Host and microbiota-derived proteases hydrolyze dietary and endogenous (host or microorganism-derived) proteins in the intestinal lumen into peptides and AA that can be used by gut bacteria after uptake (14). Available AA can be used by intestinal bacteria for protein synthesis or as carbon and energy sources (15). Luminal AA of dietary and endogenous origin are the main constituents of bacterial protein in the pig ileum, indicating it is likely that de novo synthesis of AA by the intestinal bacteria of the foregut of non-ruminants is limited (16). The capacity to synthetize AA differs greatly across bacterial taxa (14). For instance, Escherichia coli encodes genes for the biosynthesis of all 20 α-AA while Lactobacillus has limited capacity for AA biosynthesis and thus relies on the uptake of extracellular AA (14, 17). It has been proposed that some commensal and pathogenic gut bacteria might have lost biosynthetic pathways for AA due to the high availability of AA in the gut environment (18). It is also important to consider that the autotrophy for AA in gut bacteria can be strain dependent (14). In addition to exogeneous AA, some species of intestinal bacteria such as E. coli, use ammonia as the preferred nitrogen source (19). Intestinal bacteria utilize AA in a species-dependent manner, as demonstrated in bacteria derived from the pig microbiota (20, 21). For example, in vitro incubation with ¹⁴C-labeled AA demonstrated that intestinal E. coli and Klebsiella spp. and Streptococcus spp. have differential utilization of AA for protein synthesis (20). The bacterial intracellular AA composition also seems to be species specific compatible with the concept of different AA requirements (22). Interestingly, the saccharolytic pathogen Campylobacter jejuni uses a limited range of AA (serine, aspartate, asparagine, glutamate, glutamine, and proline) (23). Further to the roles of protein synthesis and energy source, luminal AA also play an important signaling role in the gut ecosystem, which may have significant impact on the development of enteric pathogens (24). The sensing of arginine by Enterohemorrhagic E. coli (EHEC) induces the expression of virulence genes (25). In contrast, the presence of some AA in the medium can impair growth of specific bacteria strains, such as high concentrations of valine and leucine inhibiting E. coli growth (26). Overall, the bacterial use of exogenous AA can be classified as nutritionally essential (as a protein building block), non-essential (as energy source), preferred, or avoided/toxic for the growth of specific bacterial species as shown in Table 1.

The microbial catabolism of AA may impact the host intestinal lumen caused by the release of multiple metabolites resulting from a combination of deamination, decarboxylation, or desulfurization reactions (12). The deamination of AA releases ammonia which may negatively impair mitochondrial respiration, resulting in decreased cell proliferation and barrier function in the intestinal epithelium (27, 28). In addition, the degradation of cysteine by the gut microbiota releases hydrogen sulfide which can reduce mitochondrial respiration and increase inflammation when present at high concentration (29). Microbial catabolism of tyrosine releases p-cresol which can induce DNA damages and reduce mitochondrial respiration in intestinal epithelial cells and has been implicated in renal, cardiovascular and neurological disorders (30). Imidazole propionate, a bacterial metabolite derived from histidine, was shown to disrupt insulin signaling and was implicated in diabetes (31). Based on these observations, AA fermentation (also called putrefaction) has often been considered detrimental for health (32).

In contrast, other bacterial metabolites derived from AA were shown to have beneficial effects for host health. Deamination and decarboxylation of glutamate, threonine, alanine, lysine, glycine, and aspartate produces short-chain fatty acids (SCFA; acetate, propionate, and butyrate) which have protective effects against infection and enhance the gut barrier function and immunity (12). The microbial catabolism of branched-chain AA (BCAA) releases branched chain fatty acids (isovalerate, isobutyrate, isocaproate, and 2-methylbutyrate) that can serve as an energy substrate for epithelial cells and promote the barrier function in vitro (12, 13, 33). Valerate, a bacterial metabolite derived from proline but also from propionate and ethanol, directly inhibits the growth of Clostridioides difficile but not of commensal bacteria (34). Decarboxylation of arginine and lysine produces the polyamines agmatine, spermine, and cadaverine, respectively (35). These metabolites influence mitochondrial function, epithelial proliferation, gut barrier function, and have trophic effects on the developing gut (35). However, the specific effects of gut microbiota-derived polyamines has not been clearly distinguished from those derived from the diet or from host cells and detrimental effects of polyamines have also been described (36). The histidine-derived metabolite histamine reduced the secretion of pro-inflammatory cytokines ex vivo (37). The gut microbiota also produces numerous catabolites from tryptophan, including indole, indole-3-propionate, indole-3-aldehyde (38). These bacterial metabolites have protective effects for the gut barrier since they reduce epithelial permeability and inflammation (38, 39) and can also contribute to the effects of the gut microbiota on the brain (40). Interestingly, neurotransmitters (GABA, histamine, serotonin, dopamine) which may have an important role in the gut-brain axis, can also be produced by the gut microbiota through AA catabolism (14). Thus, many AA-derived bacterial metabolites have protective effect on host health.

In summary, AA are used by intestinal bacteria in a species (or strain) specific manner, which highlights the potential of specific AA used as prebiotics for promoting the selective growth of beneficial over pathogenic gut microbes. Moreover, stimulating the production of protective AA-derived metabolites by the gut microbiota has the potential to mediate beneficial effects of AA used as prebiotics on host health.

Modification of dietary protein intake would be the most straightforward approach to modify AA supply to the gut microbiota. Increasing protein intake results in a larger amount of dietary protein reaching the distal part of the gut where the microbiota is mostly located (14, 41, 42). The digestibility and AA profiles of dietary protein also influences the availability of AA for the gut microbiota. In general, plant are less digestible than animal proteins and the biological value of the AA composition is commonly higher in the latter compared to the first (43). Modifying dietary protein intake in terms of quality and quantity can also change AA availability for the gut microbiota, which might have both detrimental and beneficial consequences for health (44, 45). It has been suggested in the literature that casein or whey protein, particularly rich in BCAA, could protect against obesity and modulate microbiota in humans and rodents. Similarly, lean seafood or meat with high amounts of aromatic acids, glycine, and taurine could be associated with increased energy expenditure, anti-obesogenic effect, and modulation of microbiota (44). It is also well described in the literature that high-protein intake has been associated with negative effects on gut health, such as inflammatory bowel disease in humans and postweaning diarrhea in piglets (46). In contrast, reducing crude protein level in piglet’s diets has been associated with reduced diarrhea score as reported in a recent meta-analysis (47). As discussed above, pathogenic, and commensal bacteria utilize AA in a specific manner and detrimental or protective metabolites are produced from AA by the gut microbiota. Thus, changing protein intake does not facilitate a targeted supply of AA to the gut microbiota to promote health. Alternatively, dietary supplementation with specific AA is a targeted approach with potential beneficial consequences for host health through a selective growth promotion of beneficial bacteria and through the production of protective metabolites.

Accumulating evidence is showing that dietary supplementation with free AA can modulate the microbiota composition and activity both in vitro (33) and in vivo (Tables 2–4). This is associated with consequences for the host as reported in mice and humans (Table 2), pigs (Table 3), and chickens (Table 4). Most studies reveal an effect of AA supplementation on the gut microbiota diversity or composition. Thus, the comparison between studies presented in Tables 2–4 does not reveal general trends regarding the effects of AA supplementation on the gut microbiota. The divergence of the results obtained after AA supplementation can be explained by multiple differences between studies including the AA tested, host species, gut segment, dose, and duration of AA supply and exposition or not to an inflammatory or infectious challenge. It is interesting to notice that some effects of the AA supplementations were observed in the large intestine, despite that free-AA are anticipated to be absorbed mostly in the upper part of the intestine. It can be hypothesized that a high level of free-AA might temporally overwhelm the absorptive capacity of the small intestine. A surprising observation is that no linear dose-dependent effects were observed on the microbiota in studies testing the same AA at different level of supplementation (Table 3). Thus, further studies are clearly needed to define more clearly what are the effects of AA supplementation on the gut microbiota. This future work should help determine which AA have the most favorable effects on the gut microbiota and what is the effective level of supplementation. In addition, only few studies presented in Tables 2–4 have investigated the effects of AA supplementation on the production of AA-derived metabolites, the latter being potentially more predictable than the effects on the composition of the microbiota due to functional redundancy (i.e., different bacterial communities can express similar metabolic capabilities).

The evaluation of host parameters focused on intestinal barrier function, immunity and metabolism revealed modulations associated with the modification of the gut microbiota induced by AA. However, it is not clear yet if these modifications at the gut level are beneficial for the host, which is a requirement to fulfill the definition of prebiotics. In farm animals, the effects of AA supplementation on the microbiota were associated with either no or beneficial effects on growth performance. An important perspective will be to demonstrate that the modulation of the gut microbiota by AA is directly involved in the effect observed at the host level.

The potential synergistic effect of AA supplementation with probiotics has been investigated. Probiotics are “live microorganisms which when administered in adequate amounts confer a health benefit on the host” (46). Combining AA and probiotics corresponds with the concept of “symbiotic” which is “a mixture comprising live microorganisms and substrate(s) selectively utilized by host microorganisms that confers a health benefit on the host” (48). One potential mechanism is that AA could promote the survival of the exogenous microbial species (i.e., the probiotic) in addition of being used as substrates for their growth. For instance, the catabolism of glutamine has been shown to improve the acid tolerance of Lactobacillus (49, 50). Therefore, the association of glutamine and the probiotic bacteria L. plantarum was expected to increase its survivability and thereby improve its positive effect on gut health. Accordingly, the authors showed that the combination of glutamine (1–4 mM) and L. plantarum decreased the translocation of E. coli in weanling rabbit ileal loops (51). They observed a synergistic effect indicating that the provision of the two compounds (AA and probiotics) together was more efficient than the anticipated sum of effects resulting from each compound alone. Other studies investigated the effects of the combination of arginine and Lactobacillus in rats with acute liver injury. The authors showed that the co-administration of L. plantarum and arginine reduced the hepatocellular necrosis and inflammatory cell infiltration, whereas the effect of individual administration of probiotics or arginine alone had lower effects than the two together (52). The potential mechanism of this synergistic effect may involve the metabolization of arginine by L. plantarum into polyamines, nitric oxide or its utilization as an energy source. Another study showed that a supplementation with L. plantarum and arginine 10 days before an LPS-challenge induced a synergistic reduction of liver damage and inflammation (53). The authors hypothesized that probiotics could direct arginine toward polyamines rather than NO synthesis by decreasing inflammation level and promoting cell proliferation and healing in the liver (53). Altogether, these results suggest that symbiotics composed of AA and probiotics have the potential to promote health to a larger extent than the simple sum of both dietary supplements alone. Multiple combination of probiotics and AA should be tested in future studies, notably by selecting the most promising association based on the capacity of the probiotic strain to metabolize specific AA (Table 1).