Review
Gut microbiota: Changes throughout the lifespan from infancy to elderly

https://doi.org/10.1016/j.idairyj.2009.11.010Get rights and content

Abstract

Our understanding of the composition and function of the human gut microbiota has improved dramatically in recent years. In this review, major milestones along this path will be reviewed. The methodological developments that underpinned this acceleration of scientific progress are discussed. We review the infant microbiota with special reference to colonization, succession and stabilization events. The healthy adult microbiota is then described, including reference to selected conditions that perturb the microbiota such as antibiotic treatment, bowel dysfunction and obesity. We put special emphasis on the special issues that characterize elderly subjects, including the challenges provided by “inflamm-aging”, with reference to how the microbiota might interact with these processes. Lastly, the elderly intestinal metagenomics project ELDERMET is described, which aims to establish the composition and function of the gut microbiota in several hundred Irish subjects.

Section snippets

General introduction

The human gut microbiota has been the subject of intense research in recent years. From a relatively obscure field, over-shadowed by targeted analysis of microbial pathogens, and latterly, beneficial commensals, studies of whole-gut community structure have blossomed. This has been due in large part to the development of culture-independent techniques, which have also been applied to soil, water and other environmental samples. Solving of the “plate count anomaly” (the discrepancy between

Historical aspects and method development

The increasing interest in recent years in the human gut microbiota has been accompanied by a growing number of molecular methods that can be used for studying such environments. Traditional culture-based techniques offer the ability to recover isolates of interest for further phenotypic studies e.g. investigating growth substrate-specificities, growth requirements and stress tests, under both anaerobic and aerobic conditions. Although isolation approaches are constantly being improved (Aagot

The infant gut microbiota

The infant gut microbiota is inherently interesting to many microbiologists because of the fascinating ecological parameters that affect it. What are the key steps in the colonization process of the infant in transiting from a sterile in utero environment to a bacterium-loaded every-day world? What factors control this process? How long does it take for the microbiota to reach an adult-like pattern? Do early-life microbiota changes affect health in later life? We are beginning to be able to

The healthy adult gut microbiota

Once the microbiota of the infant gut has stabilized following the first few year of life, and converged towards a more adult community structure (Palmer, Bik, DiGiulio, Relman, & O'Brown, 2007), it is dominated by a small number of phyla. Eckburg et al. (2005) were the first to employ a high-throughput culture-independent methodology, based on sequencing of cloned 16S rRNA amplicons, in order to compare gut community structures from faeces and six colonic sites in three healthy individuals.

The elderly gut microbiota

Most western countries are experiencing a significant increase in the proportion of their elderly citizens (>65 years), as a result of improved sanitation, hygiene, and healthcare. The US Census Bureau recently estimated that by 2040, the proportion of older people will double from 7 percent to 14 percent of the total world population (Kinsella & He, 2009). Within 10 years, for the first time in human history there will be more people aged 65 and older than children under 5 in the world (

The Eldermet study: preliminary findings

Scientists in Cork, Ireland, have studied the biology of individual members of the human microbiota for many years, primarily from the perspective of elucidating how single species or even strains impact upon the host (Corr et al., 2007, O'Toole and Cooney, 2008, Leahy et al., 2005, Ventura et al., 2009, Wall et al., 2009). In 2008, we formed the ELDERMET consortium (http://eldermet.ucc.ie) with the objective of characterizing the gut microbiota of elderly Irish subjects. With a target of

Acknowledgements

PWO'T and MJC are scientists in the ELDERMET consortium (http://eldermet.ucc.ie), which is supported by the (Govt. of Ireland) Dept. Agriculture Fisheries and Food/Health Research Board FHRI award to the ELDERMET project. PWOT's laboratory is also supported in part by a CSET award from Science Foundation Ireland to the Alimentary Pharmabiotic Centre. MJC is funded by a fellowship from the Health Research Board of Ireland.

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