Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians

Elena Biagi, Lotta Nylund, Marco Candela, Rita Ostan, Laura Bucci, Elisa Pini, Janne Nikkïla, Daniela Monti, Reetta Satokari, Claudio Franceschi, Patrizia Brigidi, Willem De Vos, Elena Biagi, Lotta Nylund, Marco Candela, Rita Ostan, Laura Bucci, Elisa Pini, Janne Nikkïla, Daniela Monti, Reetta Satokari, Claudio Franceschi, Patrizia Brigidi, Willem De Vos

Abstract

Background: Age-related physiological changes in the gastrointestinal tract, as well as modifications in lifestyle, nutritional behaviour, and functionality of the host immune system, inevitably affect the gut microbiota, resulting in a greater susceptibility to infections.

Methodology/principal findings: By using the Human Intestinal Tract Chip (HITChip) and quantitative PCR of 16S rRNA genes of Bacteria and Archaea, we explored the age-related differences in the gut microbiota composition among young adults, elderly, and centenarians, i.e subjects who reached the extreme limits of the human lifespan, living for over 100 years. We observed that the microbial composition and diversity of the gut ecosystem of young adults and seventy-years old people is highly similar but differs significantly from that of the centenarians. After 100 years of symbiotic association with the human host, the microbiota is characterized by a rearrangement in the Firmicutes population and an enrichment in facultative anaerobes, notably pathobionts. The presence of such a compromised microbiota in the centenarians is associated with an increased inflammatory status, also known as inflammageing, as determined by a range of peripheral blood inflammatory markers. This may be explained by a remodelling of the centenarians' microbiota, with a marked decrease in Faecalibacterium prauznitzii and relatives, symbiotic species with reported anti-inflammatory properties. As signature bacteria of the long life we identified specifically Eubacterium limosum and relatives that were more than ten-fold increased in the centenarians.

Conclusions/significance: We provide evidence for the fact that the ageing process deeply affects the structure of the human gut microbiota, as well as its homeostasis with the host's immune system. Because of its crucial role in the host physiology and health status, age-related differences in the gut microbiota composition may be related to the progression of diseases and frailty in the elderly population.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1. Hierarchical clustering, with heat map,…
Figure 1. Hierarchical clustering, with heat map, of the HITChip profiles of centenarians, elderly and young adults.
Subjects belonging to the groups C, E, and Y are indicated by green, blue, and yellow squares, respectively. Darkness of the spot corresponds to the bacterial abundance in the sample. Pearson correlation and Ward's clustering method were used. Genus-like bacterial groups belonging to Proteobacteria (P), Bacilli (B), Clostridium cluster IV (C.IV) and XIVa (C.XIVa) are indicated. The two phylogenetic groups members of the Clostridium cluster IV located within the Clostridium cluster XIVa (bottom) are Faecalibacterium prausnitzii et rel. and Papillibacter cinnamovorans et rel.
Figure 2. Triplot of the RDA of…
Figure 2. Triplot of the RDA of the microbiota composition of centenarians, elderly and young adults.
Subjects belonging to group C, E, and Y are indicated by green circles, blue squares and yellow diamonds, respectively. Constrained explanatory variables (C, E, and Y) are indicated by red triangles. Responding bacterial subgroups that explained more than 10% of the variability of the samples are indicated by black arrows. First and second ordination axes are plotted, showing 5.2% and 0.9% of the variability in the dataset, respectively. Log transformed data were used for the analysis. Bottom-left, P value obtained by MCPP is reported. Abbreviations: C., Clostridium; E., Eubacterium; F., Faecalibacterium; R., Ruminococcus; K., Klebsiella.
Figure 3. Relative contribution of the phylum/order-like…
Figure 3. Relative contribution of the phylum/order-like phylogroups to the microbiota of centenarians, elderly and young adults.
In the legend, phylum/order-like phylogroups which contribute for at least 0.5% to one of the profiles are indicated.
Figure 4. Correlation between microbiota composition and…
Figure 4. Correlation between microbiota composition and plasma levels of pro-inflammatory cytokines.
In the RDA blood cytokine levels (red arrows) and age groups (C, S, and Y, red triangles) are used as linear and nominal environmental variables, respectively. Samples belonging to C, S and Y groups are indicated by green circles, blue squares and yellow diamonds, respectively. Responding bacterial subgroups that explained more than 20% of the variability of the samples are indicated by black arrows. First and second ordination axes are plotted, showing 5.8% and 3.1% of the variability in the dataset, respectively. Red arrows which are not labelled corresponds to (clockwise, starting from the left) TNF-α, IFN-γ, IL-2, IL-1α, IL-12p70, and IL-1β. Log transformed data were used for this analysis. Bottom-left, P value obtained by MCPP is reported. Top-left, average blood levels of IL-6 and IL-8 in groups C, S and Y are reported.

References

    1. Imahori K. How I understand ageing. Nutr Rev. 1992;50:351–352.
    1. Kleessen B, Sycura B, Zunft HJ, Blaut M. Affects of inulin and lactose on fecal microflora, microbial activity and bowel habits in elderly constipated persons. Am J Clin Nutr. 1997;65:1397–1402.
    1. Brocklehurst JC. Bowel management in the neurologically disabled. The problem of old age. Proc R Soc Med. 1972;65:66–70.
    1. Macfarlane GT, Cummings JH, Macfarlane S, Gibson GR. Influence of retention time on degradation of pancreatic enzymes by human colonic bacteria grown in a 3-stage continuous culture system. J Appl Bacteriol. 1989;67:520–527.
    1. Ostan R, Bucci L, Capri M, Salvioli S, Scurti M, et al. Immunosenescence and immunogenetics of human longevity. Neuroimmunomodulation. 2008;15:224–240.
    1. Franceschi C. Inflammaging as a major characteristic of old people: can it be prevented or cured? Nutr Rev. 2007;65:S173–S176.
    1. Franceschi C, Capri M, Monti D, Giunta S, Olivieri F, et al. Inflammaging and anti-inflammaging: systemic perspective on aging and longevity emerging from studies in humans. Mech Ageing Dev. 2007;128:92–105.
    1. Larbi A, Franceschi C, Mazzatti D, Solana R, Wikby A, et al. Aging of the immune system as a prognostic factor for human longevity. Physiology. 2008;23:64–74.
    1. Neish AS. Microbes in gastrointestinal health and disease. Gastroenterology. 2009;136:65–80.
    1. Guigoz Y, Doré J, Schiffrin J. The inflammatory status of old age can be nurtured from the intestinal environment. Curr Op Clin Nutr Metab Care. 2008;11:13–20.
    1. Flint HJ, Duncan SH, Scott KP, Louis P. Interactions and competition within the microbial community of the human colon: links between diet and health. Environ Microbiol. 2007;9:1101–1111.
    1. Woodsmansey EJ. Intestinal bacteria and ageing. J Appl Micriobiol. 2007;102:1178–1186.
    1. Hopkins MJ, Macfarlane GT. Changes in predominant bacterial populations in human feces with age and with Clostridium difficile infection. Microb Ecol. 2002;51:448–454.
    1. Bartosch S, Fite A, Macfarlane GT, McMurdo MET. Characterization of bacterial communities in feces from healthy elderly volunteers and hospitalized elderly patients by using real time PCR and effects of antibiotic treatment on the fecal microbiota. Appl Environ Microbiol. 2004;70:3575–3581.
    1. Woodsmansey EJ, McMurdo MET, Macfarlane CT, Macfarlane S. Comparison of compositions and metabolic activities of fecal microbiotas in young adults and in antibiotic-treated and non-antibiotic treated elderly subjects. Appl Environ Microbiol. 2004;70:6113–6122.
    1. Mueller S, Saunier K, Hanisch C, Norin E, Alm L, et al. Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study. Appl Environ Microbiol. 2006;72:1027–1033.
    1. Mariat D, Firmesse O, Levenez F, Guimaraes VD, Sokol H, et al. The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiol. 2009;9:123.
    1. Satokari R, Rantanen R, Pitkälä K, Salminen S. Cho SS, Finocchiaro ET, editors. Probiotics and prebiotics in the elderly individuals. 2010. pp. 341–353. Handbook of prebiotics and probiotics incredients – Health benefits and food applications (ISBN 978-1-4200-6213-7) Taylor and Francis, CRC Press, Boca Raton.
    1. Zoetendal EG, Rajilic-Stojanovic M, de Vos WM. High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut. 2008;57:1605–1615.
    1. Rajilic-Stojanovic M, Heilig HGHJ, Molenaar D, Kajander K, Surakka A, et al. Development an application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. 2009. Environ Microbiol, Epub ahead of print.
    1. Claesson MJ, O'Sullivan O, Wang Q, Nikkila J, Marchesi JR, et al. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS ONE. 2009;4:e6669.
    1. Franceschi C, Motta L, Valensin S, Rapisarda R, Franzone A, et al. Do men and women follow different trajectories to reach extreme longevity? Italian Multicenter Study on Centenarians (IMUSCE). Aging. 2000;12:77–84.
    1. Clarke KR. Non-parametric multivariate analyses of changes in community structure. Aust J Ecol. 1993;18:117–143.
    1. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Human gut microbes associated with obesity. Nature. 2006;444:1022–1023.
    1. Andersson AF, Lindberg M, Jakobsson H, Backhed F, Nyrén P, et al. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PloS ONE. 2008;3:e2836.
    1. Tap J, Mondot S, Levenez F, Pelletier E, Caron C, et al. Towards the human intestinal microbiota phylogenetic core. Environ Microbiol. 2009;11:2574–2584.
    1. Salonen A, Nikkilä J, Jalanka-Tuovinen J, Immonen O, Rajilić-Stojanović M, et al. 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 Epub ahead of print.
    1. Sansonetti PJ, Di Santo JP. Debugging how bacteria manipulate the immune response. Immunity. 2007;26:149–161.
    1. Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol. 2009;9:313–323.
    1. Vanhoutte T, Huys G, De Brandt E, Swings J. Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers. FEMS Microbiol Ecol. 2004;48:437–446.
    1. Leser TD, Molbak L. Better living through microbial action: the benefits of the mammalian gastrointestinal microbiota on the host. Environ Microbiol. 2009;11:2194–2206.
    1. Hayashi H, Sakamoto M, Kitahara M, Benno Y. Molecular analysis of fecal microbiota in elderly individuals using 16S rDNA library and T-RFLP. Microbiol Immunol. 2003;47:557–570.
    1. Zwielehner J, Liszt K, Handschur M, Lassl C, Lapin A, et al. Combined PCR-DGGE fingerprinting and quantitative-PCR indicates shifts in fecal population sizes and diversity of Bacteroides, bifidobacteria and Clostridium cluster IV in institutionalized elderly. Experimen Gerontol. 2009;44:440–446.
    1. Barcenilla A, Pryde SE, Martin JC, Duncan SH, Stewart CS, et al. Phylogenetic relationships of butyrate-producing bacteria from human gut. Appl Environ Microbiol. 2000;66:1654–1661.
    1. Pryde SE, Duncan SH, Hold GL, Stewart CS, Flint HJ. The microbiology of butyrate formation in the human colon. FEMS Microbiol Lett. 2002;217:133–139.
    1. Louis P, Flint HJ. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiol Lett. 2009;294:1–8.
    1. Thibault R, Blachier F, Darcy-Vrillon B, de Coppet P, Bourreille A, et al. Butyrate utilization by the colonic mucosa in inflammatory bowel diseases: a transport deficiency. Inflamm Bowel Dis. 2009;16:684–695.
    1. Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermudez-Humaran LG, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn's disease patients. Proc Natl Acad Sci USA. 2008;105:16731–16736.
    1. Sokol H, Seksik P, Furet JP, Firmesse O, Nion-Larmurier I, et al. Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm bowel Dis. 2009;15:1183–1189.
    1. Pédron T, Sansonetti P. Commensals, bacterial pathogens and intestinal inflammation: an intriguing ménage à trois. Cell Host & Microbes. 2008;3:344–347.
    1. Sansonetti PJ, Medzhitov R. Learning tolerance while fighting ignorance. Cell. 2009;138:416–420.
    1. Collado MC, Derrien M, Isolauri E, de Vos WM, Salminen S. Intestinal integrity and Akkermansia muciniphila, a mucin-degrading member of the intestinal microbiota present in infants, adults, and the elderly. Appl Environ Microbiol. 2007;73:7767–7770.
    1. Swidsinski A, Doerffel Y, Loening-Baucke V, Theissig F, Rückert JC, et al. Acute appendicitis is characterized by local invasion with Fusobacterium nucleatum/necrophorum. Gut. 2009 Epub ahead of print.
    1. Fagnoni FF, Vescovini R, Passeri G, Bologna G, Pedrazzoni M, et al. Shortage of circulating naive CD8+ T cells provides new insights on immunodeficiency in aging. Blood. 2000;95:2860–2868.
    1. Zanni F, Vescovini R, Biasini C, Fagnoni F, Zanlari L, et al. Marked increase with age of type 1 cytokines within memory and effector/cytotoxic CD8+ T cells in humans: a contribution to understand the relationship between inflammation and immunosenescence. Exp Gerontol. 2003;38:891–987.
    1. Alberti S, Cevenini E, Ostan R, Capri M, Salvioli S, et al. Age dependent modifications of type 1 and type 2 cytokines within virgin and memory CD4+ T cells in human. Mech Ageing Dev. 2006;127:560–566.
    1. Nasi M, Troiano L, Lugli E, Pinti M, Ferraresi R, et al. Thymic output and functionality of the IL-7/IL-7 receptor system in centenarians: implications for the neolymphogenesis at the limit of human life. Aging Cell. 2006;5:167–175.
    1. Koch S, Larbi A, Derhovanessian E, Ozcelik D, Naumova E, et al. Multiparameter flow cytometric analysis of CD4 and CD8 T cell subsets in young and old people. Immun Ageing. 2008;25:5–6.
    1. Franceschi C, Bonafè M, Valensin S, Olivieri F, De Luca M, et al. Inflamm-aging. An evolutionary perspective on immunosenescence. Ann N Y Acad Sci. 2000;908:244–254.
    1. Baggio G, Donazzan S, Monti D, Mari D, Martini S, et al. Lipoprotein(a) and lipoprotein profile in healthy centenarians: a reappraisal of vascular risk factors. FASEB J. 1998;12:433–437.
    1. Passeri G, Pini G, Troiano L, Vescovini R, Sansoni P, et al. Low vitamin D status, high bone turnover, and bone fractures in centenarians. J Clin Endocrinol Metab. 2003;88:5109–5115.
    1. Kanauchi O, Fukada M, Matsumoto Y, Ishii S, Ozawa T, et al. Eubacterium limosum ameliorates experimental colitis and metabolite of microbe attenuates colonic inflammatory action with increase of mucosal integrity. World J Gastroenterol. 2006;12:1071–1077.
    1. Hur H, Rafii F. Biotransformation of the isoflavonoids biochanin A, formononetin, and glycitein by Eubacterium limosum. FEMS Microbiol Lett. 2000;192:21–25.
    1. Possemiers S, Rabot S, Espín JC, Bruneau A, Philippe C, et al. Eubacterium limosum activates isoxanthohumol from hops (Humulus lupulus L.) into the potent phytoestrogen 8-prenylnaringenin in vitro and in rat intestine. J Nutr. 2008;138:1310–1316.
    1. Adlercreutz H. Phyto-oeastrogens and cancer. Lancet Oncol. 2002;3:364–373.
    1. Cohen JE. Human population: the next half century. Science. 2003;302:1172–1175.
    1. Lane DJ. 16S/23S Sequencing. In: Stackebrandt E, Goodfellow M, editors. Nucleic acids techniques in bacterial systematics. Chichester, UK: Wiley&Sons; 1991. pp. 115–175.
    1. Leps J, Smilauer P. Cambridge University Press: Multivariate analysis of ecological data using CANOCO. 2003.
    1. Simpson EH. Measurements of diversity. Nature. 1949;163:688.
    1. Matsuki T, Watanabe K, Fujimoto J, Takada T, Tanaka R. Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in human feces. Appl Environ Microbiol. 2004;70:7220–7228.
    1. Kaufmann P, Pfefferkorn A, Teuber M, Meile L. Identification and quantification of Bifidobacterium species isolated from food with genus-specific 16S rRNA-targeted probes by colony hybridization and PCR. Appl Environ Microbiol. 1997;63:1268–1273.
    1. Marteau P, Pochart P, Dore J, Bera-Maillet C, Bernalier A, et al. Comparative study of bacterial groups within the human cecal and fecal microbiota. Appl Environ Microbiol. 2001;67:4939–4942.
    1. Rinttilä T, Kassinen A, Malinen E, Krogius L, Palva A. Development of an extensive set of 16S rDNA-targeted primers for quantification of pathogenic and indigenous bacteria in faecal samples by real-time PCR. J Appl Microbiol. 2004;97:1166–1177.
    1. Kullen MJ, Sanozky-Dawes RB, Crowell DC, Klaenhammer TR. Use of the DNA sequence of variable regions of the 16S rRNA gene for rapid and accurate identification of bacteria in the Lactobacillus acidophilus complex. J Appl Microbiol. 2000;89:511–516.
    1. Baker G, Smith J, Cowan D. Review and re-analysis of domain-specific 16S primers. J Microbiol Methods. 2003;55:541–555.
    1. Recasens M, López-Bermejo A, Ricart W, Vendrell J, Casamitjana R, et al. An inflammation score is better associated with basal than stimulated surrogate indexes of insulin resistance. J Clin Endocrinol Metab. 2005;90:112–116.
    1. Duncan BB, Schmidt MI, Pankow JS, Ballantyne CM, Couper D, et al. Low-grade systemic inflammation and the development of type 2 diabetes: the atherosclerosis risk in communities study. Diabetes. 2003;52:1799–1805.

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