Full disclosure: My institution isn't doing all of this yet. Most aren't.
That's the problem.
We're still practicing reactive infection treatment when a good body of evidence suggests we could be practicing preventive microbiome medicine.
Over the past five editions, we've established:
Microbiome health is fundamental to infection prevention
Antimicrobial stewardship is microbiome stewardship
We can see colonization resistance failing before infections occur
ID physicians should be leading this transformation
Now the question is: What does that actually look like?
The Four Components of Preventive Microbiome Programs
It goes without saying, not every patient needs microbiome monitoring. It makes sense to focus on populations where microbiome disruption predictably increases infection risk:
High-risk populations would include the following:
Prolonged ICU stays with broad-spectrum antibiotics
Multiple antibiotic courses
Immunocompromised hosts
Recurrent infections (CDI, UTIs, bacteremia)
Predictable microbiome disruption (critical illness, bowel prep, prolonged NPO)
The framework:
Identify patients where microbiome disruption is likely and infection risk is high.
Studies show up to 90% of gut commensals can be lost within hours of critical illness.
Patients who develop hospital-acquired infections show earlier microbiome disruption than those who don't.
We can predict who's at risk. The question is whether we act on it.
This is microbiome stewardship applied systematically:
Antimicrobial optimization:
Narrowest-spectrum agent appropriate
Shortest effective duration
Explicit microbiome-preserving rationale
Heightened scrutiny for prolonged courses in high-risk patients
Supportive strategies:
Early enteral nutrition when feasible
Evidence-based probiotics in specific populations
Avoidance of unnecessary antimicrobial exposure
The framework:
Default to microbiome preservation unless clinical necessity dictates otherwise.
Where microbiome diagnostics are available:
Routine baseline assessment in high-risk patients
Serial monitoring to identify loss of diversity, pathogen dominance, resistance genes
Intervention triggers based on microbiome signatures
When diagnostics aren't available, use clinical proxies such as antimicrobial exposure history, development of secondary infections, clinical deterioration.
The framework:
Make colonization resistance visible so you can act before infection occurs.
When monitoring reveals high-risk microbiome states:
Microbiome restoration:
FMT for recurrent CDI (established)
Emerging microbiome therapeutics
Targeted probiotic strategies
Modified prophylaxis:
Adjustment based on microbiome composition
Heightened surveillance for specific patients
Antimicrobial modification:
Earlier discontinuation when patterns are concerning
Alternative agents preserving beneficial bacteria
The framework:
Intervene based on microbiome state, not just clinical infection.
The Cost Barrier (And Why It's Not the Real Problem)
To be honest: Cost is real.
mNGS runs $300-500 per sample.
Not every institution can afford routine surveillance.
Insurance coverage is inconsistent.
But we are missing the point:
The question isn't "Can we afford microbiome diagnostics?"
The question is "Can we afford NOT to prevent infections?"
The math:
One C. difficile case: $15,000-30,000
One ICU bacteremia: $40,000+
One VAP: adds 4-13 days to mechanical ventilation
If microbiome-focused prevention prevents even a fraction of these infections, the ROI is compelling.
And here's the critical point: You don't need expensive diagnostics to start practicing preventive microbiome medicine.
You can start TODAY with:
Better microbiome stewardship (you're already doing this)
Risk stratification (clinical assessment, no cost)
Microbiome-protective protocols (better antimicrobial decisions)
Early intervention for high-risk patients (clinical judgment)
Better tools help. But better decisions can come first.
When diagnostic tools become more accessible—and they will—the institutions practicing preventive thinking will be ready to integrate them effectively.
The institutions waiting for perfect tools will be playing catch-up.
Better Tools → Better Decisions → Better Outcomes
This is my mantra for a reason.
Better microbiome diagnostics are coming. They'll enable better decisions about when and how to intervene.
But you don't need to wait for better tools to start making better decisions.
You can practice preventive microbiome medicine today by:
Thinking about colonization resistance, not just pathogens
Identifying patients at risk before infection occurs
Preserving microbiomes through smart stewardship
Intervening based on ecological understanding
Better decisions lead to better outcomes. The tools just make those decisions more precise.
What's Next
In the next edition, I'll show you what these four components actually look like in practice:
How preventive microbiome medicine transforms ICU care
What it means for managing recurrent infections
The practical roadmap from where you are today to where you want to be
Because frameworks are useful. But implementation is everything.
Your Turn
Which of these four components is your institution strongest in?
Which one represents your biggest gap?
What would it take to start addressing that gap?
Let's talk in the comments.
👋🏿 Hi! I'm Dr Tina Agbaosi
👩🏿⚕️ Infectious Diseases physician and Metagenomics enthusiast. Approaching science and patients, with curiosity and kindness opens doors that pure clinical knowledge alone never could.