Caroline Young1, Henry M Wood2, Ramakrishnan Ayloor Seshadri3, Pham Van Nang4, Carlos Vaccaro5, Luis Contreras Melendez6, Mayilvahanan Bose3, Mai Van Doi4, Tamara Alejandra Piñero5, Camilo Tapia Valladares6, Julieta Arguero5, Alba Fuentes Balaguer2, Kelsey N Thompson7, Yan Yan7, Curtis Huttenhower7, Philip Quirke2. 1. Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Level 4 Wellcome Trust Brenner Building, Leeds, LS9 7TF, UK. c.young@leeds.ac.uk. 2. Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Level 4 Wellcome Trust Brenner Building, Leeds, LS9 7TF, UK. 3. Cancer Institute (WIA), Chennai, India. 4. Can Tho University of Medicine and Pharmacy, Can Tho, Vietnam. 5. Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano de buenos Aires (HIBA), Buenos Aires, Argentina. 6. Universidad de los Andes, Santiago, Chile. 7. Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, USA.
Abstract
BACKGROUND: 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. 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. METHODS: We 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. RESULTS: The 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). CONCLUSIONS: This 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.
BACKGROUND: 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. 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. METHODS: We 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. RESULTS: The 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). CONCLUSIONS: This 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.
Authors: Cayetano Pleguezuelos-Manzano; Jens Puschhof; Axel Rosendahl Huber; Arne van Hoeck; Henry M Wood; Jason Nomburg; Carino Gurjao; Freek Manders; Guillaume Dalmasso; Paul B Stege; Fernanda L Paganelli; Maarten H Geurts; Joep Beumer; Tomohiro Mizutani; Yi Miao; Reinier van der Linden; Stefan van der Elst; K Christopher Garcia; Janetta Top; Rob J L Willems; Marios Giannakis; Richard Bonnet; Phil Quirke; Matthew Meyerson; Edwin Cuppen; Ruben van Boxtel; Hans Clevers Journal: Nature Date: 2020-02-27 Impact factor: 49.962
Authors: Belén Carbonetto; Mónica C Fabbro; Mariela Sciara; Analía Seravalle; Guadalupe Méjico; Santiago Revale; María S Romero; Bianca Brun; Marcelo Fay; Fabián Fay; Martin P Vazquez Journal: Front Microbiol Date: 2016-02-01 Impact factor: 5.640
Authors: Wendy S W Wong; Nicole Clemency; Elisabeth Klein; Marina Provenzano; Ramaswamy Iyer; John E Niederhuber; Suchitra K Hourigan Journal: Microbiome Date: 2017-09-05 Impact factor: 14.650
Authors: Ramnik J Xavier; Curtis Huttenhower; Jason Lloyd-Price; Cesar Arze; Ashwin N Ananthakrishnan; Melanie Schirmer; Julian Avila-Pacheco; Tiffany W Poon; Elizabeth Andrews; Nadim J Ajami; Kevin S Bonham; Colin J Brislawn; David Casero; Holly Courtney; Antonio Gonzalez; Thomas G Graeber; A Brantley Hall; Kathleen Lake; Carol J Landers; Himel Mallick; Damian R Plichta; Mahadev Prasad; Gholamali Rahnavard; Jenny Sauk; Dmitry Shungin; Yoshiki Vázquez-Baeza; Richard A White; Jonathan Braun; Lee A Denson; Janet K Jansson; Rob Knight; Subra Kugathasan; Dermot P B McGovern; Joseph F Petrosino; Thaddeus S Stappenbeck; Harland S Winter; Clary B Clish; Eric A Franzosa; Hera Vlamakis Journal: Nature Date: 2019-05-29 Impact factor: 49.962