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Eyeballing your gut microbiome


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How's your microbiome? You can get tested, or you can eyeball it.


Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates





The assessment of potentially confounding factors affecting colon microbiota composition is essential to the identification of robust microbiome based disease markers. Here, we investigate the link between gut microbiota variation and stool consistency using Bristol Stool Scale classification, which reflects faecal water content and activity, and is considered a proxy for intestinal colon transit time.



Through 16S rDNA Illumina profiling of faecal samples of 53 healthy women, we evaluated associations between microbiome richness, Bacteroidetes:Firmicutes ratio, enterotypes, and genus abundance with self-reported, Bristol Stool Scale-based stool consistency. Each sample’s microbiota growth potential was calculated to test whether transit time acts as a selective force on gut bacterial growth rates.



Stool consistency strongly correlates with all known major microbiome markers. It is negatively correlated with species richness, positively associated to the Bacteroidetes:Firmicutes ratio, and linked to Akkermansia and Methanobrevibacter abundance. Enterotypes are distinctly distributed over the BSS-scores. Based on the correlations between microbiota growth potential and stool consistency scores within both enterotypes, we hypothesise that accelerated transit contributes to colon ecosystem differentiation. While shorter transit times can be linked to increased abundance of fast growing species in Ruminococcaceae-Bacteroides samples, hinting to a washout avoidance strategy of faster replication, this trend is absent in Prevotella-enterotyped individuals. Within this enterotype adherence to host tissue therefore appears to be a more likely bacterial strategy to cope with washout.



The strength of the associations between stool consistency and species richness, enterotypes and community composition emphasises the crucial importance of stool consistency assessment in gut metagenome-wide association studies.


See also:


Population-level analysis of gut microbiome variation


  1. Gwen Falony1,2,*
  2. Marie Joossens1,2,3,*
  3. Sara Vieira-Silva1,2,*
  4. Jun Wang1,2,*
  5. Youssef Darzi1,2,3
  6. Karoline Faust1,2,3
  7. Alexander Kurilshikov4,5
  8. Marc Jan Bonder6
  9. Mireia Valles-Colomer1,2
  10. Doris Vandeputte1,2,3,
  11. Raul Y. Tito1,2,3
  12. Samuel Chaffron1,2,3
  13. Leen Rymenans1,2,3
  14. Chloë Verspecht1,2
  15. Lise De Sutter1,2,3
  16. Gipsi Lima-Mendez1,2
  17. Kevin D’hoe1,2,3
  18. Karl Jonckheere2,3
  19. Daniel Homola2,3,
  20. Roberto Garcia2,3
  21. Ettje F. Tigchelaar6,7
  22. Linda Eeckhaudt2,3
  23. Jingyuan Fu6,8
  24. Liesbet Henckaerts1,9
  25. Alexandra Zhernakova6,7
  26. Cisca Wijmenga6
  27. Jeroen Raes1,2,3,
“Normal” for the gut microbiota


For the benefit of future clinical studies, it is critical to establish what constitutes a “normal” gut microbiome, if it exists at all. Through fecal samples and questionnaires, Falony et al. and Zhernakova et al. targeted general populations in Belgium and the Netherlands, respectively. Gut microbiota composition correlated with a range of factors including diet, use of medication, red blood cell counts, fecal chromogranin A, and stool consistency. The data give some hints for possible biomarkers of normal gut communities.

Science, this issue pp. 560 and 565




Fecal microbiome variation in the average, healthy population has remained under-investigated. Here, we analyzed two independent, extensively phenotyped cohorts: the Belgian Flemish Gut Flora Project (FGFP; discovery cohort; N = 1106) and the Dutch LifeLines-DEEP study (LLDeep; replication; N = 1135). Integration with global data sets (Ncombined = 3948) revealed a 14-genera core microbiota, but the 664 identified genera still underexplore total gut diversity. Sixty-nine clinical and questionnaire-based covariates were found associated to microbiota compositional variation with a 92% replication rate. Stool consistency showed the largest effect size, whereas medication explained largest total variance and interacted with other covariate-microbiota associations. Early-life events such as birth mode were not reflected in adult microbiota composition. Finally, we found that proposed disease marker genera associated to host covariates, urging inclusion of the latter in study design.


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