Research Findings


  1. Gut microbiota composition correlates with diet and health in the elderly (Lay summary) (MS Word) – Right Click to Download
  2. SGM Spring Conference,
    Manchester 25-28th March 2013,
    The Human Microbiome: overdue recognition for our fellow travellers
    (Powerpoint Presentation) – Right Click to Download

The range of data published from the ELDERMET project to date is broad-ranging and illustrates the intra-disciplinary nature of the research.  High-throughput, culture-independent molecular technologies have elucidated microbial community structure at much higher resolution than was previously possible. Two such methods, pyrosequencing and a phylogenetic array were compared to evaluate microbial classification potential.  Sequence comparisons of the V4 and V6 regions of the 16S ribosomal RNA gene, present in all prokaryotes, amplified using 454 FLX Pyrosequencing and HITChip hybridizations showed good correlation between the phylogenetic classifications, especially at lower-order ranks (phylum, class, order, and to a lesser extent, family).  The Ribosomal Database Project (RDP)-classifier consistently assigned most V4 sequences from human intestinal samples down to genus level with good accuracy and speed. Results show that HITChip hybridizations and resulting community profiles correlated well with pyrosequencing-based compositions, especially for lower-order ranks, indicating high robustness of both approaches.  This was the first study illustrating the deepest sequencing of individual gastrointestinal samples (Claesson et al. 2009, 2010).

The microbiota is in a state of flux during dynamic life periods such as older age (O’Toole & Claesson, 2010).  The biological consequences of such change are still being explored. Pyrosequencing characterisation of the faecal microbiota in 161 ELDERMET subjects and 9 younger control subjects found a distinct difference in core microbiota composition to that of younger adults.  The faecal microbiota of elderly subjects was characterized by unusual phylum proportions and extreme variability. In addition, temporal stability of the microbiota at three months was illustrated in 85% of subjects (Claesson et al. 2011).

Culture technologies have been the traditional method of microbiological exploration of the microbiota.  The degree of correlation between measurements generated from culture-dependent microbiological techniques and from next generation sequencing technologies were explored in three groups of intestinal bacteria.  Bifidobacterium sp., Lactobacillus sp. and Enterobacteriaceae were enumerated on selective media through culture-dependent techniques, and proportional representation of these bacteria in the microbiota was determined through sequencing technology.  Correlation between the two methods implies that a single method is capable of profiling intestinal Bifidobacterium, Lactobacillus and Enterobacteriaceae populations.  However, both methods have advantages that justify their use in tandem.  This was the first, extensive study to compare bacterial counts from culture-dependent microbiological techniques and from next generation sequencing technologies (O’Sullivan et al. 2011).

Clostridium difficile is an important nosocomial pathogen associated particularly with diarrhoeal disease in elderly individuals in hospitals and long-term care facilities. Carriage rate was examined by culture as a function of faecal microbiota composition in elderly subjects recruited from the community, including outpatient, short-term respite, and long-term hospital stay subjects.  The highest rate was found in those in short and long-term hospital care.  The dominant 072 ribotype was carried by 43% (12/28) of subjects while the hypervirulent strain R027 (B1/NAP1/027) was isolated from 3 subjects (11%), 2 of whom displayed C. difficile-associated diarrhoea (CDAD) symptoms at the time of sampling. A marked reduction in microbial diversity at genus level was observed in patients who had been diagnosed with CDAD at the time of sampling and from whom C. difficile R027 was isolated (Rea et al. 2012)

Analysis of ELDERMET Food Frequency Data provided the opportunity to determine correlations between diet, distinct microbiota profiles, and clinical biomarkers of health and/or disease.  A range of focused studies also investigated compliance with Irish food based dietary guidelines in elderly subjects across a range of health strata. From those residing in both community and institutional settings (rehabilitation wards/out-patients clinics), a high consumption of low nutrient density foods was prominent, with poor compliance to recommended intakes of other food groups including dairy, breads and cereals which may have negative health implications. Fruit and vegetable consumption by those in institutionalised care were low compared to current dietary recommendations.  As a consequence, a large proportion of older Irish adults may be at risk of inadequate intakes of important vitamins and minerals (Power et al. 2011) in particular those of relevance for health promotion and brain-ageing, where gender differences in folate status have been associated with cognition (O’Connor et al. 2011).

At present, there is no information, based on the compelling role of the intestinal bacteria, upon which to develop foods for the promotion or maintenance of health in the elderly.  Food products / ingredients / functional foods (pre- or probiotics) or supplements based on ELDERMET research findings could be used in the management of common health problems where links with the composition of the intestinal microbiota have been associated such as allergies, cancer, digestive disorders, obesity and its related conditions (Clemente et al. 2012).  In addition, the recent discovery by ELDERMET scientists through unbiased correlation analysis of new microbiota associations with multiple clinical parameters (Claesson et al. 2012) will form the basis for the provision of strategies that modulate the microbiota to promote and maintain health in the elderly.



  1. Claesson MJ, Jeffery IB, Conde S, Power SE, O’Connor EM, Cusack S, Harris HMB, Coakley M,Laks B, O’Sullivan O,Fitzgerald G, Deane J, O’Connor M, Harnedy N, O’Connor K, O’Mahony D, van Sinderen D, Wallace M, Brennan L, Stanton C, Marchesi JR, Fitzgerald AP, Shanahan F, Hill C, Ross RP, O’Toole PW (2012). Gut microbiota composition correlates with diet and health in the elderly. Nature. 488(7410):178-84.
  2. Claesson, MJ, O. O’Sullivan , Q. Wang , J. Nikkilä, JR Marchesi, H. Smidt, W. M. de Vos, RP Ross, and PW O’Toole. (2009). Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine. PLoS One. 4(8): e6669.
  3. Claesson et al.  Evaluating the latest high-throughput molecular techniques for the exploration of microbial gut communities.  Gut microbes (4):277-278. 2010.
  4. Claesson et al.  Composition, variability and temporal stability of the intestinal microbiota of the elderly.  Proc Natl Acad Sci USA. (2011) 15; 108 Suppl 1:4586-91. Published online before print June 22, 2010, doi: 10.1073/pnas.1000097107.
  5. O’Connor E.M., Fitzgerald G.F, O’ Toole P.W. Gender differences in folate status are associated with cognition in healthy Irish elderly adults. Proceedings of the Nutrition Society (2011) 70 (OCE3) E64. DOI:10.1017/S0029665111001042
  6. O’Sullivan Ó, Coakley M, Lakshminarayanan B, Claesson MJ, Stanton C, O’Toole PW, Ross RP. Correlation of rRNA gene amplicon pyrosequencing and bacterial culture for microbial compositional analysis of faecal samples from elderly Irish subjects. J Appl Microbiol. 2011; 111(2):467-73.
  7. O’Toole P.W. & Claesson M.J. Gut microbiota: Changes throughout the lifespan from infancy to elderly. International Dairy Journal (2010) 20(4): 281-291.
  8. Power S.E., O’Toole P.W., O’Connor E.M., Fitzgerald G.F. Consumption of fruit and vegetables among elderly Irish people in long term institutionalised care: the ELDERMET project. Proceedings of the Nutrition Society (2011) 70 (OCE3) E116. DOI:10.1017/S002966511100156X
  9. Rea MC, O’Sullivan O, Shanahan F, O’Toole PW, Stanton C, Ross RP, Hill C. Clostridium difficile carriage in elderly subjects and associated changes in the intestinal microbiota. J Clin Microbiol. 2012; 50(3):867-75.