Impact of doxycycline post-exposure prophylaxis for sexually transmitted infections on the gut microbiome and antimicrobial resistome.

Name: Αlpha¹ Rigor Record — Impact of doxycycline post-exposure prophylaxis for sexually transmitted infections on the gut microbiome and antimicrobial resistome.
Item: Impact of doxycycline post-exposure prophylaxis for sexually transmitted infections on the gut microbiome and antimicrobial resistome.
Rating: 100
Author: Αlpha¹

Chu VT, Glascock A, Donnell D, Grabow C, Brown CE, Ward R, Love C, Kalantar KL, Cohen SE, Cannon C, Woodworth MH, Kelley CF, Celum C, Luetkemeyer AF, Langelier CR

Paper source

Read full text (PMC)

Embed this Rigor badge

Αlpha¹ Rigor Review — 4.5★ (Strong), 0 critical, 2 high issues for “Impact of doxycycline post-exposure prophylaxis for sexually transmitted infections on the gut microbiome and antimicrobial resistome.”

Links back to this Rigor Record.

Αlpha¹ Editorial

This rigor review was examined and confirmed by Αlpha¹ Editorial · August 16, 2026

Αlpha¹ Rigor Review

Rigor Reviewed

4.5 / 5

Strong — minor issues to address

Observational Study

Critical

High-priority

How this rating was calculated▸

Started at 5★ — deductions

IntegrityIntegrity concern−0.5★

Model-reported confidence: highReviewer agreement: highEngine: 7.39.0Source: full text

Problems surfaced2 types

Numerical inconsistencies1

Values that contradict each other or are impossible for the stated sample: recomputed p-values and test statistics, GRIM/GRIMMER checks on summary numbers, percentages against their own counts, totals against their parts, and estimates against their own confidence intervals.

Internal contradictions in the reported numbersAssessed

Overstated conclusions1

Conclusions that reach past what the paper's own results support — including a significance claim that no longer holds when the statistic is recomputed, and efficacy resting on an unvalidated surrogate endpoint.

Conclusions only partially backed by the presented evidenceAssessed

This Αlpha¹ Rigor Review uses AI Rigor Reviewers trained on a curated corpus of high-fidelity and retracted papers, with expert supervision and curation. It can still make mistakes; verify each finding against the source before relying on it.

This is a well-conducted secondary analysis of a randomized trial, with strong reporting of study design, ethics, key resources, data/code availability, and transparency. The main weaknesses are minor: lack of explicit blinding and power analysis for the secondary analysis, and a few copyedit issues including an internal inconsistency in participant count (501 vs 510).

This is an observational secondary analysis of a randomized trial; both reviewers agreed on this classification. The statistics verification covered only a subset of tests (3 tests, 2 consistent, 0 inconsistent) and cannot confirm the correctness of all reported statistics. The citation check found no retracted or unresolved references. The copyedit pass flagged minor issues, including a participant-count inconsistency.

6 major claims checked against the paper's own evidence: 1 only partially supported (evidence backs part of the claim; gaps or caveats remain); the rest adequately supported.

Recomputed 2 tests: 2 consistent, 0 inconsistent; 2 via agent-written checks.

1 integrity concern flagged (0 high).

Reporting

Eight Dimensions8 pass

The introduction cites randomized trials of doxy-PEP and notes the lack of data on its impact on the gut microbiome and resistome. It acknowledges limitations of prior studies (culture-based or 16S rRNA) and justifies the use of metagenomics and metatranscriptomics. The hypothesis follows logically from the cited evidence.

Sub-criteria

prior work citedADEQUATE

premise rationaleADEQUATE

limitations addressedADEQUATE

Per reviewer (2) — the votes behind the verdict

PASSReviewer 1· 90% conf

The paper establishes a clear scientific premise by citing prior work on doxy-PEP efficacy and concerns about antimicrobial resistance, and it logically motivates the study of the gut resistome.

Evidence

paraphrase[Introduction, paragraph 1]

“Doxycycline post-exposure prophylaxis (doxy-PEP) is highly efficacious in preventing bacterial sexually transmitted infections (STIs) in randomized, controlled clinical trials among men who have sex with men (MSM) and transgender women living with HIV or on pre-exposure prophylaxis (PrEP) to prevent HIV infection.”

paraphrase[Introduction, paragraph 3]

“The few studies that have evaluated the impact of doxycycline exposure on the human microbiome involved daily doxycycline use and were based primarily on bacterial culture or 16S rRNA gene amplicon sequencing, limiting their ability to evaluate the antimicrobial resistance genes (ARGs) in the microbiome, termed the resistome.”

direct quote[Introduction, paragraph 4]

“To address the outstanding question of whether doxy-PEP impacts the ecology of the gut microbiome and resistome, we studied longitudinally collected rectal swabs from DoxyPEP clinical trial participants using a combination of DNA-seq and RNA-seq approaches.”