Untitled Flashcards Set

Lecture 1: 

• Microbiota: The assemblage of individual microorganisms present in a defined environment

• Microbiome: The totality of microbes, their genetic elements (genomes), and environmental interactions within a defined environment.

  • Environments: Gut or soil

  • Microbiome contains microbiota and their complete genetic elements 

• Organs: 

  • A collection of tissues joined in a structural unit to serve a commoner function.

• Symbiotic Relationships

  • Gut bacteria outnumber animal cells 

  • Microbial genes far outweigh the human or animal genome 

  • Gut microbes have many functions 

    • Metabolic: Breakdown of complex sugars, production of vitamins utilized by the host

    • Protective: Educate the immune system

    • Structural: Epithelial cell growth/differentiation

• Community:

  • Bacteria, archaea, bacteriophage, protozoa, fungi

• Classification of gut microbes

• Trophic Guilds are driven by dietary intake

  • Herbivores vs omnivores vs insectivore vs carnivore 

• Biological Functions of the GI tract

  • Connection to environment:  Lumen of GI is technically outside the body

  • Anatomical Features: Vary across carnivores, omnivores, herbivores, insectivores

  • Motility: Transport digesta 

    • Progressive breakdown of polymers to monomers in specific regions for absorption.

  • Digestion: Solubilize feedstuff and nutrients for absorption

    • Mechanical- chewing, GI contractions, gizzard contraction

    • Enzymatic hydrolysis (protein to amino acids, complex carbs to monosaccharides) to aid in absorption. 

    • Microbial fermentation 

  • Absorption: nutrients via active and passive transport

  • Excretion: undigested residues and metabolic waste

  • Protection: prevent absorption of non-beneficial diet/environmental components 

• Mouth

  • Prehension: Gathering of feed (lips, tongue, teeth)

  • Salivary secretions: Lubricates feed (mucins) - bolus formation

    • Facilitates taste

    • Enzyme secretions (amylase)

    • Buffers- bicarbonate, phosphate

  • Palatability: taste and olfactory stimuli 

  • Chewing, grinding, tearing: Reduce particle size, swallowing, regurgitate bolus

• Function and Glandular Stomach

  • ECFP

  • Esophageal region (no glandular secretions) 

  • Cardiac glandular (secretes mucins) 

  • Fundic Glandular (secretes pepsin, rennin in neonates)

  • Pyloric glandular (secretes mucins) 

• Autoenzymatic: “monogastrics” - most of the enzymes produced for digestion are made by “self” or “auto” 

• Alloenzymatic: term for animals that rely on fermentation as their main source of enzymes for breakdown of the diet.

• Types of Enzymatic Digestion:

  • Host-derived (hydrolysis) 

    • Enzymes produced by host tissues

    • Convert starch to glucose, protein to amino acids, triglycerides to fatty acids. 

    • Complex carbs (cellulose, hemicellulose) cannot be degraded 

  • Microbially-derived (fermentation) 

    • Enzymes produced by microorganisms (bacteria, protozoa, fungi) 

    • Microbes utilize and release monomers (sugars, amino acids) for their own purposes to maintain a niche in the microbial community

    • Microbial products of fermentation performed in the absence of of oxygen, such as volatile fatty acids, are not used by the microbes and are instead available to the host 

• Endogenous secretions and hydrolysis in the small intestine 

  • Comprised of the duodenum (shortest), jejunum, and ileum (longest)

  • Pancreatic and bile duct enter the duodenum (common duct in some species) 

  • Primary absorption site for simple sugars, amino acids, vitamins, minerals, and lipids 

• Cecum

  • Most animals have 1, birds have two

  • Size varies: may be large in herbivores

  • Site of fermentation, continues to colon

  • Appendix is an undeveloped cecum in humans

• Colon: Large intestine

  • Length varies: short in carnivores, long in herbivores

  • Site of water and mineral absorption

  • May be important site for fermentation 

    • VFAs produced are absorbed here

    • Not major site of amino acid absorption 

  • Rectum = storage for feces

    • birds/reptiles/amphibians/sharks have a cloaca (urinary tract and colon empty into cloaca)

  • Anus (birds = vent) = elimination 

• Rumen: largest compartment covered in non glandular squamous epithelium, muscular walls for mixing.

  • Grooves along the outside segments the rumen, internal is segmented by pillars 

  • Esophageal groove: functions in young ruminants. Two muscular folds which when given stimulus (drinking) close to form a passage directly from esophagus to the omasum. 

  • Reticulo-rumen: (rumen and reticulum are essentially one major compartment) honeycomb structure, fermentation occurs here, very muscular for movement of feed, rumination, and eructation

  • Omasum: 3rd compartment, characterized by leaves with horny papillae, fermentation occurs, but to much lower extent and residence time is shorter. Water and VFAs are removed (prevent buffering in the abomasum). 

• Hydrolysis vs Fermentation

  • Forestomach and hind gut fermenters are supported by microbial fermentation

  • Monogastric animals rely on enzymatic hydrolysis for digestion although all species have varied combinations of both. 

  • Functions of stomach, small intestine, and colon are similar across species.

• Microbial digestion = fermentation

  • Enzymes are produced by microbes (bacteria, protozoa, archaea) 

• Mucus layers:

  • Single layer in intestines to allow for water absorption

  • Double layer in stomach to protect lining from acid

  • Double layer in colon to protect from higher number of microbes in fecal matter

• Conserved functionality and transit times of GI tracts across species:

  • Chicken:

    • Caeca: 10-20 hrs and pH 6-7

    • Crop: up to 6 hrs, pH 5.5-6

    • Proventriculus: 45 min, pH 2.5-3.5

    • Gizzard: 2-3 hrs, pH 2.5-3.5

    • Pancreas and small intestine: 2.5 hrs, pH 5-7.5

  • Rumen/reticulum: 

    • Feed microbial fermentation (vitamins, amino acids, volatile fatty acids)

    • pH 5.5-7

    • Smooth muscle undergoing rhythmic contractions

    • Mean retention time (MRT) = 30-60 hrs

  • Abomasum: 

    • True stomach that digests protein from feed and ruminal microbes

    • Releases gastric juices

    • pH 2-3

  • Omasum:

    • Absorbs water, vitamins, minerals

    • Reduces particle size

    • pH 6

• Intestinal epithelial cell (IEC) heterogeneity

  • Single layer lines the entire GI 

    • Aid in digestion and absorption of food

    • Maintain barrier function/protect against microbes and potential toxins 

  • Rich adult stem cell population with near indefinite capacity for self-renewal

    • Why? Cells are killed and undergo anoikis daily

    • Intestinal stem cells (ISC) are located at the base of the crypts of glands, depending on the region. 

  • Five main cell types:

    • Absorptive enterocyte

    • Enteroendocrine cell (secretes GI hormones)

    • Tuft cell

    • Goblet cell

    • Paneth cell (mainly small intestine)

• How do some microbes create a niche in the stomach under harsh conditions?

  • Secrete urease which neutralizes HCl through ammonia production

• Parietal cells secrete HCl to acidify stomach contents

• Small intestinal purpose/anatomy:

  • Enhance absorptive area for nutrient acquisition

  • Folds of kerchkring: circular folds/flaps that project into the lumen

  • Contains villi 

• Specialized intestinal regions continuously sample the mucosal and luminal contents

  • Microfold cells

    • Part of gut associated with lymphoid tissue

    • Cover mucosa-associated lymphoid tissues in small intestine

    • Contribute to local and systemic immune responses

  • Peyer’s patches

    • Aggregated lymphoid follicles

    • House immune cells mitigate pathogen invasion