Microbiome Analysis Platform Studies
Are some bacterial genera more commonly associated with quarters prone to mastitis?
A common use of 16S rRNA targeted amplicon sequencing (TAS) is to identify correlations between the bacterial population present in an environment and some aspect of metadata associated with that population. In one ongoing study in the Ronholm lab, Soyoun Park is trying to determine if some bacteria genera more commonly co-occur with S. aureus mastitis.
Soyoun collected about 600 samples from healthy and mastitic quarters from 10 cows on 5 different dairy farms over the course of about a year. In Figure 1, she demonstrates that there is a relationship, in terms of beta-diversity, between which farm the sample was collected from and the composition of the bacterial community in raw milk.
Figure 1. PCoA ordination of the beta-diversity observed in raw milk samples taken from 5 dairy farms in Quebec. Each colour is used to represent a farm.
LefSE can then be used with the 16S rRNA TAS for bio-marker discovery. Bio-marker discovery allows us to use correlations between different groups of samples (mastitic or healthy) and certain taxa to identify markers of disease or susceptibility to disease. In Figure 2 Soyoun has identified a bacterial genus that is strongly correlated with mastitic milk when compared to healthy milk from a different quarter on the same cow.
Figure 2. LefSE analysis used to identify differential abundance of specific taxa between mastitic and healthy quarters. Significantly different abundances of certain genera may be useful for bio-marker discovery.
A more intense correlational analysis can also be preformed. In Figure 3, Soyoun has shown the direct correlations between different genera and SCC.
Figure 3. Correlational analysis between various bacterial taxa and SCC in milk sample. This analysis requires that measurements of SCC and 16S rRNA TAS are recorded from the same milk samples.