Microbiome studies that don’t embarrass you in diligence.
I help biotech teams reduce confounding, batch effects, and claim inflation by turning messy evidence into an executive-ready plan.
Get a 72-hour Defensibility Memo
What you get is simple
Clear risks. Clear fixes. Clear language you can defend.
Microbiome programs fail for reasons that nobody wants to admit:
Confounding (diet, meds, antibiotics) drowns the signal in noise
Batch effects make your “finding” a lab artifact
Multiple testing turns p-values into a slot machine
Claim inflation makes your deck stronger and your data weaker
Unclear endpoints and shifting analyses kill credibility with reviewers and investors
You don’t need more experiments. You need the right next experiment and a plan that holds up under scrutiny
What I do
I’m your external scientific quality system.
I use structured tools to audit the evidence, quantify claim risk, and recommend the cheapest next step that increases defensibility.
If your program is solid, you’ll leave with sharper claims and a cleaner story.
If it’s shaky, you’ll find out before the world does.
Rapid Triage (72 hours)
A fast, fixed-scope assessment designed for founders, CSOs, and investors who need a decision.
You send: protocol, manuscript, preprint, or deck (PDF is fine)
You get: a concise memo with:
Top failure modes and what they cost you
Claim defensibility rating (and what language is safe right now)
Recommended “next best experiment” plan with ranked steps
Specific fixes for confounders, batch effects, and analysis fragility
SERVICES
Claim Defensibility Audit
Align your claims to your evidence so you don’t get destroyed in diligence.
Includes PRΔ scoring, claim language rewrite, and evidence-to-claim mapping.
Best for: investor decks, press releases, product claims
Batch Effect + Chain-of-Custody Audit
A hard operational audit to keep your microbiome data from lying to you.
Includes a standardized audit report and corrective action plan.
Best for: multi-site studies, vendor pipelines, scaling programs
Trial Readiness Sprint
Pre-study design sprint to remove confounders and protocol failure modes before enrollment.
Includes confounder blueprint, sampling and shipping rules, and analysis guardrails.
Best for: teams about to launch a study
What you actually receive
You won’t get vague advice. You’ll get documents your team can execute.
Examples:
Defensibility Memo (PDF)
Next Best Experiment plan (ranked steps)
Batch Effect and Chain-of-Custody audit report
Confounder control blueprint
Trial readiness checklist
R. William DePaolo, PhD (Immunology & Microbiology). Former founding director of a university microbiome center. 25+ peer reviewed publications.
• Built and led multi-team microbiome programs from bench to clinic
• Deep expertise in immunology, microbiome science, study design, and clinical translation
• Known for calling out weak methods and fixing them fast
What I do
a reality check that turns into a roadmap.
I audit your pipeline, study plan, and reporting claims end to end. You get specific fixes, prioritized by impact and effort, plus language you can safely use with clinicians, partners, and investors.
Ways to Work Together
Offer 1: Microbiome Pipeline Reality Check (2 weeks)
A fast, high impact audit of your sampling, wet lab workflow, bioinformatics, stats, reporting, and claim boundaries.
You get
• Red flag list and root cause analysis
• Priority fixes ranked by impact and effort
• A reporting and claims guardrail sheet
• A short readout call with next steps
Offer 2: Study Design and Trial Readiness Sprint (2 to 6 weeks)
For teams about to spend real money on a study. We tighten endpoints, confounders, analysis plans, and decision criteria before you lock anything in.
You get
• Study design critique and redesign recommendations
• Endpoint and heterogeneity strategy
• Analysis plan guardrails and prereg ready outline
• Risk register (what could sink the study and how to prevent it)
Offer 3: Team Workshop (half day or full day)
Training for scientists, clinicians, and product teams on what breaks microbiome inference and how to prevent it.
Popular sessions
• How microbiome results get distorted (by accident or incentives)
• QC, batch, compositional pitfalls, and reporting honesty
• ML for microbiome (what works, what’s hype, what to demand)
Most microbiome programs aren’t failing from lack of data. They’re failing from weak foundations.
If you’ve ever felt unsure whether your results would replicate across labs, survive reviewer criticism, or justify clinical recommendations, you’re not alone. The field is full of avoidable failure modes.
• Batch effects and preprocessing choices quietly drive your “findings”
• Compositional data errors and multiple testing inflate false positives
• Study design and confounders make signals look real when they aren’t
• Reports overpromise, then trust collapses with clinicians and partners
• Teams chase taxonomy lists instead of meaningful function and outcomes
You don’t need more sequencing. You need tighter science and cleaner decision making.
Who this is for
If you’re in one of these seats, this will help.
• Founders and product leads building microbiome tests
• Scientific leads preparing clinical pilots or partnerships
• Sequencing and bioinformatics cores supporting multiple investigators
• Clinics offering microbiome programs that need credibility and restraint
• Investors and due diligence teams evaluating microbiome claims
How it works
Simple process. No chaos.
Step 1
Fit call (20 minutes). We define the goal and decide if the work makes sense.
Step 2
Intake. You share what you have (methods, pipeline overview, reports, study plan).
Step 3
Audit and synthesis. I review, stress test, and map failure modes to fixes.
Step 4
Delivery. You get a written roadmap plus a readout call to align the team.
About
I’m William DePaolo, PhD. I’ve led microbiome and immunology programs across academia and industry, built interdisciplinary research infrastructure, and worked across preclinical and human studies. My style is direct, practical, and evidence first. I’m here to make your results real, not just publishable.
Your Questions, Answered
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Usually within one to two weeks, depending on scope.
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Yes
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I focus on audit, strategy, and governance. If implementation support is needed, we can scope it or I can collaborate with your team.
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We offer flexible pricing based on project type and complexity. After an initial conversation, we’ll provide a transparent quote with no hidden costs.
Want a blunt read on what’s working and what’s quietly breaking?
Book a 20 minute fit call and I’ll tell you quickly if I can help. If not, I’ll point you toward the right next move.