Article Text

Original research
Blue poo: impact of gut transit time on the gut microbiome using a novel marker
  1. Francesco Asnicar1,
  2. Emily R Leeming2,
  3. Eirini Dimidi3,
  4. Mohsen Mazidi2,
  5. Paul W Franks4,
  6. Haya Al Khatib3,5,
  7. Ana M Valdes6,
  8. Richard Davies5,
  9. Elco Bakker5,
  10. Lucy Francis5,
  11. Andrew Chan7,
  12. Rachel Gibson3,
  13. George Hadjigeorgiou5,
  14. Jonathan Wolf5,
  15. Timothy D Spector8,
  16. Nicola Segata9,
  17. Sarah E Berry3
  1. 1Department Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
  2. 2Twins Research and Epidemiology, King's College London, London, UK
  3. 3Diabetes and Nutritional Sciences Division, King's College London, London, UK
  4. 4Department of Clinical Sciences, Lund University, Lund, Sweden
  5. 5Zoe Global, London, UK
  6. 6NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals Trust and the University of Nottingham, Nottingham, UK
  7. 7Clinical and Translational Epidemiology Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
  8. 8Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
  9. 9Department CIBIO, University of Trento, Trento, Trentino-Alto Adige, Italy
  1. Correspondence to Dr Sarah E Berry, Diabetes and Nutritional Sciences Division, King's College London, London WC2R 2LS, UK; sarah.e.berry{at}


Background and aims Gut transit time is a key modulator of host–microbiome interactions, yet this is often overlooked, partly because reliable methods are typically expensive or burdensome. The aim of this single-arm, single-blinded intervention study is to assess (1) the relationship between gut transit time and the human gut microbiome, and (2) the utility of the ‘blue dye’ method as an inexpensive and scalable technique to measure transit time.

Methods We assessed interactions between the taxonomic and functional potential profiles of the gut microbiome (profiled via shotgun metagenomic sequencing), gut transit time (measured via the blue dye method), cardiometabolic health and diet in 863 healthy individuals from the PREDICT 1 study.

Results We found that gut microbiome taxonomic composition can accurately discriminate between gut transit time classes (0.82 area under the receiver operating characteristic curve) and longer gut transit time is linked with specific microbial species such as Akkermansia muciniphila, Bacteroides spp and Alistipes spp (false discovery rate-adjusted p values <0.01). The blue dye measure of gut transit time had the strongest association with the gut microbiome over typical transit time proxies such as stool consistency and frequency.

Conclusions Gut transit time, measured via the blue dye method, is a more informative marker of gut microbiome function than traditional measures of stool consistency and frequency. The blue dye method can be applied in large-scale epidemiological studies to advance diet-microbiome-health research. Clinical trial registry website and trial number NCT03479866.

  • intestinal bacteria
  • gastrointestinal transit

Data availability statement

Data are available upon reasonable request. Metagenomes are deposited in EBI ENA under accession number PRJEB39223. The non-metagenomic data used for analysis in this study are held by the Department of Twin Research at King’s College London and access can be requested from to allow for anonymisation and compliance with GDPR standards.

This is an open access article distributed in accordance with the Creative Commons Attribution 4.0 Unported (CC BY 4.0) license, which permits others to copy, redistribute, remix, transform and build upon this work for any purpose, provided the original work is properly cited, a link to the licence is given, and indication of whether changes were made. See:

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Data availability statement

Data are available upon reasonable request. Metagenomes are deposited in EBI ENA under accession number PRJEB39223. The non-metagenomic data used for analysis in this study are held by the Department of Twin Research at King’s College London and access can be requested from to allow for anonymisation and compliance with GDPR standards.

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  • TDS, NS and SEB are joint senior authors.

  • Twitter @EmilyLeemingRD, @EiriniDimidi, @nsegata, @saraheeberry

  • FA, ERL and ED contributed equally.

  • Correction notice This article has been corrected since it published Online First. The joint senior author statement has been updated.

  • Contributors Conceptualisation: SB, AV, JW, GH, HAK, RD, NS, PF and TDS. Data curation: SB, NS, FA, TDS and RD. Formal analysis: FA, SB, NS, ERL, ED, MM and LF. Funding acquisition: JW, GH and TDS. Investigation: SB, GH, HAK, ERL, NS and FA. Methodology: SB, AV, JW, GH, HAK, RD, NS, PF, TDS, FA and ERL. Project administration: SB, NS, ERL, TDS, FA, GH, JW and ED. Resources: TDS, NS, JW and GH. Software: NS, FA, RD and EB. Supervision: SB, NS, PF and ERL. Validation: FA, NS and RD. Visualisation: NS, SB, ED, FA, MM and ERL. Writing—original draft: NS, FA, SB, ED, ERL, MM, TDS and PF. Writing—review and editing: NS, FA, SB, ED, ERL, MM, RG, AC, TDS, PWF, AV, JW, GH, HAK, RD, EB and LF.

  • Funding This work was supported by Zoe Global Ltd and by the European Research Council (ERC-STG project MetaPG) to NS; by MIUR ‘Futuro in Ricerca’ (grant No. RBFR13EWWI_001) to NS; by the European H2020 programme (ONCOBIOME-825410 project and MASTER-818368 project) to NS; by the National Cancer Institute of the National Institutes of Health (1U01CA230551) to NS; by the Premio Internazionale Lombardia e Ricerca 2019 to NS. AMV was supported by the NIHR Nottingham BRC. TwinsUK is funded by the Wellcome Trust, Medical Research Council, European Union, Chronic Disease Research Foundation (CDRF), Zoe Global Ltd and the National Institute for Health Research (NIHR)-funded BioResource, Clinical Research Facility and Biomedical Research Centre based at Guy’s and St Thomas’ NHS Foundation Trust in partnership with King’s College London.

  • Competing interests TDS, SB, FA, PF, AV, AC, ERL and NS are consultants to Zoe Global Ltd (“Zoe”). JW, GH, RD, HAK, LF and EB are or have been employees of Zoe. Other authors have no conflict of interest to declare. The study sponsors (Zoe Global Ltd; JW and GH) contributed as part of the Scientific Advisory Board for the PREDICT 1 study in the study design and collection. ED has received an education grant from Alpro, research funding from the British Dietetic Association, Almond Board of California, the International Nut and Dried Fruit Council and Nestec Ltd and has served as a consultant for Puratos. SB has received research funding from the Almond Board of California and from the Malaysian Palm Oil Board.

  • Provenance and peer review Not commissioned; externally peer reviewed.

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