Canine Gastrointestinal Microbiome in Health and Disease

Introduction

The intestinal microbiota is defined as the aggregate of all living micro-organisms (bacteria, fungi, protozoa, and viruses) that inhabit the gastrointestinal (GI) tract. The word microflora is often used in older textbooks, but microbiota (from the word bios in ancient Greek meaning "life") is the more appropriate term.

Until a few years ago, culture was the principal method used to identify bacteria inhabiting the canine GI tract, and this technique still yields useful result when employed for detection of specific enteropathogens (e.g. Salmonella, Campylobacter jejuni). However, it is now well recognized that the vast majority of intestinal microbes present in the GI tract remain undetected using culture-based methods (1). A new molecular method, known as 16S rRNA sequencing, allows bacteria to be identified in a much more reliable way using a culture-independent approach. Bacterial DNA is extracted from an intestinal sample and the 16S rRNA gene is amplified and processed via PCR using a high-throughput sequencer, allowing a more comprehensive identification of the bacteria present in the sample (Figure 1). Such molecular studies have revealed that the canine GI tract is home to a highly complex microbial ecosystem, referred to as the intestinal microbiome, consisting of several hundred different bacterial genera and probably more than a thousand bacterial phylotypes (2). It has been estimated that the intestinal microbiome consists of approximately 10 times more microbial cells (1012-1014) than the number of host cells, and the microbial gene pool is 100-fold larger compared to the host gene pool. It is emerging that this highly complex microbial ecosystem plays a crucial role in regulation of host health and immunity, as demonstrated in various studies in humans, animal models, and (most recently) dogs and cats (1). [...]

Key Points

• Advances in microbiology have revealed a much more abundant, diverse, and complex gastrointestinal microbiota than was previously appreciated using culture-based methods.

• Contemporary culture–independent microbiology, based on the detection of molecular signatures of bacteria such as 16S and 23S rRNA genes, enables in-depth evaluation of the presence and localization of bacteria in the gut.

• The intestinal microbiota has a key role in maintaining health and immunity.

• Dysbiosis, or imbalances in the intestinal microbiota, are increasingly associated with inflammatory bowel disease (IBD).

• Culture-independent methods have enabled the discovery of mucosally invasive bacteria in dogs with granulomatous colitis.

• A combination of dysbiosis and host susceptibility may influence the response to antibiotics seen in dogs with antibiotic-responsive enteropathies.

• Elucidating the factors that shape the intestinal microbiome will provide novel opportunities for prophylaxis and therapeutic intervention.