Intest Res.  2019 Jul;17(3):419-426. 10.5217/ir.2018.00149.

Is stool frequency associated with the richness and community composition of gut microbiota?

  • 1Department of Internal Medicine, Kosin University College of Medicine, Busan, Korea.
  • 2Cell Biotech, Co., Ltd., Gimpo, Korea.


Recently, a number of studies have reported that the gut microbiota could contribute to human conditions, including obesity, inflammation, cancer development, and behavior. We hypothesized that the composition and distribution of gut microbiota are different according to stool frequency, and attempted to identify the association between gut microbiota and stool frequency.
We collected fecal samples from healthy individuals divided into 3 groups according to stool frequency: group 1, a small number of defecation (≤2 times/wk); group 2, normal defecation (1 time/day or 1 time/2 day); and group 3, a large number of defecation (≥2-3 times/day). We evaluated the composition and distribution of the gut microbiota in each group via 16S rRNA-based taxonomic profiling of the fecal samples.
Fecal samples were collected from a total of 60 individuals (31 men and 29 women, aged 34.1±5.88 years), and each group comprised 20 individuals. The microbial richness of group 1 was significantly higher than that of group 3 and tended to decrease with increasing number of defecation (P<0.05). The biological community composition was fairly different according to the number of defecation, and Bacteroidetes to Firmicutes ratio was higher in group 1 than in the other groups. Moreover, we found specific strains at the family and genus levels in groups 1 and 3.
Bacteroidetes to Firmicutes ratio and the abundance of Bifidobacterium were different according to the stool frequency, and specific bacteria were identified in the subjects with large and small numbers of defecation, respectively. These findings suggest that stool frequency might be associated with the richness and community composition of the gut microbiota.


Feces; Gastrointestinal microbiome; Composition; Distribution

MeSH Terms

Gastrointestinal Microbiome*


  • Fig. 1. Violin plot for the α-diversity of bacterial communities in the 3 different groups according to the number of defecation. The violin plot presents the full range of values obtained from the source data, where the width of the orange, blue, or red-colored area presents the probability density of the sample values at that level (aP<0.05). The Seaborn package in Python 3 was used for visualization.

  • Fig. 2. Principal coordinate analysis plot according to the Bray Curtis dissimilarity for bacterial associations in the 3 groups. Each dot presents the bacterial community of each sample (individual). It was generated using the Microbial Genomics Module in CLC Genomics Workbench V10.0.1 (QIAGEN). Group 1, a small number of defecation (≤2 times/wk); group 2, normal defecation (1 time/1–2 day); group 3, a large number of defecation (≥2–3 times/day).

  • Fig. 3. Composition of bacterial communities in the 3 different groups. (A) Relative abundance of the gut microbiota in the 3 different groups at the phylum level against the Greengenes database. (B) Abundance of the gut microbiota at the genus level. It was generated using the Microbial Genomics Module in CLC Genomics Workbench V10.0.1 (QIAGEN). NA, not available.

  • Fig. 4. Significant co-occurrence relationships among the abundances of bacteria according to the number of defecation at the family and genus levels. Visualization for a microbial interaction network is shown with nodes and clades. Each node presents different bacteria, and each edge presents significant co-occurrence relationships. The size of the node indicates the abundance of each bacterium at the phylum and genus levels. The CoNet application in Cytoscape 3.6 was used for visualization. Group 1, a small number of defecation (≤ 2 times/wk); group 3, a large number of defecation (≥ 2–3 times/day).

  • Fig. 5. Significantly different bacterial compositions in the groups classified by the number of defecation at the family (A) and genus levels (B). The box plots present the relative abundance of the significantly different bacteria between the individuals with a small number of defecation (group 1) and a large number of defecation (group 3). Each groups represent group 1 (≤2 times/wk), group 2 (1 time/1–2 day), and group 3 (≥2–3 times/day). It was generated by using the Seaborn package in Python 3.


1. Gill SR, Pop M, Deboy RT, et al. Metagenomic analysis of the human distal gut microbiome. Science. 2006; 312:1355–1359.
2. Bäckhed F, Ding H, Wang T, et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A. 2004; 101:15718–15723.
3. Collins SM, Surette M, Bercik P. The interplay between the intestinal microbiota and the brain. Nat Rev Microbiol. 2012; 10:735–742.
4. Endt K, Stecher B, Chaffron S, et al. The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal Salmonella diarrhea. PLoS Pathog. 2010; 6:e1001097.
5. LeBlanc JG, Milani C, de Giori GS, Sesma F, van Sinderen D, Ventura M. Bacteria as vitamin suppliers to their host: a gut microbiota perspective. Curr Opin Biotechnol. 2013; 24:160–168.
6. Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol. 2009; 9:313–323.
7. Diaz Heijtz R, Wang S, Anuar F, et al. Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci U S A. 2011; 108:3047–3052.
8. Feng Q, Liang S, Jia H, et al. Gut microbiome development along the colorectal adenoma-carcinoma sequence. Nat Commun. 2015; 6:6528.
9. Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010; 464:59–65.
10. Qin J, Li Y, Cai Z, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012; 490:55–60.
11. Zhang X, Zhang D, Jia H, et al. The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment. Nat Med. 2015; 21:895–905.
12. Buermans HP, den Dunnen JT. Next generation sequencing technology: advances and applications. Biochim Biophys Acta. 2014; 1842:1932–41.
13. Vandeputte D, Falony G, Vieira-Silva S, Tito RY, Joossens M, Raes J. Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates. Gut. 2016; 65:57–62.
14. Tigchelaar EF, Bonder MJ, Jankipersadsing SA, Fu J, Wijmenga C, Zhernakova A. Gut microbiota composition associated with stool consistency. Gut. 2016; 65:540–542.
15. Törnblom H, Van Oudenhove L, Sadik R, Abrahamsson H, Tack J, Simrén M. Colonic transit time and IBS symptoms: what’s the link? Am J Gastroenterol. 2012; 107:754–760.
16. Heaton KW, Radvan J, Cripps H, Mountford RA, Braddon FE, Hughes AO. Defecation frequency and timing, and stool form in the general population: a prospective study. Gut. 1992; 33:818–824.
17. Hadizadeh F, Walter S, Belheouane M, et al. Stool frequency is associated with gut microbiota composition. Gut. 2017; 66:559–560.
18. Smith P, Haenssler E, Adams E, O’Neil D. Automated DNA purification from diverse microbiome samples using dedicated microbiome kits on the QIAcube®. QIAGEN Web site. Accessed July 15, 2019.
19. Faust K, Sathirapongsasuti JF, Izard J, et al. Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol. 2012; 8:e1002606.
20. Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13:2498–2504.
21. Tap J, Furet JP, Bensaada M, et al. Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults. Environ Microbiol. 2015; 17:4954–4964.
22. Le Chatelier E, Nielsen T, Qin J, et al. Richness of human gut microbiome correlates with metabolic markers. Nature. 2013; 500:541–546.
23. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature. 2006; 444:1022–1023.
24. Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A. 2005; 102:11070–11075.
25. Ridaura VK, Faith JJ, Rey FE, et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 2013; 341:1241214.
26. Jeffery IB, O’Toole PW, Öhman L, et al. An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota. Gut. 2012; 61:997–1006.
27. Ibarra A, Latreille-Barbier M, Donazzolo Y, Pelletier X, Ouwehand AC. Effects of 28-day Bifidobacterium animalis subsp. lactis HN019 supplementation on colonic transit time and gastrointestinal symptoms in adults with functional constipation: a double-blind, randomized, placebo-controlled, and dose-ranging trial. Gut Microbes. 2018; 9:236–251.
28. Eskesen D, Jespersen L, Michelsen B, Whorwell PJ, Müller-Lissner S, Morberg CM. Effect of the probiotic strain Bifidobacterium animalis subsp. lactis, BB-12®, on defecation frequency in healthy subjects with low defecation frequency and abdominal discomfort: a randomised, double-blind, placebo-controlled, parallel-group trial. Br J Nutr. 2015; 114:1638–1646.
29. Del Piano M, Carmagnola S, Anderloni A, et al. The use of probiotics in healthy volunteers with evacuation disorders and hard stools: a double-blind, randomized, placebo-controlled study. J Clin Gastroenterol. 2010; 44 Suppl 1:S30–S34.
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