What is the microbiome and microbiota?
The microbiota refers to the collection of microorganisms (bacteria, fungi, protozoa and viruses) that inhabit a specific environment. The term microbiome refers to the microorganisms, their genes and “theatre of activity” (eg metabolites, structural elements) and has superseded the outdated term “microflora” (Figure 1).
The gut, skin and urogenital tract harbour their own microbiomes which are remarkably different from each other. Further, variation is seen between species, or even within the same species or individual. The skin microbiome can feature different bacterial populations in the same animal depending on the body location tested (Cuscó et al., 2017). Despite these variations, there does appear to be a core bacterial community found within the majority of healthy individuals which is generally stable over time. The canine intestinal microbiome, for example, is dominated by three main phyla (Fusobacteriota, Bacteroidetes and Firmicutes) (Pilla and Suchodolski, 2020).
The gut, skin and urogenital tract harbour their own microbiomes which are remarkably different from each other
What factors can impact the microbiome?
Within the gastrointestinal tract, microbiome composition is affected by the local microenvironment which is determined by factors such as pH level, oxygen availability, motility, lumen patency and the presence of bile acids (Gorkiewicz and Moschen, 2018). For example, anaerobic bacteria are found in their greatest numbers in the large intestine where oxygen levels are low, compared to the proximal small intestine where oxygen is more readily available. The composition of the microbiome is also influenced by external factors such as diet, lifestyle, environment and even seasonality, as well as internal factors such as host immunity, genetics and early microbial exposure. This becomes increasingly relevant when different microbiome compositions in individuals born via caesarean section compared with vaginal delivery have been evidenced, with the former lacking certain commensal bacteria important in the development of immunity.
Are there “good” and “bad” bacteria?
To some degree, the functionality of a particular bacterial species within the microbiome is not black and white, but can be influenced by several factors including the abundance/presence of other bacterial species, the microenvironment they reside within and the immunity of the host. Therefore, the assignment of labels such as “good” or “bad” to bacteria may be too simplistic. Despite this, there are certain bacterial species that are generally considered to have beneficial roles on host health as well as those which are known pathogens.
the functionality of a particular bacterial species within the microbiome is not black and white, but can be influenced by several factors including the abundance/presence of other bacterial species, the microenvironment they reside within and the immunity of the host
What are mutually beneficial organisms?
Mutually beneficial organisms are organisms from two different species that exist together, each providing the other with some benefit from their individual activity. For example, Ruminococcus is a cellulose-digesting bacteria, which exists within the microbiome of many herbivores, and is vital in allowing these animals to extract nutrients and energy (primarily glucose) from otherwise undigestible fibres. In return, the host provides a continual supply of fibre through grazing.
Commensal organisms
Commensal organisms are those that benefit from the host without affecting the host in any way (positively or negatively). However, this term is controversial among 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.
Occasionally, should the environment become more favourable to a specific commensal organism, they may have the ability to increase in abundance at the expense of other “competitors”. For example, S. pseudintermedius is part of a healthy canine skin microbiome, yet under certain conditions, such as reduced skin barrier function and inflammation, it can proliferate to abnormal levels and cause a secondary pyoderma, something that is seen relatively commonly in canine atopic dermatitis. Any imbalance or disruption of the normal microbiome equilibrium is termed a dysbiosis (Older et al., 2020; Hata and Gallo, 2008).
What are pathogenic organisms?
the microbiome has been shown to be very important in the normal development of the gastrointestinal tract, with germ-free mice reported to have poor capillary development in their intestinal villi, which can be reversed by faecal microbial transplantation
Pathogenic or parasitic organisms are those that will gain some benefit from the host but simultaneously cause some degree of harm in the process. A normal, healthy microbiome does contain pathogenic bacteria (eg E. coli); however, numbers of these bacteria are kept under control by commensal organisms through competition for nutrients, space and binding sites (termed competitive exclusion), as well as direct inhibition through the production of bacteriocins. In certain situations, pathogenic organisms can override this protective microbial barrier and out-compete the commensal community resulting in infection or disease (Rolhion and Chassaing, 2016). Antibiotic administration can have devastating effects on the commensal community, reducing colonisation resistance and allowing pathogens to thrive (Kennedy et al., 2008). Furthermore, the microbiome has been shown to be very important in the normal development of the gastrointestinal tract, with germ-free mice reported to have poor capillary development in their intestinal villi, which can be reversed by faecal microbial transplantation (Stappenbeck et al., 2002).
Summary
The mammalian microbiome comprises between 10 and 100 trillion bacterial cells, outnumbering host cells by approximately 3 to 1, and in humans adding over 8 million genes to our set of 22,000. Over recent years our understanding of the microbiome has moved from infancy to toddlerhood; however, there is much work still to be done in establishing its true impact on host physiology. It is clear that a symbiotic relationship exists between the host and microbiome which has led to a new paradigm in our consideration of this system, viewing the microbiome as a “virtual organ” in its own right.
