BIOL1XX8 2024 Lecture 15: Microbes PDF

The Yin and Yang of Human Microbiomes: Diseases and Benefits A/Prof. Andrew Holmes Charles Perkins Centre & School of Life & Environmental Sciences PART 1 – Microbes are normal and part of us. Understand that microbes are inevitable and you require microbe exposure to be normal. Ø Can describe th...

The Yin and Yang of Human Microbiomes: Diseases and Benefits A/Prof. Andrew Holmes Charles Perkins Centre & School of Life & Environmental Sciences PART 1 – Microbes are normal and part of us. Understand that microbes are inevitable and you require microbe exposure to be normal. Ø Can describe three main route of exposure and primary sites of permanent microbes residence Ø Can give examples of evidence from germ-free animal models of postnatal development in gut tissues that requires microbes to occur. Ø Can give examples outside the gut of systemic body functions that are influenced by gut microbe-mediated developmental outcomes. Just because microbes are normal does not mean they are all good. Apply concepts for categorizing biological interactions to the human-microbe context - our body system evolved to accommodate resident microbes in our gut and exclude microbes from systemic tissues. Ø Can explain the distinction between interaction categories of amensal, pathogen/parasite, commensal and mutualist and recognize the challenges of applying these to classify microbes found on humans. Ø Can use examples from gut anatomy and postnatal development to illustrate that gut microbes should be considered normal participants in animal systems biology. Ø Can identify patterns of similarity for the gut microbes of all mammals (what is normal) - examples of phyla that are ‘always’ dominant components and examples of microbe functions (their physiology) that are always found. Critical Fact: Exposure to foreign and resident microbes is continuous Our exterior surfaces (skin) and internal cavities (respiratory, urogenital and gastrointestinal tracts) are all exposed to huge numbers of diverse microbes. Humans estimated to inhale daily: Ø Viruses 6 × 106 Ø Bacteria 6 × 106 Ø Fungi 6 x 104 The microbes we are exposed to may: fail to colonize; become short-term residents; Our skin surface and become long-term residents digestive tract are exposed to BILLIONS per day. Critical Fact: We don’t have microbes in utero BUT after birth the residence of TRILLIONS of microbes is normal. Our gut is very densely packed with Bacterial Our Body Composition cells. Human + Bacteria Bacteria - much smaller than human cells, very By weight 98% 2% much more numerous (1011 cells/g) By cell No. ~30% ~70% Microbial metagenome is much larger than By genes 99% human genome. Critical Fact: Our microbe composition is controlled - the presence of microbes in tissues is NOT normal. Extremely high density of diverse bacterial cells inside gut Tight gut barrier is formed by mucin layer over tightly joined epithelial cells (nuclei in blue). Microbes are excluded from the underlying tissues of our body. Tropini et al. (2017) Cell Host & Microbe 21:433 If microbes are normal, but can also cause disease, how do we tell good microbes from bad microbes? Traditional classification of interactions between organisms Incompatible – At least one partner benefits and no ongoing interaction long-term interactions occur Amensal-----Parasites-----Commensals-----Mutualists Parasitism category: Commensalism category: Mutualism category: Partner one benefits Partner one benefits Partner one benefits increased growth output for parasite increased growth output for commensal increased growth output for mutualist Partner two harmed Partner two neutral. Partner two benefits reduced growth output for ‘host’ no growth change for host improved growth for host Host better without parasite Host same with/without commensal Host needs microbe for optimal fitness To use these concepts need to assess outcomes over time in both presence and absence of each interacting partner species – very difficult for animal-microbe interactions. We interact with many species simultaneously at multiple body sites Critical Fact: Resident microbes collectively influence animal outcomes via mechanisms involving many species. Amensal-----Parasites-----Commensals-----Mutualists Microbe not normally present – Microbe one of hundreds normally present can simply assess affect of – cannot assess outcome of pairwise interaction. pairwise interaction. If interested look up Koch’s postulates Pathogens--Parasites---Commensals---Co-operators---Mutualists We can’t easily determine outcomes for individual resident microbe species – but we can look at all or none effects. What happens after we acquire trillions of resident microbes? We can test effect of presence or absence of all microbes. Our postnatal development happens simultaneously with Ante-natal microbe exposure (in utero) The foetus develops in a sac that is typically not exposed to microbes Microbe signals are required to trigger much gut postnatal development – we need microbes to be normal. Epithelial cell surface Gut vascularization Maturation of gut tissues (EEC, GALT, ENS) Normal Major regulatory systems of the body located in the gut require microbes for full development. Immune functions e.g. Fucose on e.g. IgA secretion GALT (Gut-associated lymphoid tissue) epithelial surface e.g. capillary network into colon Germ free Endocrine functions EEC (Entero-endocrine cells) Neural functions ENS (Enteric nervous system) Adapted from Hooper & Gordon (2001) Glycobiology, Stappenbeck et al., (2002) PNAS Microbe signals are required to trigger much gut postnatal development – we need microbes to be normal. In the absence of Microbes: Gut functions are different – reduced digestive capacity Immune functions are different – essentially no adaptive immunity Metabolic regulation is different – altered neuro-endocrine signalling pathways Cognitive functions & mood are different – underdeveloped enteric nervous system A stable gut microbial community – gut microbiome – develops at approximately the same time postnatal development finishes. These effects emerge from interaction with hundreds of gut microbes over time. Presence of gut microbiome affects the entire body system – not just the gut. Thinking Points: Many modern diseases show associations between diet, microbiome and immuno- metabolic functions – factors that develop after birth. What happens here à à impacts Adult health Factors in normal microbiome development: Microbe exposure (birth canal, skin) Infant diet (breast milk) Immune system development Disturbances to microbiome development: Antibiotics (at birth or during infancy) Microbe exposure (C-section, infection) Key Concept: DOHAD - there is interaction between microbiome Diet (breast/formula; weaning pattern) development and development of immune and metabolic regulation. Developmental Origins of Health and Disease Key Concept: A gut microbiome refers to the stable resident microbial community of a defined habitat (gut) in an individual person. Low - Moderate Very high bacterial numbers bacterial numbers Ileum Duodenum Colon 103 - 105 108 1011 - 1012 < 104 g-1 Jejunum Stomach Appendix We require microbes, but we have different microbiomes at different body sites. The gut microbiome is by far the most influential. The stomach is continually exposed to microbes, but very few actually grow there. The distal Small intestine (mainly ileum) is a site of stable occupation by microbes. Lower numbers than colon. The Large intestine (colon) has distinct conditions for microbial growth and far higher microbe cell density than ileum. Most other internal organs are sites where presence of microbes is not tolerated. Prescott’s Microbiology 10th edition 32.2  Gut microbiomes are specialized, diverse communities. Hundreds of species (diverse) but from small number of Bacterial phyla (specialised). Over 98% of the total microbial cells in our gut are Bacteria. There are typically some Archaea cells present. Eukarya microbes such as fungi and protists are present in small numbers Universal tree of life Broad similarity: Most gut microbes in all mammals are from two Bacterial phyla and have fermentative metabolism (anaerobic). Bacteria Tens to hundred of Bacteroidetes species. Bacteroidetes (10- Vast majority show fermentative metabolism. 90% of all cells) Diverse growth substrates commonly polysaccharides Hundreds of Firmicutes species. Firmicutes Vast majority show fermentative metabolism. (10-90% of all cells) Diverse growth substrates commonly polysaccharides Tens of Proteobacteria species. Proteobacteria respiratory and fermentative metabolism (1–5% of all cells) Growth substrates rarely polysaccharides, commonly small molecules (sugars, amino acids and fatty acids). Archaea One or two species. Methanobrevibacter (1- One type of metabolism (methanogenesis). 2%) Growth on one-carbon compounds and hydrogen. Other Bacterial phyla - Actinobacteria, Verrucomicrobia, and Deferribacteres  PART 2 – Primary direct function of gut microbiome is delivery of nutritional benefits. Can describe why primary function of gut microbes is considered to be as significant contributor to nutrition. Ø Can give simple explanation of why multiple microbe species are required to efficiently obtain energy from plant foods. Ø Can explain the role of fermentation-derived SCFA as nutrients and contrast their contribution to energy in humans with that in other animals. Ø Can list other microbial metabolites that impact nutrition (vitamins, amino acids). Can apply concepts of microbial activity and location to explain the need for microbial control to maintain a balanced co-operative interaction. Ø Can explain why metabolites from fermentation are typically beneficial, but some metabolites from anaerobic respiration may be harmful. Ø Can describe why ‘overgrowth’ of microbes can cause pain or other intestinal problems. Ø Can relate functional anatomy (distinct properties of stomach, SI and LI) to promotion of beneficial microbial contributions to nutrition. Silverthorn Human Physiology Chapter 21 Prescott’s Microbiology Chapter 3, Chapter 32 Our microbiome influences our nutrition: Evidence from comparing the presence/absence of microbes Germ free Normal Food eaten (g/day) No F al G rm The presence of microbes changes our food requirements. Quantity - Less food is eaten by animals that are colonized. Quality - The diet fed to germ-free animals requires vitamin supplementation and a simple carbohydrate profile. Digestion in stomach / small intestine is driven by exocrine secretions. Most non- starch polysaccharide carbohydrates from plants are ‘digestion-resistant’ à fibre. Small intestine: Tank for further hydrolysis. Cells of accessory organs secrete enzymes and bile. Intestinal epithelial cells absorb nutrients. Ileum Duodenum Jejunum Stomach: An acid hydrolysis tank. Material passing to the colon includes: Gastric cells secrete acid and enzymes. Ø Indigestible - chemically inaccessible to human enzymes (e.g. fibre) Ø Inaccessible – particle structure prevents enzyme access (e.g. intact corn kernel) Ø Excess – exceeded digestion/absorption capacity of small intestine. Plant-based foods are potentially rich sources of macronutrients but only if you can digest the cell wall polysaccharides. Whole plant foods come in well- Micrograph of starch stored in wrapped packages. plant cells Plant cell walls are digestion resistant (e.g. cellulose, xylan). Starch, must be released to be degraded by amylases. Other storage polysaccharides of plants are typically also digestion-resistant (e.g. inulin, arabinogalactans). Microbes have a far wider repertoire of carbohydrate-degrading enzymes than humans. Multiple microbe species co-operate to solubilize fibre  Gastrointestinal tracts evolved to accommodate large ‘fermentative microbial communities’ – especially in herbivores. Large foregut-fermenting Mammalian Mammalian monogastrics include herbivores (horses), omnivores (pigs, mammalian herbivores. carnivores. humans) and carnivores (cats, dogs). The colon is the site of high density microbial populations and fermentation. Colon: Site of water resorption/stool formation and in herbivores/omnivores also extended digestion via microbial metabolism. Ileum Duodenum Jejunum Plant-specialists have complex Meat- digestive tract with a specialists have Ruminants: up to 70% of calories via rumen microbes specialised fermentation a simple Humans: 10 – 15% of calories via colon microbes chamber. digestive tract. Stevens & Hume (1998) Physiol Revs 1998;78:393-427 Key concept: Healthy gut microbiomes aid energy harvesting. Bacteria have enzymes to solubilize fibre – animals don’t. Only fermentative metabolism has high yields of short chain fatty acids. enzyme degrades fibre Non-starch Uptake of polysaccharides released sugars in diet (Fibre) Energy for growth and synthesis Fermentative metabolism Bacterial enzyme of sugars secretion Terminal metabolites for excretion Short Chain Fatty acids (Acetate, SCFA are fermentation metabolites Propionate, Butyrate and others) that are valuable energy sources CO2 for animals H2 Key Concept: The energy and nutrients obtained from plant foods is only accurately predictable if you know the microbiome contribution Fats Carbohydrates Proteins Mechanical, chemical, and enzymatic digestion Soluble molecules that are released (not synthesized) from Fatty acids (>c10) Amino the ingested food. Glucose + monoglycerides acids Avail nutrients varies with food types. Absorption (small intestine) Soluble molecules produced by bacterial metabolism of Short Chain Fatty undigested food. Absorption (colon) Avail nutrients varies with food type AND microbiome. Acids (