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

Official title

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

Overview

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.

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.

Interventions

• 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

Primary outcome measures

• Feasibility of logistics of the study protocol: Deliveries [Time frame: 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]
• Feasibility of logistics of the study protocol: Recruitment rate [Time frame: 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]

Secondary outcome measures (5)

• Participant compliance to the study protocol [Time frame: 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]
• Sample completeness [Time frame: 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]
• Differences in phytonutrient levels in serum [Time frame: Baseline, Day 8, Day 21, and Day 29]

Eligibility criteria

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

Criteria are shown verbatim from the registry (in English). Final eligibility is always assessed by the study center.

Healthy volunteers: Yes

Study design

Allocation

Randomized

Model

Crossover

Masking

Triple blind

Primary purpose

Prevention

Study locations

Netherlands · 1 center

• Leids Universitair Medisch Centrum — Leiden

Publications

• Julious, S.A. (2005), Sample size of 12 per group rule of thumb for a pilot study. Pharmaceut. Statist., 4: 287-291. https://doi.org/10.1002/pst.185
• Hirt H. Healthy soils for healthy plants for healthy humans: How beneficial microbes in the soil, food and gut are interconnected and how agriculture can contribute to human health. EMBO Rep. 2020 Aug 5;21(8):e51069. doi: 10.15252/embr.202051069. Epub 2020 Jul 31. PMID 32734701
• Blum WEH, Zechmeister-Boltenstern S, Keiblinger KM. Does Soil Contribute to the Human Gut Microbiome? Microorganisms. 2019 Aug 23;7(9):287. doi: 10.3390/microorganisms7090287. PMID 31450753
• Fierer N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol. 2017 Oct;15(10):579-590. doi: 10.1038/nrmicro.2017.87. Epub 2017 Aug 21. PMID 28824177
• David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014 Jan 23;505(7484):559-63. doi: 10.1038/nature12820. Epub 2013 Dec 11. PMID 24336217
• Leeming ER, Louca P, Gibson R, Menni C, Spector TD, Le Roy CI. The complexities of the diet-microbiome relationship: advances and perspectives. Genome Med. 2021 Jan 20;13(1):10. doi: 10.1186/s13073-020-00813-7. PMID 33472701
• Johnson AJ, Zheng JJ, Kang JW, Saboe A, Knights D, Zivkovic AM. A Guide to Diet-Microbiome Study Design. Front Nutr. 2020 Jun 12;7:79. doi: 10.3389/fnut.2020.00079. eCollection 2020. PMID 32596250
• Sanna S, van Zuydam NR, Mahajan A, Kurilshikov A, Vich Vila A, Vosa U, Mujagic Z, Masclee AAM, Jonkers DMAE, Oosting M, Joosten LAB, Netea MG, Franke L, Zhernakova A, Fu J, Wijmenga C, McCarthy MI. Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases. Nat Genet. 2019 Apr;51(4):600-605. doi: 10.1038/s41588-019-0350-x. Epub 2019 Feb 18. PMID 30778224

Identifiers

NCT: NCT07742319 · NL-010026

Primary sources (government registries)

• ClinicalTrials.gov (US NIH)

View this study on ClinicalTrials.gov ↗