10 Facts about the Microbiome that you may not know

  1. The terms ‘microbiome’ and ‘microbiota’ have different meanings. The collection of living microorganisms (bacteria, fungi, protozoa and viruses) that inhabit a specific environment are referred to interchangeably as the microbiota or microbiome. In fact, there is a subtle difference between the terms; the former refers to the microorganisms themselves, whereas the latter refers to the microorganisms plus their ‘theatre of activity’, which includes their genetic material, microbial structures, metabolites and microenvironment (specific habitat in which they reside).1
  2. Bacteria are the predominant micro-organism within the gastrointestinal microbiome.  The human gastrointestinal microbiome is comprised of 10-100 trillion microbial cells, including bacteria, fungi, archaea and viruses. However, when this microbial DNA is sequenced, 99% of the genes detected are of bacterial origin, demonstrating their predominance in microbiome composition.2
  3. A diverse microbiome is a marker of a health. Microbiome diversity is a measure of how many different species are present (richness) and how evenly distributed they are in the community (evenness). The presence of more bacterial species allows for greater functionality and resistance to pathogenic invasion.3 Furthermore, low diversity has been associated with numerous health conditions in dogs, including chronic enteropathies, acute diarrhoea, and obesity.4,8
  4. Pathogenic bacteria exist within a normal, healthy microbiome. The microbiome maintains a fine balance of both commensal and pathogenic organisms. In health, commensal organisms act to provide ‘colonisation resilience’ in which they impede the growth of pathogenic microorganisms through a number of inhibitory mechanisms.  Occasionally, pathogens can override this microbial barrier, out-competing the commensal community resulting in infection or disease.5 For example, a reduction in colonisation resistance can be seen following antibiotic administration as their non-specific bactericidal action can deplete the commensal community, opening a window of opportunity for pathogens to proliferate.6 Interestingly, even some commensal organisms can become opportunistic pathogens if the environment becomes more favourable to that specific organism.7
  5. Different microbiomes exist within the same animal. Although the gastrointestinal microbiome seems to get the most attention, there are distinct ecosystems of micro-organisms that live in various other organs including the skin, urogenital tract and respiratory tract, all with a unique composition.
  6. Each individual has a unique microbiome composition, almost like a fingerprint. Every individual has their own unique microbiome composition which is reflective of many factors, including diet, genetics, medication use, and lifestyle. However despite these individual variations, there does appear to be a core bacterial community which is common to animals of the same species. For example, the canine gastrointestinal microbiome is co-dominated by three phyla, Fusobacterium, Bacteroidetes, and Firmicutes.8
  7. Microbiome composition can vary within the same organ. The relative abundance of each bacterial 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.5 In fact, even within the skin microbiome we can see microbial variations within the same animal as different cutaneous bacterial populations appear to exist at different locations on the body.9
  8. The microbiome evolves over time. From birth, a puppies microbiome is constantly evolving, until it reaches a stable adult state at approximately 18 months of age. Once established, external factors such as diet, environment, lifestyle, illness and stress can impact microbiome composition, however in general a healthy adult state is maintained over time. In humans, more than 70% of faecal bacterial species within an individual were stable over a 1 year period, which may extend to decades for weight-stable individuals.6 Although long-term studies are not available in dogs, the microbiome was shown to be relatively stable over a 2 week period, and it is reasonable to expect that this may persist in healthy adult animals.6
  9. Ageing leads to a reduction in microbiome diversity. An ageing microbiome tends to show signs of reduced diversity, almost resembling a mirror image of juvenile microbiome development, only in reverse. It is thought that an age-related decline in normal immune function and gastrointestinal physiology can lead to reduced gut motility, intestinal barrier disruption and inflammation within the gut. Inevitably, these changes can affect microbiome composition and functionality, which can result in reduced bacterial diversity.10
  10. Our understanding of the microbiome is ever-advancing. At present, it is widely accepted that a symbiotic relationship exists between the microbiome and host which plays a significant role in health, both within the gastrointestinal tract and on distant body systems, such as immunity and metabolic health. However, our knowledge on the microbiome is constantly expanding and it is a research field with infinite potential and great clinical application. Eventually, findings from microbiome research could revolutionise the diagnosis and treatment of certain diseases in human and veterinary medicine.11