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Challenges and issues in analysing and interpreting microbiota sequencing data

Microorganisms in the intestine can have multifaceted effects on the health and productivity of animals and birds. The advancement in DNA sequencing technology has enabled scientists to study these microorganisms and their effects on unprecedented depth and scale. This resulted in thousands of studies about intestinal microbiota (term to describe all microorganisms in an environment) and their role.  This led to hundreds of commercial animal supplements with claims to positively modify intestinal microbiota to improve health and productivity. However, a depth of knowledge and skills is required to correctly analyse and interpret the sequencing data. There are several limitations and complexities in analysing such data and misrepresentation and misinterpretation of such data is common.

Scientists from the Institute for Future Farming System, Central Queensland University Australia have recently published a review entitled “the role of microbiota in animal health and productivity: misinterpretations and limitations” in the journal “Animal Production Science”. This review is focused on the issues and challenges regarding the analysis and interpretation of microbiota research. In addition, current trends in microbiota research in different livestock (specifically ruminants, pig and poultry) have also been discussed. 

The article has summarised the role of microbiota as “the most prominent and well-known roles include control of fat storage and weight gain, gut barrier defence, breaking down complex nutrients, development and training of the immune system, biosynthesis of vitamins and amino acids, communication with the nervous system, pathogen exclusion and control, mood, behaviour and food craving influence, short-chain fatty acid production and much more”.  Moreover, microbiota play specific roles during production stress such as heat stress, stress during transport, stress due to disease etc. 

The article emphasized that “the microbiota investigation is now a highly regarded methodology that solidified its role in livestock health and welfare research; however, the levels of complexity of each individual step, taken from animal trial to data analysis, need to be thoroughly understood and addressed.” The review has discussed how highly variable nature of microbiota population between animals and different gut sections, choice of marker genes and their specific regions and PCR primers affect the microbiota research. Similarly, the article has also highlighted the challenges in designing the microbiota research and selecting the right method and tools to analyse the data. The paper has affirmed that “regardless of the immense advancements in computational analysis tools, many factors in data analysis introduce biases and errors.”

The paper has concluded that “Despite some methodology shortfalls, microbiome research is far from slowing down, and a trend of shifting the focus towards animal and environmental welfare rather than productivity is emerging.”

The article can be accessed by clicking the article title below:

The role of microbiota in animal health and productivity: misinterpretations and limitations


  1. I will summarize commonly used computational
    tools used for the analysis of different types of sequencing data in the gut microbiome
    studies, which help to extend our knowledge in the role gut microbiome plays in human
    health and disease pathogenesis.


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