Belda et al. have conducted a potentially interesting study that is, I believe, marred by flaws in methodology and sampling design.

The most important issue is that conclusions were drawn from a comparison of two unreplicated samples. All individual gut communities from each group (lab and field) were pooled and a single metagenome generated from each pool. Thus we have no idea of the variability within each group, and you will find no mention of statistical tests anywhere in the paper -- yet there are statements such as "Lab-reared and field-collected ECB also differ significantly in terms of their GH and CBM profiles." See Prosser (“Replicate or Lie,” Environmental Microbiology, 2010 12(7), 1806-1810) about the importance of replicates in microbial ecology studies.

There are additional issues with the methods. One is that the lab larvae were fed an (apparently) nonsterile artificial diet, and that the larvae were not starved prior to gut collection (which is commonly done in caterpillar gut microbe sampling; e.g. Broderick 2004). It is very likely that the lab larvae's Staph, Bacilli, etc. were all from diet "contaminants" present in the gut lumen and not so interesting in terms of insect-specific microbiota. It would have been valuable to have sequenced the diets themselves.

Some other comments. The age and number of caterpillars (and their guts) do not seem to have been very carefully controlled. The amplification on artificial media and the exposure of the lab caterpillars to antibiotics (as Belda et al. do mention in the paper) are very important to note when interpreting their results. There are a number of typos, and there does not appear to be a legend in Fig 5. In Fig 1 there is a “Bacteroidetes” bin and also a “Bacteroidetes-Chlorobi” bin.

Nevertheless, the finding of a high diversity of genera in the wild caterpillars’ guts is interesting, in a descriptive sense, and the paper illustrates how metagenomics could be valuable in insect gut censuses.