Complex Carbohydrate Utilization by the Healthy Human Microbiome

Laurentian University, Canada
PLoS ONE (Impact Factor: 3.23). 06/2012; 7(6):e28742. DOI: 10.1371/journal.pone.0028742
Source: PubMed


The various ecological habitats in the human body provide microbes a wide array of nutrient sources and survival challenges. Advances in technology such as DNA sequencing have allowed a deeper perspective into the molecular function of the human microbiota than has been achievable in the past. Here we aimed to examine the enzymes that cleave complex carbohydrates (CAZymes) in the human microbiome in order to determine (i) whether the CAZyme profiles of bacterial genomes are more similar within body sites or bacterial families and (ii) the sugar degradation and utilization capabilities of microbial communities inhabiting various human habitats. Upon examination of 493 bacterial references genomes from 12 human habitats, we found that sugar degradation capabilities of taxa are more similar to others in the same bacterial family than to those inhabiting the same habitat. Yet, the analysis of 520 metagenomic samples from five major body sites show that even when the community composition varies the CAZyme profiles are very similar within a body site, suggesting that the observed functional profile and microbial habitation have adapted to the local carbohydrate composition. When broad sugar utilization was compared within the five major body sites, the gastrointestinal track contained the highest potential for total sugar degradation, while dextran and peptidoglycan degradation were highest in oral and vaginal sites respectively. Our analysis suggests that the carbohydrate composition of each body site has a profound influence and probably constitutes one of the major driving forces that shapes the community composition and therefore the CAZyme profile of the local microbial communities, which in turn reflects the microbiome fitness to a body site.

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Available from: Brandi L Cantarel
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    • "The human gut harbors the most substantial microbial communities within our bodies, with these communities exhibiting considerable inter-and intra-personal variability (Eckburg et al., 2005; Ley et al., 2006; Qin et al., 2010). Several diseases and disorders have been linked to dysbiosis (imbalance) in these gut communities, and recent studies have sought to identify changes to microbial community structure and function during health and disease (Bäckhed et al., 2004; Cantarel et al., 2012; Claesson et al., 2012; Qin et al., 2012; Hsiao et al., 2013; Gevers et al., 2014). Gut microbial community composition varies less within an individual than among different individuals, suggesting a strong environmental component (Turnbaugh et al., 2006; Qin et al., 2010; Caporaso et al., 2011; The Human Microbiome Project Consortium, 2012; Schloissnig et al., 2013). "
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    • "The entire gene repertoire involved in the breakdown of carbohydrates is termed as the ‘glycobiome’ [23]. Studies on the human gut metagenome has revealed the presence of an extensive glycobiome harbored by the gut microbial community [24], [25]. This feature has been studied in most of the bacteria associated with the human gut. "
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    • "For example, the human genome encodes fewer than 20 complex carbohydrate-utilizing enzymes, which indicates that humans cannot digest most of the carbohydrates present in their diet. The microbial populations within the gut serve this important function by degrading the complex plant polysaccharides from sources such as vegetables into simple products that the human body can digest [24]. The gut microbiome serves various functions that have an effect on different aspects of its host health. "
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