When the diets of monogastric production animals are being formulated to achieve the protein and amino acid concentrations required by the host, the role of intestinal microbiota has been generally ignored. While bacteria in the upper intestine use dietary amino acids as building blocks of essential proteins, bacteria in lower intestine use them also as substrates in fermentation (also known as putrefaction).

Proteins in the upper intestine offer food for the host.

The upper intestine is dominated by lactic acid bacteria the growth of which is fully dependent on feed-derived amino acids. Therefore, they directly compete for amino acids with the host. However, these bacteria, not only utilise dietary amino acids, but are also involved in the hydrolysis of complex proteins by the proteases and peptidases they express.
The role of these bacterial enzymes is pronounced in poultry, where the dietary proteins and amino acids are exposed to the highly dense bacterial community of the crop before they are processed by the host’s hydrolysis machinery of the proventriculus- gizzard-duodenum.
In an ideal case, the majority of dietary protein is hydrolysed by pepsin, trypsin and peptidases, and the released amino acids and small peptides become effectively absorbed in the duodenum/jejunum.
Often that is not the case due to the characteristics of the dietary protein, anti-nutritional factors, compromised secretion of digestive enzymes, suboptimal pH in the proventriculus-gizzard, etc. The further the proteins/amino acids pass through the small intestine the more likely they are consumed by intestinal bacteria and are unavailable for the host. Inevitably, small-intestinal bacteria use some dietary sugars, amino acids and vitamins.
However, while commensal lactic acid bacteria take their part of these valuable nutrients, at the same time they help to maintain homeostasis in the intestinal habitat and prevent overgrowth of intestinal pathogens.
Protein bypassing ileum only feeds bacteria of the lower intestine In the distal ileum there are proteins of at least three origins:
• dietary proteins resistant to digestion
• endogenous proteins synthesised and secreted by the host, and
• endogenous proteins of the intestinal bacteria.

Protein bypassing ileum only feeds bacteria of the lower intestine

The residual proteins in ileal digesta are practically inert to microbial hydrolysis under the conditions of distal ileum. However, the fraction that enters the caeca is readily attacked by a highly diverse and efficient caecal microbial community. In the caecum, there are bacteria that are specialised in protein digestion and can capture energy from amino acid degradation; some also use amino acids as a source of carbon for all the building blocks of their biomass. Often, amino acids are not the preferred source of energy but in the absence of metabolisable carbohydrates can be utilised by some bacteria.

In caecal bacterial metabolism, most amino acids are being metabolised to common volatile fatty acids such as acetic, propionic and butyric acid. These are the same metabolites that anaerobic bacteria also produce in the metabolism of carbohydrates.

Indeed, by the analysis of major VFAs alone it is not possible conclude whether the boost in VFA production is coming from the fermentation of non-starch polysaccharides (which is considered beneficial) or bypass protein (which is a negative sign).

There are some compounds that are only being produced in the metabolism of specific amino acids. For example, the branched chain fatty acids valine, leucine and isoleucine are converted by intestinal bacteria to isobutyrate, 2-methylbutyrate and isovalerate, respectively. Also, aromatic amino acids tryptophan and tyrosine are converted to indole, skatole, cresol and phenol. It is worth noting that many of the fermentation products of the aromatic amino acids are detrimental, and their presence alone may impair performance.

Although the amino acids that produce amino acid-specific metabolites represent only a fraction of total amino acids, the corresponding metabolites can be used as biomarkers of anaerobic protein fermentation, also referred to as putrefaction.

References to literature upon request.