Slide 1 Year 1 MBChB Lecture 15 Introduction to the Gut Microbiota Professor Barry Campbell Gastroenterology Research Unit Cellular & Molecular Physiology, Institute of Translational Medicine bjcampbl@liv.ac.uk http://pcwww.liv.ac.uk/~bjcampbl/microbiota.htm Slide 2 Learning outcomes Lecture 15: Introduction to the gut microbiota o Define the gut microbiota and microbiome, and its role in development and health o Explain how diet impacts on the microbiota and microbial activity o Describe the role of the microbiota in the production and absorption of short chain fatty acids from dietary fibre in the large intestine o Introduce the concept of dysbiosis (microbial imbalance), reduced diversity and gut disease Slide 3 The microbiome The importance of microbiota Joshua Lederberg - argued that microorganisms inhabiting the human body should be included as part of the human genome, because of their influence on human physiology. Lederberg & McCray 2001 Scientist 15: 8 Human microbiome. ~100 trillion bugs NIH Human Microbiome Project Genome Res 2009; 19, 2317-23
Slide 4 Estimated numbers of bacteria on/within the human body Original dogma: We are only 10% human (more or less) Revised estimates: 3 x 10 13 Human cells 3.9 x 10 13 Bacteria 10 trillion cells vs. ~100 trillion bugs Approx. 76% Human now!! Sender et al. Plos Biol 2016; doi:10.1371/journal.pbio 10002533 Slide 5 What do we know about our gut microbial community (microbiota)? Established in the 1 st year of life Co-evolves with the immune system Highly variable between individuals In 154 individuals no single shared abundant species About 160 bacterial species in each faecal sample gene set ~150 times human genome The range of bacteria appears to be fairly stable with time But influenced by diet Turnbaugh & Gordon 2009 J Physiol 587:4153-8 Turnbaugh et al. 2009. Nature 457:480-4 Qin et al. 2010. Nature 464, 59-65 Slide 6 Early development of the human faecal microbiota during first 10 days of life The meconium was sterile. On the second day of life, coliform bacteria, Lactobacilli and Enterococci could be isolated On third day strains of Bacteroides On fifth day Bifidobacteria. Hoogkamp-Korstanje et al. 1979. Antonie van Leeuwenhoek 45; 35-40
Slide 7 Host-Microbiota mutualism i.e. the way two organisms of different species exist in a relationship in which each individual benefits from the activity of the other In blood only 1000 bacteria are required to induce an inflammatory response. Yet, 10 14 bacteria in the gut induce no such response!! WHY? Bacteria are confined to the mucosal immune compartment by the intestinal barrier & the innate immune system where they are not recognised as foreign Slide 8 Gut microbiota shapes intestinal immune system Healthy individuals have: Higher taxonomic diversity Higher gene diversity Microbial communities are important for development and stability of immunity Cerf-Bensussan & Gaboriau-Routhiau 2010; Nat. Rev. Immunol. 10(10):735-44 Slide 9 Bacteria in the normal distal gut % of bacteria 13,000 16S rrna sequences analysed from healthy young adults and non-ibd controls. Six major phyla Firmicutes Bacteroidetes Actinobacteria Proteobacteria Fusobacteria Verrucomicrobia >90% Petersen et al. 2008 Cell Host & Microbe 3, 417-27
Slide 10 The importance of the mucus barrier Colonic mucus is continuous with two layers inner layer is normally free from bacteria Small intestinal mucus is discontinuous MUC2 bacteria Johansson et al. PNAS 2011; 108, 4659-65 Slide 11 Mucosa-associated bacteria differ from faecal bacteria! includes bacteria that are asaccharolytic (eg some Firmicutes) or aerobic/ microaerophilic bacteria typically absent from the faeces (eg E. coli) Aldenburg et al. Gastroenterology 2014; 147, 1055-63 Slide 12 High fruit/ legume fibre diet More Gram +ve saccharolytic spp. High SCFA levels Habitual diet shapes the gut microbiota 16S rrna gene surveys reveal a clear separation of two child populations from Burkina Faso and EU High milk fat/animal protein diet Low SCFA levels More Gram -ve Proteobacteria De Filippo et al. 2010 PNAS 107, 14691-6
Slide 13 Dietary SCFAs All dairy Microbiota fermentation of dietary fibre generates short chain fatty acids SCFAs from Dietary fibre fermentation soluble and insoluble SCFAs.. a subset of fatty acids that contain 6 or less carbon molecules Acetate Propionate Butyrate Firmicutes Bacteroidetes High numbers of anaerobic, sacchrolytic species >90% Slide 14 Absorption of SCFAs in the large intestine MCT transporter/receptor uptake of SCFAs Also diffusion through apical membrane and tight junctions Butyrate (BT) is the major source of energy for the bowel and a potent inhibitor of histone deacetylases (HDAC), BT enhances tumour suppressor gene expression. SCFA receptors link the metabolic activity of the gut microbiota with host body energy homeostasis Also immunomodulatory Gill & Dudeja 2011. Am. J. Physiol. 301: C977-C979 Kimura et al. 2013 Nat. Commun. 4, # 1829 Also GPR41 (SCFAs) and GPR109a (butyrate) G-protein coupled receptors Slide 15 Systemic metabolism of SCFA SCFA entering into the portal vein undergoes first-pass metabolism by the liver within the liver the may enter a number of metabolic pathways depending on the metabolic state Acetate and butyrate may be converted to the central metabolite, acetyl-coa and utilized to form lipids and ketone bodies. SCFA may also enter the citric acid cycle and become utilized for glucose production via gluconeogenesis. Acetate may also pass through into the peripheral circulation and can be detected in peripheral blood.
Slide 16 Even short-term dietary intervention alters the human gut microbiota and microbial activity. Bacterial 16S ribosomal RNA gene sequencing Microbial diversity (the difference between each subject s baseline and dietassociated gut microbiota) changed within 1 day on animal-based diet reaching the colon (blue marker). David et al. 2014 Nature 505:559-63 Slide 17 Summary of how diet shapes the gut microbiota Simpson & Campbell 2015. Aliment Pharmacol Ther. 42:158-79 Slide 18 Dysbiosis An alteration in the microbiome caused by a change in microbiota composition, a change in microbial metabolic activity, and/or a shift in local distribution of communities of microbes Homeostasis symbionts commensals pathobionts Reduced diversity Loss of beneficial microbes Pathobiont expansion
Slide 19 Factors shaping intestinal microbial composition and effects of dysbiosis on host health Sommer & Bäckhed. 2013. Nature Reviews Microbiology 11, 227 238 Slide 20 Inflammation re-shapes the gut microbiome % of bacteria % of bacteria 5,405 16S rrna sequences from patients with Inflammatory bowel diseases [IBD], i.e. Crohn s disease & ulcerative colitis. Petersen et al. 2008 Cell Host & Microbe 3, 417-27 Slide 21 Diet, microbiota and colonic health a long history 1852-1943 Dr John Harvey Kellogg 90% of the diseases of civilization are due to improper functioning of the colon poor diet favors harmful bacteria that can then infect other tissues in the body; that the intestinal flora is changed by the diet of the individual, and is changed for the better
Slide 22 Diet, microbiota and colonic health a long history 1856-1943 Sir William Arbuthnot Lane A full colon is the root of all suffering? An early advocate of dietary prevention of cancer. Promoted whole foods, fruits and vegetables, sunshine and exercise: his plan to foster health and longevity via 3 bowel movements daily. By Photogravure after Elliott & Fry. - [1], CC BY 4.0, https://commons.wikimedia.org/w/index.php?curid=33387516 Slide 23 High intake of fruit fibre (but not cereal or legumes) protects against Crohn s disease Prospective Nurses health study 170,776 women followed up for 3,317,425 person years 1.4g/d vs. 6.4 g/d fruit fibre Ananthakrishnan et al. 2013 Gastroenterology 145:970-77