Although this is a slightly older paper, the role of fungi in the gut microbiota is becoming an increasingly prevalent topic of discussion among microbiome groups, making this discussion a timely one. This group also previously published two papers on the role of antibiotics and fungal microbiota in allergic airway disease (Noverr et al 2004 & Noverr et al 2005). The primary finding of the paper at hand was that the introduction of C.albicans following antibiotic treatment causes marked changes in the reassembly of the microbiome, even in the absence of inflammation.
As discussed in journal club, there were several positive aspects to the study. First, the authors demonstrated the importance of the role of fungi in the gut despite relatively small numbers compared to that of bacteria. This is an aspect of the microbiome that has largely been neglected in recent years but fungi are large organisms and as illustrated, possess a significant ability to impact community reassembly following a disturbance. The inclusion of a multiplex qPCR array was helpful in examining changes to gene expression in response to various microbiome disturbances, although many aspects of this data were not addressed in the discussion. Finally, the relative abundance graphs were a good way to summarize taxonomic distribution, though we did discuss the challenges of pooling this type of data when samples are vastly different from one another.
There were a few other suggested areas for improvement to the study and paper that were discussed as well. For example, it was difficult to compare the bands from the graphs in Fig. 7 as their relative abundances may have been different (ie. Graph C: band for undisturbed ~10% versus band for disturbed + C.albicans ~1%). As a result some of the graphs were difficult to interpret with accuracy. The practice of using a log scale to demonstrate relative abundance followed by a non-log scale to plot taxa is also misleading. In addition, the authors’ use of rarefaction curves was not ideal. Finally, the title of Fig. 7 should read Day 21, not Day 7. Overall there were no major issues with the study or its findings.
We found this paper helpful in demonstrating the need for addressing fungi in microbiome analyses. However, there are still many obstacles to overcome in this area, such as limited fungal databases.
May 2015 Journal Club Paper: