Abstract
BackgroundThe incidence of colorectal cancer (CRC) is increasing in developing countries, yet limited research on the CRC- associated microbiota has been conducted in these areas, in part due to scarce resources, facilities, and the difficulty of fresh or frozen stool storage/transport. Here, we aimed (1) to establish a broad representation of diverse developing countries (Argentina, Chile, India, and Vietnam); (2) to validate a ‘resource-light’ sample-collection protocol translatable in these settings using guaiac faecal occult blood test (gFOBT) cards stored and, importantly, shipped internationally at room temperature; (3) to perform initial profiling of the collective CRC-associated microbiome of these developing countries; and (4) to compare this quantitatively with established CRC biomarkers from developed countries.MethodsWe assessed the effect of international storage and transport at room temperature by replicating gFOBT from five UK volunteers, storing two in the UK, and sending replicates to institutes in the four countries. Next, to determine the effect of prolonged UK storage, DNA extraction replicates for a subset of samples were performed up to 252 days apart. To profile the CRC-associated microbiome of developing countries, gFOBT were collected from 41 treatment-naïve CRC patients and 40 non-CRC controls from across the four institutes, and V4 16S rRNA gene sequencing was performed. Finally, we constructed a random forest (RF) model that was trained and tested against existing datasets from developed countries.ResultsThe microbiome was stably assayed when samples were stored/transported at room temperature and after prolonged UK storage. Large-scale microbiome structure was separated by country and continent, with a smaller effect from CRC. Importantly, the RF model performed similarly to models trained using external datasets and identified similar taxa of importance (Parvimonas, Peptostreptococcus, Fusobacterium, Alistipes, and Escherichia).ConclusionsThis study demonstrates that gFOBT, stored and transported at room temperature, represents a suitable method of faecal sample collection for amplicon-based microbiome biomarkers in developing countries and suggests a CRC-faecal microbiome association that is consistent between developed and developing countries.
Highlights
The incidence of colorectal cancer (CRC) is increasing in developing countries, yet limited research on the CRC- associated microbiota has been conducted in these areas, in part due to scarce resources, facilities, and the difficulty of fresh or frozen stool storage/transport
The median age of non-CRC controls from Argentina, Chile, and India was substantially younger than the corresponding CRC patients, and the median age of CRC patients from India and Vietnam was younger than that of CRC patients from Chile and Argentina (Table 1)
This allowed us to further profile the faecal microbiomes of CRC patients and non-CRC controls from Argentina, Chile, India, and Vietnam, and, through comparison with external datasets, to demonstrate that the CRC-associated microbiome of these developing countries resembles that of developed countries
Summary
The incidence of colorectal cancer (CRC) is increasing in developing countries, yet limited research on the CRC- associated microbiota has been conducted in these areas, in part due to scarce resources, facilities, and the difficulty of fresh or frozen stool storage/transport. There is growing evidence of an association between CRC and an altered faecal microbiome, with the potential to develop novel screening, prognostic or therapeutic markers. The majority of CRC-microbiome research has profiled developed cohorts. Of the limited number of studies conducted in developing countries, most have been small pilot studies [3,4,5,6,7]. It cannot be assumed that results from developed countries will be generalisable to developing populations, as the health-associated microbiome of developed and developing populations has been shown to differ taxonomically and functionally [8]
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