Additional file 1 of The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries
Creators: name: Young, Caroline
name: Wood, Henry M.
name: Seshadri, Ramakrishnan Ayloor
name: Van Nang, Pham
name: Vaccaro, Carlos
name: Melendez, Luis Contreras
name: Bose, Mayilvahanan
name: Van Doi, Mai
name: Piñero, Tamara Alejandra
name: Valladares, Camilo Tapia
name: Arguero, Julieta
name: Balaguer, Alba Fuentes
name: Thompson, Kelsey N.
name: Yan, Yan
name: Huttenhower, Curtis
name: Quirke, Philip
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology

description: Additional file 1: Table S1. PERMANOVA analysis. P-values &lt; 0.05 are shaded grey. R2 values are recorded to two decimal places. Fig. S1A. Distribution of Bray-Curtis distances between UK volunteer samples. The five UK volunteers are labelled A1-E5. Within individual Bray-Curtis distances are low, despite differences in sample storage. Fig. S1B. Genus-level taxonomic profile of UK volunteer samples. Each bar represents a sample labelled as: UK volunteer (A1-E5); country of storage (AR = Argentina; CH = Chile; IN = India; VI = Vietnam; UK); storage duration (S = short-term storage; L = long-term storage (i.e. the duration of CRC/non-CRC control sample collection); R = samples which remained in the UK). The key contains the top 20 taxa (where a genus was described as family_group, groups were merged and only the family name is included for brevity); additional taxa are coloured grey. There is minimal taxonomic variability between samples from the same individual, and taxonomic variability affects both samples which remained in the UK and samples which were transported and stored internationally. Fig. S2A. PCoA of Bray-Curtis distances for extraction replicates. Points are coloured as extraction replicate pairs. Fig. S2B. Distribution of Bray-Curtis distances between extraction replicate samples. Fig. S2C. Genus-level taxonomic profile of extraction replicate samples. Each bar represents a sample labelled as follows: country of origin (AR = Argentina; CH = Chile; IN = India; VI = Vietnam); disease status (CRC = CRC; NC = non-CRC control); sample ID; whether the sample is an extraction replicate (indicated by .R). For ease of comparison, taxa are coloured as per Supplementary Fig. 1B. Replicate pairs have similar taxonomic profiles. Fig. S3A. Genus-level taxonomic profile of CRC and non-CRC control samples. Each bar represents a sample labelled as follows: country of origin (AR = Argentina; CH = Chile; IN = India; VI = Vietnam); disease status (CRC = CRC; NC = non-CRC control). For ease of comparison, taxa are coloured as per Supplementary Fig. 1B. South American samples generally have a high relative abundance of Bacteroides, and Asian samples a high relative abundance of Prevotella. Fig. S3B. The mean taxonomic composition (genus-level) of CRC and non-CRC control samples. Each bar represents the mean taxonomic composition of a group labelled as follows: country of origin (AR = Argentina; CH = Chile; IN = India; VI = Vietnam); disease status (CRC = CRC; NC = non-CRC control). For ease of comparison, taxa are coloured as per Supplementary Fig. 1B. South American samples have a high relative abundance of Bacteroides, and Asian samples a high relative abundance of Prevotella. Fig. S3C. LEfSe plot illustrating taxa enriched in South American (SA) compared with Asian (AS) samples. Fig. S4A. Distributions of relative abundance of genera of greatest importance to random forest models. The boxplots labelled ‘All’ are a summary of all of the studies, including the current study. The first 19 taxa are CRC-enriched (mean relative abundance) in the majority of studies; the final 5 taxa are control-enriched (mean relative abundance) in the majority of studies. Fig. S4B. LEfSe plot illustrating taxa enriched in CRC compared with non-CRC controls for the current study cohort as a whole. Fig. S4C. LEfSe plot illustrating taxa enriched in CRC compared with non-CRC controls (Argentina). Fig. S4D. LEfSe plot illustrating taxa enriched in CRC compared with non-CRC controls (Chile). Fig. S4E. LEfSe plot illustrating taxa enriched in CRC compared with non-CRC controls (India). Fig. S4F. LEfSe plot illustrating taxa enriched in CRC compared with non-CRC controls (Vietnam).