Mucosa-associated gut microbiome in Japanese patients with functional constipation.

1 Mearin F, Lacy BE, Chang L, et al. Bowel disorders. Gastroenterology 2016;

150: 1393–1407.

2 Vazquez Roque M, Bouras EP. Epidemiology and management of chronic

constipation in elderly patients. Clin Interv Aging 2015; 10: 919–930.

3 Kawamura Y, Yamamoto S, Funaki Y, et al. Internet survey on the actual

situation of constipation in the Japanese population under 70 years old: focus

on functional constipation and constipation-predominant irritable bowel

syndrome. J Gastroenterol 2020; 55: 27–38.

4 Kosako M, Akiho H, Miwa H, Kanazawa M, Fukudo S. Impact of symptoms

by gender and age in Japanese subjects with irritable bowel syndrome with

constipation (IBS-C): a large population-based internet survey. Biopsychosoc

Med 2018; 12: 12.

5 Rautava S, Luoto R, Salminen S, Isolauri E. Microbial contact during

pregnancy, intestinal colonization and human disease. Nat Rev Gastroenterol

Hepatol 2012; 9: 565–576.

6 Goldsmith JR, Sartor RB. The role of diet on intestinal microbiota metabolism:

downstream impacts on host immune function and health, and therapeutic

implications. J Gastroenterol 2014; 49: 785–798.

7 Sheehan D, Moran C, Shanahan F. The microbiota in inflammatory bowel

disease. J Gastroenterol 2015; 50: 495–507.

8 Kostic AD, Xavier RJ, Gevers D. The microbiome in inflammatory bowel

disease: current status and the future ahead. Gastroenterology 2014; 146:

1489–1499.

9 Li J, Butcher J, Mack D, Stintzi A. Functional impacts of the intestinal

microbiome in the pathogenesis of inflammatory bowel disease. Inflamm

Bowel Dis 2015; 21: 139–153.

10 Parthasarathy G, Chen J, Chen X, et al. Relationship between microbiota of

the colonic mucosa vs feces and symptoms, colonic transit, and methane

production in female patients with chronic constipation. Gastroenterology

2016; 150: 367–379.e1.

11 Sundin J, Aziz I, Nordlander S, et al. Evidence of altered mucosa-associated

and fecal microbiota composition in patients with irritable bowel syndrome.

Sci Rep 2020; 10: 593.

12 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.

13 Ringel Y, Maharshak N, Ringel-Kulka T, Wolber EA, Sartor RB, Carroll

Y. Sugitani et al.

14

15

16

17

18

19

20

21

22

23

24

25

26

27

IM. High throughput sequencing reveals distinct microbial populations

within the mucosal and luminal niches in healthy individuals. Gut Microbes

2015; 6: 173–181.

Sartor RB. Gut microbiota: optimal sampling of the intestinal microbiota for

research. Nat Rev Gastroenterol Hepatol 2015; 12: 253–254.

Kashiwagi S, Naito Y, Inoue R, et al. Mucosa-associated microbiota in the

gastrointestinal tract of healthy Japanese subjects. Digestion 2020; 101: 107–

120.

Fukui A, Takagi T, Naito Y, et al. Higher levels of streptococcus in upper

gastrointestinal mucosa associated with symptoms in patients with functional

dyspepsia. Digestion 2020; 101: 38–45.

Nishino K, Nishida A, Inoue R, et al. Analysis of endoscopic brush samples

identified mucosa-associated dysbiosis in inflammatory bowel disease. J

Gastroenterol 2018; 53: 95–106.

Nishijima S, Suda W, Oshima K, et al. The gut microbiome of healthy

Japanese and its microbial and functional uniqueness. DNA Res 2016; 23:

125–133.

Kawada Y, Naito Y, Andoh A, Ozeki M, Inoue R. Effect of storage and

DNA extraction method on 16S rRNA-profiled fecal microbiota in Japanese

adults. J Clin Biochem Nutr 2019; 64: 106–111.

Inoue R, Sakaue Y, Sawai C, et al. A preliminary investigation on the

relationship between gut microbiota and gene expressions in peripheral

mononuclear cells of infants with autism spectrum disorders. Biosci Biotechnol

Biochem 2016; 80: 2450–2458.

Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of

high-throughput community sequencing data. Nat Methods 2010; 7: 335–336.

Edgar RC. Search and clustering orders of magnitude faster than BLAST.

Bioinformatics 2010; 26: 2460–2461.

Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile

open source tool for metagenomics. PeerJ 2016; 4: e2584.

DeSantis TZ, Hugenholtz P, Larsen N, et al. Greengenes, a chimera-checked

16S rRNA gene database and workbench compatible with ARB. Appl Environ

Microbiol 2006; 72: 5069–5072.

McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 2013; 8:

e61217.

Segata N, Izard J, Waldron L, et al. Metagenomic biomarker discovery and

explanation. Genome Biol 2011; 12: R60.

Langille MG, Zaneveld J, Caporaso JG, et al. Predictive functional profiling

J. Clin. Biochem. Nutr. | March 2021 | vol. 68 | no. 2 | 191

©2021 JCBN

28

29

30

31

32

33

34

192

of microbial communities using 16S rRNA marker gene sequences. Nat

Biotechnol 2013; 31: 814–821.

Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M. Data,

information, knowledge and principle: back to metabolism in KEGG. Nucleic

Acids Res 2014; 42: D199–D205.

Parks DH, Tyson GW, Hugenholtz P, Beiko RG. STAMP: statistical analysis

of taxonomic and functional profiles. Bioinformatics 2014; 30: 3123–3124.

Ohkusa T, Koido S, Nishikawa Y, Sato N. Gut microbiota and chronic

constipation: a review and update. Front Med (Lausanne) 2019; 6: 19.

Forbes JD, Van Domselaar G, Bernstein CN. Microbiome survey of the

inflamed and noninflamed gut at different compartments within the gastrointestinal tract of inflammatory bowel disease patients. Inflamm Bowel Dis

2016; 22: 817–825.

Parkes GC, Rayment NB, Hudspith BN, et al. Distinct microbial populations

exist in the mucosa-associated microbiota of sub-groups of irritable bowel

syndrome. Neurogastroenterol Motil 2012; 24: 31–39.

Zhu L, Liu W, Alkhouri R, et al. Structural changes in the gut microbiome of

constipated patients. Physiol Genomics 2014; 46: 679–686.

Tyrrell KL, Warren YA, Citron DM, Goldstein EJC. Re-assessment of

phenotypic identifications of Bacteroides putredinis to Alistipes species using

molecular methods. Anaerobe 2011; 17: 130–134.

35 Nagai F, Morotomi M, Watanabe Y, Sakon H, Tanaka R. Alistipes indistinctus

sp. nov. and Odoribacter laneus sp. nov., common members of the human

intestinal microbiota isolated from faeces. Int J Syst Evol Microbiol 2010; 60

(Pt 6): 1296–1302.

36 O'Mahony SM, Clarke G, Borre YE, Dinan TG, Cryan JF. Serotonin,

tryptophan metabolism and the brain-gut-microbiome axis. Behav Brain Res

2015; 277: 32–48.

37 Carbonero F, Benefiel AC, Gaskins HR. Contributions of the microbial

hydrogen economy to colonic homeostasis. Nat Rev Gastroenterol Hepatol

2012; 9: 504–518.

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