Standardizing a Protocol for Microbiota Analysis in Poultry
Published:November 14, 2023
A roundtable featuring Mike Kogut (USDA), Annelies Kers (Utrecht University), Monika Proszkowiec-Weglarz (USDA) and Tim Johnson (University of Minnesota) starts an open discussion on how to agree on standard procedures for microbiome analysis, during the 11th Symposium on Gut Health in Production of Food Animals in St. Louis, USA.
This is probably one of the fundamental questions of modern microbiology, which has always focused on the search for criteria for identifying microorganisms. Remember Bergey's classic bacteria guide? The morphology of the colonies was supported by the composition of the nutrient medium. Then the criterion was the ability to metabolize specific carbohydrates. And now 16s sequencing has been added to all this, which raises more questions than answers. Why can't there be organisms that are able to metabolize the same substrate even if sequencing gives a completely different answer? What is more important in poultry farming, the ability to act on the substrate, or the result of sequencing? The ability of microorganisms to produce a variety of strains with completely different characteristics with amazing speed leads to the conclusion that it is the characteristics that need to be compared, and not the origin of the strains. Let's say that my great-grandfather was the king of Sweden. For me, as a biochemist, this only matters when I look at family photographs and nothing more.
We have the notion that one of the key factors to achieve and maintain the adequate structure and functions of the digestive tract is the microbiota that resides there; which in turn influences the level of general health and productivity of the animals.
This round table addresses the need to use more standardized methodologies to characterize the composition of the microbiota in birds (metagenomics), since it is considered that the way in which these studies have been carried out, presents such a level of heterogeneity that it does not allow an objective comparison of the results that have been obtained in different research centers.
But the task doesn´t end there. It is necessary to have greater knowledge of the functions of the microbiota (metabolomics, metatranscriptomics) that is being characterized taxonomically……..As some experts on the subject say: to go from knowing who there are and how many there are, to knowing what they are doing there, and how they are doing it……….Also for this, it is presumed that the standardization of the methodologies to be used will be necessary.
I agree, it is a very important topic. On point was not discussed enough I think: standardisation of the bioinformatics. While new developments are always happening overall, the 16s sequencing bioinformatics is now mostly established to use ASV or mOTUs based on the DADA2 pipeline. It might be useful to agree at least on a best practice and recommended tools for the bioinformatics as well. This will make hopefully comparing results described in a paper easier without reanalysing data.
This is an important issue. It will be interesting to see/hear how similar the results are from different laboratories using the proposed protocol when analysing the same mock communities or sample(s) in developing/validating the standardised methodology.
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