Falcon gut microbiota is shaped by diet and enriched in Salmonella

Abstract

The gut microbiome is increasingly being appreciated as a master regulator of animal health. However, avian gut microbiome studies commonly focus on birds of economic importance and the gut microbiomes of raptors remain underexplored. Here we examine the gut microbiota of 29 captive falcons—raptors of historic importance—in the context of avian evolution by sequencing the V4 region of the 16S rRNA gene. Our results reveal that evolutionary histories and diet are significantly associated with avian gut microbiota in general, whereas diet plays a major role in shaping the falcon gut microbiota. Multiple analyses revealed that gut microbial diversity, composition, and relative abundance of key diet-discriminating bacterial genera in the falcon gut closely resemble those of carnivorous raptors rather than those of their closest phylogenetic relatives. Furthermore, the falcon microbiota is dominated by Firmicutes and contains Salmonella at appreciable levels. Salmonella presence was associated with altered functional capacity of the falcon gut microbiota as its abundance is associated with depletion of multiple predicted metabolic pathways involved in protein mass buildup, muscle maintenance, and enrichment of antimicrobial compound degradation, thus increasing the pathogenic potential of the falcon gut. Our results point to the necessity of screening for Salmonella and other human pathogens in captive birds to safeguard both the health of falcons and individuals who come in contact with these birds.

Detection of Salmonella Reservoirs in Birds of Prey Hosted in an Italian Wildlife Centre: Molecular and Antimicrobial Resistance Characterisation

“…This change can already occur after a month of direct contact between animals and humans, and the diet, especially if based on raw food, represents the first determining causal factor [ 39 , 40 , 41 ]. Some studies have shown that birds of prey fed poultry meat develop a wider range of Gram-negative bacterial flora [ 38 ]; in particular, a study on falcons has shown that the diets most commonly fed to these birds increase the levels of Salmonella in the intestinal flora [ 42 ].…”

Antimicrobial Resistance and Virulence Potential of Bacterial Species from Captive Birds of Prey—Consequences of Falconry for Public Health

“…Captivity is presently known to affect gut and oral microbiome diversity in birds of prey when compared to their wild counterparts, with observable changes within just one month of direct human contact, and diet is being pointed to as the main factor responsible for alterations in the oral microbiome [ 60 , 61 , 62 , 63 , 64 , 65 ]. For example, studies have shown that birds who are fed chicken are linked to a wider diversity of Gram-negative bacteria [ 66 ], and that the diet commonly provided to captive animals increases the levels of Salmonella in falcons [ 65 ]. Some other factors responsible for altering the microbiome in birds of prey are also shown in Figure 1 .…”

“… Some variables suspected to alter the microbiome of birds of prey in captivity: contact with wildlife; direct contact with human and animal waste; contact with synanthropic species; contact with domestic waterfowl; contact with other pet birds; diet; and previous exposure to antibiotics. Based on [ 25 , 27 , 32 , 33 , 34 , 35 , 36 , 60 , 61 , 62 , 63 , 64 , 65 ] and created using BioRender ( ). …”

“…Moreover, more studies are required to confirm the importance of captive birds of prey in resistant bacteria dissemination, as the information available is still scarce. Based on [25,27,[32][33][34][35][36][60][61][62][63][64][65] and created using BioRender (https://www.biorender.com/).…”

“…All leftover food should be removed at least once daily, ideally at the same time as water changes are also performed [94]. As previously mentioned, food can be an important vector of pathogenic bacteria and should always be checked for contamination and spoilage before storage, and good hygiene practices should be applied when meal prepping to avoid cross-contamination [64,65,96].…”