The Human Gut Microbiota Part 3
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NUTRITION & SUPPLEMENTATION THE HUMAN GUT MICROBIOTA THE COMPOSITION OF THE HUMAN GUT MICROBIOTA - PART THREE Written by ACA Contributor Andrew Chappell BSc (Hons), MSc, PhD, RNutr Sport As previously stated the complexity and number of bacteria that inhabit the GIT increases with progression down the GIT from the small intestine to the large intestine (Figure 12). The continual supply of nutrients delivered to the large intestine and fairly consistent pH makes the GIT a perfect environment for gut microbes (Moore & Holdeman 1974, and Finegold et al. 1977). Advances in genome sequencing technologies, combined with the reduction in cost of these technologies, has meant our understanding of the bacteria that inhabit the human GIT has increased significantly over the past 20 years (Zoetendal et al. 2008). The microbiota is relatively stable throughout adult life, with the exception of disease states, although a certain degree of fluctuation is possible with antibiotic treatment, infections and changes in dietary patterns (Duncan et al. 2007, David et al. 2014a, and David et al. 2014b). In infancy the microbiota seems to be less complex and is dominated by species belonging to the Actinobacteria phylum predominantly Bifidobacteria spp. commonly sold as probiotics, and similarly as we age and become infirm there may be a tendency towards a less diverse microbiota (Penders et al. 2007 and Claesson et al. 2012). Increased understanding has resulted in a renaissance in research categorising the microbiota. Previously researchers could only study microbes that they could grow in the lab; this meant that Bifidobacterium and Lactobacillus were disproportionately studied. Moreover, for a long period of time one, Firmicutes one of the major phylum (which can make up to 50 % of a person's microbiota) went unstudied until the late 80s. The result of all this means that prior to the 1990's there was considerable focus placed on the easily grown probiotic species Lactobacillus and Bifidobacterium which make up relatively small proportions (<0.5% and 1% respectively) of the colonic microbiota in the healthy adult (with Lactobacilli undetected in the previous Italian and Hadza examples) by comparison to far more abundant microbes like Faecalibacterium prausnitzii (up to 9%). This has resulted in a lasting legacy whereby the Lactobacillus and Bifidobacterium have been prescribed as cure all's and go to probiotics for all ailments of the gut despite a lack of efficacy and the removal of probiotic status by the European Food Safety Authority. Figure 12. Summary of the most prevalent microbes occupying different regions along the Gastrointestinal Tract: TM7 (candidate division). Taken from Brown et al. (2013). © ADVANCED COACHING ACADEMY LTD NUTRITION & SUPPLEMENTATION The Healthy Adult Microbiota The four main phyla found within the healthy adult make up to 95.5 % of all bacterium found within the gut (Ley et al. 2008, DeFilippo et al. 2010, and Schnorr et al. 2014). The remaining bacteria that populate the gut belong to the Cyanobacteria, Fusobacteria, Spirochaeta, Fibrobacteres and Verrucomicrobia phyla, with much lower and variable proportions and abundances. It was previously thought that the ratio of Firmicutes and Bacteroidetes may have important consequences for health, however data from large scale projects like the HMP have demonstrates that the ratio within a cohort of healthy volunteers can vary between 95:5 to 5:95 % in favour of either phyla. This suggesting that even within the healthy state the microbiota can occupy a range of configurations (Figure 13) (The HMPC 2012). Interestingly despite the range of configurations there is considerable similarity in the metabolic potential of those microbes. Or in other words the microbes perform similar roles despite their difference in composition if you recall the ecosystem example I gave previously. Figure 13. Diversity of the human microbiota from sites around the body. Panel A reflects different bacterial phyla at seven different sites around the body. Anterior nares (nostrils), RC, retroauricular crease (behind ears) Buccal mucosa (cheek), supra- and subgingival dental plaque (tooth biofilm above and below the gum), Tongue dorsum (tongue soft tissues), Stool (colon microbiota), posterior fornix (vaginal sample). Panel B refers to the metabolic capability of the microbial population. Firmicutes belonging to the butyrate producing Lachnospiraceae and Ruminococcaceae Genus have been shown to make up to 35.5 % of all bacterial counts from healthy human faecal samples (Chassard et al. 2008). Within these clusters, bacteria belonging to the Roseburia genus and F. prausnitzii species comprised as much as 8.9 and 12.2 % of all bacteria while Bacteroides-Prevotella, Actinobacteria and Negativicutes make up 15.1, 5.1 and 9.9 % of counts respectively Chassard et al. (2008), at least in Western populations. Below the genus level, the microbiota becomes harder to classify, due in part to the large number of different species present within and individual (Qin et al. 2010). Despite difficults in characterising beyond species bacteria recovered from faecal samples show 18 species to be present in at least 57 % of individuals and 75 species in 50 % of individuals which suggests some form of common core as mentioned earlier (Qin et al. 2010). However even for the 57 most common species present in over 90 % of individuals their abundance ranged 12 to 2,187 fold between individuals. Or in other words a person may possess a common microbe, but that microbe may play a significant role in one person and an insignificant in another. © ADVANCED COACHING ACADEMY LTD NUTRITION & SUPPLEMENTATION Another way the gut microbiota can be considered is as a “communities of genes”. This is perhaps my favourite way to consider the microbiota. This is where different bacteria with similar genetic potential may fill an environmental niche. You therefore look at a person’s genetic richness within the microbiome and it’s potential, rather than trying to determine the gut microbiomes potential by looking at the species. If we look at Human Microbiome Project example we can see variation between subjects in bacteria but, metabolic pathways are ubiquitous (Figure 13b) (The HMPC 2012, and Chantelier et al. 2013). The Hadza vs Italian cohort again provides as with a great example of microbiota potential with the Hadza microbiota more capable of digesting nutrients than Italian microbiota measured by the number of enzymes they possess (Figure 14). Figure 14. Differences in the number of digestive enzymes possessed by the microbiota between Hadza hunter gathers and Italians. The Black line across the box plot represents the Median number of enzymes, the box corresponds to where 50% of all subjects data points lie. On average the Hadza microbiota is capable of digesting far more different types of carbohydrate than the Italian microbiota. The presence of bacterial specialists should however not be discounted, and subjects lacking Ruminococcus bromii have been shown to be incapable of degrading type III resistant starch (Xiaolei et al. 2012). Indeed, there is differences in the ability for people to extract energy from fibre across a population as a result. For example, one individual may be able to extract 0 to 1 kcal of energy from a gram of fibre compared to 2 or 4 kcal in a different individual. There does appear to be few truly keystone species eve Bifidobacteria who had previously thought to be the sole target of prebiotic compounds inulin and fructo-oligosaccharides is not immune with many gut microbes beyond the Bifids seemingly capable of fermenting these prebiotics. Interestingly microbial genes and thus microbial richness may negatively correlate with disease. In experiments where healthy weight individuals have been compared to obese subject’s higher numbers of genes have been counted in the healthy weight individuals compared to the obese individuals. This © ADVANCED COACHING ACADEMY LTD NUTRITION & SUPPLEMENTATION indicates that those with low gene counts were more likely to be obese and have a lower species diversity than non-obese individuals (Chantelier et al. 2013). Those with low gene counts were found to have an increased capacity for potentially deleterious metabolites: β-glucuronide, degradation of aromatic amino’s, nitrate reduction, sulphate producing capacity and lower production of the beneficial SCFAs. There is also the suggestion that there may be an increase in inflammatory molecules such as lipopolysaccharides P (LPS) (drinkers of butter and bulletproof coffee may recognise LPS) and oxidative stress which might contribute towards subsequent N disease of the lower bowel (Chantelier et al. 2013). The Microbiota in Growth and Development During birth, the previously sterile GIT is colonised by microbes from the mother’s vagina, faeces (Ardissone et al. 2014). The mode of delivery therefore has a bearing on the early infant microbiota, and infants born by caesareans have microbiotas resembling their surrounding environment compared to one resembling the mother (Dominguez–Bello et al. 2010, Ardissone et al. 2014, and Backhed et al. 2015). Bacterial diversity increases with infant’s age, although those born by caesarean still differ compared to their vaginally born peers at 12 months (Backhed et al. 2015). The developing microbiota is also influenced by whether infants is breast or formula fed (Penders et al. 2007, Boehm & Moro 2008, and Oozeer et al. 2013). Human breast milk is high in oligosaccharides (medium chain carbohydrates) with over 1000 structurally diverse and distinct molecules (Boehm & Moro 2008). Human milk acts like a prebiotics and selectively increases Bifidobacteria in the infant (Bohehm & Moro 2008). Breast milk also contains specialist molecules that interact with the immune system and prevent harmful bacteria from colonising the GIT as well as assisting in the immune systems development (Oozeer et al. 2013). The microbiota of the breast fed infant microbiota is therefore different from that of the formula fed and is dominated by the Actinobacteria phylum of which 75 % of species belonging to the Bifidobacterium genus (Oozeer et al. 2013).