A study published in the journal Animals has shed new light on the relationship between different methods of analysing the canine gut microbiome. The research, led by Dr Jan Suchodolski and colleagues at Texas A&M University, compared targeted quantitative PCR (qPCR) assays and a qPCR-based dysbiosis index (DI) with untargeted DNA shotgun metagenomic sequencing in dogs with various clinical conditions.
The study, which included 296 dogs with diverse clinical phenotypes, aimed to evaluate the correlation between these different analytical approaches and determine whether the qPCR-based DI accurately reflects global shifts in the gut microbiome. The researchers analysed faecal samples from healthy dogs, dogs with chronic enteropathy, acute diarrhoea, non-gastrointestinal diseases, and dogs on antibiotics.
One of the key findings of the study was the robust correlation between the qPCR-based DI and the untargeted metagenomic sequencing data. The researchers found that higher DI values indicated a more pronounced deviation from the healthy reference group, which was supported by analysis of similarity (ANOSIM) on beta diversity. As the DI value increased, there was a corresponding increase in the R value, indicating larger dissimilarities in the microbiome composition.
Interestingly, the study also revealed that an increase in the DI was correlated with a decrease in alpha diversity metrics such as Shannon index, Chao1, and observed features. This suggests that dogs with higher DI scores tend to have less diverse and less rich bacterial communities in their gut.
The researchers identified several bacterial groups that were positively correlated with alpha diversity metrics, including Faecalibacterium, Fusobacterium, and Clostridium hiranonis. These findings align with previous research suggesting that these bacteria may have beneficial effects in dogs, such as producing short-chain fatty acids with anti-inflammatory properties or playing a role in bile acid metabolism.
A particularly noteworthy aspect of the study was the comparison between qPCR and shotgun sequencing results. While significant correlations were found between the two methods for all bacterial groups targeted in the DI, the researchers observed that certain taxa were only detectable by qPCR and not by sequencing in some samples. This highlights the complementary nature of these two approaches and the potential advantages of using targeted assays for specific bacterial groups.
The study also provided insights into the core microbiota of healthy dogs. Surprisingly, less than 2% of bacterial species (17 out of 1190) were consistently present in all healthy dogs based on sequencing data. This finding underscores the high degree of individual variation in the canine gut microbiome and the challenges in defining a “normal” microbiome.
Dr Suchodolski and his team emphasised the clinical relevance of their findings, particularly in relation to dogs with chronic enteropathy (CE). They noted that approximately 36% of dogs with CE in their study population had a normal DI, consistent with findings from other studies. This suggests that not all dogs with CE exhibit dysbiosis, and those with a normal DI may have a different underlying pathophysiology compared to those with dysbiosis.
The researchers also highlighted the strengths and limitations of both targeted and untargeted approaches to microbiome analysis. While untargeted sequencing provides a comprehensive overview of the microbial community, it can be influenced by factors such as sequencing depth and data processing methods. In contrast, qPCR assays offer high reproducibility, sensitivity, and specificity for known targets, but cannot detect unexpected or novel microbial taxa.
The study’s findings have important implications for both research and clinical practice in veterinary medicine. The strong correlation between the qPCR-based DI and non-targeted sequencing results suggests that the DI could be a valuable tool for assessing overall shifts in the canine gut microbiome. This could be particularly useful in clinical settings, where a rapid and cost-effective method for evaluating microbiome health is desirable.
However, the researchers caution that both approaches have their place in microbiome research. They suggest that combining targeted and untargeted methods can provide a more comprehensive understanding of the gut microbiome and its role in health and disease.
In conclusion, this study represents a significant advancement in our understanding of canine gut microbiome analysis methods. By demonstrating the strong correlation between targeted qPCR assays and untargeted metagenomic sequencing, the research provides validation for the use of the dysbiosis index as an indicator of overall microbiome health in dogs. As our understanding of the complex relationship between the gut microbiome and canine health continues to grow, tools like the DI may play an increasingly important role in both research and clinical practice, potentially leading to improved diagnostic and therapeutic approaches for gastrointestinal disorders in dogs.