Skip to main content
Top
Published in: European Journal of Clinical Microbiology & Infectious Diseases 9/2018

01-09-2018 | Review

How human microbiome talks to health and disease

Authors: Jing Cong, Xiaochun Zhang

Published in: European Journal of Clinical Microbiology & Infectious Diseases | Issue 9/2018

Login to get access

Abstract

Microbes are ubiquitous in the human body. They usually live in communities, and each of these communities has a distinct taxonomical structure. Due to its close relationship with human health and disease, the human microbiome has received great attention and is probably considered to be the most valuable biomarker in preventing and solving human diseases. In this paper, we first review the value of the human microbiome. Then, we focus on the role of the human microbiome in influencing human health and disease. Furthermore, we intensively discuss the relationship between intestinal microbiota and cancer therapy. Finally, we briefly summarize the significance of the human microbiome based on the development of sequencing and bioinformatic techniques.
Literature
1.
go back to reference Fontaneto D, Hortal J (2012) Microbial biogeography: is everything small everywhere? Caister Academic Press, Poole, p 87–98 Fontaneto D, Hortal J (2012) Microbial biogeography: is everything small everywhere? Caister Academic Press, Poole, p 87–98
2.
go back to reference Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308(5728):1635–1638CrossRefPubMedPubMedCentral Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308(5728):1635–1638CrossRefPubMedPubMedCentral
3.
go back to reference Grice EA, Segre JA (2012) The human microbiome: our second genome. Annual Rev Genomics Human Genetics 13(1):151–170CrossRef Grice EA, Segre JA (2012) The human microbiome: our second genome. Annual Rev Genomics Human Genetics 13(1):151–170CrossRef
4.
go back to reference Dethlefsen L, Mcfallngai M, Relman DA (2007) An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 449(7164):811–818CrossRefPubMed Dethlefsen L, Mcfallngai M, Relman DA (2007) An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 449(7164):811–818CrossRefPubMed
5.
go back to reference Zhu GZ, Li JT (2008) Substantial alterations of the cutaneous bacterial biota in psoriatic lesions. PLoS One 3(7):550–550 Zhu GZ, Li JT (2008) Substantial alterations of the cutaneous bacterial biota in psoriatic lesions. PLoS One 3(7):550–550
6.
go back to reference Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444 (7122):1027–1031 Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444 (7122):1027–1031
7.
go back to reference Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R (2011) Bacterial community variation in human body habitats across space and time. Science 326(5960):1694–1697CrossRef Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R (2011) Bacterial community variation in human body habitats across space and time. Science 326(5960):1694–1697CrossRef
8.
go back to reference Wei L, Lei H, Yu P, Ma C, Wu X, Xu J (2014) Nested PCR-denaturing gradient gel electrophoresis analysis of human skin microbial diversity with age. Microbiol Res 169(9–10):686–692 Wei L, Lei H, Yu P, Ma C, Wu X, Xu J (2014) Nested PCR-denaturing gradient gel electrophoresis analysis of human skin microbial diversity with age. Microbiol Res 169(9–10):686–692
9.
go back to reference Wylie KM, Mihindukulasuriya KA, Zhou Y, Sodergren E, Storch GA, Weinstock GM (2014) Metagenomic analysis of double-stranded DNA viruses in healthy adults. BMC Biol 12(1):1–10CrossRef Wylie KM, Mihindukulasuriya KA, Zhou Y, Sodergren E, Storch GA, Weinstock GM (2014) Metagenomic analysis of double-stranded DNA viruses in healthy adults. BMC Biol 12(1):1–10CrossRef
10.
go back to reference Clavaud C, Jourdain R, Barhen A, Tichit M, Bouchier C, Pouradier F, Rawadi CE, Guillot J, Ménardszczebara F, Breton L (2013) Dandruff is associated with disequilibrium in the proportion of the major bacterial and fungal populations colonizing the scalp. PLoS One 8(3):e58203CrossRefPubMedPubMedCentral Clavaud C, Jourdain R, Barhen A, Tichit M, Bouchier C, Pouradier F, Rawadi CE, Guillot J, Ménardszczebara F, Breton L (2013) Dandruff is associated with disequilibrium in the proportion of the major bacterial and fungal populations colonizing the scalp. PLoS One 8(3):e58203CrossRefPubMedPubMedCentral
11.
go back to reference Keisha F, Julia O, Joy Y, Sean C, Clayton D, Meyer JA, Deborah S, Effie N, Morgan P, Kong HH (2013) Topographic diversity of fungal and bacterial communities in human skin. Nature 498(7454):367–370CrossRef Keisha F, Julia O, Joy Y, Sean C, Clayton D, Meyer JA, Deborah S, Effie N, Morgan P, Kong HH (2013) Topographic diversity of fungal and bacterial communities in human skin. Nature 498(7454):367–370CrossRef
12.
go back to reference Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308(5728):1635–1638CrossRefPubMedPubMedCentral Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308(5728):1635–1638CrossRefPubMedPubMedCentral
13.
go back to reference Perez Perez GI, Gao Z, Jourdain R, Ramirez J, Gany F, Clavaud C, Demaude J, Breton L, Blaser MJ (2016) Body site is a more determinant factor than human population diversity in the healthy skin microbiome. PLoS One 11(4):e0151990 Perez Perez GI, Gao Z, Jourdain R, Ramirez J, Gany F, Clavaud C, Demaude J, Breton L, Blaser MJ (2016) Body site is a more determinant factor than human population diversity in the healthy skin microbiome. PLoS One 11(4):e0151990
14.
go back to reference Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, Bouffard GG, Blakesley RW, Murray PR, Green ED (2009) Topographical and temporal diversity of the human skin microbiome. Science 324(5931):1190–1192CrossRefPubMedPubMedCentral Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, Bouffard GG, Blakesley RW, Murray PR, Green ED (2009) Topographical and temporal diversity of the human skin microbiome. Science 324(5931):1190–1192CrossRefPubMedPubMedCentral
15.
16.
go back to reference Chiller K, Selkin BA, Murakawa GJ (2001) Skin microflora and bacterial infections of the skin. J Investig Dermatol Symp Proc 6(3):170–174CrossRefPubMed Chiller K, Selkin BA, Murakawa GJ (2001) Skin microflora and bacterial infections of the skin. J Investig Dermatol Symp Proc 6(3):170–174CrossRefPubMed
18.
go back to reference Biedermann T (2006) Dissecting the role of infections in atopic dermatitis. Acta Dermato Venereologica 86(2):99–109PubMed Biedermann T (2006) Dissecting the role of infections in atopic dermatitis. Acta Dermato Venereologica 86(2):99–109PubMed
19.
go back to reference Iwase T, Uehara Y, Shinji H, Tajima A, Seo H, Takada K, Agata T, Mizunoe Y (2010) Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization. Nature 465(7296):346–349CrossRefPubMed Iwase T, Uehara Y, Shinji H, Tajima A, Seo H, Takada K, Agata T, Mizunoe Y (2010) Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization. Nature 465(7296):346–349CrossRefPubMed
20.
go back to reference Lai Y, Di NA, Nakatsuji T, Leichtle A, Yang Y, Cogen AL, Wu ZR, Hooper LV, Schmidt RR, Von AS (2009) Commensal bacteria regulate Toll-like receptor 3-dependent inflammation after skin injury. Nat Med 15(12):1377–1382CrossRefPubMedPubMedCentral Lai Y, Di NA, Nakatsuji T, Leichtle A, Yang Y, Cogen AL, Wu ZR, Hooper LV, Schmidt RR, Von AS (2009) Commensal bacteria regulate Toll-like receptor 3-dependent inflammation after skin injury. Nat Med 15(12):1377–1382CrossRefPubMedPubMedCentral
21.
go back to reference Shu M, Wang Y, Yu J, Kuo S, Coda A, Jiang Y, Gallo RL, Huang CM (2013) Fermentation of Propionibacterium acnes, a commensal bacterium in the human skin microbiome, as skin probiotics against methicillin-resistant Staphylococcus aureus. PLoS One 8(2):1060–1064CrossRef Shu M, Wang Y, Yu J, Kuo S, Coda A, Jiang Y, Gallo RL, Huang CM (2013) Fermentation of Propionibacterium acnes, a commensal bacterium in the human skin microbiome, as skin probiotics against methicillin-resistant Staphylococcus aureus. PLoS One 8(2):1060–1064CrossRef
22.
go back to reference Volz T, Skabytska Y, Guenova E, Chen KM, Frick JS, Kirschning CJ, Kaesler S, Röcken M, Biedermann T (2014) Nonpathogenic bacteria alleviating atopic dermatitis inflammation induce IL-10-producing dendritic cells and regulatory Tr1 cells. J Investig Dermatol 134(1):96–104CrossRefPubMed Volz T, Skabytska Y, Guenova E, Chen KM, Frick JS, Kirschning CJ, Kaesler S, Röcken M, Biedermann T (2014) Nonpathogenic bacteria alleviating atopic dermatitis inflammation induce IL-10-producing dendritic cells and regulatory Tr1 cells. J Investig Dermatol 134(1):96–104CrossRefPubMed
23.
go back to reference Lai Y, Cogen AL, Radek KA, Park HJ, Macleod DT, Leichtle A, Ryan AF, Nardo AD, Gallo RL (2010) Activation of TLR2 by a small molecule produced by Staphylococcus epidermidis increases antimicrobial defense against bacterial skin infections. J Investig Dermatol 130(9):2211–2221CrossRefPubMed Lai Y, Cogen AL, Radek KA, Park HJ, Macleod DT, Leichtle A, Ryan AF, Nardo AD, Gallo RL (2010) Activation of TLR2 by a small molecule produced by Staphylococcus epidermidis increases antimicrobial defense against bacterial skin infections. J Investig Dermatol 130(9):2211–2221CrossRefPubMed
24.
go back to reference Grice EA, Kong HH, Renaud G, Young AC, Bouffard GG, Blakesley RW, Wolfsberg TG, Turner ML, Segre JA (2008) A diversity profile of the human skin microbiota. Genome Res 18(7):1043–1050CrossRefPubMedPubMedCentral Grice EA, Kong HH, Renaud G, Young AC, Bouffard GG, Blakesley RW, Wolfsberg TG, Turner ML, Segre JA (2008) A diversity profile of the human skin microbiota. Genome Res 18(7):1043–1050CrossRefPubMedPubMedCentral
25.
go back to reference Sanmiguel A, Grice EA (2015) Interactions between host factors and the skin microbiome. Cellular Molecular Life Sci Cmls 72(8):1499–1515CrossRef Sanmiguel A, Grice EA (2015) Interactions between host factors and the skin microbiome. Cellular Molecular Life Sci Cmls 72(8):1499–1515CrossRef
26.
27.
go back to reference Flint HJ, Scott KP, Louis P, Duncan SH (2012) The role of the gut microbiota in nutrition and health. Nat Rev Gastroenterol Hepatol 9(10):577–589CrossRefPubMed Flint HJ, Scott KP, Louis P, Duncan SH (2012) The role of the gut microbiota in nutrition and health. Nat Rev Gastroenterol Hepatol 9(10):577–589CrossRefPubMed
28.
go back to reference Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE (2006) Metagenomic analysis of the human distal gut microbiome. Science 312(5778):1355–1359CrossRefPubMedPubMedCentral Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE (2006) Metagenomic analysis of the human distal gut microbiome. Science 312(5778):1355–1359CrossRefPubMedPubMedCentral
29.
go back to reference Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T (2014) An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol 32(8):834–841CrossRefPubMed Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T (2014) An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol 32(8):834–841CrossRefPubMed
30.
go back to reference Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R (2008) Evolution of mammals and their gut microbes. Science 320(5883):1647–1651CrossRefPubMedPubMedCentral Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R (2008) Evolution of mammals and their gut microbes. Science 320(5883):1647–1651CrossRefPubMedPubMedCentral
31.
go back to reference Consortium THMP (2012) Structure, function and diversity of the healthy human microbiome. Nature 486(7402):207–214CrossRef Consortium THMP (2012) Structure, function and diversity of the healthy human microbiome. Nature 486(7402):207–214CrossRef
32.
go back to reference Paola MD, Filippo CD, Cavalieri D, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G, Lionetti P (2010) PP90 impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A 107(33):S445–S446 Paola MD, Filippo CD, Cavalieri D, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G, Lionetti P (2010) PP90 impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A 107(33):S445–S446
33.
go back to reference Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP (2012) Human gut microbiome viewed across age and geography. Nature 486(7402):222–227CrossRefPubMedPubMedCentral Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP (2012) Human gut microbiome viewed across age and geography. Nature 486(7402):222–227CrossRefPubMedPubMedCentral
34.
go back to reference Mardis ER, Gordon JI, Mahowald MA, Turnbaugh PJ, Ley RE, Magrini V (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444(7122):1027–1031CrossRefPubMed Mardis ER, Gordon JI, Mahowald MA, Turnbaugh PJ, Ley RE, Magrini V (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444(7122):1027–1031CrossRefPubMed
35.
go back to reference Koren O, Goodrich J, Cullender T, Spor A, Laitinen K, Bäckhed HK, Gonzalez A, Werner J, Angenent L, Knight R (2012) Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 150(3):470–480CrossRefPubMedPubMedCentral Koren O, Goodrich J, Cullender T, Spor A, Laitinen K, Bäckhed HK, Gonzalez A, Werner J, Angenent L, Knight R (2012) Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 150(3):470–480CrossRefPubMedPubMedCentral
36.
go back to reference Mulders RJ, Git KCGD, Schéle E, Dickson SL, Sanz Y, Adan RAH (2018) Microbiota in obesity: interactions with enteroendocrine, immune and central nervous systems. Obes Rev 19(4) Mulders RJ, Git KCGD, Schéle E, Dickson SL, Sanz Y, Adan RAH (2018) Microbiota in obesity: interactions with enteroendocrine, immune and central nervous systems. Obes Rev 19(4)
38.
go back to reference Jobin C (2017) Human intestinal microbiota and colorectal cancer: moving beyond associative studies. Gastroenterology 153(6):1475–1478 Jobin C (2017) Human intestinal microbiota and colorectal cancer: moving beyond associative studies. Gastroenterology 153(6):1475–1478
39.
go back to reference Round JL, Mazmanian SK (2010) Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc Natl Acad Sci U S A 107(27):12204–12209CrossRefPubMedPubMedCentral Round JL, Mazmanian SK (2010) Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc Natl Acad Sci U S A 107(27):12204–12209CrossRefPubMedPubMedCentral
41.
go back to reference Abu-Shanab A, Quigley EM (2010) The role of the gut microbiota in nonalcoholic fatty liver disease. Nat Rev Gastroenterol Hepatol 7(12):691–701CrossRefPubMed Abu-Shanab A, Quigley EM (2010) The role of the gut microbiota in nonalcoholic fatty liver disease. Nat Rev Gastroenterol Hepatol 7(12):691–701CrossRefPubMed
42.
go back to reference Bäckhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, Semenkovich CF, Gordon JI (2004) The gut microbiota as an environmental factor that regulates fat storage. Proceedings of the National Academy of Sciences of the United States of America 101 (44):15718–15723 Bäckhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, Semenkovich CF, Gordon JI (2004) The gut microbiota as an environmental factor that regulates fat storage. Proceedings of the National Academy of Sciences of the United States of America 101 (44):15718–15723
43.
go back to reference Fei N, Zhao L (2013) An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice. Isme J Multidisciplinary J Microbial Ecology 7(4):880–884 Fei N, Zhao L (2013) An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice. Isme J Multidisciplinary J Microbial Ecology 7(4):880–884
44.
go back to reference Everard A, Belzer C, Geurts L, Ouwerkerk JP, Druart C, Bindels LB, Guiot Y, Derrien M, Muccioli GG, Delzenne NM (2013) Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc Natl Acad Sci U S A 110(22):9066–9071CrossRefPubMedPubMedCentral Everard A, Belzer C, Geurts L, Ouwerkerk JP, Druart C, Bindels LB, Guiot Y, Derrien M, Muccioli GG, Delzenne NM (2013) Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc Natl Acad Sci U S A 110(22):9066–9071CrossRefPubMedPubMedCentral
45.
go back to reference Gupta A, Madani R, Mukhtar H (2010) Streptococcus bovis endocarditis, a silent sign for colonic tumour. Color Dis 12(3):164–171CrossRef Gupta A, Madani R, Mukhtar H (2010) Streptococcus bovis endocarditis, a silent sign for colonic tumour. Color Dis 12(3):164–171CrossRef
46.
go back to reference Viljoen KS, Dakshinamurthy A, Goldberg P, Blackburn JM (2015) Quantitative profiling of colorectal cancer-associated bacteria reveals associations between fusobacterium spp., enterotoxigenic Bacteroides fragilis (ETBF) and clinicopathological features of colorectal cancer. PLoS One 10(3):e0119462CrossRefPubMedPubMedCentral Viljoen KS, Dakshinamurthy A, Goldberg P, Blackburn JM (2015) Quantitative profiling of colorectal cancer-associated bacteria reveals associations between fusobacterium spp., enterotoxigenic Bacteroides fragilis (ETBF) and clinicopathological features of colorectal cancer. PLoS One 10(3):e0119462CrossRefPubMedPubMedCentral
47.
go back to reference Ahn J, Sinha R, Pei Z, Dominianni C, Wu J, Shi J, Goedert JJ, Hayes RB, Yang L (2013) Human gut microbiome and risk for colorectal cancer. J Natl Cancer Inst 105(24):1907–1911CrossRefPubMedPubMedCentral Ahn J, Sinha R, Pei Z, Dominianni C, Wu J, Shi J, Goedert JJ, Hayes RB, Yang L (2013) Human gut microbiome and risk for colorectal cancer. J Natl Cancer Inst 105(24):1907–1911CrossRefPubMedPubMedCentral
48.
go back to reference Gonçalves P, Araújo JR, Di SJ (2018) A cross-talk between microbiota-derived short-chain fatty acids and the host mucosal immune system regulates intestinal homeostasis and inflammatory bowel disease. Inflamm Bowel Dis 24(3):558CrossRefPubMed Gonçalves P, Araújo JR, Di SJ (2018) A cross-talk between microbiota-derived short-chain fatty acids and the host mucosal immune system regulates intestinal homeostasis and inflammatory bowel disease. Inflamm Bowel Dis 24(3):558CrossRefPubMed
50.
go back to reference Consortium HMP (2012) Structure, function and diversity of the healthy human microbiome. Nature 486(7402):207–214CrossRef Consortium HMP (2012) Structure, function and diversity of the healthy human microbiome. Nature 486(7402):207–214CrossRef
51.
go back to reference Wade WG (2012) The oral microbiome in health and disease. Pharmacological Research the Official Journal of the Italian Pharmacological Society 69 (1):137–143 Wade WG (2012) The oral microbiome in health and disease. Pharmacological Research the Official Journal of the Italian Pharmacological Society 69 (1):137–143
52.
go back to reference Crielaard W, Zaura E, Schuller AA, Huse SM, Montijn RC, Keijser BJ (2011) Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health. BMC Med Genet 4(1):22 Crielaard W, Zaura E, Schuller AA, Huse SM, Montijn RC, Keijser BJ (2011) Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health. BMC Med Genet 4(1):22
53.
go back to reference Zheng H, Xu L, Wang Z, Li L, Zhang J, Zhang Q, Chen T, Lin J, Chen F (2015) Subgingival microbiome in patients with healthy and ailing dental implants. Sci Rep 5:10948 Zheng H, Xu L, Wang Z, Li L, Zhang J, Zhang Q, Chen T, Lin J, Chen F (2015) Subgingival microbiome in patients with healthy and ailing dental implants. Sci Rep 5:10948
54.
go back to reference Segal LN, Alekseyenko AV, Clemente JC, Kulkarni R, Wu B, Chen H, Berger KI, Goldring RM, Rom WN, Blaser MJ (2013) Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation. Microbiome 1(1):19CrossRefPubMedPubMedCentral Segal LN, Alekseyenko AV, Clemente JC, Kulkarni R, Wu B, Chen H, Berger KI, Goldring RM, Rom WN, Blaser MJ (2013) Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation. Microbiome 1(1):19CrossRefPubMedPubMedCentral
55.
go back to reference Twigg HL, Morris A, Ghedin E, Curtis JL, Huffnagle GB, Crothers K, Campbell TB, Flores SC, Fontenot AP, Beck JM (2013) Use of bronchoalveolar lavage to assess the respiratory microbiome: signal in the noise. Lancet Respiratory Medicine 1(5):354–356CrossRefPubMed Twigg HL, Morris A, Ghedin E, Curtis JL, Huffnagle GB, Crothers K, Campbell TB, Flores SC, Fontenot AP, Beck JM (2013) Use of bronchoalveolar lavage to assess the respiratory microbiome: signal in the noise. Lancet Respiratory Medicine 1(5):354–356CrossRefPubMed
56.
go back to reference Venkataraman A, Bassis CM, Beck JM, Young VB, Curtis JL, Huffnagle GB, Schmidt TM (2015) Application of a neutral community model to assess structuring of the human lung microbiome. MBio 6(1) Venkataraman A, Bassis CM, Beck JM, Young VB, Curtis JL, Huffnagle GB, Schmidt TM (2015) Application of a neutral community model to assess structuring of the human lung microbiome. MBio 6(1)
57.
go back to reference Dickson RP, Erbdownward JR, Freeman CM, Mccloskey L, Beck JM, Huffnagle GB, Curtis JL (2015) Spatial variation in the healthy human lung microbiome and the adapted island model of lung biogeography. Annals Am Thoracic Soc 12(6):821–830CrossRef Dickson RP, Erbdownward JR, Freeman CM, Mccloskey L, Beck JM, Huffnagle GB, Curtis JL (2015) Spatial variation in the healthy human lung microbiome and the adapted island model of lung biogeography. Annals Am Thoracic Soc 12(6):821–830CrossRef
58.
go back to reference Sze MA, Dimitriu PA, Hayashi S, Elliott WM, Mcdonough JE, Gosselink JV, Cooper J, Sin DD, Mohn WW, Hogg JC (2012) The lung tissue microbiome in chronic obstructive pulmonary disease. Am J Respiratory Critical Care Medicine 185(10):1073-1080CrossRef Sze MA, Dimitriu PA, Hayashi S, Elliott WM, Mcdonough JE, Gosselink JV, Cooper J, Sin DD, Mohn WW, Hogg JC (2012) The lung tissue microbiome in chronic obstructive pulmonary disease. Am J Respiratory Critical Care Medicine 185(10):1073-1080CrossRef
59.
go back to reference Zachariah R, Spielmann MP, Harries AD, Gomani P, Graham SM, Bakali E, Humblet P (2003) Passive versus active tuberculosis case finding and isoniazid preventive therapy among household contacts in a rural district of Malawi. Int J Tuberculosis Lung Disease 7(11):1033–1039 Zachariah R, Spielmann MP, Harries AD, Gomani P, Graham SM, Bakali E, Humblet P (2003) Passive versus active tuberculosis case finding and isoniazid preventive therapy among household contacts in a rural district of Malawi. Int J Tuberculosis Lung Disease 7(11):1033–1039
60.
go back to reference Piters WAADS, Sanders EAM, Bogaert D (2015) The role of the local microbial ecosystem in respiratory health and disease. Philos Trans R Soc Lond 370(1675) Piters WAADS, Sanders EAM, Bogaert D (2015) The role of the local microbial ecosystem in respiratory health and disease. Philos Trans R Soc Lond 370(1675)
61.
go back to reference Marri PR, Stern DA, Wright AL, Billheimer D, Martinez FD (2013) Asthma-associated differences in microbial composition of induced sputum. J Allergy Clinical Immunology 131(2):1–3CrossRef Marri PR, Stern DA, Wright AL, Billheimer D, Martinez FD (2013) Asthma-associated differences in microbial composition of induced sputum. J Allergy Clinical Immunology 131(2):1–3CrossRef
62.
go back to reference Garcianuñez M, Millares L, Pomares X, Ferrari R, Pérezbrocal V, Gallego M, Espasa M, Moya A, Monsó E (2014) Severity-related changes of bronchial microbiome in chronic obstructive pulmonary disease. J Clin Microbiol 52(12):4217–4223CrossRef Garcianuñez M, Millares L, Pomares X, Ferrari R, Pérezbrocal V, Gallego M, Espasa M, Moya A, Monsó E (2014) Severity-related changes of bronchial microbiome in chronic obstructive pulmonary disease. J Clin Microbiol 52(12):4217–4223CrossRef
63.
go back to reference Wu D, Hou C, Li Y, Zhao Z, Liu J, Lu X, Shang X, Xin Y (2014) Analysis of the bacterial community in chronic obstructive pulmonary disease sputum samples by denaturing gradient gel electrophoresis and real-time PCR. Bmc Pulmonary Medicine 14(1):179CrossRefPubMedPubMedCentral Wu D, Hou C, Li Y, Zhao Z, Liu J, Lu X, Shang X, Xin Y (2014) Analysis of the bacterial community in chronic obstructive pulmonary disease sputum samples by denaturing gradient gel electrophoresis and real-time PCR. Bmc Pulmonary Medicine 14(1):179CrossRefPubMedPubMedCentral
64.
go back to reference Han MK, Zhou Y, Murray S, Tayob N, Noth I, Lama VN, Moore BB, White ES, Flaherty KR, Huffnagle GB (2014) Lung microbiome and disease progression in idiopathic pulmonary fibrosis: an analysis of the COMET study. Lancet Respiratory Medicine 2(7):548–556CrossRefPubMed Han MK, Zhou Y, Murray S, Tayob N, Noth I, Lama VN, Moore BB, White ES, Flaherty KR, Huffnagle GB (2014) Lung microbiome and disease progression in idiopathic pulmonary fibrosis: an analysis of the COMET study. Lancet Respiratory Medicine 2(7):548–556CrossRefPubMed
65.
go back to reference Dickson RP, ErbDownward JR, Huffnagle GB (2014) Towards an ecology of the lung: new conceptual models of pulmonary microbiology and pneumonia pathogenesis. Lancet Respir Med 2(3):238–246CrossRefPubMedPubMedCentral Dickson RP, ErbDownward JR, Huffnagle GB (2014) Towards an ecology of the lung: new conceptual models of pulmonary microbiology and pneumonia pathogenesis. Lancet Respir Med 2(3):238–246CrossRefPubMedPubMedCentral
66.
go back to reference Smith SB, Ravel J (2017) The vaginal microbiota, host defence and reproductive physiology. Journal of Physiology 595 (2):451-463 Smith SB, Ravel J (2017) The vaginal microbiota, host defence and reproductive physiology. Journal of Physiology 595 (2):451-463
67.
go back to reference Si J, You HJ, Yu J, Sung J, Ko G (2017) Prevotella as a hub for vaginal microbiota under the influence of host genetics and their association with obesity. Cell Host & Microbe 21(1):97–105 Si J, You HJ, Yu J, Sung J, Ko G (2017) Prevotella as a hub for vaginal microbiota under the influence of host genetics and their association with obesity. Cell Host & Microbe 21(1):97–105
68.
go back to reference Digiulio DB, Callahan BJ, Mcmurdie PJ, Costello EK, Lyell DJ, Robaczewska A, Sun CL, Goltsman DS, Wong RJ, Shaw G (2015) Temporal and spatial variation of the human microbiota during pregnancy. Proc Natl Acad Sci U S A 112(35):11060CrossRefPubMedPubMedCentral Digiulio DB, Callahan BJ, Mcmurdie PJ, Costello EK, Lyell DJ, Robaczewska A, Sun CL, Goltsman DS, Wong RJ, Shaw G (2015) Temporal and spatial variation of the human microbiota during pregnancy. Proc Natl Acad Sci U S A 112(35):11060CrossRefPubMedPubMedCentral
69.
go back to reference Bogaert D, Keijser B, Huse S, Rossen J, Veenhoven R, Gils EV, Bruin J, Montijn R, Bonten M, Sanders E (2011) Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis. PLoS One 6(2):e17035CrossRefPubMedPubMedCentral Bogaert D, Keijser B, Huse S, Rossen J, Veenhoven R, Gils EV, Bruin J, Montijn R, Bonten M, Sanders E (2011) Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis. PLoS One 6(2):e17035CrossRefPubMedPubMedCentral
70.
go back to reference Yan M, Pamp SJ, Fukuyama J, Hwang PH, Cho DY, Holmes S, Relman DA (2013) Nasal microenvironments and interspecific interactions influence nasal microbiota complexity and S. aureus carriage. Cell Host Microbe 14(6):631–640CrossRefPubMedPubMedCentral Yan M, Pamp SJ, Fukuyama J, Hwang PH, Cho DY, Holmes S, Relman DA (2013) Nasal microenvironments and interspecific interactions influence nasal microbiota complexity and S. aureus carriage. Cell Host Microbe 14(6):631–640CrossRefPubMedPubMedCentral
71.
go back to reference Yu J, Feng Q, Wong SH, Zhang D, Liang QY, Qin Y, Tang L, Zhao H, Stenvang J, Li Y (2017) Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer. Gut 66(1):70–78CrossRefPubMed Yu J, Feng Q, Wong SH, Zhang D, Liang QY, Qin Y, Tang L, Zhao H, Stenvang J, Li Y (2017) Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer. Gut 66(1):70–78CrossRefPubMed
72.
go back to reference Touchefeu Y, Montassier E, Nieman K, Gastinne T, Potel G, de Bruley VS, Vacon FL, La Cochetière MF (2014) Systematic review: the role of the gut microbiota in chemotherapy- or radiation-induced gastrointestinal mucositis-current evidence and potential clinical applications. Alimentary Pharmacology Therapeutics 40(5):409–421PubMed Touchefeu Y, Montassier E, Nieman K, Gastinne T, Potel G, de Bruley VS, Vacon FL, La Cochetière MF (2014) Systematic review: the role of the gut microbiota in chemotherapy- or radiation-induced gastrointestinal mucositis-current evidence and potential clinical applications. Alimentary Pharmacology Therapeutics 40(5):409–421PubMed
73.
go back to reference Yu T, Guo F, Yu Y, Sun T, Ma D, Han J, Qian Y, Kryczek I, Sun D, Nagarsheth N (2017) Fusobacterium nucleatum promotes chemoresistance to colorectal cancer by modulating autophagy. Cell 170(3):548–563CrossRefPubMedPubMedCentral Yu T, Guo F, Yu Y, Sun T, Ma D, Han J, Qian Y, Kryczek I, Sun D, Nagarsheth N (2017) Fusobacterium nucleatum promotes chemoresistance to colorectal cancer by modulating autophagy. Cell 170(3):548–563CrossRefPubMedPubMedCentral
74.
go back to reference Routy B, Le CE, Derosa L, Cpm D, Alou MT, Daillère R, Fluckiger A, Messaoudene M, Rauber C, Roberti MP (2018) Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. Science 359(6371):91–97CrossRefPubMed Routy B, Le CE, Derosa L, Cpm D, Alou MT, Daillère R, Fluckiger A, Messaoudene M, Rauber C, Roberti MP (2018) Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. Science 359(6371):91–97CrossRefPubMed
75.
go back to reference Gopalakrishnan V, Spencer CN, Nezi L, Reuben A, Andrews MC, Karpinets TV, Prieto PA, Vicente D, Hoffman K, Wei SC (2018) Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science 359(6371):97–103CrossRefPubMed Gopalakrishnan V, Spencer CN, Nezi L, Reuben A, Andrews MC, Karpinets TV, Prieto PA, Vicente D, Hoffman K, Wei SC (2018) Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science 359(6371):97–103CrossRefPubMed
76.
go back to reference Matson V, Fessler J, Bao R, Chongsuwat T, Zha Y, Alegre ML, Luke JJ, Gajewski TF (2018) The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients. Science 359(6371):104–108CrossRefPubMed Matson V, Fessler J, Bao R, Chongsuwat T, Zha Y, Alegre ML, Luke JJ, Gajewski TF (2018) The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients. Science 359(6371):104–108CrossRefPubMed
77.
go back to reference Chitapanarux I, Chitapanarux T, Traisathit P, Kudumpee S, Tharavichitkul E, Lorvidhaya V (2010) Randomized controlled trial of live lactobacillus acidophilus plus bifidobacterium bifidum in prophylaxis of diarrhea during radiotherapy in cervical cancer patients. Radiat Oncol 5(1):31CrossRefPubMedPubMedCentral Chitapanarux I, Chitapanarux T, Traisathit P, Kudumpee S, Tharavichitkul E, Lorvidhaya V (2010) Randomized controlled trial of live lactobacillus acidophilus plus bifidobacterium bifidum in prophylaxis of diarrhea during radiotherapy in cervical cancer patients. Radiat Oncol 5(1):31CrossRefPubMedPubMedCentral
78.
go back to reference Ciorba MA, Hallemeier CL, Stenson WF, Parikh PJ (2015) Probiotics to prevent gastrointestinal toxicity from cancer therapy: an interpretive review and call to action. Current Opinion Supportive Palliative Care 9(2):157–162CrossRef Ciorba MA, Hallemeier CL, Stenson WF, Parikh PJ (2015) Probiotics to prevent gastrointestinal toxicity from cancer therapy: an interpretive review and call to action. Current Opinion Supportive Palliative Care 9(2):157–162CrossRef
79.
go back to reference Blijlevens N, Donnelly JP, Pauw BD (2000) Mucosal barrier injury: biology, pathology, clinical counterparts and consequences of intensive treatment for haematological malignancy: an overview. Bone Marrow Transplant 25(12):1269–1278CrossRefPubMed Blijlevens N, Donnelly JP, Pauw BD (2000) Mucosal barrier injury: biology, pathology, clinical counterparts and consequences of intensive treatment for haematological malignancy: an overview. Bone Marrow Transplant 25(12):1269–1278CrossRefPubMed
80.
go back to reference Montassier E, Gastinne T, Vangay P, Alghalith GA, Bruley dVS, Massart S, Moreau P, Potel G, Mf DLC, Batard E (2015) Chemotherapy-driven dysbiosis in the intestinal microbiome. Aliment Pharmacol Ther 42(5):515–528CrossRefPubMed Montassier E, Gastinne T, Vangay P, Alghalith GA, Bruley dVS, Massart S, Moreau P, Potel G, Mf DLC, Batard E (2015) Chemotherapy-driven dysbiosis in the intestinal microbiome. Aliment Pharmacol Ther 42(5):515–528CrossRefPubMed
81.
go back to reference Viaud S, Saccheri F, Mignot G, Yamazaki T, Daillère R, Hannani D, Enot DP, Pfirschke C, Engblom C, Pittet MJ (2013) The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide. Science 342(6161):971–976CrossRefPubMedPubMedCentral Viaud S, Saccheri F, Mignot G, Yamazaki T, Daillère R, Hannani D, Enot DP, Pfirschke C, Engblom C, Pittet MJ (2013) The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide. Science 342(6161):971–976CrossRefPubMedPubMedCentral
83.
go back to reference Ciorba MA, Riehl TE, Rao MS, Clara M, Xueping E, Nava GM, Walker MR, Marinshaw JM, Stappenbeck TS, Stenson WF (2012) Lactobacillus probiotic protects intestinal epithelium from radiation injury in a TLR-2/cyclo-oxygenase-2-dependent manner. Gastroenterology 140(6):829–838 Ciorba MA, Riehl TE, Rao MS, Clara M, Xueping E, Nava GM, Walker MR, Marinshaw JM, Stappenbeck TS, Stenson WF (2012) Lactobacillus probiotic protects intestinal epithelium from radiation injury in a TLR-2/cyclo-oxygenase-2-dependent manner. Gastroenterology 140(6):829–838
84.
go back to reference Wang A, Ling Z, Yang Z, Kiela PR, Wang T, Wang C, Cao L, Geng F, Shen M, Ran X (2015) Gut microbial dysbiosis may predict diarrhea and fatigue in patients undergoing pelvic cancer radiotherapy: a pilot study. PLoS One 10(5):e0126312CrossRefPubMedPubMedCentral Wang A, Ling Z, Yang Z, Kiela PR, Wang T, Wang C, Cao L, Geng F, Shen M, Ran X (2015) Gut microbial dysbiosis may predict diarrhea and fatigue in patients undergoing pelvic cancer radiotherapy: a pilot study. PLoS One 10(5):e0126312CrossRefPubMedPubMedCentral
85.
go back to reference LloydPrice J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall A, Brady A, Creasy H, McCracken C, Giglio M (2017) Strains, functions and dynamics in the expanded Human Microbiome Project. Nature 550(7674):61–66 LloydPrice J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall A, Brady A, Creasy H, McCracken C, Giglio M (2017) Strains, functions and dynamics in the expanded Human Microbiome Project. Nature 550(7674):61–66
Metadata
Title
How human microbiome talks to health and disease
Authors
Jing Cong
Xiaochun Zhang
Publication date
01-09-2018
Publisher
Springer Berlin Heidelberg
Published in
European Journal of Clinical Microbiology & Infectious Diseases / Issue 9/2018
Print ISSN: 0934-9723
Electronic ISSN: 1435-4373
DOI
https://doi.org/10.1007/s10096-018-3263-1

Other articles of this Issue 9/2018

European Journal of Clinical Microbiology & Infectious Diseases 9/2018 Go to the issue
Obesity Clinical Trial Summary

At a glance: The STEP trials

A round-up of the STEP phase 3 clinical trials evaluating semaglutide for weight loss in people with overweight or obesity.

Developed by: Springer Medicine

Highlights from the ACC 2024 Congress

Year in Review: Pediatric cardiology

Watch Dr. Anne Marie Valente present the last year's highlights in pediatric and congenital heart disease in the official ACC.24 Year in Review session.

Year in Review: Pulmonary vascular disease

The last year's highlights in pulmonary vascular disease are presented by Dr. Jane Leopold in this official video from ACC.24.

Year in Review: Valvular heart disease

Watch Prof. William Zoghbi present the last year's highlights in valvular heart disease from the official ACC.24 Year in Review session.

Year in Review: Heart failure and cardiomyopathies

Watch this official video from ACC.24. Dr. Biykem Bozkurt discuss last year's major advances in heart failure and cardiomyopathies.