Module Outline 1. Microbiome overview: getting a sense of the microbiome, research, what we know 2. Bacteria: features, functions, communities & taxonomy 3. Other microbes: archaea, fungi, viruses, parasites (protozoa & helminths)
Bacteria Outline 1. Overview 2. Structural & Functional Features 3. Taxonomy 4. Communities
Bacteria 1. Appear to be the most functionally important 99% of the metagenome contribute the majority of the functional capacity and diversity of the microbiome Most of the biomass Extensive known interactions with human physiology 2. They are the best-characterized so far Most other microbes have been harder to study, for various reasons
Metagenome Source: WGO Handbook on Gut Microbes (World Gastroenterology Organisation)
Bacteria Hundreds of species per individual Main groups (phyla) Firmicutes Bacteroidetes Proteobacteria Actinobacteria Form complex communities that vary along digestive tract
Bacteria: Categorization Commensals vs. transients Beneficial vs. harmful Gram positive vs. gram negative Aerobic, anaerobic, facultative anaerobic Taxonomy
INTERNAL (Long-term) Commensals (Symbionts) Dysbiosis & Pathobionts EXTERNAL (Transient) Beneficial Microbes Pathogens & Parasites
Bacteria: Categorization Commensals vs. transients Beneficial vs. harmful Gram positive vs. gram negative Aerobic, anaerobic, facultative anaerobic Taxonomy
Bacteria Outline 1. Overview 2. Structural & Functional Features 3. Taxonomy 4. Communities
Microbiome MAMPs Metabolites Mucosal Barrier
Structural Components Major determinants of intestinal barrier response to microbiome Major determinants of virulence Major determinants of morphology and some functions of bacteria
Key Bacterial Components Capsule, cell wall / membrane components Lipopolysaccharide (LPS or endotoxin gram negative) Peptidoglycans & lipoteichoic acid (gram positive) Glycoproteins Others Flagella and pili (if present) DNA (circular chromosome and plasmids) Proteins and other components
Immune System Perspective MAMPS > Receptors Microbe-associated molecular patterns - recognized by specialized receptors Important for innate immune response Antigens > Antibodies Recognized by antibodies Important for adaptive immune response Metabolites Can have direct and indirect effects on immune system
Immune Responses Innate and Adaptive Innate more general, first-line defense (MAMPs) Adaptive more specific, can be delayed (antigens) Inflammation & immunotolerance Inflammation - Inflammatory immune cells & cytokines Anti-inflammatory or immunotolerance Involves antiinflammatory immune cells & cytokines
Do bacteria need to be alive to elicit a mucosal (immune, epithelial) response? No. Isolated components can elicit a response.
Source: Wikipedia
Source: Wikipedia
Source: CellsAlive.com
Capsule / Slime Layer Gelatinous outer layer made of polysaccharides Some have it, others don t Variable thickness Some have defined capsule, others amorphous Helps mediate adherence Virulence factor (limit phagocytosis) Source: Todar s Online Textbook of Bacteriology
Lipopolysaccharide (Endotoxin) Gram-negative bacteria Lipid + polysaccharide Essential structural role + adhesion Elicits a strong inflammatory response (e.g. septic shock) Used routinely in research to generate inflammation in lab animals Plays a role in chronic inflammation (bacterial overgrowth, leaky gut)
Summary: Structural Components 1. There are many structural features of gut microbes that the gut mucosa can recognize & respond to 2. Specific MAMPs and antigens allow immune system to recognize and respond specifically to different types of bacteria & other microbes
Functional Testing No routine clinical tests measure structural components directly Indirect tests: Microbiome (bacterial) composition tests (stool culture, DNA) LPS antibodies (Cyrex) Intestinal permeability tests (lactulose/mannitol test, zonulin test) Immune system responses (inflammatory markers)
Microbiome MAMPs Metabolites Mucosal Barrier
Key Functions of Bacteria Survival & reproduction (replicate as fast as 20-30 minutes) Energy production & biosynthesis (available substrates + functional capacity) Adaptation, defense & competition, interaction & cooperation (communities), attachment & motility, etc.
Anaerobic (fermentation) Vast majority of gut microbes are anaerobic Tolerance to oxygen varies among anaerobes, some are strict anaerobes Aerobic respiration Energy Production Facultative anaerobes Aerobic respiration if oxygen present; anaerobic if not
Oxygen AGE Availability Longitudinal: Lower GI lumen is anaerobic, upper GI has higher oxygen availability Cross-sectional: Lumen has less (or no) oxygen, mucosal tissue has higher oxygen (diffusion from circulation)
O 2 Tolerance & Metabolism IMPORTANCE? A DETERMINANT OF What they consume and produce Where they thrive in GI tract Pathogenic potential: higher oxygen levels may favor pathogens & pathobionts Which ones can be easily cultured in a lab or commercial (probiotic) production facility
Sources of Metabolic Substrates DIET Carbohydrate residues Protein residues Fats Phytochemicals / polyphenols Some drugs, toxins, etc. BODY Mucus Digestive enzymes Bile acids, liver detox products, etc. Dead cell components MICROBES Microbial metabolites Dead microbe components
Variability in Substrates Meal-to-meal and day-to-day variations in composition, quality, amount and timing Digestive health, physiology & circadian rhythms Response to diet, stress, other factors Changes in microbe composition: daily, longerterm, infections
Metabolic Products (Metabolites) Short-chain fatty acids Branched-chain fatty acids Lactate, succinate, other organic acids Gases: H 2, CO 2, CH 4, H 2 S Amino acids Biogenic amines Vitamin K, B vitamins Polyphenol derivatives Secondary bile acids Ethanol Drug and toxin derivatives Neurotransmitters Wide range of other metabolites (METABOLOME)
Metabolic Products (Metabolites) Hundreds/thousands, most are uncharacterized May be beneficial, harmful, or neutral Effects often context-dependent (e.g., diet, genes) Microbial metabolism adds a layer of complexity (and opportunity!) to nutrition & physiology
1 absorption microbiome 2 absorption 3 microbial use 4 elimination
Metabolic Diversity BACTERIAL GROUPS Bacteroides, Prevotella, Bifidobacteria, Fusobacterium Oxalobacter, Lactobacillus, Bifidobacterium Bacteroides Prevotella ENRICHED PATHWAYS Carbohydrate metabolism Oxalate metabolism Biotin and riboflavin biosynthesis Thiamine and folate biosynthesis
Short Chain Fatty Acids Major products produced by gut bacteria Produced primarily from undigested carbohydrates via fermentation Also produced from protein fermentation > 95% absorbed from the gut (testing caveat!)
Benefits of SCFAs Anti-inflammatory (promote Treg cells) Intestinal barrier maintenance Primary energy source for colon cells Contribute to caloric intake (up to 10%) Contribute to acidic conditions in colon (inhibits pathogens) Metabolic regulation (satiety, fat metabolism, glucose metabolism) Promote brain health Influence cell growth & differentiation Influence gene expression (epigenetics)
Lactate L-lactate produced by many gut bacteria mainly from starch, not fiber Not a major fermentation product but critical for maintaining redox balance during fermentation Contributes to acidic conditions in colon Used by other gut bacteria as well as by intestinal mucosa cells D-lactate also produced by a few species, can be toxic at high concentrations
Hydrogen & Methane HYDROGEN (H 2 ) Produced by a wide range of bacteria from carbohydrate and protein breakdown Roughly 1 liter per day produced (majority is usually consumed by other bacteria - e.g., methanogens) Measurement of H 2 in breath used as an indicator of SIBO In SIBO / IBS, associated with diarrhea-predominant symptoms METHANE (CH 4 ) Produced by methanogens (Archeae) from H 2 Measurement of CH 4 in breath used as an indicator of small intestinal bacterial overgrowth (SIBO) In SIBO / IBS, associated with constipationpredominant symptoms
SOURCE: Protein Fermentation
Protein Fermentation Products SCFAs and branched-chain fatty acids (BCFAs), primarily by Clostridia Putrefactive / autointoxication products Ammonia Phenol Amines (putrescine, cadaverine, etc.) Hydrogen sulfide Thiols Indolic compounds
Protein Fermentation Products Generally increase toward distal colon May produce toxic effects in the body (e.g., cancer in distal colon), but likely depends on dose & context But, some have beneficial effects Many products metabolized by other bacteria
p-cresol Potential toxin produced via protein fermentation from some commensal bacteria (produced from tyrosine) May contribute to risk or disease progression for colon cancer, cardiovascular disease, chronic kidney disease, and autism (associated with elevated p-cresol) Tends to be higher in those with higher protein and slowed transit (constipation) Levels have been shown to be reduced via various dietary fibers, resistant starches, and some polyphenols Diet + microbiome interactions = individual variability
Trimethylamine N-Oxide (TMAO) Associated with increased risk for cardiovascular disease and a few other diseases The precursor TMA is produced by gut bacteria from phosphatidylcholine (lecithin), L-carnitine, and betaine, and then converted to TMAO by the liver TMAO is also produced directly by some gut bacteria TMAO is a bundant in some seafood TMA levels depend on microbiome composition and diet; levels tend to be lower in vegetarians and vegans
Summary Points: Metabolites Wide range of metabolites produced by microbial metabolism in the gut Many have been shown to have beneficial or harmful effects Many have been linked to various diseases and conditions Various microbes have been shown to be primary producers of key metabolites, making them desirable targets for therapeutic interventions
Functional Testing Microbial organic acids (urine) Modified and unmodified Stool tests SCFAs Secondary bile acids Protein fermentation products TMAO test (Cleveland HeartLab)
Microbiome MAMPs Metabolites Mucosa
Microbiome MAMPs Metabolites Receptors Receptors Mucosa
Bacteria Outline 1. Overview 2. Structural & Functional Features 3. Taxonomy 4. Communities