Cecum and Rumen Natural Bioreactors

bioreactor

→ create medium and environmental conditions that mimic intestine

→ change diet composition (swap media reservoir)

→ monitor changes in volatile fatty acid synthesis, gas production, etc

→ monitor changes in the microbial population

need to cool culture vessel to maintain desired temp (37 C → 98 F)

first stage of catabolism

proteins, polysaccharides, and lipids → constituent parts (amino acids, sugars, fatty acids, and glycerol)

second stage of catabolism

amino acids, sugars, fatty acids, and glycerol → acetyl CoA, pyruvate and tricarboxylic acid intermediates

energy is generated

third stage of catabolism

CO₂ , ATP, NADH+, H+, FADH₂ (TCA cycle and electron transport)

more energy is generated, and oxidizing agents are regenerated

Carbohydrate-active enzymes (CAZymes)

→ very specific (sugars)

→ “endo”- glycoside hydrolase (GH)

→ “exo”-glycoside hydrolase (GH)

carbohydrate-binding modules (CBM)

binds CAZymes or bacteria to carbohydrates

lignocellulolytic digestion

Eubacteria (NOT methanogenic Archaea AND only SOME members)

→ bacteroidetes (gram-neg)

→ firmicutes (gram-pos)

Anaerobic fungi

Ciliophora (ciliated protozoans)

(all of these do fermentation)

cell-bound CAZyme complex + Secreted CAZymes

cellulosome

→ binds cell to substrate

→ easy access to “liberated” sugars

Polysaccharide Utilization Loci (PUL) of Gram-Neg Bacteria

→ pulls sugar into the cell, helps stop competition for sugars

secreted CAZymes (Gram-Pos bacteria)

the disadvantage of using “secreted” CAZymes is other organisms can complete for sugars liberated by these enzymes

Fermentation

Problem: catabolism involves the oxidation of organic compounds, which requires NAD+ as an oxidizing agent (NAD+ → NADH + H⁺ )

→ there is a limiting amount of NAD+ in the cell

→ if NAD+ is not regenerated, then the catabolic process ceases

Solution: Re-oxidize NAD+ through:

→ e^- transport

→ use organic compounds as oxidizing agents (fermentation)

Acidophiles

optimal growth between pH 1-5.5

neutrophile

optimal growth between pH 5.5-8, preferably 6.5-7.5

alkalophiles

optional growth between pH 8.5-11.5

Internal pH of ALL cells

is maintained close to neutrality (pH 7)

pathogens/symbionts pH

6.5-7.5 pH

what does lactic acid do to pH

it drops the pH