Effects of Gastric Acid on Colonic Microbiome: Complete Statistical Analysis

1. Trial at a Glance

This page covers the registry results for Effects of Gastric Acid on Colonic Microbiome (NCT01901276), a na phase 4 study. The primary outcome is Shannon Diversity Index Measuring Change in Microbiome Diversity.

2. Clinical Question

The scientific rationale in the registry record is that antibiotics can perturb the microbiome and allow Clostridium difficile to proliferate, while long-term PPI use has been associated with Clostridium difficile-associated diarrhea in observational studies. The record describes the mechanism linking PPIs and that association as unknown. This study was designed to examine a proposed microbiome mechanism, not to measure whether PPI use changes the occurrence of diarrhea or infection.

The planned microbiome questions included whether PPI use diminishes overall diversity, whether it diminishes the relative abundance of Bacteroidetes, whether duration affects diversity, and whether diversity recovers after a defined course. The primary outcome named in the registry record is the Shannon diversity index. The outcome description specifies changes across Week 0, Week 4, and Week 8; the record does not report numerical estimates for those changes. As a single-group study, its comparisons are changes over time in the study group, not differences between randomized treatment groups.

3. Trial Design

This is a completed Phase 4 study with a single-group model and no masking. Allocation is listed as NA, and the registry record explicitly identifies the study as not being a randomized comparison. Enrollment is 14. The record lists a start date of 2013-08 and primary completion in 2015-03. The sponsor is Daniel Freedberg, MD.

The intervention is listed as Omeprazole 40 mg bid. The arm description names Omeprazole 40 mg Bid x 4-8 Weeks. The primary outcome timeframe is Baseline (Week 0), Week 4, and Week 8. Its description frames the first planned change as Week 0 versus Week 4, after four weeks of no acid suppression, and the next as Week 4 versus Week 8, after four weeks of twice-daily PPI. The registry record does not provide further details about the schedule of visits or adherence assessment.

Fecal samples were to be used to describe the colonic flora with pyrosequencing of the hypervariable V4 region of the bacterial 16S ribosomal subunit gene. The primary outcome is a median Shannon diversity index with a 95% confidence interval. The record does not state the statistical test or model used to estimate changes, nor does it provide a detailed analysis plan.

With no control arm, the design can describe patterns of change in the participants observed over time. It cannot, by design alone, separate a change associated with the intervention from changes due to other influences that vary over time. The registry record does not report randomization, masking, or a concurrent comparison group. The record also does not explain the basis for the enrollment target or give a sample-size justification for the original study design.

4. Participant Flow and Accounting

The registry reports how participants moved through each stage of the study. All counts below are exactly as posted; missing counts are not inferred from other stages.

No PPI: Week 0 to Week 4

Reasons for not completing this period:

On PPI: Week 4 to Week 8

Randomization: Week 8 to Week 12

5. Baseline Characteristics

The table reproduces the baseline characteristics posted in the registry, which describe the participants analysed at baseline and help show whether the randomized groups were comparable.

Population: Healthy volunteers.

6. Primary Endpoint

The registry lists the primary outcome as Shannon Diversity Index Measuring Change in Microbiome Diversity, measured over Baseline (Week 0), Week 4, Week 8.

The primary outcome is the Shannon diversity index, a mathematical measure of species diversity in a community. The registry description defines it using the proportions of the different species in the community: the index is higher when diversity is higher. It states that a value of 0 represents no diversity, with only one species present, and that the index has no upper limit.

The stated unit is the Shannon index. The outcome is summarized as a median with a 95% confidence interval. The planned time points are Baseline (Week 0), Week 4, and Week 8. The description specifies assessment of change from Week 0 to Week 4 during four weeks without acid suppression, then from Week 4 to Week 8 during four weeks of twice-daily PPI. This makes the endpoint relevant to the study's proposed question about whether microbiome diversity changes over time in relation to PPI exposure.

In general, a diversity index condenses information about the mix of species into a measure that can be compared across samples. It does not, by itself, identify which species account for a change or establish why that change occurred. The registry record does not report the observed median values or confidence intervals, so the size and precision of the measured changes cannot be described from the registry results presented.

7. Why No Re-analysis Is Shown

8. Statistical Interpretation

9. Statistical Methods Explained

The primary outcome is a median Shannon diversity index with a 95% confidence interval. The index is calculated from the proportions of species in a community, as described in the registry record. In general, a median is the middle value when observations are ordered. It can be useful when a distribution is asymmetric or includes values far from the center, but a median alone does not describe the full distribution. The registry record does not state whether the median is calculated separately at each time point or how the changes between time points are summarized.

What does the Shannon index represent?

In general, diversity measures capture more than the presence of species: they reflect the distribution of observations across the species in a community. The registry description identifies the Shannon index as increasing with species diversity and explains that its minimum is 0, corresponding to a community with only one species. There is no upper limit. A value is therefore interpreted in relation to the species composition and proportions represented in the sample. The index does not on its own identify which organisms changed, and it is not a direct measure of clinical illness.

The study planned to characterize fecal samples using pyrosequencing of the hypervariable V4 region of the bacterial 16S ribosomal subunit gene. This describes the assay approach named in the registry record. The record does not report further laboratory procedures, quality-control criteria, or how sequencing observations were processed into index values. Those details are not reported in the registry record.

How should a confidence interval be read?

In general, a confidence interval presents a range of values compatible with an estimate under the statistical procedure and its assumptions. It communicates precision as well as the central estimate: an interval that spans a broad range is less precise than one spanning a narrower range. A confidence interval is not a guarantee that the true value lies within the particular observed interval, and its interpretation depends on the method used to construct it. The registry record specifies a 95% confidence interval for the median but does not identify the interval-construction method or give the interval limits. Its precision therefore cannot be evaluated from the posted results.

The planned assessments compare Week 0 with Week 4, then Week 4 with Week 8. Because the study is single-group, these are comparisons over time in the study group rather than randomized between-arm contrasts. In general, repeated measurements can help describe how an outcome changes within participants. Analysis of repeated observations must account for the fact that measurements from the same participant may be related. The registry record does not state whether the analysis used a paired method, a longitudinal model, or another approach. It would be inappropriate to attribute a particular method to the investigators without that information.

What is not specified about the analysis?

The registry record names the endpoint, summary measure, confidence level, and time points, but does not report a hypothesis test, model, covariate adjustment, handling of ties or missing observations, or criteria for excluding samples. It also does not state whether the analysis was prespecified in a detailed statistical analysis plan. These are not reported in the registry record. Without them, the assumptions behind any inferential result cannot be checked, and no inferential result is available in the posted outcome information in any case.

The study summary describes several scientific questions: overall diversity, relative abundance of Bacteroidetes, duration of PPI exposure, and recovery after the course. In general, when multiple outcomes or comparisons are examined, the chance of at least one apparently unusual result can increase if each is assessed separately without accounting for multiplicity. A multiplicity strategy can set out how to interpret related tests collectively. The registry record does not report such a strategy. It also lists one outcome measure and one analysis, but that count does not clarify whether all of the questions described in the study summary were addressed or how comparisons were handled.

A sample-size planning illustration is described using a two-sided significance level of 0.05, equal allocation between two arms, and a normal approximation, with the effect to detect stated as a fraction of the observed effect. The assumptions are for a planning illustration, not a description of the study's single-group design. Any sample-size values from such an illustration are planning quantities, not observed power and not evidence that the study had a particular probability of detecting an effect. The registry record does not report a sample-size justification for the original study design, and the stated illustration does not convert the single-group study into a randomized comparison.

In general, over-dispersion occurs when variability is greater than a statistical model assumes. If ignored, uncertainty estimates can be too small and tests can be misleading. Whether over-dispersion is relevant depends on the outcome and model. The registry record does not describe a model for which over-dispersion can be assessed, so no claim about its presence or handling can be made for this study.

10. Multiplicity, Missing Data and Analysis Populations

The study summary names several questions: overall microbiome diversity, relative abundance of Bacteroidetes, effects of PPI duration, and recovery of diversity after a defined course. The primary outcome record specifies Shannon diversity and two planned time comparisons, but the registry record does not report how the other questions were analyzed or how multiple outcomes and comparisons were handled. A multiplicity adjustment or hierarchy for interpreting results is not reported in the registry record.

In general, examining multiple outcomes or time contrasts can make isolated findings harder to interpret if each is treated as a separate confirmatory test. A prespecified approach can clarify which outcome is primary and how secondary findings should be viewed. The record names a primary outcome, but does not give a detailed statistical analysis plan or a stated strategy for controlling multiplicity. The number of listed outcome measures and analyses does not, by itself, show how the broader set of scientific questions was handled.

The outcome information does not report the number of participants with usable samples at each time point, missing-data reasons, or the method used for missing observations. The registry record does not state whether all enrolled participants were included in each analysis or define an analysis population. These details are not reported in the registry record. It is therefore not possible to assess whether incomplete sampling could have affected the summaries or whether the participants contributing data differed across time points.

In general, missing observations matter when the probability of missingness is related to participant characteristics or outcomes. Different approaches to missing data rely on different assumptions, and the assumptions should be described to interpret estimates. No such approach is reported for the primary endpoint. The record also does not report sensitivity analyses exploring the effect of missing samples. The information available is insufficient to judge the completeness or robustness of the primary outcome analysis.

11. Safety Results

The registry reports serious adverse events as affected participants divided by participants at risk.

Deaths

Other (non-serious) adverse events

Participants with at least one non-serious event at or above the registry's 0% reporting threshold.

The safety record lists the Omeprazole 40 mg Bid x 4-8 Weeks group with 12 participants at risk for serious adverse events and 0 affected. It also lists 12 at risk for other adverse events and 0 affected, and deaths are listed as 0. No top serious terms are listed. These are the counts recorded for the displayed safety categories.

These figures should be read as registry counts, not as a complete description of all possible safety outcomes. The record does not give additional detail about how adverse events were defined, collected, or followed, and it does not report event-level descriptions beyond the empty list of top serious terms. The enrollment figure is 14, whereas the safety record lists 12 at risk; the reason for this difference is not reported in the registry record. The safety denominator should not be assumed to represent every enrolled participant.

In general, a count of zero observed events does not prove that an event cannot occur, and it does not establish safety beyond the participants and observation captured by the record. These counts also do not provide a randomized comparison. They should not be read as an estimate of a difference between omeprazole and another treatment or no treatment.

12. What the Result Does, and Does Not, Mean

The registry record documents a completed single-group study of omeprazole exposure and planned assessment of colonic microbiome diversity. It identifies the Shannon diversity index as the primary outcome and specifies samples at baseline (Week 0), Week 4, and Week 8. The record does not report numerical primary outcome results. It therefore does not show the observed direction or magnitude of change, nor how precisely change was estimated.

The study's rationale concerns a proposed mechanism for the association between long-term PPI use and Clostridium difficile-associated diarrhea. Its primary endpoint is a microbiome diversity measure, not a clinical endpoint such as diarrhea or infection. Even if changes in diversity were reported, such a finding would not by itself demonstrate a change in clinical risk or confirm a causal pathway. The registry record does not report clinical outcome results for those conditions.

Because the study has no randomized comparison group, the time comparisons cannot establish that any change was caused by omeprazole. In general, before-and-after observations can describe how measurements vary over time, but do not independently control for other factors that may also change over time. This limitation applies to the design whether or not a numerical change is observed.

The planned questions about Bacteroidetes, PPI duration, and recovery are also described in the study summary. Numerical results for these questions are not reported in the registry record. Their mention as aims should not be confused with evidence that an effect was found, or that each question was answered.

The serious and other adverse-event categories list 0 affected among 12 at risk, and deaths are listed as 0. These are the posted counts, with the limitations of the safety information. Overall, the registry record supports a description of the study design and its intended endpoint, but not a conclusion about the observed microbiome result or a causal clinical effect.

13. Why This Trial Matters Statistically

This study illustrates a common statistical challenge in mechanistic clinical research: a biological measure can be informative about a proposed pathway without directly measuring the clinical outcome that motivated the hypothesis. Here, the registry record links its rationale to PPI use, microbiome changes, and Clostridium difficile-associated diarrhea, while the primary outcome is the Shannon diversity index. Keeping those levels of evidence distinct is essential when interpreting a study.

The repeated time points are also important to the question being asked. The outcome description distinguishes a period without acid suppression from a later period of twice-daily PPI. Repeated measurements can describe patterns within participants, but the absence of a concurrent randomized control group limits causal attribution. The design can address change over time in the study group; it cannot, by itself, determine what would have happened over the same period without the intervention.

The record's reporting gaps make the distinction between planned measurement and observed evidence especially clear. It names the endpoint and its summary form, but does not report the median values or confidence intervals. Without those estimates, neither direction nor precision can be evaluated. The record also does not detail the analysis approach, missing-data handling, or multiplicity strategy. These omissions limit statistical interpretation independently of the study's sample size.

Finally, the posted safety counts demonstrate why denominators and analysis populations matter. Enrollment is 14, while 12 are listed at risk in the adverse-event categories, and the reason is not given. A reader cannot assume that the same participants contributed to every endpoint. Transparent reporting of outcome estimates, uncertainty, analysis populations, and the handling of missing observations is necessary to evaluate both the strength and limits of a clinical study's evidence.

14. Limitations

• The posted summary statistics are the only data these results rest on; patient-level data, full protocols and statistical analysis plans are not available.
• Recalculated results are simple, unadjusted calculations from posted summaries. They do not replace the sponsor's prespecified analysis.

The most important limitation for interpreting the primary outcome is that numerical results are not reported in the registry record. The median Shannon values, confidence interval limits, and estimated changes are absent. Thus, the direction, size, and precision of any change cannot be evaluated. The record also does not give the number of participants contributing outcome data at each time point.

The study is unblinded and single-group, with allocation listed as NA. There is no randomized control arm, so changes over time cannot be separated from other time-varying influences by a concurrent comparison. This limits causal interpretation of any observed before-and-after pattern. The registry record does not report further details about participant eligibility, recruitment, adherence, or the timing of sample collection beyond the stated time points.

The methods description identifies the sequencing approach and the Shannon index but does not report key analytical details, including the statistical test or model, missing-data approach, sample-processing criteria, or multiplicity strategy. The registry record does not say whether the primary outcome was analyzed as specified or whether the additional questions in the study summary were analyzed. These details are not reported in the registry record.

The record lists enrollment as 14 and safety denominators of 12, but does not explain the difference. It also does not report a sample-size justification for the original study. The planning illustration described in the record is separate from the single-group design and is not evidence of observed power. Finally, the study's microbiome endpoint is not a direct measure of Clostridium difficile-associated diarrhea or infection, so it cannot alone answer the clinical question that motivated the proposed mechanism.

15. Related Tutorials

16. Related Statistical Calculators

17. Sources

• ClinicalTrials.gov: Effects of Gastric Acid on Colonic Microbiome — NCT01901276.
• Registry record last updated 2024-08-15; status last verified 2024-07.
• Results first posted 2024-08-15.
• Data retrieved from ClinicalTrials.gov on 2026-11-09.
• Group sizes, means, event counts and sponsor-reported p-values are reproduced as posted. Effect estimates, confidence intervals and p-values not attributed to the sponsor are independently calculated from the posted summary statistics.

18. Record Summary

NCT01901276 is a completed Phase 4, unblinded, single-group study titled “Effects of Gastric Acid on Colonic Microbiome.” Enrollment is listed as 14. The intervention is Omeprazole 40 mg bid, with the arm described as treatment for 4-8 weeks. The primary outcome is the median Shannon diversity index with a 95% confidence interval, assessed at Baseline (Week 0), Week 4, and Week 8.

The study summary describes fecal sampling and pyrosequencing of the bacterial 16S gene's V4 region to examine microbiome diversity and related questions. The registry record does not report numerical primary outcome results, analysis details, or the number contributing data at each time point. The safety record lists 0 serious adverse events and 0 other adverse events among 12 at risk, with 0 deaths.