Introduction
This article analyzes the concept of the holobiont, in which an animal and its microbiome form a single, inseparable biological unit. Rather than searching for individual "good" bacteria, the text proposes viewing health as the functional balance of an entire ecosystem.
The reader will discover how permeable the boundaries are between an organism and its environment. They will also learn why anthropocentric models for assessing bacterial flora fail when applied to dogs and cats, and how diet and surroundings govern animal immunity.
The Avian Microbiome as an Open Exchange System
In industrial farming, the avian microbiome is an open system. Chicks, separated from their parents, are colonized by microorganisms found in feed, water, and hatchery surfaces.
A key role here is played by competitive exclusion. This process involves the rapid colonization of niches by desirable bacteria, which blocks access for pathogens such as Salmonella or Campylobacter.
This system encompasses not only the intestines but also the respiratory tract and feathers. Bacteria and resistance genes (resistome) circulate in a loop between the bird and its environment, making the poultry house a micro-scale model of One Health.
Efficiency and Health as a Result of Functional Ecosystem Balance
Animal health does not depend on the presence of specific strains, but rather on the stability of functions. An example is short-chain fatty acids (SCFAs), including butyrate, which supports the intestinal barrier.
Supplementing metabolites or single bacteria alone does not guarantee high performance or immunity. The feed conversion ratio (FCR) is a result of intestinal ecology, not the presence of a single "super-bacteria."
Dysbiosis is not always the direct cause of disease, but rather a signal of lost resilience. Pathologies, such as necrotic enteritis, develop only when multiple environmental and nutritional factors overlap.
Litter as an External Ecological Organ of the Flock
Litter is not a dead substrate, but rather an "external organ" of the flock. It is a reservoir of microorganisms and resistance genes that directly shapes the intestinal and respiratory microbiomes of the birds.
It affects health through the emission of ammonia (NH₃), which damages the respiratory epithelium. Conversely, microbiologically mature litter can paradoxically support chick immunity by providing a complex flora.
This dependency shows that the boundary of an organism is negotiable. Managing the moisture and pH of the substrate is, in reality, managing the metabolism of the entire holobiont, which directly translates to food safety.
Summary
If microorganisms do not recognize human divisions between what is domestic, wild, or sterile, where exactly does the biological unit end? A dog, cat, or fish are nodes in a vast network of genetic exchange.
Humans cease to be external observers of nature. They become part of a shared, permeable ecosystem in which every breath and touch is an act of microbiological negotiation.
Frequently Asked Questions
How is the microbiome of a bird in industrial farming shaped and how does it interact with its environment?
The microbiome of a bird in industrial farming is shaped through the rapid succession of microorganisms that the chick acquires from feed, water, litter, as well as surfaces in the hatchery and during transport. The bird functions as an open system, constantly exchanging microbes with the environment and other individuals via the beak, skin, feathers, and respiratory tracts.
1. Does the presence of specific bacteria or supplementation with metabolites guarantee health and high performance in animals?
2. No, the presence of specific bacteria or supplementation with a single metabolite does not guarantee animal health and performance. High productivity depends on many factors (including genetics, feed, and husbandry systems), and the mere presence of a given bacterium does not ensure an appropriate level of its products nor replace the natural microbiological network.
3. How does the external environment, e.g., bedding, affect the health and microbiome of animals?
4. The external environment, including bedding, serves as a reservoir of pathogens and a source of complex microbiota that influences the development of animal cecal communities. Dust from bedding carries microorganisms into the respiratory system, and ammonia released from it can damage the respiratory epithelium and conjunctiva, increasing susceptibility to infections.
5. How do the farm environment and the surface biology of birds influence the development of fungal infections and the spread of resistance genes?
6. Damp bedding, contaminated feed, dust, and intensive farming increase birds' exposure to fungal spores and promote infections. The farm environment may participate in the selection of azole-resistant fungi, and poultry litter can contain an extensive set of antibiotic resistance genes (ARGs) for numerous antibiotics.
7. How do bacteria and resistance genes move between animals and the external environment?
8. Bacteria and resistance genes enter the environment, among other things, through the use of manure-containing bedding as fertilizer, which enables their transfer to the soil. They are also transported by wild birds, which, living in anthropogenic environments, become AMR reservoirs and can subsequently spread these traits during migration.
9. Can a dog's microbiome composition be assessed based on human patterns, and is there one ideal ancestral diet model?
10. A dog's microbiological health cannot be assessed based on human patterns because evolution has created a different biological niche for dogs. There is no single ideal ancestral diet model, as the process of domestication and co-evolution with humans has led to genetic differences in starch digestion depending on the population.
Does the composition of the dog's microbiome depend on the breed, and how do changes in its structure affect the course of intestinal diseases?
Breed may be one of the factors differentiating the composition of the dog's microbiome, even with a similar diet and environmental conditions. In the course of intestinal diseases, changes in the microbiome structure lead to functional dysbiosis, manifested by lower bacterial diversity and disruption of chemical pathways, such as butyrate production or bile acid metabolism.
Does the presence of bacteria such as Staphylococcus pseudintermedius on a dog's skin always indicate disease?
No, the presence of S. pseudintermedius on a dog's skin does not always indicate disease, as it is a common inhabitant of the skin and mucous membranes. This bacterium may transition from commensalism to pathogenicity only under appropriate conditions, e.g., when the skin barrier is damaged.
How do the dog-human relationship and the home environment illustrate the concept of the holobiont?
The dog-human relationship illustrates the concept of the holobiont through the sharing of the microbiome, particularly on the skin, making the home a shared microbiological field. The dog acts as a "microbiological ferry," transporting microorganisms between the external environment and humans, meaning that the biological unit is no longer ecologically closed.
Why is the cat a difficult subject for microbiome science, and how does its metabolism differ from that of omnivores?
The cat is a difficult research subject because, as an obligate carnivore, it deviates from models developed for humans and omnivorous animals. Its metabolism differs from theirs due to the constant activity of amino acid metabolizing pathways and a limited ability to synthesize key substances such as taurine or arginine.
How does a cat's diet affect the composition and functioning of its microbiome?
Diet modifies the intestinal environment, influencing the composition and functions of the microbiome through the provided substrates. High protein intake shifts metabolism toward proteolytic fermentation, while a diet richer in easily fermentable carbohydrates increases the significance of microorganisms that utilize these compounds.
Why is the presence of specific bacteria or high levels of metabolites not sufficient indicators of an animal's health?
The impact of bacteria and metabolites on the organism depends on many factors, such as their site of origin, bioavailability, or absorption. A higher level of a given substance does not always mean improved health, as it may result from, for example, lower absorption rather than increased production.
Are changes in the composition of gut and skin bacteria in cats a direct cause of diseases, and can they be permanently repaired?
There is no confirmed evidence that changes in the microbiome are a direct cause of diseases; they may create an environment conducive to the development of enteropathy or lymphoproliferative processes. There is no universal method for permanent ecosystem repair, as the effects of probiotic support depend on the specific strain, disease, and context.
Does greater microbiome diversity in free-living animals always mean better health, and are there universal bacterial composition patterns for all species?
Greater microbiome diversity in free-living animals does not always mean better health, as it is associated with exposure to pathogens, parasites, and toxins. There are no universal bacterial composition patterns for all species, since host physiology takes precedence over statistics, and the same ratio of bacteria can have different meanings in different animals.
How do ambient temperature and diet affect the microbiome of poikilothermic animals?
Ambient temperature affects the rate of enzymatic reactions of microorganisms and modifies digestion time, content passage, and substrate availability, which may give an advantage to certain bacterial species or lead to microbiota destabilization. Diet determines the composition of the microbiome; an example is Iguanidae, which have developed a dependence on microorganisms that break down complex polysaccharides in a specialized hindgut fermentation system.
Is there a universal bacterial core in reptiles, and what determines the composition of their microbiome?
There is no single universal bacterial core for reptiles, as comparisons between different species show enormous variability. The composition of the microbiome is primarily determined by dietary niches and diet, as well as evolutionary factors.
How do animals acquire the necessary microbiome, and is it possible to recover it after a period of captivity?
Young animals, such as green iguanas, acquire the necessary microbiome through contact with soil microorganisms and coprophagy, which is the consumption of feces from older individuals. The microbiome can be recovered after a period of captivity; returning to the natural environment can trigger the process of ecological reconstruction of the microbiota.
Does a change in the composition of gut bacteria following a dietary change always signify the destruction of the microbiome and disease?
No, changes in the microbiome due to diet are an expected phenomenon and can be adaptive in nature. Pathology occurs only when these changes lead to a permanent loss of function, impaired resilience, or negative consequences for the host.
Why is protecting the animal's DNA alone not enough to preserve a species, and how does the environment (especially aquatic) influence this relationship?
Protecting DNA alone is not sufficient because preserving a species requires maintaining functional relationships with the microbiome, which enables processes such as food digestion. In aquatic environments, this dependency is particularly strong, as animals live within an active microbiological ecosystem, and their gills and skin remain in constant contact with a medium that influences their microbiota.
Is there one ideal composition of gut bacteria for all farmed fish?
There is no single, ideal gut microbiome profile for all farmed fish. This is due to biological differences between species, such as diet (e.g., herbivorous tilapia vs. carnivorous salmon), the structure of the digestive tract, and environmental salinity.
Is there a universal set of beneficial bacteria for fish and crustaceans?
Creating a universal list of beneficial bacteria is problematic due to differences in farming temperatures, species, and the diversity of microbiomes within a single organism. The composition of microorganisms depends on many factors, such as diet, environment, and host homeostasis, and some genera of bacteria (e.g., Vibrio) include both beneficial and pathogenic strains.
How does feeding fish larvae affect their microbiome, and why are traditional probiotics in aquaculture sometimes ineffective?
Live feed serves as an inoculation vector, transporting microorganisms from the water to the gastrointestinal tract of the larvae and influencing their initial microbial colonization. Traditional probiotics can be ineffective under field conditions due to inconsistent results depending on various factors such as strain, dose, host species, or environmental parameters.
In modern animal husbandry, is the pursuit of complete sterility and biosecurity beneficial for their health and performance?
The pursuit of complete sterility is not beneficial because systems such as RAS rely on the activity of microorganisms responsible for purifying water from toxic nitrogen compounds. Instead of sterility, the goal should be controlled ecological stability, as the total elimination of microbes would prevent the system from functioning properly.
Do animal health and performance depend on the presence of specific bacterial strains?
No, the mere presence of a specific microorganism does not determine its significance. Function and health result from the relationship between the host, the microbial community, available substrates, and environmental conditions.
