BMS 150 Gut Physiology and Microbiome PDF

Physiology 5.01 Physiology of the Gastrointestinal Tract and Introduction to Gut Microbiome Dr. Maria Shapoval BMS 150 Week 10 Overview Overview of Gastrointestinal Tract Gut Physiology Motility Digestion Absorption Regulation Microbiome Amounts p...

Physiology 5.01 Physiology of the Gastrointestinal Tract and Introduction to Gut Microbiome Dr. Maria Shapoval BMS 150 Week 10 Overview Overview of Gastrointestinal Tract Gut Physiology Motility Digestion Absorption Regulation Microbiome Amounts per GI Typical families Value/ function/ role of microbiome in health Bidirectional relationship between microbiome and human physiology and health Learning Objectives Describe the different types of movements specific to the digestive tract Discuss the role of ICC, smooth muscle cells, enteric and central nervous systems in regulating gut motility Briefly explore additional hormones that can influence GI motility Summarize the function and mechanism of digestion Compare and contrast the absorption of carbohydrates, amino acids and fats Describe the gut microbiome, including the different bacterial families and their locations within the GI tract Discuss the role of the gut microbiome in digestive function and intestinal health Consider pathological implication of gut dysbiosis Learning Objectives Discuss the relationship between dietary factors and microbiome Describe the role that antibiotics play in influencing the gut microbiome Big Picture – Gut Function Gastrointestinal Tract (GI) is involved in transporting food by- products at appropriate times to areas that are functionally designed to break them down and others that are designed for absorption 60 tonnes of food pass through GI tract through average life time It is also involved in some degree of decontamination of the food by-products as well as facilitating and maintaining appropriate relationships with live non-human cells (bacteria, viruses, fungi, etc) with the help of the immune system Largest interface between host, environmental factors and antigens Overview of the GI Tract Here are the different structures that contribute to the function of the gastrointestinal tract. We will cover some of these today and some we will be covering in future. Mouth, teeth, salivary glands Esophagus, lower esophageal sphincter (LES), stomach, pyloric sphincter Small Intestine (SI): duodenum, jejunum, ileum Large Intestine (LI) Ascending, transverse, descending, sigmoid colon Rectum, anus Supporting organs: liver, gallbladder, pancreas Future lectures will dive into anatomy and physiology of discrete components and organs Today we are talking about physiology overall and introduce role of microbiome Motility There are 3 basic movements that take place along the GI tract: Peristalsis Involves entire GI tract, starting with esophagus Waves of smooth muscle contractions that propel food bolus throughout GI tract Rhythm is believed to be produced by interstitial cells of Cajal (located with the myenteric plexuses; enteric nervous system) Involves contraction behind (proximal) the food bolus and relaxation in front (distal) of the food bolus May also be stimulated or promoted by distention of smooth muscle cells (aka stretch) Function: propel food further along GI tract Some problems: esophageal spasms, atonic colon (an example of cause of constipation), gastroparesis Motility There are 3 basic movements that take place along the GI tract: Segmentation Occurs within SI and LI Produced by the coordination of smooth muscle cells and interstitial cells of Cajal (ICC) Function: promote mixing the food particles to increase interaction between the villi of the enterocytes and various food particles to promote absorption Motility There are 3 basic movements that take place along the GI tract: Migrating motor complex (MMC) Occurs within stomach and SI (and a few other locations) Small movement, almost a vibration, that occurs predominantly during fasting 1.5-2 hr intervals Movement is promoted by motilin, secreted by Mo-cells located in the duodenum (upper SI) Function: suspected that it is a self-cleaning mechanism, as this movement causes small food particles and bacteria to be dislodged from the intestinal wall and prevents bacteria from traveling from LI into SI Some problems: lack of MMC has been implicated in pathogenesis of small intestinal bacterial overgrowth, reduced during pregnancy and may explain or contribute to constipation and heartburn  Interstitial Cells of Cajal (ICC) Pacemakers of the GI Form a network with each other and smooth muscle cells via gap junctions, as well as enteric motor neurons Found throughout the entire GI tract Generate slow waves - these do not typically lead to muscle contractions Can also cause spike potentials that do trigger smooth muscle contractions à contribute to all types of different movements Interstitial Cells of Cajal (ICC) Pacemakers of the GI Excitability of smooth muscle can be increased by additional factors such as: Muscle stretch (distention) Acetylcholine Other GI hormones Excitability can be decreased by: Norepinephrine (causes hyperpolarization) Enteric Nervous System (ENS) Composed of sensory, motor and interneurons Organized into: Submucosal Plexus Located between the layers of submucosa and circular muscle (only present in SI and LI) Function to regulate motility, local blood flow, regulate secretions and epithelial cell function Myenteric Plexus Located between longitudinal and circular muscles (entire GI) Function to regulate motility CNS and GI Motility While the enteric NS can function independently, the CNS does innervate the GI tract in several places and provides additional regulation and modification of the ENS Examples of nerves that connect CNS and ENS Vagus Nerve Pelvic Splanchnic Nerves Thoracic Sympathetic Trunk In general, sympathetic NS opposes GI motility (as well as digestive secretions) Parasympathetic role is not as straightforward as it can both stimulate and inhibit motility Transport Throughout GI Tract Timing is key! If the food is transported too quickly, may not have enough time to digest or absorb it For example, if the food is allowed to enter the duodenum before being properly digested in the stomach the digestive enzymes in the duodenum may not be able to complete digestion limiting what can be absorbed from the food …And then someone else might eat our food, like gut bacteria! If the food is transported too slowly, it may irritate the local or neighboring mucosa For example, if the food content stays in the stomach for too long this increases likelihood that stomach acid will enter the esophagus (i.e. heartburn) Regulating Timing of GI Motility Many different cells/tissues can influence motility Already discussed smooth muscle cells, ICC, ENS and CNS Some of these cells response to mechanical stimulation (i.e. distention) while others respond to chemical cues (i.e. presence of peptides or free fatty acids can trigger cholecystokinin to be released) Secretion promoting motility: I-cells – cholecystokinin Enterochromaffin cells – serotonin G-cells – gastrin Mo-cells – motilin Beta-pancreatic cells – insulin Regulating Timing of GI Motility Many different cells/tissues can influence motility Already discussed smooth muscle cells, ICC, ENS and CNS Some of these cells response to mechanical stimulation (i.e. distention) while others respond to chemical cues (i.e. presence of peptides or free fatty acids can trigger cholecystokinin to be released) Secretions reducing motility: S-cells – secretin D-cells – somatostatin Pancreatic cells - Pancreatic peptide YY Alpha-pancreatic cells – glucagon These hormones have multiple functions beyond regulating motility, such as regulating other endocrine cells, metabolism, appetite and much more  Digestion – Overview Digestion = breaking down macromolecules into smaller molecules to increase absorption Two major types: Mechanical digestion: physically cutting, crushing, and churning food so that the volume of each food particle decreases (and therefore SA:volume ratio favours chemical digestion) Mouth – chewing Stomach – the segmentation-like movements of the stomach (churning) “smashes” food against the firm bumps and ridges in the mucosa of the stomach (rugae) Food is broken down into smaller and smaller pieces as it is mixed with the fluid secretions of the stomach Digestion – Overview Digestion = breaking down macromolecules into smaller molecules to increase absorption Two major types: Chemical Digestion: chemical processes that allows absorption of food particles. Can be described as: Enzymatic digestion – enzymes Lipid solubilization – emulsifiers (bile break macronutrients down into salts, lecithin) secreted by the liver smaller and smaller particles emulsify ingested lipids so that through the process of hydrolysis enzymes can break them down to smaller, absorbable molecules  Digestion – Overview Carbohydrate digestion – begins in the mouth with salivary amylase (minority), further broken down by pancreatic amylase and brush border enzymes within SI (majority of CHO digestion) Protein digestion – begins in the stomach with HCL and pepsin, further digested by pancreatic enzymes and brush border enzymes Fat digestion – begins in the stomach with HCl and lipase (minority), further digested by pancreatic lipase and emulsified by bile acids released by the liver (majority of lipid digestion) The mechanics of digestion will be further explored in other lectures Thoughts to ponder: what complications would you expect to see if any of these digestive processes were struggling or incomplete? Digestion - Summary Location Enzymes/ Contributing What is being Secretion organs/ structures digested? Mouth Salivary amylase Salivary glands Carbohydrates, all Mucus, water Teeth else broken into Mastication smaller particles Stomach HCl, lipase, pepsin Vagus nerve Proteins, fats, carbs promotes HCl – limited digestion release other than protein Small Intestine Bile acids, Liver contributes Proteins – pancreatic bile, pancreas pancreatic enzymes, Most enzymes, brush release numerous brush border important site border enzymes enzymes including enzymes; of chemical lipase and amylase Carbs – brush digestion border enzyme and amylase Lipids – lipase and bile acids Large Intestine Gut microbiota some of what hasn’t been digested yet Absorption Absorption: movement of any substance across the mucosal epithelium of the alimentary tract and into the bloodstream (most substances) or lymphatics (lipids) Largely takes place in the small intestine and is dependent on the health of the villus and microvilli of enterocytes Effective absorption is dependent on a large surface area at the apex of the epithelial cell (brush border, villi) Supported by segmentation to increase food bolus contact with microvilli and villi Proper timing required (transit that is too quick won’t allow enough time for absorption) Chyme (“watery” product of gastric digestion) needs to be mechanically digested into small particles and chemically digested into small molecules for absorption to occur Carbohydrate Absorption Digestion breaks polysaccharides into monosaccharides Galactose, glucose, fructose Only monosaccharides can be transported across the epithelial cells of the small intestine – disaccharides and polysaccharides cannot be transported Na+/glucose (galactose) co-transporter (SGLT1) Transports glucose and galactose (hexoses) from lumen into enterocyte Depends on high concentration of Na+ within lumen to power the transport of the hexoses (Na+ moves down its concentration gradient) If defective, can’t absorb these into the body Na+/K+ pump needs to continue to maintain low intracellular [Na+] Carbohydrate Absorption GLUT-5 Passive transport (facilitated diffusion) of fructose from lumen into enterocyte GLUT-2 and GLUT-5 basolateral side Transport of monosaccharides from enterocyte into blood stream (hepatic portal vein) Protein Absorption Majority of protein is absorbed in the duodenum and jejunum (very little left for ileum) Only 2-3% of protein escapes digestion and absorption (under healthy conditions) Absorption of undigested protein (by adults) has been linked with allergic symptoms Na+ symporters (similar to SGLT1) for amino acids 5 different types PepT1 transporter Transports dipeptides and tripeptides into enterocyte Relies in H+ instead of Na+ concentration gradient These are hydrolyzed into amino acids by intracellular enzymes (cytosolic digestion) within the enterocyte Amino acids are released into blood stream; hepatic portal vein Nucleic Acid Absorption Nucleic acids are broken into nucleotides and further broken into nucleoside and phosphoric acid via digestion Split further into sugars and purines and pyrimidine bases Bases absorbed via nucleoside transporters (active transporters) Fat Absorption Passive diffusion (and possible carrier proteins) Free fatty acids 10-12 carbons long Pass through enterocyte unmodified and enter portal circulation Remain free and unesterified Chylomicron Free fatty acids >10-12 carbons long Re-esterified into triglyceride once inside enterocyte Cholesterol (also esterified), transported via NPC1L1 transporter FFA’s and cholesterol are coated with proteins, more cholesterol and phospholipids à chylomicron Enters lymphatics (too big to pass between endothelial cells into blood stream) Fat Absorption Majority of ingested fats are absorbed (95% in adults, 85- 90% in infant) Assuming moderate amount of fat in the diet Steatorrhea Impaired fat digestion and absorption resulting in high amount of fat in the stool What kind of problems or pathological processes would you expect to contribute to this finding? Vitamin and Nutrient Absorption Fat-soluble vitamins (A, D, E, K) Depend on incorporation into micelle for absorption (similar process as with other fats) Majority absorbed in duodenum (upper SI), however vitamin B12 is absorbed in the ileum Most of the B-vitamins and vitamin C require Na+ cotransporters for absorption Iron absorption: Occurs within duodenum via divalent metal transporter 1 (DMT1) – Fe2+ (ferrous) enters enterocytes Transported out of enterocyte by ferroportin 1 and hephaestin In plasma Fe2+ is converted into Fe3+ (ferric) and is transported by being bound to transferrin The Human Microbiome What is the microbiome? The collection of all organisms living on and in a given environment or habitat (i.e., the human body) Also known as microbiota or commensal organisms Human microbiome project - the catalog of the microbes in human and their genes (within entire organism) Composition: Recent estimates ~1014 cells (100 trillion) Bacteria, viruses, fungi, etc. Virus composition outnumbers bacterial composition ~ 5:1 Bacteria vs. fungi ~ 10:1 Distribution determined in part by environment (pH, O2 access, tropism, etc.) Composition varies from person to person Bacterial Amounts within GI Tract Oral Cavity (Mouth) 1011 /g: Spirochaetes Esophagus 102 – 104/ mL: Streptococci, Lactobacilli, gram negative bacilli Genus: Prevotella, Veillonella, Megasphaera, Granulicatella, Rothia, Fusobacterium, Gemella, TM7, etc Stomach 103/mL: Helicobacter pylori Small Intestine 104-106/mL: Lactobacilli, gram positive cocci Large Intestine 1012 /g: Bacteroides, Bifidobacteria, Clostridia, Peptostreptococci, Fusobacteria, Lactobacilli, Enterobacteria, Enterococci, Eubacteria, Methanogens, Sulphate reducers, etc Microbiome Impact on Humans All species live in symbiosis with other organisms, and this codependency has shaped our evolutionary development We share significant homology with many bacterial, viral, and fungal organisms at the genetic level The human body has evolved to develop in the context of a microbial presence The body relies on microorganisms to perform vital functions – prevent colonization by pathogens, improve digestion and metabolism, develop immune competency FYI illustration. Gut Microbiome: 93.5% of gut bacteria belong to the following phyla: Firmicutes (major composition) Bacteroidetes (major composition) Proteobacteria (minor composition) Actinobacteria (minor composition) Gut Microbiome: Firmicutes Genus: Lactobacillus, Clostridium, Enterococcus Examples: Lactobacillus reuteri, Enterococcus caecium Bacteroidetes Bacteroides, Prevotella Examples: Bacteroides fragilis, Prevotella spp. Proteobacteria –Helicobacter, E. coli, Shigella, Salmonella, Yersinia (some commensal and some pathological bacteria) Actinobacteria – Bifidobacterium longum, Bif. Bifidum Homework: Look at the composition of a probiotic – what phyla is it composed of? Which of these are producers of SCFA? Gut Microbiome: Functions of the gut microbiome: Harvesting energy (digesting and absorbing nutrients that we can’t utilize) Strengthen gut integrity Shape intestinal epithelium Regulation of immune function Regulate intestinal motility Protection against pathogenic microbes Production of some nutrients Vitamin K2 (menaquinone), short-chain fatty acids Considered an “endocrine organ” Gut Microbiome Development Birth process plays a role in determining the types of amounts of bacteria that will colonize the infant’s GI tract C-section: less Bacteroides and more Clostridium species Vaginal: more characteristic of mom’s microbiota Initial food: Breastfeed: Bifidobacterium high Formula fed: Bifidobacterium low, higher diversity and altered ratio of E. coli, Clostridium difficile, Bacteroides fragilis Under fed: increase in entero-pathogens like Enterobacteriaceae By 2.5 years of age the composition, diversity and functional capabilities of child’s gut flora is similar to that of an adult microbiota Remains fairly stable throughout life, meaning there are some fluctuations but the majority of the ratio’s of different phyla and families will remain consistent Diet and Gut Microbiome Many different factors can influence the composition of the gut microbiota, including genetics, diet, medications and other factors. Example of dietary impact: Starch, fiber and plant diet Infant microbiota is composed of Actinobacteria (10.1%) and Bacteroidetes (57.7%) Prevotella – present; produce short-chain fatty acids (SCFA’s) Diet high in sugar, starch and animal protein Infant microbiota Actinobacteria (6.7%) and Bacteroidetes (22.4%) Prevotella – largely absent Short-Chain Fatty Acid (SCFA): Microbiome metabolite Produced duration fermentation of indigestible carbohydrates (fibers) by gut microbiota Acetate, propionate, butyrate Promote intestinal integrity by: Regulating luminal pH Regulate mucus production Produce fuel for the epithelial cells Modify mucosal immune function Influence overall metabolism: Appetite regulation Energy expenditure Glucose homeostasis Immunomodulation FYI illustration. FYI illustration. Microbiome Metabolites SCFA – already discussed Trimethylamine (TMA) Choline, phosphatidylcholine and L-carnitine can be metabolized into TMA by microbiome. TMA can be further converted into trimethylamine oxide (TMAO) which has been linked to increasing risk factor for atherosclerosis and thrombosis Bile acids Produced by the liver and secreted into the intestines can be further modified by gut microbiome Bile acids have been correlated with changes in energy metabolism (i.e. high cholesterol, insulin insensitivity) Indoles Produced by metabolism of tryptophan Maintain intestinal barrier and influence immune response Gut Microbiome and Intestinal Integrity The presence of various bacterial species has been correlated with changes in epithelial cell function and structure Examples of healthy and beneficial changes: Non-pathogenic E. coli – increase epithelial mucus secretion and reduce epithelial permeability Lactobacillus rhamnossus – increase expression of occludin and ZO-1 proteins Review: what was the function of these proteins? L. rheuteri – increase epithelial cell proliferation Gut Microbiome and Intestinal Integrity The presence of various bacterial species has been correlated with changes in epithelial cell function and structure Examples of pathological changes: Salmonella entetica – reduced ZO-1 and occluding proteins and tight junction complexes What would be the impact on intestinal permeability? Clostridium difficile – reduced mucin production Enterovirus E11 – direct cytotoxicity Gut Microbiome and Intestinal Motility Observations: Giving probiotics (live bacteria) to adults with constipation improves gut motility and increases number of bowel movements per day Transplanting fecal flora from patients with constipation to germ-free mice results in constipation symptoms Mechanisms: SCFA’s promote serotonin production and thus increase motility SCFA’s (butyrate) increase ratio of intermuscular cholinergic neurons – speeds up transmission of ENS signals and increase motility Gut bacteria can modified bile composition which can also influence gut motility Methane gas released by some intestinal bacteria can slow down motility by influencing smooth muscle cell contractions Gut Microbiome and Intestinal Motility Bi-Directional Relationship: Changes in motility influence the survival of different bacterial groups Constipation (related to irritable bowel syndrome) causes changes to gut bacteria: Increased: Bacteroides and Enterobacter Decreased: Bifidobacterium and Prevotella Diarrhea: Increased: Prevotella Decreased: Bifidobacterium, Bacteroides and Lactobacillus Antibiotics Terms and Concepts Bacteriostatic Mechanism of action interferes with bacterial cell activity (including replication) without directly causing death Require host immune function to fully clear the overgrowth Example: macrolides and tetracyclines Bactericidal Mechanism of action directly kills the bacteria Increased risk of adverse events compared to bacteriostatic antibiotics Broad spectrum Antibiotic is able to effect different types of bacteria’s including gram positive, gram negative, and others (spirochetes, atypical) Antibiotics and Gut Microbiome Negative Effects on Gut Microbiome: Reduce species diversity Altered metabolic activity Select the antibiotic-resistant organisms May lead to development of Clostridium difficile overgrowth resulting in antibiotic-associated diarrhea However, in most cases, the gut bacteria will recover to their baseline state within a few weeks after antibiotic is discontinued However, several studies argue that long-term dysbiosis is also frequent Not all antibiotics have the same impact on gut microbiome Doxycycline (tetracycline class) – reduce Bifidobacterium diversity Clarithromycin – reduce Bifidobacterium spp and Lactobacillus sp Nitrofurantoin (used for UTI) and amoxicillin – little impact on gut bacteria Antibiotics and Gut Microbiome Antibiotic-associated diarrhea (AAD): Occurs in 5-30% initially during antibiotic treatment or within 2 months after discontinuation Host factors that increase likelihood: age >65, immunosuppression, ICU or prolonged hospitalization Caused by disruption in normal gut microbiome C. difficile accounts for 10-25% of AAD cases Symptoms: mild diarrhea ranging to acute pseudomembraneous colitis (100% due to C. difficile) Note yellowish Watery diarrhea, fever, leukocytosis pseudomembranes seen on (increased WBC in blood) colonoscopy. Antibiotics and Gut Microbiome Antibiotics in childhood Association with development of asthma, juvenile arthritis, type 1 diabetes, Crohn’s disease (IBD) and mental illness Thought to be due to dysbiosis: Reduced richness of microbiome; diversity and abundance Reduction of Bifidobacteria and Lactobacillus Increase in E. coli Study Guiding Questions Compare and contrast the different types of movement; location? purpose? Cells/ chemicals involved? Compare and contrast the absorption mechanism of proteins, nucleic acids, carbohydrates and fats Summarize the impact of gut microbiome on intestinal function and overall health Summarize the impact of the environment on the different populations of gut microbiome References Zhou M, Zhao J. A review on the health effects of pesticides based on host gut microbiome and metabolomics. Front Mol Biosci. 2021; 8. Ganong’s Review of Medical Physiology – 25th edition – Chapters 25, 26 and 27 Gierynska M, et al. Integrity of the intestinal barrier: the involvement of epithelial cells and microbiota- a mutual relationship. Animals (Basel). 2022; 12(2): 154 Liu Q, et al. Interaction between the gut microbiota and intestinal motility. Evid Based Complement Alternat Med. 2022 Rinninella E, et al. What is the healthy gut microbiota composition? A changing ecosystem across age, environment, diet and disease. Microorganisms. 2019; 7(1): 14 Silva YP, et al. The role of short-chain fatty acids from gut microbiota in gut-brain communication. Front Endocrinol. 2020; 11