An Introduction to the Microbiota

What is the Microbiota?

The collection of living microorganisms (bacteria, fungi, protozoa and viruses) that inhabit a specific environment are referred as the microbiota or microbiome, (the latter referring to the microorganisms and their genes) and are terms which now supersede the outdated ‘microflora’.

The microbes occupying habitats such as gut, skin and the urogenital tract differ remarkably between and within species. Even within the same habitat variations can occur, with different bacterial populations existing at different skin sites on the same animal.[1] However despite these variations, there does appear to be a core bacterial community, demonstrated by the canine intestinal microbiota which is dominated by three main phyla (Fusobacterium, Bacteroidetes, and Firmicutes)[2]. However, the relative abundance of each taxa can be extremely variable and reflects the microenvironment of the gastrointestinal tract location which is dictated by factors such as pH, oxygen, motility, lumen patency and presence of bile acids.[3] Other external factors such as diet, environment, season, host genetics and even early microbial exposure have all been implicated in the development of the microbiota.

These microbes form complex and dynamic associations with humans, animals and plants that range from mutually beneficial to commensal or pathogenic.

Mutually Beneficial Organisms

Mutually beneficial organisms are organisms from two different species that exist together and each provides the other with some benefit from their individual activity. An example of this would be Ruminococcus, a cellulose-digesting bacteria present in herbivores: the host provides these bacteria with a constant supply of nutrients (from fibre), and in return the bacterial products of digestion (primarily glucose) supply the host with energy and nutrition from a food source they would otherwise be unable to utilise.

Commensal Organisms

Commensal organisms are those that benefit from the host without affecting the host in any way (positively or negatively). This term is, however, controversial amongst many biologists who do not truly believe that an organism can ‘take’ from another organism without exerting any change at all; this theory promotes the idea that all commensal organisms must have some mutualistic or parasitic effect on the host, no matter how subtle or small that effect may be.

Interestingly, some commensal organisms can become pathogenic if the environment becomes more favourable to that specific organism at the expense of other ‘competitors’. An example of this would be Staphylococcus pseudintermedius in dogs with atopic dermatitis. S.pseudintermedius is part of a healthy canine skin microbiota yet under certain conditions, such as reduced skin barrier function and inflammation, these commensal organisms can proliferate to abnormal levels thereby contributing to the disease process.

This imbalance to the normal, diverse equilibrium of micro-organisms is termed a dysbiosis.[4][5]

Pathogenic or Parasitic Organisms

Pathogenic or parasitic organisms are those that will gain some benefit from the host but simultaneously cause some degree of harm in the process. The microbiota provides protection against colonisation by these pathogenic microorganisms through a number of complex mechanisms, however occasionally organisms can override this microbial barrier, out-competing the commensal community resulting in infection or disease.[6] Factors such as antibiotic administration can reduce colonisation resistance against pathogens[7], and germ- free mice have shown a greater susceptibility to epithelial injury in induced colitis.[8] Thus, the importance of a harmonious and diverse microbiota in preventing the proliferation of pathogenic species and driving normal gut development is widely accepted.

Mammalian Microbiota

The mammalian microbiota is comprised of 10-100 trillion microbial cells, outnumbering host cells by 10 to 1 and in humans adding over 8 million genes to our set of 22,000. Our understanding of the microbiota it still in its infancy, however its huge impact on host physiology is clear and the symbiotic relationship that exists between the host and microbiota has led to a new paradigm in our consideration of this system; is the microbiota actually a ‘virtual organ’ in its own right?

In Partnership With Protexin Veterinary

Author: Pippa Coupe BVSc MRCVS, Veterinary Product Manager at Protexin Veterinary. Protexin Veterinary is a brand of ADM Protexin Ltd

Read more

Development of the Microbiota

Functions of the Microbiota


Canine and Human Microbiome

The Microbiota and Antibiotics


  1. Cuscó A, Belanger JM, Gershony L. et al. Individual signatures and environmental factors shape skin microbiota in healthy dogs. Microbiome 2017; 5:139
  2. Pilla R, Suchodolski JS. The Role of the Canine Gut Microbiome and Metabolome in Health and Gastrointestinal Disease. Front Vet Sci 2020;14(6):498
  3. Gorkiewicz G, Moschen A. Gut microbiome: a new player in gastrointestinal disease. Virchows Archiv 2018; 472(1):159–172
  4. Older CE, Rodrigues Hoffmann A, Hoover K, Banovic F. Characterization of Cutaneous Bacterial Microbiota from Superficial Pyoderma Forms in Atopic Dogs. Pathogens 2020; 9(8):638
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  8. Hernández-Chirlaque C, Aranda CJ, Ocón B et al. Germ-free and Antibiotic-treated Mice are Highly Susceptible to Epithelial Injury in DSS Colitis. Journal of Crohn's and Colitis 2016; 10(1):1324–1335