[논문]Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals

Vaga, Stefania; Lee, Sunjae; Ji, Boyang; Andreasson, Anna; Talley, Nicholas J.; Agré; us, Lars; Bidkhori, Gholamreza; Kovatcheva-Datchary, Petia; Park, Junseok; Lee, Doheon; Proctor, Gordon; Ehrlich, Stanislav Dusko; Nielsen, Jens; Engstrand, Lars; Shoaie, Saeed

doi:10.1038/s41598-020-71939-2

[해외논문] Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals 원문보기

Scientific reports, v.10, 2020년, pp.14977 -

Vaga, Stefania (Centre for Host-Microbiome Interactions, Dental Institute, King’s College London, London, UK) , Lee, Sunjae (Centre for Host-Microbiome Interactions, Dental Institute, King’s College London, London, UK) , Ji, Boyang (Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden) , Andreasson, Anna (Stress Research Institute, Stockholm University, Stockholm, Sweden) , Talley, Nicholas J. (University of Newcastle, Newcastle, NSW Australia) , Agréus, Lars (Division of Family Medicine and Primary Care, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden) , Bidkhori, Gholamreza (Centre for Host-Microbiome Interactions, Dental Institute, King’s College London, London, UK) , Kovatcheva-Datchary, Petia (Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, 41345 Gothenburg, Sweden) , Park, Junseok (Department of Bio and Brain Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea) , Lee, Doheon (Department of Bio and Brain Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Kor) , Proctor, Gordon , Ehrlich, Stanislav Dusko , Nielsen, Jens , Engstrand, Lars , Shoaie, Saeed

Abstract ▼ AI-Helper

Gut mucosal microbes evolved closest to the host, developing specialized local communities. There is, however, insufficient knowledge of these communities as most studies have employed sequencing technologies to investigate faecal microbiota only. This work used shotgun metagenomics of mucosal biopsies to explore the microbial communities’ compositions of terminal ileum and large intestine in 5 healthy individuals. Functional annotations and genome-scale metabolic modelling of selected species were then employed to identify local functional enrichments. While faecal metagenomics provided a good approximation of the average gut mucosal microbiome composition, mucosal biopsies allowed detecting the subtle variations of local microbial communities. Given their significant enrichment in the mucosal microbiota, we highlight the roles of Bacteroides species and describe the antimicrobial resistance biogeography along the intestine. We also detail which species, at which locations, are involved with the tryptophan/indole pathway, whose malfunctioning has been linked to pathologies including inflammatory bowel disease. Our study thus provides invaluable resources for investigating mechanisms connecting gut microbiota and host pathophysiology.

참고문헌 (76)

1. Thursby E Juge N Introduction to the human gut microbiota Biochem. J. 2017 474 1823 1836 28512250

상세보기
2. Dethlefsen L McFall-Ngai M Relman DA An ecological and evolutionary perspective on humang-microbe mutualism and disease Nature 2007 449 811 818 17943117
3. Desselberger U The Mammalian intestinal microbiome: composition, interaction with the immune system, significance for vaccine efficacy, and potential for disease therapy Pathogens 2018 7 1 2
4. Zhang Z Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota ISME J. 2014 8 881 893 24132077

상세보기
5. Mcmahon T Van Zijl PCM Gilad AA Eating for two: how metabolism establishes interspecies cell host microbe interactions in the gut Gut 2015 27 320 331
6. Goodrich JK Genetic determinants of the gut microbiome in UK twins Cell Host Microbe 2016 19 731 743 27173935

상세보기
7. Donaldson GP Lee SM Mazmanian SK Gut biogeography of the bacterial microbiota Nat. Rev. Microbiol. 2015 14 20 32 26499895
8. Qin J Europe PMC Funders Group Europe PMC Funders. A human gut microbial gene catalog established by metagenomic sequencing Gut 2013 464 59 65
9. Vogtmann E Colorectal cancer and the human gut microbiome: reproducibility with whole-genome shotgun sequencing PLoS ONE 2016 11 1 13
10. VichVila A Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome Sci. Transl. Med. 2018 10 1 12
11. Kuang YS Connections between the human gut microbiome and gestational diabetes mellitus Gigascience 2017 6 1 12 29046044

상세보기
12. Jandhyala SM Role of the normal gut microbiota World J. Gastroenterol. 2015 21 8836 8847 26269673
13. Ottman N Geerlings SY Aalvink S De Vos WM Belzer C Best practice & research clinical gastroenterology action and function of akkermansia muciniphila in microbiome ecology, health and disease Best Pract. Res. Clin. Gastroenterol. 2017 31 637 642 29566906
14. Lee H Modulation of the gut microbiota by metformin improves metabolic profiles in aged obese mice Gut Microbes 2018 9 155 165 29157127

상세보기
15. Cekanaviciute E Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models Proc. Natl. Acad. Sci. 2017 114 201711235
16. Bedarf JR Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naive Parkinson’s disease patients Genome Med. 2017 9 1 13 28081715
17. Ghotaslou R Yekani M Memar MY The role of e ffl ux pumps in Bacteroides fragilis resistance to antibiotics Microbiol. Res. 2018 210 1 5 29625653

상세보기
18. Cirkeline K Anaerobe antimicrobial resistance in the Bacteroides fragilis group in faecal samples from patients receiving broad-spectrum antibiotics Anaerobe 2017 47 79 85 28445776
19. Deng H Bacteroides fragilis prevents clostridium difficile infection in a mouse model by restoring gut barrier and microbiome regulation Front. Microbiol. 2018 9 1 12 29403456
20. Mazmanian SK Liu CH Tzianabos AO Kasper DL Of symbiotic bacteria directs maturation of the host immune system Cell 2005 122 107 118 16009137
21. Sommer F Backhed F The gut microbiota-masters of host development and physiology Nat. Rev. Microbiol. 2013 11 227 238 23435359

상세보기
22. Howell KJ DNA methylation and transcription patterns in intestinal epithelial cells from pediatric patients with inflammatory bowel diseases differentiate disease subtypes and associate with outcome Gastroenterology 2018 154 585 598 29031501
23. Li G Diversity of duodenal and rectal microbiota in biopsy tissues and luminal contents in healthy volunteers J. Microbiol. Biotechnol. 2015 25 1136 1145 25737115

원문보기 상세보기
24. Suez J Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT Cell 2018 174 1406 1423.e16 30193113

상세보기
25. Gevers D Kugathasan S Denson L Vazquez-Baeza Y Van Treuren W The treatment-naive microbiome in new-onset Crohn’s disease Cell Host Microbe 2014 15 382 392 24629344

상세보기
26. Beaumont M Quantity and source of dietary protein influence metabolite production by gut microbiota and rectal mucosa gene expression: a randomized, parallel, double-blind trial in overweight humans Am. J. Clin. Nutr. 2017 106 1005 1019 28903954

상세보기
27. Hillmann B Evaluating the information content of shallow shotgun metagenomics MSystem 2018 3 1 12
28. Kjellstrom L A randomly selected population sample undergoing colonoscopy: prevalence of the irritable bowel syndrome and the impact of selection factors Eur. J. Gastroenterol. Hepatol. 2014 26 268 275 24384686

상세보기
29. Le Chatelier E Richness of human gut microbiome correlates with metabolic markers Nature 2013 500 541 546 23985870

상세보기
30. Rangel I The relationship between faecal-associated and mucosal-associated microbiota in irritable bowel syndrome patients and healthy subjects Aliment. Pharmacol. Ther. 2015 42 1211 1221 26376728

상세보기
31. Leite AZ Detection of increased plasma interleukin-6 levels and prevalence of Prevotella copri and Bacteroides vulgatus in the feces of type 2 diabetes patients Front. Immunol. 2017 10.3389/fimmu.2017.01107 28966614

상세보기
32. Chiodini RJ Transitional and temporal changes in the mucosal and submucosal intestinal microbiota in advanced crohn’s disease of the terminal ileum J. Med. Microbiol. 2018 67 549 559 29458679

상세보기
33. Chiodini RJ Dowd SE Galandiuk S Davis B Glassing A The predominant site of bacterial translocation across the intestinal mucosal barrier occurs at the advancing disease margin in Crohn’s disease Microbiology 2016 162 1608 1619 27418066
34. Øyri SF Muzes G Sipos F Dysbiotic gut microbiome: A key element of Crohn’s disease Comp. Immunol. Microbiol. Infect. Dis. 2015 43 36 49 26616659

상세보기
35. van Schaik W The human gut resistome Philos. Trans. R. Soc. B 2015 370 20140087
36. 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 26476454

상세보기
37. Kanehisa M Goto S KEGG: Kyoto encyclopedia of genes and genomes Nucleic Acids Res. 2000 28 27 30 10592173

상세보기
38. Kanehisa M Toward understanding the origin and evolution of cellular organisms Protein Sci. 2019 28 1947 1951 31441146

상세보기
39. Lyu Y Wu L Wang F Shen X Lin D Carotenoid supplementation and retinoic acid in immunoglobulin A regulation of the gut microbiota dysbiosis Exp. Biol. Med. 2018 243 613 620
40. Medema MH AntiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences Nucleic Acids Res. 2011 39 339 346
41. Schoner TA Aryl polyenes, a highly abundant class of bacterial natural products, are functionally related to antioxidative carotenoids ChemBioChem 2016 17 247 253 26629877

상세보기
42. Cummings JH Pomare EW Branch HWJ Naylor CPE MacFarlane GT Short chain fatty acids in human large intestine, portal, hepatic and venous blood Gut 1987 28 1221 1227 3678950

상세보기
43. Gao J Impact of the gut microbiota on intestinal immunity mediated by tryptophan metabolism Front. Cell Infect. Microbiol. 2018 8 1 22 29404279
44. Zoetendal EG Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces Appl. Environ. Microbiol. 2002 68 3401 3407 12089021

상세보기
45. Nayfach S Pollard KS Toward accurate and quantitative comparative metagenomics Cell 2016 166 1103 1116 27565341

상세보기
46. Wexler HM Bacteroides: the good, the bad, and the nitty-gritty Clin. Microbiol. Rev. 2007 20 593 621 17934076

상세보기
47. Tzianabos AO Structural features of polysaccharides that abscesses induce intra-abdominal Science 1993 262 416 419 8211161
48. Hiippala K The potential of gut commensals in reinforcing intestinal barrier function and alleviating inflammation Nutrients 2018 10 988

상세보기
49. Round JL The Toll-like receptor pathway establishes commensal gut colonization Science 2011 332 974 977 21512004
50. Hsiao EY Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders Cell 2013 155 1451 1463 24315484

상세보기
51. Chang YC TLR2 and interleukin-10 are involved in Bacteroides fragilis-mediated prevention of DSS-induced colitis in gnotobiotic mice PLoS ONE 2017 12 1 16
52. An D Na C Bielawski J Hannun YA Kasper DL Membrane sphingolipids as essential molecular signals for Bacteroides survival in the intestine Proc. Natl. Acad. Sci. 2011 108 4666 4671 20855611
53. Maskell JP The resolution of bacteroides lipopolysaccharides by polyacrylamide gel electrophoresis J. Med. Microbiol. 1991 34 253 257 2030500

상세보기
54. Jacobson AN Choudhury BP Fischbach MA The Biosynthesis of Lipooligosaccharide from Bacteroides thetaiotaomicron MBio 2018 9 1 14
55. Jalanka J Long-term effects on luminal and mucosal microbiota and commonly acquired taxa in faecal microbiota transplantation for recurrent Clostridium difficile infection BMC Med. 2016 14 1 10 26728489
56. Goodman AL Identifying genetic determinants needed to establish a human gut symbiont in its habitat Cell Host Microbe 2009 6 279 289 19748469

상세보기
57. Pumbwe L Skilbeck CA Wexler HM The bacteroides fragilis cell envelope: quarterback, linebacker, coach-or all three? Anaerobe 2006 12 211 220 17045496

상세보기
58. Forslund K Country-specific antibiotic use practices impact the human gut resistome Genome Res. 2013 23 1163 1169 23568836

상세보기
59. Crofts TS Gasparrini AJ Dantas G Next-generation approaches to understand and combat the antibiotic resistome Nat. Rev. Microbiol. 2017 15 422 434 28392565

상세보기
60. Forsberg K The shared antibiotic resistome of soil bacteria and human pathogens Science 2012 337 1107 1111 22936781

상세보기
61. Halstead JM The effects of micronutrient deficiencies on bacterial species from the human gut microbiota Science 2015 347 1367 1671 25792328
62. Kau AL Ahern PP Griffin NW Goodman AL Gordon JI Human nutrition, the gut microbiome and the immune system Nature 2011 474 327 336 21677749

상세보기
63. Roager HM Licht TR Microbial tryptophan catabolites in health and disease Nat. Commun. 2018 9 1 10 29317637
64. Agus A Planchais J Sokol H Review gut microbiota regulation of tryptophan metabolism in health and disease Cell Host Microbe 2018 23 716 724 29902437
65. Nikolaus S Increased tryptophan metabolism is associated with activity of inflammatory bowel diseases Gastroenterology 2017 153 1504 1516.e2 28827067
66. Nagata N Effects of bowel preparation on the human gut microbiome and metabolome Sci. Rep. 2019 9 1 8 30626917
67. Arango-Argoty G DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data Microbiome 2018 6 1 15 29291746
68. Salonen A Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis J. Microbiol. Methods 2010 81 127 134 20171997

상세보기
69. Dore J Dietary intervention impact on gut microbial gene richness Nature 2013 500 585 588 23985875

상세보기
70. Wen C Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis Genome Biol. 2017 18 1 13 28077169
71. Nielsen HB Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes Nat. Biotechnol. 2014 32 822 828 24997787

상세보기
72. Le Chatelier E Gut microbiome influences efficacy of PD-1？based immunotherapy against epithelial tumors Science 2017 359 91 97 29097494
73. Kanehisa M Sato Y Furumichi M Morishima K Tanabe M New approach for understanding genome variations in KEGG Nucleic Acids Res. 2019 47 D590 D595 30321428

상세보기
74. Forrester J Ury H The signed-rank (Wilcoxon) test in the rapid analysis of biological data Lancet 1969 1 239 241 4178594
75. McArthur AG The comprehensive antibiotic resistance database Antimicrob. Agents Chemother. 2013 57 3348 3357 23650175

상세보기
76. Blin K AntiSMASH 4.0: improvements in chemistry prediction and gene cluster boundary identification Nucleic Acids Res. 2017 45 W36 W41 28460038

상세보기

LOADING...

활용도 분석정보

상세보기

다운로드

내보내기

활용도 Top5 논문

해당 논문의 주제분야에서 활용도가 높은 상위 5개 콘텐츠를 보여줍니다.
더보기 버튼을 클릭하시면 더 많은 관련자료를 살펴볼 수 있습니다.

표제어: PCR

동의어: Packet Collision Rate

용어 설명 출처 목록 (6)

용어 설명: PCR은 세균 특이성이 있는 primer를 이용하여 적은 수의 세균이 있을지라도 쉽게 검출할 수 있는 유용한 방법이며, 이를 이용하여 구강 내 치면세균막이나 타액에서 직접 세균을 검출할 수 있게 되었다[8].

내보내기 구분	파일저장 인쇄 메일전송
구성항목	기본정보 상세정보 관리번호, 논문명, 저널/프로시딩명, 저자 , 발행년, 권, 호, 시작페이지, 끝페이지, 발행기관 관리번호, 논문명, 대등논문명, 저자 , 저널/프로시딩명, 발행기관, 발행년, 발행언어, 권, 호, 시작페이지, 끝페이지, ISBN, ISSN, 주제분야, 키워드, 초록(한글), 초록(영문), 저자(소속기관)
저장형식	Text(ASCII format) Excel format RefWorks Direct Export RIS format (for Reference Manager, ProCite, EndNote), Scholar's Aids, Mendeley
메일정보	받는사람 (필수) @ 보내는사람 (선택) @ 제목 내용 KISTI 검색결과 이메일 서비스
안내	총 건의 자료가 검색되었습니다. 다운받으실 자료의 인덱스를 입력하세요. (1-10,000) 검색결과의 순서대로 최대 10,000건 까지 다운로드가 가능합니다. 데이타가 많을 경우 속도가 느려질 수 있습니다.(최대 2~3분 소요) 다운로드 파일은 UTF-8 형태로 저장됩니다. 파일의 내용이 제대로 보이지 않을실 때는 웹브라우저 상단의 보기 -> 인코딩 -> 자동선택 여부를 확인하십시오. ~ Text(ASCII format) Excel format

연합인증