How to understand microbiota published research

Marcio Costa, Cécile Crost, Université de Montréal, CRIPA-Fonds de recherche du Québec

The modulation and analyses of digestive microbiota has become a no feature in infectious disease management and animal husbandry. Marcio Costa, professor at Universite de Montreal and Scott Weese, professor at University of Guelph published for veterinary practitioners, a handguide to interpret the published data of this field of research. This review paper presents how to screen any science advancement proposed by the research community.

Despite more than a century of advancement in microbe in vitro culture, the vast majority of microbes are very difficult to culture. 20th century molecular microbe identification methods such as DGGE, RFLP and first DNA sequencing technologies are nowadays obsolete.

NGS or Next Generation Sequencing technology allowing analysis of several thousands of DNA fragments in parallel, is the gold standard method. NGS can be design in two ways, one to assess the taxonomic information of a community (classification of bacteria), this kind of analysis describes which microbe taxa are present in the community; targeted amplicon sequencing is used for taxonomic studies (to obtain the name of a bacteria). The other type of NGS analysis describes the metabolic function profile in a microbiota (the genetic potential of the community); metagenomics or shotgun analysis are used for metabolic function analysis. However, NGS yields a relative proportion of between the different bacterial populations and other techniques, such as quantitative PCR, are required for a real total count.

To confirm presence of a microbe in anatomic lesion, researchers can use Fluorescent in situ hybridization.

However, at present, most of the microbiota studies performed in animals are merely descriptive; no cause-consequence relationship can be inferred. So, in order to asses for example if a specific bacteria induces weight loss (or gain), researchers need to use mechanistic methodologies (e.g.: studies of pathways and gene expression analysis). Mechanistic methodologies help to identify interaction of molecules with identified mechanical molecular cascade in several organs or microbe cells. Molecular interactions can then trigger or cause symptoms (anorexia, fever, vomit).

In conclusion, the research about the impact of the microbiota on the host are just at the beginning and need to be interpreted with caution to avoid false extrapolation in cases of purely descriptive studies.

Source: Methods and basic concepts for microbiota assessment. Vet J. 2019 Jul;249:10-15. Marcio Costa, J Scott Weese. Epub 2019 May 13.