefit of NGS: it delivers a more complete picture of the microbes at the site of infection. It can detect slow-growing, hard-to-culture, rare, or anaerobic microbes that don’t grow well on a culture dish in a lab.
After microbes are identified, the report delivers key details to help your provider interpret those findings. This includes how much microbial DNA was found, if bacteria are Gram-positive or Gram-negative, and whether they can tolerate oxygen. These details help your provider assess which microbes can be clinically relevant and which medications are worth considering.
Bacterial & Fungal Load
It starts with a list of the detected bacteria and fungi, with each put in a separate table by type of microbe. It goes into bacterial load, counting how much bacterial DNA was found in your sample, measured as copies of identified genes per gram of tissue (or volume of fluid). Fungal load does the same for fungi DNA.
These numbers give your provider a sense of scale: is this a small, low-level microbial presence or a heavy load that’s more likely to be causing infection? To make it easier to gauge at a glance, your report classifies each load level as High, Medium, or Low.
Gram Stain
For every bacterial species detected, you will see a gram stain reference. It is a decades-old lab technique that sorts bacteria into two broad groups based on their cell wall structure, “gram-positive” or “gram-negative” — labeled (+) or (-) respectively.
Knowing which group a bacterium belongs to helps the doctor know which type of antibiotic is more likely to work against it. Note gram-staining is not clinically relevant for fungi, so the record is labeled “N” for not applicable.
Respiration Type
Each microbe is also classified by its respiration type, or how it handles oxygen, as it’s a helpful data point for treatment selection:
Since a fungus’s ability to process oxygen isn’t clinically relevant, the report labels all fungi as Unknown (Unk) in this column.
Using qPCR, MicroGenDX checks your sample for up to 17 antimicrobial resistance genes. Resistance genes are like tiny instruction manuals that some bacteria carry, teaching them how to survive a specific antibiotic, essentially building armor against that particular weapon.
These instruction manuals can be shared. Bacteria can pass resistance genes to each other, spreading that same protection to neighboring microbes, even across different species.
This kind of sharing happens especially easily inside biofilms: dense, protective bacterial communities that make infections harder to detect and treat. Learn more about biofilms.
If your report shows a resistance gene tied to a common first-choice antibiotic, it can help your provider know a drug is unlikely to work — saving you from a frustrating trial-and-error cycle of treatment.
This is one of the most clinically important sections of the report because resistance genes can help identify antimicrobials that can be less likely to work, giving your provider key context when reviewing the considerations listed in Section 4.
This is the section patients are most eager to read, and it’s easy to see why.
It lists antibiotics or antifungals that are worth exploring with your provider, based on the microbes and drug resistance genes detected in your sample. Below each antimicrobial, you’ll see shorthand for how it’s taken:
A checkmark (√) shows the drug has been shown effective against a specific microbe in your sample. A blank box means that connection is unknown, as there isn’t established data connecting it to that specific microbe. That doesn’t mean it won’t work.
Our lab conducts this analysis by examining published scientific research along with information from the Sanford Guide and Johns Hopkins Guides, two of the most widely trusted clinical references U.S. doctors use for antimicrobial treatments. These suggested antimicrobials can be used as a starting point by your provider as they consider your treatment.
Think of this as a curated shortlist, not a prescription.
It narrows down possible treatments based on what your sample showed, but it isn’t complete. Your provider may recommend something that isn’t listed here, and that’s ok. They’re weighing your medical history, other medications, local resistance patterns, and more, with clinical judgment no list could capture. Treatment planning is the doctor’s responsibility.
Marked as Pathogenicity on the report, this section appears only on reports for tests including urine samples as the urinary microbiome is more diverse than others. It’s not part of tests for other specimen types like wound or sinus swabs.
For each microbe found in a urine sample, MicroGenDX adds a classification to reflect its pathogenicity, meaning how likely it is to negatively impact urinary health. Each is labeled:
This label is generated through an ongoing, AI-assisted physician review of what the scientific literature says about how each microbe impacts the urinary tract. It’s another way to help your provider perform their best work.
The same organism can pose an issue or be benign depending on where in the body it lives. E. coli, for example, is an expected part of a healthy gut, but if it appears in a urine sample it could be the cause of a UTI. That’s why your provider considers your results and symptoms together.
Some sites carry more bacteria than others like the ear canals, mouth, sinuses, and urinary tract which isn’t a cause for concern. Lactobacillus, for instance, is usually the single most abundant organism in a healthy vaginal microbiome, where it actually helps protect against infection — so seeing it dominate a result is often a sign of health, not a problem.
Everything above is meant to help you understand what your report delivers. MicroGenDX generates data, your provider uses that data, along with your medical history and symptoms to drive their diagnosis and treatment plan.
Please don’t start, stop, or change any medication based solely on this report without talking to your provider first.
If you have questions on your report, NGS, billing, or finding a doctor who knows MicroGenDX, you can:
Providers reviewing an unfamiliar report format, or managing a particularly complex case, also have free support options:
This kind of peer support exists because complex infections deserve more than a one-way lab report; they deserve a second set of helpful eyes when needed.
These questions can help you take your understanding of your report into a productive conversation at your next appointment:
A MicroGenDX report can be a powerful tool for getting to the bottom of a stubborn infection, but like any tool, it works best in the right hands: yours for reading it, your provider’s for acting on it. Get comfortable with the format, know what type of information it provides, and lean on the free support available to you and your provider along the way.
This article is for educational purposes only and is not a substitute for professional medical advice, diagnosis, or treatment. Always talk to your healthcare provider about your MicroGenDX lab report.
It’s normal for the lists not to match exactly. qPCR and NGS are two separate testing methods that look for microbes in different ways. qPCR checks for a specific, known list of organisms and drug resistance genes. NGS reads the full genetic material in your sample against a database of over 60,000 bacteria and fungi.
MicroGenDX returns results, both the qPCR and NGS portions, in as soon as 24 hours after the lab receives your sample. Our turnaround is considerably faster than traditional culture, which can take days to weeks and may report an incomplete picture.
MicroGenDX qPCR + NGS testing is 99.2% accurate, having been independently validated by the College of American Pathology (CAP) on an ongoing basis. A breakdown of this extensive process is detailed here. Note this doesn’t replace the clinical judgment needed to interpret what those results mean for your care.
MicroGenDX is a medical testing laboratory that identifies the root cause of infectious disease by reading microbial DNA at the site of infection. Its testing uses qPCR and Next-Generation DNA Sequencing (NGS) technologies to detect the bacteria, fungi, and drug-resistance genes behind your infection, including microbes that don’t grow well in a culture dish and may go undetected.
The result is a picture of the microbial landscape causing infection, delivered in as little as 24 hours after our lab receives your sample. It also has a shortlist of options your provider can consider for treatment.
Possibly. Biofilms are thought to play a role in 65–80% of chronic microbial infections, in part because they resist both detection and treatment. If your infection keeps returning despite treatment, it’s worth asking your provider if a biofilm could be a factor.
No, many of the microbes on your report are normal, helpful residents of your body. Treating all microbes can wipe out the protective ones. A completely sterile microbiome can cause more problems to the functioning of your body, including making you more vulnerable to future infections.
Your provider decides which microbes to treat based on your full clinical picture.
A low or negative result can happen for several reasons:
If you have questions on your sample collection or results, give our Customer Service team a call. Otherwise, your provider is best positioned to interpret what a negative result means for your situation.
Authors
Staff Writer
