Westlake Frequent-sampling Cohort 2

The Westlake Frequent-sampling Cohort 2 (WeF2) is an observational follow-up study that re-enrolls healthy adults who previously completed a 15-day intensive gut microbiome sampling study (WeF) at Westlake University in China. The core idea is to understand not just what your gut microbiome looks like on any given day, but how stable or variable it is across months and years of normal life. Participants will return for periodic low-frequency sample collections and will also repeat the intensive 15-day daily-sampling protocol at intervals beginning roughly six months after the original baseline. By layering sparse routine sampling on top of recurring high-density windows, the study can tease apart the 'stable core' microbiome from fluctuations driven by season, diet, illness, or other life events. This design is methodologically important because most microbiome studies take just one or two snapshots, making it impossible to know whether an observed community is typical for that person or a transient state. WeF2 aims to determine whether short-term day-to-day variability patterns identified at baseline are reproducible features of an individual's microbiome years later. If they are, it would validate short intensive sampling bursts as a reliable 'fingerprint' of personal microbiome dynamics—a finding with broad implications for clinical microbiome testing and research design.

• No results are yet available — the study is actively recruiting as of May 2026; all findings below reflect study objectives, not outcomes.
• Primary objective: determine whether day-to-day gut microbiome variability patterns observed during the original 15-day WeF protocol persist and are reproducible over multi-year follow-up under free-living conditions.
• Secondary objective: distinguish a stable 'core' personal microbiome from transient or seasonally driven community fluctuations by combining sparse longitudinal sampling with repeated high-density 15-day sampling windows.

WeF2 is a prospective observational longitudinal cohort study enrolling adults who completed the prior WeF baseline protocol (15 consecutive days of daily stool and oral biospecimen collection). Follow-up visits are designed at extended intervals (starting ~6 months post-baseline and continuing thereafter), with each interval including both sparse routine biospecimen collection and a repeat of the full 15-day intensive daily-sampling protocol. No intervention is administered; participants continue free-living conditions throughout. Sample size and exact visit schedule are not disclosed in the available registration metadata, and the study is currently in the recruiting phase with an estimated completion horizon extending to at least 2026.

Because this is an observational study of a single previously assembled healthy-adult cohort, findings may not generalise to other populations, age groups, or disease states. Retention bias is a significant concern in multi-year longitudinal designs: participants who remain in the study through repeated intensive sampling windows may differ systematically from those lost to follow-up, potentially inflating estimates of microbiome stability. The study cannot establish causality between microbiome dynamics and any health outcome, nor can it determine whether identified stability patterns are driven by host genetics, diet, geography, or their interaction. A natural next experiment would pair WeF2's observational trajectory data with a controlled dietary or antibiotic perturbation to test whether the stable core microbiome is resilient or merely quiescent.

WeF2 directly extends the methodological framework interrogated in [§100], which argues that human microbiome research needs ecological and causal longitudinal designs to move beyond cross-sectional snapshots—WeF2's repeated high-density sampling windows represent a practical implementation of that framework. It parallels [§75], which also tracks gut microbial colonisation dynamics over time but in a very different population (infants rather than healthy adults), making the two studies jointly informative about the timescales over which microbiome stability is established and maintained across the lifespan. The study also runs parallel to [§72], which characterises microbiota remodelling trajectories in obese patients after bariatric surgery; comparing those procedure-induced community shifts against the natural free-living drift captured in WeF2 will help calibrate what magnitude of change is clinically meaningful versus within normal individual variation. Finally, WeF2's oral microbiota component offers a point of comparison with [§86], where integrated metagenomic signatures are linked to cognitive outcomes, since oral-gut microbial co-dynamics remain poorly characterised in healthy longitudinal cohorts.

• The human microbiome at translational crossroads: an ecological and causal perspective
  Directly argues for the ecological and causal longitudinal study design that WeF2 implements — reading both together clarifies the theoretical motivation behind repeated high-density sampling windows.
• Influence of Probiotics on Early Gut Microbial Colonization
  Also tracks gut microbial colonisation dynamics longitudinally but in infants, providing a developmental contrast that helps contextualise what 'stability' means at different life stages.
• Microbiota remodeling after bariatric surgery: Procedure-specific dynamics and metabolic implications
  Characterises procedure-driven microbiome remodelling trajectories post-bariatric surgery; comparing those perturbation-induced dynamics against WeF2's free-living drift will help define the boundary between pathological and normal community change.
• A single-strain dropout screen reveals mechanistic links between microbial ecology and metabolism
  Uses a single-strain dropout screen to link microbial ecology to metabolism at mechanistic resolution — a useful complement to WeF2's community-level stability data when interpreting which ecological shifts have functional consequences.
• Integrated gut microbiota and metabolome signatures revealed by deep metagenomic sequencing in post-stroke cognitive impairment with type 2 diabetes
  Deploys deep metagenomic sequencing to derive integrated gut microbiota and metabolome signatures in a longitudinal disease context, offering a methodological benchmark for the kind of multi-omic readouts WeF2's biospecimen archive could support in future analyses.