How Differences in the Composition of Microorganisms in the Soil Affect the Microorganisms in the Human Gut, Through the Vegetables That Grow in it: a Process Pilot Study With Healthy Participants (HUMANITAS)

July 29, 2026 updated by: Pieter Maljaars, Leiden University Medical Center

The Effect of Soil Biodiversity on Human Gut Microbiome: a Process Pilot Study (The HUMANITAS Study)

There are two objectives for this clinical trial. The first is to test whether, with the current logistics and study setup it is possible to perform the study well and see where there might be bottlenecks we couldn't predict. The second objective is to investigate the relation between the composition of the microorganisms in the soil, the crops that grow in that soil, and the human gut. During the study participants will drink three vegetable smoothies a day, for two periods of one week. The only difference between the two periods is whether the vegetables come from a farm with a low diversity of microorganisms in the soil or a high diversity. Participants will be asked to give blood samples and turn in fecal samples before and after each period.

Study Overview

Status

Not yet recruiting

Conditions

Intervention / Treatment

Detailed Description

This randomized, double-blind, crossover pilot study will be used to assess the feasibility of logistics including vegetable delivery and preparation of the intervention product by the participants themselves. Besides feasibility, we will aim to identify live bacteria and fungi present in the intervention product (smoothies) and trace these back in stool samples.

The gut microbiome is also called the "second genome" to which many protective and life-supporting functions have been externalized. It orchestrates the crosstalk between our own cells and environmental metagenome. Diet and food choices can modulate gut microbiome species and functional diversity, but the mechanisms by which this occurs are unclear. The nutritional quality of crops, the crop microbiome and the soil microbiome may therefore all be involved.

Ten participants will be randomized in a cross-over design, with each participant drinking three 150 mL vegetable smoothies per day for two separate intervention weeks (HiDi vs LoDi soil origin, randomized 1 : 1). During the first week, smoothies will be prepared with the vegetables derived from microbiome-enriched soil (HiDi) or microbiome-impoverished soil (LoDi). Vegetables, a blender, and detailed instructions to prepare the smoothies on-site will be delivered to the participant. Each participant is asked to keep a diary (in the form of a daily Castor questionnaire), with special attention to dietary habits and intake. Furthermore, before and after this specified diet week, blood and stool samples will be collected. After a washout period of two weeks, participants will be offered identical meals in a crossover design.

Study Type

Interventional

Enrollment (Estimated)

10

Phase

  • Not Applicable

Contacts and Locations

This section provides the contact details for those conducting the study, and information on where this study is being conducted.

Study Contact

Study Contact Backup

Study Locations

  • Netherlands
    • South Holland
      • Leiden, South Holland, Netherlands, 2333ZA
        • Leids Universitair Medisch Centrum
        • Contact:
        • Principal Investigator:
          • Jeroen Maljaars, MD, PhD

Participation Criteria

Researchers look for people who fit a certain description, called eligibility criteria. Some examples of these criteria are a person's general health condition or prior treatments.

Eligibility Criteria

Ages Eligible for Study

  • Adult
  • Older Adult

Accepts Healthy Volunteers

Yes

Description

Inclusion Criteria:

  • Aged 18 to 70 years
  • Written informed consent
  • Inhabitant of Leiden

Exclusion Criteria:

  • Any documented causes of chronic disease
  • Suspicion of or present excessive alcohol use defined as >2 units/day (>14/week)
  • Recent use (<3 months) of antibiotics
  • Any known food allergy or restriction, or following a vegan/vegetarian diet
  • Use of possible drugs interfering microbiota or recent (< 3 months) changes in dosages
  • A psychiatric, addictive or any other disorder that compromises the participants ability to understand the study content and to give written informed consent for participation in the study

Study Plan

This section provides details of the study plan, including how the study is designed and what the study is measuring.

How is the study designed?

Design Details

  • Primary Purpose: Prevention
  • Allocation: Randomized
  • Interventional Model: Crossover Assignment
  • Masking: Triple

Arms and Interventions

Participant Group / Arm
Intervention / Treatment
Active Comparator: Crops derived from Low followed by High diversity soil
Participants will be given vegetables, originating from low- or high-microbial diversity soil, to prepare smoothies with. In this arm participants start with vegetables from a low diversity soil, after a washout period of two weeks they will receive vegetables from a high diversity soil.
Other: Low diversity vegetable smoothie
Vegetable smoothie prepared with crops grown in low-microbial diversity soil
Other: High diversity vegetable smoothie
Vegetable smoothie prepared with crops grown in high-microbial diversity soil
Active Comparator: Crops derived from High followed by Low diversity soil
Participants will be given vegetables, originating from low- or high-microbial diversity soil, to prepare smoothies with. In this arm participants start with vegetables from a high diversity soil, after a washout period of two weeks they will receive vegetables from a low diversity soil.
Other: Low diversity vegetable smoothie
Vegetable smoothie prepared with crops grown in low-microbial diversity soil
Other: High diversity vegetable smoothie
Vegetable smoothie prepared with crops grown in high-microbial diversity soil

What is the study measuring?

Primary Outcome Measures

Outcome Measure
Measure Description
Time Frame
Feasibility of logistics of the study protocol: Deliveries
Time Frame: From start enrollment to the end of treatment at 4 weeks
The percentage of successful deliveries to the participants in the pre-agreed time window.
From start enrollment to the end of treatment at 4 weeks
Feasibility of logistics of the study protocol: Preparation of the intervention product
Time Frame: From the start of the treatment period until the end at 4 weeks
Using the Daily diary (Castor questionnaire), successful preparation of the intervention product is assessed.
From the start of the treatment period until the end at 4 weeks
Feasibility of logistics of the study protocol: Recruitment rate
Time Frame: From the start of recruitment until the start of the study
Number of recruited participants per month until the start of the study.
From the start of recruitment until the start of the study
Tracing back life microorganisms from the smoothie in stool samples
Time Frame: Day 1, Day 7, Day 22, and Day 28
Life bacteria present in the smoothies will be cultured and sequenced to then compare to feces samples of participants
Day 1, Day 7, Day 22, and Day 28

Secondary Outcome Measures

Outcome Measure
Measure Description
Time Frame
Participant compliance to the study protocol
Time Frame: From start enrolment until the end of treatment at the end of 4 weeks
Compliance with the protocol will be assessed through the daily lifestyle diary (in the form of a Castor questionnaire). Which will capture the number of consumed smoothies (≥95.2%) and number of consumed smoothies at the correct time window (≥80%). As well whether the duration and time of exercise (≥80%), duration and time of nighttime sleeping period (≥80%), timing and content of main meals (≥80%) between the two periods are comparable. For each of the parameters the compliance threshold is indicated above. Based on these parameters we will get a percentage of participants that were compliant.
From start enrolment until the end of treatment at the end of 4 weeks
Shifts in gut microbiome composition
Time Frame: Baseline, Day 8, Day 21, and Day 29
Metagenomics will be performed on feces samples from participants to get an compositional view of the gut microbiome. Samples will be taken at baseline, Day 8, Day 21, and Day 29
Baseline, Day 8, Day 21, and Day 29
Sample completeness
Time Frame: From start of treatment to the end of treatment at 4 weeks
percentage of complete sampling sets
From start of treatment to the end of treatment at 4 weeks
Asses willingness of participants to create their own intervention product
Time Frame: From start treatment to end of treatment at 4 weeks
Using the Daily diary (Castor questionnaire), the participants are required to fill in their opinion on creating their own intervention product on a daily basis. This is measured on a 10 point scale, with 1 being equal to never wanting to do it again and 10 being equal to enjoying it. There is also an optional open question where participants can justify their answer.
From start treatment to end of treatment at 4 weeks
Differences in phytonutrient levels in serum
Time Frame: Baseline, Day 8, Day 21, and Day 29
After confirmation of significant changes in gut microbiome composition, phytonutrient levels will be measured in serum. Serum will be collected at Baseline, Day 8, Day 21, and Day 29
Baseline, Day 8, Day 21, and Day 29

Collaborators and Investigators

This is where you will find people and organizations involved with this study.

Sponsor

Leiden University Medical Center

Collaborators

Maastricht University

Publications and helpful links

The person responsible for entering information about the study voluntarily provides these publications. These may be about anything related to the study.

General Publications

Study record dates

These dates track the progress of study record and summary results submissions to ClinicalTrials.gov. Study records and reported results are reviewed by the National Library of Medicine (NLM) to make sure they meet specific quality control standards before being posted on the public website.

Study Major Dates

Study Start (Estimated)

August 1, 2026

Primary Completion (Estimated)

September 1, 2026

Study Completion (Estimated)

September 1, 2026

Study Registration Dates

First Submitted

July 16, 2026

First Submitted That Met QC Criteria

July 29, 2026

First Posted (Actual)

August 3, 2026

Study Record Updates

Last Update Posted (Actual)

August 3, 2026

Last Update Submitted That Met QC Criteria

July 29, 2026

Last Verified

July 1, 2026

More Information

Terms related to this study

Keywords

Other Study ID Numbers

  • NL-010026

Plan for Individual participant data (IPD)

Plan to Share Individual Participant Data (IPD)?

YES

IPD Plan Description

Metagenomic sequencing data from feces and pythonutrient levels in serum (if available)

IPD Sharing Time Frame

Beginning 1 month after publication with no end date

IPD Sharing Supporting Information Type

  • STUDY_PROTOCOL
  • ANALYTIC_CODE

Drug and device information, study documents

Studies a U.S. FDA-regulated drug product

No

Studies a U.S. FDA-regulated device product

No

This information was retrieved directly from the website clinicaltrials.gov without any changes. If you have any requests to change, remove or update your study details, please contact register@clinicaltrials.gov. As soon as a change is implemented on clinicaltrials.gov, this will be updated automatically on our website as well.

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