Fecal Sample Collection for Gut Microbiome Research in a Prospective Cohort: A Pilot Study within the Australian Breakthrough Cancer Study

Sep 30, 2026

Uploaded by Margaret

Large prospective analyses of human gut microbiome profiles are essential to clarify how microbiome variation contributes to disease development. A pilot study evaluated whether participants could feasibly collect fecal samples at home within a cohort. Randomly selected participants were assigned to four collection and questionnaire groups, and outcomes measured participation, sample return, and downstream DNA suitability. DNA from both fecal occult blood test cards and 95% ethanol tubes supported high-quality metagenomic analyses with highly concordant microbiome profiles. Results supported home fecal collection feasibility, with added components not reducing completion likelihood.

LanguageEnglish

CategoryHealthcare

FormatPDF

Pages7

Reading Time18 min

AccessFree to download

Abstract

Feasibility and participant completion

Sample quality for metagenomic sequencing

Introduction

Microbiome measurement and collection variability

Collection approaches: FOBT cards and ethanol tubes

Study design context: ABC cohort

RESEARCH ARTICLE [https://doi.org/10.1158/2767-9764.CRC-25-0445](https://doi.org/10.1158/2767-9764.CRC-25-0445) OPEN ACCESS Fecal Sample Collection for Gut Microbiome Research in a Prospective Cohort: A Pilot Study within the Australian Breakthrough Cancer Study Simon Cheah1,2, Jared Burke3, Fiona J. Bruinsma1,2,4, Melanie Evans1, Helen Tsimiklis3, Allison M. Hodge1,2, Brigid M. Lynch1,2, Graham G. Giles1, Rashmi Sinha5, Melissa C. Southey1,2,3, and Roger L. Milne1,2,3 􀀶 ABSTRACT Large prospective analyses of human gut microbiome profiles are needed to elucidate the role of microbiome variation in the development of disease. We conducted a pilot study to assess the feasibility of home fecal sample collection within a cohort study. A subset of cohort study participants was randomly selected and randomized into four groups defined by fecal sample collection method and questionnaire components. Of 1,093 invited participants, 610 (56%) opted-in, and of those, 88% returned a sample. Of those asked to provide a fecal sample via fecal occult blood test (FOBT) card and complete a short “day-of-sample”questionnaire, 49% returned a sample. Sample return was comparable for participants additionally asked to provide a sample via ethanol tube (51%), complete a food frequency questionnaire (48%), or complete both additional activities (49%). Whole-genome sequencing and metagenomic analysis on paired FOBT and ethanol samples showed that both collection methods provided sufficient quality and quantity of DNA for downstream metagenomic analyses and displayed highly concordant microbiome profiles. Home fecal sample collection for microbiome analysis is feasible in a large prospective cohort. Including additional components did not reduce the likelihood of participants completing all requested items. Significance: The expansion of this successful pilot to the larger Australian Breakthrough Cancer Study will facilitate future metagenomic and other host- and microbiome-related analyses in this large prospective cohort and potentially as part of an extended international pooling project. Introduction The human microbiome is the ecological community of microorganisms (bacteria, archaea, fungi, protists, and viruses) and their metabolic products that inhabit the human body. The recent emergence of high-throughput DNA sequencing technologies has enabled a rapid expansion of cultureindependent research into the association between the human microbiome and health and disease ( 1, 2) . The collection and storage of host and 1Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia. 2Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia. 3Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Australia. 4Burnet Institute, Melbourne, Australia. 5Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland. Corresponding Author: Roger L. Milne, Cancer Epidemiology Division, Cancer Council Victoria, 200 Victoria Parade, East Melbourne 3002, Australia. E-mail: [roger.milne@cancervic.org.au](roger.milne@cancervic.org.au) doi: 10.1158/2767-9764.CRC-25-0445 This open access article is distributed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. ©2025 The Authors; Published by the American Association for Cancer Research microbiota samples now, for use in future multiomic analyses, could benefit the rapidly advancing field of molecular epidemiology (3) . Such analyses might be usefully integrated with prospectively collected data on variables such as diet and medical history, allowing the investigation of the temporality, direction, and causality of associations between microbiome variation and health outcomes in prospective cohorts. The gut microbiome can be reliably measured in fecal samples, but collection methods vary and have different considerations with re

FAQs

What was the purpose of this pilot study?

To assess the feasibility of collecting home fecal samples within a cohort study for gut microbiome research.

How were participants assigned in the pilot study?

A subset was randomly selected and randomized into four groups defined by fecal sample collection method and questionnaire components.

Did fecal occult blood test cards and ethanol tubes produce comparable microbiome data?

Yes. Whole-genome sequencing and metagenomic analysis of paired samples showed sufficient DNA quality and quantity and highly concordant microbiome profiles.

Sep 30, 2026

Uploaded by Margaret