Introduction
Modern veterinary medicine is undergoing a transformation, moving from treating isolated anatomy toward an ecosystem-based approach to medicine. Central to this shift is the concept of the holobiont, in which the animal and its microbiome constitute an inseparable whole.
The reader will discover how the invisible architecture of bacteria is redefining nutritional value and public health. This article analyzes the impact of metagenomics on the fight against antimicrobial resistance through the lens of One Health.
Understanding these dependencies allows for a transition from intuitive drug administration to the precise management of the biological balance between the organism and its environment.
The Biological Value of Feed Depends on the Gut Ecosystem
Simply balancing nutrients in feed does not guarantee health, as food is primarily a landscape of resources for microorganisms. These microbes determine whether a substrate is absorbed by the host or converted into a metabolically costly product.
Nutritional paradoxes illustrate this dependency: in dogs, evolutionary adaptation to starch varies between individuals, while in cats, obesity does not correlate with a single universal bacterial marker. The microbiome can even steer an animal's appetite via the gut-brain axis.
Biological value is therefore variable and dependent on ecological context, rather than solely on the chemical composition of the feed.
The Paradox of Standardization vs. Functional Microbiome Resilience
Industrial diets may homogenize the microbiome, but they do not always deplete it. Wild animals often possess greater functional potential and resilience, although they are more exposed to pathogens and toxins.
High bacterial diversity is not synonymous with health; what matters is the stability of function rather than the number of species. A pitfall of commercial sequencing tests is their focus on descriptive dysbiosis rather than causal mechanisms.
Overly sterile environments and standardization can weaken an organism's ability to respond to disturbances, making raw diets a risky compromise between naturalness and safety.
Low Metabolic Efficiency and the Microbiome's Influence on Nutritional Choices
The microbiome drastically influences metabolism—for example, in the rumen of ruminants, where a significant portion of dietary protein is wasted and converted into ammonia. This demonstrates low nitrogen conversion efficiency.
Modern medicine intervenes in this system through antibiotics, leading to the creation of the resistome—a pool of resistance genes. Bacteria transfer these genes beyond classical inheritance by utilizing the mobilome (plasmids, transposons).
The cost of antibiotic therapy is not just the price of the drug, but the loss of therapeutic efficacy on a global scale. This necessitates a shift toward microbiome engineering: moving from probiotics and prebiotics, through postbiotics, to precise bacterial consortia and bacteriophages.
Summary
Animal health within the One Health model is a dynamic equilibrium between the host, the microbiome, and the environment. An animal is not a closed entity, but a relational system of information and gene flow.
The role of the veterinarian is evolving from a physician of anatomy toward an ecosystem manager. Every clinical decision becomes an ecological intervention with a reach that extends beyond the patient's skin.
Ultimately, treating a single individual is the management of an invisible network of connections that cannot be described in isolation from the rest of the world.
Frequently Asked Questions
How does the circulation of resistance genes in the environment influence the approach to antibiotic use in veterinary medicine?
What is microbiome engineering, and how does it differ from traditional probiotic administration?
Do industrial diets and domestic conditions deplete the microbiome of animals compared to their wild counterparts?
The research results are inconclusive; in some species, microbiome diversity decreases, while in others it increases or remains at a similar level. Wild animals may exhibit greater functional potential of the microbiome, yet industrial diets and domestic conditions simultaneously protect them from parasites, toxins, and deficiencies.
What specific paradoxes in animal nutrition demonstrate that the microbiome influences the host's health and metabolism?
Paradoxes include, among others, the inefficient nitrogen cycle in cattle, where expensive protein is microbiologically converted into ammonia and excreted as urine, and the situation of horses, where excess starch in the large intestine leads to acidification and a risk of colic or laminitis. Additionally, the influence of the microbiome on behavior was highlighted, confirmed by studies on mice in which the type of inhabiting microbiota changed food preferences regarding protein and carbohydrate proportions.
How does the microbiome influence an animal's food choices, and why does the chemical composition of the diet alone not determine the nutritional effect?
The microbiome influences animals' food choices by creating a regulatory loop in which bacterial metabolites and hormonal signals act on the nervous system and the gut-brain axis. The chemical composition of the diet does not determine the nutritional effect because the same substance can be processed differently depending on the specifics of the host's metabolism and the activity of the microbiome.
How can modern medicine influence the microbiome, and what are the ecological consequences of using antibiotics?
Modern medicine can influence the microbiome by designing it using prebiotics, synbiotics, postbiotics, bacterial community transplants, or bacteriophages, as well as through the use of antibiotics. Antibiotics act as a tool for restructuring the ecosystem and abruptly change selection conditions, leading to the elimination of sensitive microorganisms and facilitating the expansion of resistant variants.
How do bacteria transmit antibiotic resistance beyond classical inheritance?
Bacteria transmit antibiotic resistance through horizontal gene transfer, utilizing mechanisms such as conjugation (direct DNA transfer), transformation (uptake of DNA from the environment), and transduction (transfer via bacteriophages). Plasmids play a key role; as mobile technological packages, they can carry multiple resistance genes simultaneously between different cells and bacterial species.
What is the actual cost of using antibiotics in veterinary medicine beyond the direct therapeutic effect?
The actual cost is a profound disruption of the microbiome, including the loss of key bacteria and changes in bile acid metabolism, which can persist long after treatment. Additionally, the use of antibiotics increases the shedding of resistance genes, generating an external social cost in the form of the risk of losing the effectiveness of entire classes of therapies.
How does the circulation of resistance genes in the environment influence the approach to antibiotic use in veterinary medicine?
The circulation of resistance genes within the animal-environment-human system requires a One Health approach, placing greater emphasis on prevention and surveillance across different sectors. In veterinary medicine, this means using antibiotics only when the therapeutic benefit outweighs the ecological cost, while simultaneously implementing vaccinations, biosecurity, and diagnostics.
What is microbiome engineering and how does it differ from traditional probiotic administration?
Microbiome engineering is the precise management of the microorganism community using tools such as probiotics, prebiotics, postbiotics, bacteriophages, or FMT. Unlike traditional probiotic administration, which involves introducing a living organism with desired properties, engineering aims to design the ecosystem by strengthening specific metabolic functions and creating an advantage for selected groups of bacteria.
What are the differences between probiotics, prebiotics, and synbiotics in terms of their practical impact on the animal microbiome?
Probiotics introduce executors of specific functions into the body, while prebiotics are substrates that alter resources within the ecosystem to support already present microorganisms. Synbiotics combine both elements, providing live microorganisms along with a suitable substrate for them.
What are the alternatives to administering live probiotics, and is whole-microbiome transplantation an effective solution?
Alternatives to live probiotics are postbiotics—preparations of non-viable microorganisms or their components, which can be more stable and easier to standardize. On the other hand, fecal microbiota transplantation (FMT) is not unequivocally an effective solution, as alongside positive effects, cases of minimal impact or even deterioration of intestinal development or weight loss have been reported.
What are the limitations of fecal microbiota transplants (FMT) and what more modern engineering alternatives does contemporary veterinary medicine offer?
The limitations of FMT include the risk of transferring undesirable microorganisms and resistance genes, as well as a lack of guarantee regarding the ecological compatibility of the donor microbiome with the recipient. Modern alternatives include synthetic communities (SynComs), which are precisely selected consortia of strains, as well as the use of bacteriophages and endolysins for the selective targeting of pathogens.
What are the modern methods of shaping animal microbiomes beyond standard feed supplementation?
Modern methods include phage therapy requiring precise diagnostics and microbiome-informed breeding aimed at animals with beneficial microbiological profiles. Other approaches include interventions in the early stages of an animal's life to shape the trajectory of microbiome development, as well as environmental modifications, such as biofilters and bioflocs in aquaculture.
What safety requirements and legal regulations apply to the use of microorganisms as feed additives in veterinary medicine?
Regulations require precise strain identification, virulence assessment, and genomic analysis for safety and antimicrobial resistance (AMR). As of April 1, 2026, documentation for feed additives must comply with new EFSA guidelines, which emphasize genomic traceability and the risk assessment of organism persistence in the environment.
Why don't we simply replace antibiotics with probiotics, and what are the real challenges in implementing microbiome engineering?
Antibiotics are cheaper, easier to apply, and better understood technologically than probiotics, which require costly production under controlled conditions and the maintenance of viability. Real challenges in microbiome engineering include difficulties in standardization, variable efficacy of preparations, and the need to introduce advanced diagnostics of the ecosystem state prior to intervention.
Why does high bacterial diversity in an animal's microbiome not always indicate better health, and what are the pitfalls of commercial sequencing tests?
High bacterial diversity does not always mean better health because quantitative indicators do not provide information about community functions, metabolic stability, or inflammatory potential. The pitfall of commercial sequencing tests is the lack of comparability of results between different platforms, as well as the limited clinical utility and validation of the obtained data.
Is the use of natural probiotics and raw diets safe for animals and humans?
The use of natural probiotics can be risky due to frequent label inconsistencies and the presence of antibiotic resistance genes. Raw diets are associated with a documented risk of bacterial and parasitic infections, and may also lead to the transmission of pathogenic bacteria from animals to humans.
Does the presence of specific bacteria in the body always indicate disease, and does the term 'dysbiosis' explain the cause of inflammation?
The presence of specific bacteria does not always indicate disease, as many microorganisms can be commensal in one niche and pathogenic in another. The term "dysbiosis" is merely a description of differences in the microbiome rather than an explanation for the cause of inflammation, as it does not determine whether the change in the microbiome is the cause, the effect, or an adaptation.
What are the main risks and pitfalls in the practical application of microbiome knowledge in veterinary medicine and livestock breeding?
The main risks include over-optimizing the microbiome for efficiency, which can increase animals' susceptibility to stress and infections, as well as mistakenly equating statistical correlations with actual mechanisms of action. Another pitfall is the pursuit of completely replacing antibiotics with biological preparations, whereas in severe disease states, these drugs remain an essential life-saving therapy.
Why is the traditional veterinary approach focused on the anatomy of the individual currently insufficient?
The traditional approach is insufficient because many bodily functions, such as digestion or immune regulation, are performed by a microbiome that transcends the physical boundary of the body. Furthermore, drugs and resistance genes affect entire microbial communities that circulate between the animal and the environment, necessitating a transition to the holobiont model and ecosystem medicine.
How are the One Health concept and microbiome research changing the approach to animal health and welfare on a global scale?
The One Health concept recognizes the close interdependence between human, animal, and ecosystem health, moving away from treating animals merely as reservoirs of threats toward recognizing the value of their own health. Microbiome research complements this approach by highlighting continuous biological flows across administrative boundaries and introducing the concept of resilience, which links microbiological functions with animal welfare.
How does microbiome research influence the ethics of animal use in science?
Microbiome research supports the 3Rs principle by implementing alternative methods (e.g., organoids, gut-on-chip), reducing the number of animals through better experimental design, and using non-invasive sampling techniques. At the same time, it is emphasized that a lack of methodological rigor in multi-omic studies is unethical, as it leads to waste and unnecessary animal suffering.
What ethical and regulatory risks and challenges are associated with introducing synthetic microbial communities into animal organisms?
The main risks include horizontal gene transfer, lack of ecological stability, and the risk of microorganism evolution, which may lead to the loss of planned functions or unforeseen interactions with the environment. Regulatory challenges include the need to assess the evolutionary trajectory of products, analyze actual genetic equipment for virulence and antibiotic resistance, and reconcile the conflicting interests of consumers, breeders, and environmental protection.
Does a systemic and ecological approach in veterinary medicine lead to the neglect of treating a specific, suffering animal?
No, the systemic approach is an extension of clinical responsibility, not its dilution. Ecosystem medicine does not replace individual care but combines the treatment of a specific animal with environment and population management.
How is the definition of animal health and the role of the veterinarian changing in light of the holobiont and One Health concepts?
Animal health is defined as the ability of the host-microbiota-environment system to maintain functions, control inflammation, and adaptively recover balance. The role of the veterinarian is evolving toward ecosystem medicine, where decision-making requires awareness of systemic ecological effects and collaboration with other specialists.
What is an animal in light of modern biology and metagenomics, and how should this change the approach of veterinary medicine?
Modern biology defines an animal as a holobiont—a dynamic regulatory system in which the host genome coexists with the microbiome and the environment. Consequently, veterinary medicine must become simultaneously more molecular and ecological, treating the organism not in isolation, but as a whole inextricably linked to its surroundings.
