Molecular Fingerprinting of the Fecal Microbiota of Children Raised According to Different Lifestyles

Abstract

In this population-based study, 90 children from three European countries were examined to determine the impact of lifestyle on the fecal microbiota. The study was designed to assess the impact of two extreme lifestyles that we hypothesized could impact the microbial composition in the gut: i.e., an anthroposophic lifestyle (restricted use of antibiotics, greater consumption of fermented vegetables, etc.) versus living on a farm (greater consumption of farm milk, contact with animals, etc.). In previous studies, these lifestyles correlated with lower prevalence of allergies. Terminal restriction fragment length polymorphism (T-RFLP) was used to assess the bacterial composition in fecal samples since recent studies have shown that the majority of this community cannot be cultivated. The T-RFLP data were used to calculate richness and evenness of the fecal microbiota. Children that were attending Steiner schools (anthroposophic children) had a significantly higher diversity of microbes in their feces than farm children, who in turn also had lower diversity than the control groups. Specific primers were also used to focus on the Lactobacillus-like community (lactic acid bacteria [LAB]). Large differences were found in the LAB subpopulations in the sampled groups. In some children, the LAB subpopulation was dominated by a species that has not yet been cultivated.

Molecular analysis of the gut microbiota of identical twins with Crohn's disease

“…The search for a causative disease agent is complicated by the great individuality of the gut microbiota with little overlap between individuals (Zoetendal et al, 1998;Eckburg et al, 2005;Dicksved et al, 2007). However, previous findings have shown that there is a high similarity in the composition of the fecal microbial communities in monozygotic twins (Van de Merwe et al, 1983;Zoetendal et al, 2001;Stewart et al, 2005).…”

“…Untangling the possible contribution of microorganisms to CD has been complicated by the large variability in the composition of the gut microbiota in humans. Basically, each human has an individual fecal microbial fingerprint (Zoetendal et al, 1998;Eckburg et al, 2005;Dicksved et al, 2007). However, the study of monozygotic twins basically eliminates the variable of host genetics, except for potential epigenetic factors.…”

“…16S rRNA genes were PCR amplified from each DNA extract (two technical replicates per extract) using the general bacterial primers Bact-8F (5 0 -AGAGTTT GATCCTGGCTCAG-3 0 ) (Edwards et al, 1989), 5 0 end-labeled with 6-carboxyfluorescein, and 926r (5 0 -CCGTCAATTCCTTTRAGTTT-3 0 ) (Muyzer et al, 1993) using conditions that have been described in detail elsewhere (Dicksved et al, 2007).…”

Long-term impacts of antibiotic exposure on the human intestinal microbiota

“…The diversity of the gut microbiota is relatively simple in infants but becomes more complex with increasing age, reaching a high degree of complexity in adults (Fanaro et al, 2003). Lifestyle factors (Dicksved et al, 2007) and diet (Flint et al, 2007;Ley et al, 2005Ley et al, , 2006 can also affect the diversity and composition of the gut microbiota. Interestingly, the relative proportions of the two most dominant bacterial phyla i.e.…”

“…Bacteroidetes and Firmicutes, were found to be correlated with obesity in mice and humans, respectively (Ley et al, 2005(Ley et al, , 2006, but a study by Duncan et al (2008) did not see this same correlation in obese and lean humans. Molecular analyses have also revealed that the composition of the human intestinal microbiota is host-specific (Dicksved et al, 2007;Jernberg et al, 2007) and relatively stable over time (Jernberg et al, 2007;Zoetendal et al, 1998). Recent metagenome sequencing data of 124 individuals suggest the existence of a common core human gut microbiome (Qin et al, 2010), but this core may exist more at the level of shared functional genes rather than shared taxa (Turnbaugh et al, 2007(Turnbaugh et al, , 2009).…”