Molecular Analysis of Fecal Microbiota in Elderly Individuals Using 16S rDNA Library and T-RFLP

Japan Collection of Microorganisms, RIKEN, Wako, Saitama 351-0198, Japan.
Microbiology and Immunology (Impact Factor: 1.24). 02/2003; 47(8):557-70. DOI: 10.1111/j.1348-0421.2003.tb03418.x
Source: PubMed


Fecal microbiota in six elderly individuals were characterized by the 16S rDNA libraries and terminal restriction fragment length polymorphism (T-RFLP) analysis. Random clones of 16S rRNA gene sequences were isolated after PCR amplification with universal primer sets from total genomic DNA extracted from feces of three elderly individuals. These clones were partially sequenced (about 500 bp). T-RFLP analysis was performed using 16S rDNA amplified from six subjects. The lengths of the terminal restriction fragment (T-RF) were analyzed after digestion by HhaI and MspI. Among 240 clones obtained, approximately 46% belonged to 27 known species. About 54% of the other clones were 56 novel "phylotypes" (at least 98% homology of clone sequence). These libraries included 83 species or phylotypes. In addition, about 13% (30 phylotypes) of these phylotypes were newly discovered in these libraries. A large number of species that are not yet known exist in the feces of elderly individuals. 16S rDNA libraries and T-RFLP analysis revealed that the majority of bacteria were Bacteroides and relatives, Clostridium rRNA cluster IV, IX, Clostridium rRNA subcluster XIVa, and "Gammaproteobacteria". The proportion of Clostridium rRNA subcluster XIVa was lower than in healthy adults. In addition, although Ruminococcus obeum and its closely related phylotypes were detected in high frequency in healthy young subjects, hardly any were detected in our elderly individuals. "Gammaproteobacteria" were detected at high frequency.

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    • "Human gut samples also spread across this second axis: infant samples from two studies and one sample from an individual with antibiotic-induced diarrhea grouped with opportunistic consortia (e.g., samples from cultured isolates ) along PC2, whereas most human gut samples resembled other complex consortia (e.g., mature soils and rumen samples) (Supplemental Fig. S3). Elderly individuals (ages 75–94) (Hayashi et al. 2003) also had an opportunistic ''signature,'' matching reports that centenarians have more gut pathobionts than younger adults (ages 20–40) (Biagi et al. 2010). To determine whether succession and antibiotic-induced community changes within an individual shared these patterns, we added samples from the infant time-series (Koenig et al. 2011): the mother's sample plus the infant at postnatal day 3 (meconium), day 100 (before establishing adultlike microbiota as determined in Koenig et al. 2011), day 206 (after establishing adult-like microbiota), and day 432 (during treatment with the broad-spectrum antibiotic Cefnidir) (see Methods). "
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    ABSTRACT: We lack a deep understanding of genetic and metabolic attributes specializing in microbial consortia for initial and subsequent waves of colonization of our body habitats. Here we show that phylogenetically interspersed bacteria in Clostridium cluster XIVa, an abundant group of bacteria in the adult human gut also known as the Clostridium coccoides or Eubacterium rectale group, contains species that have evolved distribution patterns consistent with either early successional or stable gut communities. The species that specialize to the infant gut are more likely to associate with systemic infections and can reach high abundances in individuals with Inflammatory Bowel Disease (IBD), indicating that a subset of the microbiota that have adapted to pioneer/opportunistic lifestyles may do well in both early development and with disease. We identified genes likely selected during adaptation to pioneer/opportunistic lifestyles as those for which early succession association and not phylogenetic relationships explain genomic abundance. These genes reveal potential mechanisms by which opportunistic gut bacteria tolerate osmotic and oxidative stress and potentially important aspects of their metabolism. These genes may not only be biomarkers of properties associated with adaptation to early succession and disturbance, but also leads for developing therapies aimed at promoting reestablishment of stable gut communities following physiologic or pathologic disturbances.
    Genome Research 06/2012; 22(10):1974-84. DOI:10.1101/gr.138198.112 · 14.63 Impact Factor
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    • "Age-related modification in the dominant microbiota Among the Firmicutes, Clostridium cluster XIVa (also called Clostridium coccoides/Eubacterium rectale group) was reported to decrease in Japanese healthy elderly aged 74–94 years (Hayashi et al. 2003), Italian over 60 years (Mueller et al. 2006) and Finnish over 70 years people (Mäkivuokko et al. 2010). Most recently, Biagi et al. (2010) reported the same modification in Italian centenarians. "
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    ABSTRACT: Human beings have been recently reviewed as 'metaorganisms' as a result of a close symbiotic relationship with the intestinal microbiota. This assumption imposes a more holistic view of the ageing process where dynamics of the interaction between environment, intestinal microbiota and host must be taken into consideration. Age-related physiological changes in the gastrointestinal tract, as well as modification in lifestyle, nutritional behaviour, and functionality of the host immune system, inevitably affect the gut microbial ecosystem. Here we review the current knowledge of the changes occurring in the gut microbiota of old people, especially in the light of the most recent applications of the modern molecular characterisation techniques. The hypothetical involvement of the age-related gut microbiota unbalances in the inflamm-aging, and immunosenescence processes will also be discussed. Increasing evidence of the importance of the gut microbiota homeostasis for the host health has led to the consideration of medical/nutritional applications of this knowledge through the development of probiotic and prebiotic preparations specific for the aged population. The results of the few intervention trials reporting the use of pro/prebiotics in clinical conditions typical of the elderly will be critically reviewed.
    Age 02/2011; 34(1):247-67. DOI:10.1007/s11357-011-9217-5 · 3.45 Impact Factor
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    • "A higher level of aerobes in the microbiota of elderly than among the microbiota of adults has also been observed (Guigoz et al. 2008; Tiihonen et al. 2008). Similarly, a higher frequency of gammaproteobacteria , such as Klebsiella spp. was found in a study by Hayashi et al. (2003). In a study of elderly aged 70–100 years (with a median of 86 years) by van Tongeren et al. (2005) the prevalence of Bacteroides/Prevotella, Eubacterium rectale/Clostridium coccoides, and Ruminococcus were rather similar to the levels in healthy adults aged between 20 and 55 years in a study by Harmsen et al. (2002). "
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    ABSTRACT: The human microbiota undergoes changes throughout life. From being sterile in a foetus, the gastrointestinal tract of a newborn child is rapidly colonized with bacteria from both the mother and the environment. A less complex microbiota dominates during the first two years of life where after a more complex composition of the microbiota is established in adults. The bacterial composition undergoes changes again in elderly by factors related to ageing, including reduced mobility and intestinal functionality. However, throughout the human life cycle, intrinsic factors such as genetics, aging and non-infectious diseases are not the only ones influencing the composition and activity of the intestinal microbiota. Also external events like diet, infectious diseases and medicines have an impact on the microbiota. KeywordsBacterial composition-Gastrointestinal tract-Gut health microbiota-Probiotic
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