The Cornell Net Carbohydrate and Protein System (CNCPS) has a submodel that predicts rates of feedstuff degradation in the rumen, the passage of undegraded feed to the lower gut, and the amount of ME and protein that is available to the animal. In the CNCPS, structural carbohydrate (SC) and nonstructural carbohydrate (NSC) are estimated from sequential NDF analyses of the feed. Data from the literature are used to predict fractional rates of SC and NSC degradation. Crude protein is partitioned into five fractions. Fraction A is NPN, which is trichloroacetic (TCA) acid-soluble N. Unavailable or protein bound to cell wall (Fraction C) is derived from acid detergent insoluble nitrogen (ADIP), and slowly degraded true protein (Fraction B3) is neutral detergent insoluble nitrogen (NDIP) minus Fraction C. Rapidly degraded true protein (Fraction B1) is TCA-precipitable protein from the buffer-soluble protein minus NPN. True protein with an intermediate degradation rate (Fraction B2) is the remaining N. Protein degradation rates are estimated by an in vitro procedure that uses Streptomyces griseus protease, and a curve-peeling technique is used to identify rates for each fraction. The amount of carbohydrate or N that is digested in the rumen is determined by the relative rates of degradation and passage. Ruminal passage rates are a function of DMI, particle size, bulk density, and the type of feed that is consumed (e.g., forage vs cereal grain).

The Cornell Net Carbohydrate and Protein System (CNCPS) has a kinetic submodel that predicts ruminal fermentation. The ruminal microbial population is divided into bacteria that ferment structural carbohydrate (SC) and those that ferment nonstructural carbohydrate (NSC). Protozoa are accommodated by a decrease in the theoretical maximum growth yield (.50 vs .40 g of cells per gram of carbohydrate fermented), and the yields are adjusted for maintenance requirements (.05 vs .150 g of cell dry weight per gram of carbohydrate fermented per hour for SC and NSC bacteria, respectively). Bacterial yield is decreased when forage NDF is < 20% (2.5% for every 1% decrease in NDF). The SC bacteria utilize only ammonia as a N source, but the NSC bacteria can utilize either ammonia or peptides. The yield of NSC bacteria is enhanced by as much as 18.7% when proteins or peptides are available. The NSC bacteria produce less ammonia when the carbohydrate fermentation (growth) rate is rapid, but 34% of the ammonia production is insensitive to the rate of carbohydrate fermentation. Ammonia production rates are moderated by the rate of peptide and amino acid uptake (.07 g of peptide per gram of cells per hour), and peptides and amino acids can pass out of the rumen if the rate of proteolysis is faster than the rate of peptide utilization. The protein-sparing effect of ionophores is accommodated by decreasing the rate of peptide uptake by 34%. Validation with published data of microbial flow from the rumen gave a regression with a slope of .94 and an r2 of .88.

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Ruminant animals and ruminal microorganisms have a symbiotic relationship that facilitates fiber digestion, but domestic ruminants in developed countries are often fed an abundance of grain and little fiber. When ruminants are fed fiber-deficient rations, physiological mechanisms of homeostasis are disrupted, ruminal pH declines, microbial ecology is altered, and the animal becomes more susceptible to metabolic disorders and, in some cases, infectious disease. Some disorders can be counteracted by feed additives (for example, antibiotics and buffers), but these additives can alter the composition of the ruminal ecosystem even further.

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Ruminant animals depend on cellulolytic ruminal bacteria to digest cellulose, but these bacteria cannot resist the low ruminal pH that modern feeding practices can create. Because the cellulolytic bacteria cannot grow on cellobiose at low pH, pH sensitivity is a general aspect of growth and not just a limitation of the cellulases per se. Acid-resistant ruminal bacteria have evolved the capacity to let their intracellular pH decrease, maintain a small pH gradient across the cell membrane, and prevent an intracellular accumulation of VFA anions. Cellulolytic bacteria cannot grow with a low intracellular pH, and an increase in pH gradient leads to anion toxicity. Prevotella ruminicola cannot digest native cellulose, but it grows at low pH and degrades the cellulose derivative, carboxymethylcellulose. The Prevotella ruminicola carboxymethylcellulase cannot bind to cellulose, but a recombinant enzyme having the Prevotella ruminicola catalytic domain and a binding domain from Thermomonspora fusca was able to bind and had cellulase activity that was at least 10-fold higher. Based on these results, gene reconstruction offers a means of converting Prevotella ruminicola into a ruminal bacterium that can digest cellulose at low pH.