Besides, the relative abundance of several proteins for sugar transport system (substrate-binding protein, permease protein and ATP-binding protein for multiple sugar transport system, and ATP-binding protein for simple sugar transport system) were found enriched in the HC group (q < 0.01) [Figure 10B and Table 2]. Since sugar is one of the essential substances to maintain the vital movement, the sugar transport system is playing an important role in the healthy gut microenvironment. Dysbiosis might lead to reduction of the related proteins, and meanwhile, the functions of six subunits of nicotinamide adenine dinucleotide (NADH: ubiquinone oxidoreductase) were found enriched in IBS-D (q < 0.01) [Figure 10C and Table 2]. Herein, NADH is the reduced form of nicotinamide adenine dinucleotide, and is the coenzyme in the reaction of glycolysis, during which CO2 may generate as the final product. Hence, we can indicate from the enrichment of the subunits that increased gas production existing in the bowel of patients with IBS-D may potentially lead to recurrent bloating as the symptom.
Due to high epidemicity and intricate pathological mechanism of IBS, studies on IBS have burst out in recent years, and it is commonly received that the gut microbiota has a potential association with IBS symptom. We analyzed the16S rRNA sequences of 20 HC and 40 IBS-D fecal samples of Chinese patients, where the sample size 60 is enough for the comparative analyses.[15,16,22] As is known to the field, age, BMI, illness duration, and constitution of diets may influence the gut microbial composition, but we have demonstrated in our previous study that these factors did not result in different microbial composition between the HC and IBS-D groups. Of course, how the above factors are associated with IBS-D still needs further investigation.
Hence the HC or IBS-D individuals living in the same region or from the same racial background present more similar gut microbiome composition and thus the aggregation of different populations with various backgrounds reveals a potential gut “pan-microbiome,” which is larger than a single microbial community. Unfortunately, since the ability of existing studies to contribute to the investigation of gut pan-microbiome of IBS-D population is quite limited, our current study can only give rise to a brief discussion of the gut pan-microbiome herein. However, through the comparative analysis of taxonomic composition at both phylum and genus level, it is still clear that the abundant phylotypes are even more enriched in the gut microenvironment with dysbiosis, which may disturb the interacted relationship of the community and occupy the living space of the phylotypes with low abundance, and thus become a potential factor of the disease.
Therefore, we analyzed the interactions among the gut microbiota community, and found reduced network complexity of IBS-D from the genus network. The more co-abundance correlations (than co-exclusion ones) in the networks of both HC and IBS-D indicate stronger symbiosis in the community. It is widely known that human intestine is colonized with an intricate community of indigenous microorganisms such that a symbiotic host-bacterial relationship exists in our intestine, where the microbiota with its internal interactions are shaping a reticular system to maintain the organism. Accordingly, the strong symbiosis in microbial community, or namely, a symbiotic bacterial group, is more likely to be mutualistic with the host, and thus networking with the immune system to mediate anti-inflammatory responses necessary for mammalian health. Whereas dysbiosis may weaken the symbiotic network and alter the normal function of immune system, thus become a major factor for disorders such as IBS-D.
In the end, we identified the metabolic functions in the gut microbiota of HC and IBS-D groups to indicate the associations between the gut microbiota and host enrolled in the disorder. As one might know, fucose is component of mucin in the gut epithelial barrier; hence, the enrichment of fucose permease in IBS-D may alter the normal function of the barrier, which is reported to be associated with bacterial conglutination and invasion against host cells.[53,54] It also implied that with the barrier thinner, the increased fucose synthase of gut microbiota in IBS-D provides a protection to the host. While in the case of HC, mutarotase, and isomerase of fucose may keep the normal function of the barrier. Moreover, we found the enriched functions of proteins for sugar transport system of great importance in the healthy gut microenvironment, as well as another signature NADH: ubiquinone oxidoreductase enriched in IBS-D indicating the increased gas production potentially leading to the recurrent bloating as IBS symptom. The results revealed the alteration of host functional mechanism possibly caused by the dysbiosis of gut microbiota.
The authors thank Prof. Xiao-Lei Wu and Prof. Zu-Hong Lu of Peking University for their interest to the project and useful discussions. We also thank Dr. Long-Shu Yang of Peking University for his helpful technique supporting and useful discussions. For the study, the co-author, Prof. Li-Ping Duan of Peking University Third Hospital contributed with the corresponding author Prof. Huai-Qiu Zhu.
This work was supported by grants from the National Key Research and Development Program of China (No. 2017YFC1200205), the National Natural Science Foundation of China (No. 31671366 and No. 91231119), and the Special Research Project of ‘Clinical Medicine + X’ by Peking University.
1. Kennedy PJ, Cryan JF, Dinan TG, Clarke G. Irritable bowel syndrome
: a microbiome-gut-brain axis disorder? World J Gastroenterol
2014; 20:14105–14125. doi: 10.3748/wjg.v20.i39.14105.
2. Shinozaki M, Fukudo S, Hongo M, Shimosegawa T, Sasaki D, Matsueda K, et al. High prevalence of irritable bowel syndrome
in medical outpatients in Japan. J Clin Gastroenterol
2008; 42:1010–1016. doi: 10.1097/MCG.0b013e318150d006.
3. Frank DN, Zhu W, Sartor RB, Li E. Investigating the biological and clinical significance of human dysbioses. Trends Microbiol
2011; 19:427–434. doi: 10.1016/jtim.2011.06.005.
4. Öhman L, Törnblom H, Simrén M. Crosstalk at the mucosal border: importance of the gut microenvironment in IBS. Nat Rev Gastroenterol Hepatol
2015; 12:36–49. doi: 10.1038/nrgastro.2014.200.
5. Longstreth GF, Thompson WG, Chey WD, Houghton LA, Mearin F, Spiller RC. Functional bowel disorders. Gastroenterology
2006; 130:1480–1491. doi: 10.1053/j.gastro.2005.11.061.
6. Quigley EM, Abdel-Hamid H, Barbara G, Bhatia SJ, Boeckxstaens G, De Giorgio R, et al. A global perspective on irritable bowel syndrome
: a consensus statement of the world gastroenterology organisation summit task force on irritable bowel syndrome
. J Clin Gastroenterol
2012; 46:356–366. doi: 10.1097/MCG.0b013e318247157c.
7. Rajilić-Stojanović M, Jonkers DM, Salonen A, Hanevik K, Raes J, Jalanka J, et al. Intestinal microbiota and diet in IBS: causes, consequences, or epiphenomena? Am J Gastroenterol
2015; 110:278–287. doi: 10.1038/ajg.2014.427.
8. Collins SM. A role for the gut microbiota in IBS. Nat Rev Gastroenterol Hepatol
2014; 1:497–505. doi: 10.1038/nrgastro.2014.40.
9. Simrén M. IBS with intestinal microbial dysbiosis
: a new and clinically relevant subgroup? Gut
2014; 11:1685–1686. doi: 10.1136/gutjnl-2013-306434.
10. Sajjadieh MS, Kuznetsova LV, Bojenko VB. Dysbiosis
in Ukrainian children with irritable bowel syndrome
affected by natural radiation. Iran J Pediatr
2012; 22:364–368. doi: 10.2350/12-06-1214-OA.1.
11. Tamboli CP, Neut C, Desreumaux P, Colombel JF. Dysbiosis
in inflammatory bowel disease. Gut
2004; 53:1–4. doi: 10.1136/gut.53.1.1.
12. Joossens M, Huys G, Cnockaert M, Preter VD, Verbeke K, Rutgeerts P, et al. Dysbiosis
of the faecal microbiota in patients with Crohn's disease and their unaffected relatives. Gut
2011; 60:631–637. doi: 10.1136/gut.2010.223263.
13. Duboc H, Rainteau D, Rajca S, Humbert L, Farabos D, Maubert M, et al. Increase in fecal primary bile acids and dysbiosis
in patients with diarrhea-predominant irritable bowel syndrome
. J Neurogastroenterol
2012; 24:513–520. doi: 10.1111/j.1365-2982.2012.01893.x.
14. Kassinen A, Krogius-Kurikka L, Mäkivuokko H, Rinttilä T, Paulin L, Corander J, et al. The fecal microbiota of irritable bowel syndrome
patients differs significantly from that of healthy subjects. Gastroenterology
2007; 133:24–33. doi: 10.1053/j.gastro.2007.04.005.
15. Liu YX, Zhang L, Wang XQ, Wang Z, Zhang JJ, Jiang RH, et al. Similar fecal microbiota signatures in patients with diarrhea-predominant irritable bowel syndrome
and patients with depression. Clin Gastroenterol Hepatol
2016; 14:1602–1611. doi: 10.1016/j.cgh.2016.05.033.
16. Krogius-Kurikka L, Lyra A, Malinen E, Aarnikunnas J, Tuimala J, Paulin L, et al. Microbial community analysis reveals high level phylogenetic alterations in the overall gastrointestinal microbiota of diarrhoea-predominant irritable bowel syndrome
sufferers. BMC Gastroenterol
2009; 9:95doi: 10.1186/1471-230X-9-95.
17. Rajilić-Stojanović M, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S, et al. Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome
2011; 141:1792–1801. doi: 10.1053/j.gastro.2011.07.043.
18. Salonen A, de Vos WM, Palva A. Gastrointestinal microbiota in irritable bowel syndrome
: present state and perspectives. Microbiology
2010; 156:3205–3215. doi: 10.1099/mic.0.043257-0.
19. Jeffery IB, O’Toole PW, Öhman L, Claesson JM, Deane J, Quigley EMM, et al. An irritable bowel syndrome
subtype defined by species-specific alterations in faecal microbiota. Gut
2012; 61:997–1006. doi: 10.1136/gutjnl-2011-301501.
20. Musso G, Gambino R, Cassader M. Obesity, diabetes, and gut microbiota. Diabetes Care
2010; 33:2277–2284. doi: 10.2337/dc10-0556.
21. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature
2005; 437:376–380. doi: 10.1038/nature03959.
22. Carroll IM, Ringel-Kulka T, Siddle JP, Ringel Y. Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome
. J Neurogastroenterol
2012; 24:521–530. doi: 10.1111/j.1365-2982.2012.01891.x.
23. Cole JR, Wang Q, Cardenas E, Fisher J, Chai B, Farris RJ, et al. The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res
2009; 37:D141–D145. doi: 10.1093/nar/gkn879.
24. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol
1990; 215:403–410. doi: 10.1016/S0022-2836(05)80360-2.
25. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res
2004; 32:D277–D280. doi: 10.1093/nar/gkh063.
26. Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res
2016; 44:D457–D462. doi: 10.1093/nar/gkv1070.
27. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol
2009; 75:7537–7541. doi: 10.1128/AEM.01541-09.
28. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol
2006; 72:5069–5072. doi: 10.1128/AEM.03006-05.
29. Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol
2013; 31:814–821. doi: 10.1038/nbt.2676.
30. Markowitz VM, Chen IMA, Palaniappan K, Chu K, Szeto E, Grechkin Y, et al. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res
2012; 40:D115–D122. doi: 10.1093/nar/gkr1044.
31. Zhai P, Yang LS, Guo X, Wang Z, Guo JT, Wang XQ, et al. MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics. BMC Bioinformatics
2017; 18:434doi: 10.1186/s12859-017-1849-8.
32. Storey JD. A direct approach to false discovery rates. J R Stat Soc B
2002; 64:479–498. doi: 10.1111/1467-9868.00346.
33. Friedman J, Alm EJ. Inferring correlation networks from genomic survey data. Plos Comput Biol
2012; 8:e1002687doi: 10.1371/journal.pcbi.1002687.
34. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res
2003; 13:2498–2504. doi: 10.1101/gr.1239303.
35. Bonchev D, Buck GA. Quantitative measures of network complexity. Complexity in Chemistry, Biology, and Ecology. 2005; Boston: Springer, 191–235. doi: 10.1007/0-387-25871-X_5.
36. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keibaugh SA, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science
2011; 334:105–108. doi: 10.1126/science.1208344.
37. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, et al. Enterotypes of the human gut microbiome
2011; 473:174–180. doi: 10.1038/nature09944.
38. Miquel S, Martín R, Rossi O, Bermúdez-Humarán LG, Chatel JM, Sokol H, et al. Faecalibacterium prausnitzii and human intestinal health. Curr Opin Microbial
2013; 16:255–261. doi: 10.1016/j.mib.2013.06.003.
39. Jia W, Whitehead RN, Griffiths L, Dawson C, Waring RH, Ramsden DB, et al. Is the abundance of Faecalibacterium prausnitzii relevant to Crohn's disease? FEMS Microbiol Lett
2010; 310:138–144. doi: 10.1111/j.1574-6968.2010.02057.x.
40. Shankar V, Agans R, Holmes B, Raymer M, Paliy O. Do gut microbial communities differ in pediatric IBS and health? Gut Microbes
2013; 4:347–352. doi: 10.4161/gmic.24827.
41. Hungate RE. The Rumen and its Microbes. New York-London: Academic Press; 1996.
42. Rainey FA, Janssen PH. Phylogenetic analysis by 16S ribosomal DNA sequence comparison reveals two unrelated groups of species within the genus Ruminococcus. FEMS Microbiol Lett
1995; 129:69–73. doi: 10.1111/j.1574-6968.1995.tb07559.x.
43. Chassard C, Delmas E, Robert C, Lawson PA, Bernalier-Donadille A. Ruminococcus champanellensis sp. nov., a cellulose-degrading bacterium from human gut microbiota. Int J Syst Evol Microbiol
2012; 62:138–143. doi: 10.1099/ijs.0.027375-0.
44. Flint HJ, Bayer EA, Rincon MT, Lamed R, White BA. Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nature Rev Microbiol
2008; 6:121–131. doi: 10.1038/nrmicro1817.
45. Leitch EC, Walker AW, Duncan SH, Holtrop G, Flint HJ. Selective colonization of insoluble substrates by human faecal bacteria. Environ Microbiol
2007; 9:667–679. doi: 10.1111/j.1462-2920.2006.01186.x.
46. Marteau P. Butyrate-producing bacteria as pharmabiotics for inflammatory bowel disease. Gut
2013; 62:1673doi: 10.1136/gutjnl-2012-304240.
47. Eeckhaut V, Machiels K, Perrier C, Romero C, Maes S, Flahou B, et al. Butyricicoccus pullicaecorum in inflammatory bowel disease. Gut
2013; 62:1745–1752. doi: 10.1136/gutjnl-2012-303611.
48. Whorwell PJ, Altringer L, Morel J, Bond Y, Charbonneau D, O’Mahony L, et al. Efficacy of an encapsulated probiotic Bifidobacterium infantis 35624 in women with irritable bowel syndrome
. Am J Gastroenterol
2006; 101:1581–1590. doi: 10.1111/j.1572-0241.2006.00734.x.
49. O’Mahony L, McCarthy L, Kelly P, Hurley G, Luo F, Chen K, et al. Lactobacillus and Bifidobacterium in irritable bowel syndrome
: symptom responses and relationship to cytokine profiles. Gastroenterology
2005; 128:541–551. doi: 10.1053/j.gastro.2004.11.050.
50. McCarthy J, O’Mahony L, O’Callaghan L, Sheil B, Vaughan EE, Fitzsimons N, et al. Double blind, placebo controlled trial of two probiotic strains in interleukin 10 knockout mice and mechanistic link with cytokine balance. Gut
2003; 52:975–980. doi: 10.1136/gut.52.7.975.
51. Mazmanian SK, Round JL, Kasper DL. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature
2008; 453:620–625. doi: 10.1038/nature07008.
52. Xu J, Bjursell MK, Himrod J, Deng S, Carmichael LK, Chiang HC, et al. A genomic view of the human-Bacteroides
thetaiotaomicron symbiosis. Science
2003; 299:2074–2076. doi: 10.1126/science.1080029.
53. Fearnley C, Manning G, Bagnall M, Javed MA, Wassenaar TM, Newell DG. Identification of hyperinvasive Campylobacter jejuni
strains isolated from poultry and human clinical sources. J Med Microbiol
2008; 57:570–580. doi: 10.1099/jmm.0.47803-0.
54. Stahl M, Friis LM, Nothaft H, Liu X, Li J, Szymanski CM, et al. L-fucose utilization provides Campylobacter jejuni with a competitive advantage. Proc Natl Acad Sci U S A
2011; 108:7194–7199. doi: 10.1073/pnas.1014125108.