One thing that keeps rolling in my head these days is the impact of HGT on microbial genetic diversity. I am not an expert in HGT so I can't really figure out some points. I started to get to know HGT six years ago when one of my colleagues found some Bacillus PKS in the Streptomycete strains she isolated, which was explained by HGT.
Now I am processing geochip data, which was generated from group-specific/species-specific probes. This comprehensive chip provided lots of insights into the microbial functional community in sponges.
However, I am not very confident to draw the conclusion that a probe indicates the existence of a certain strain (group) considering HGT, although in the attachment the authors believed these probes can pinpoint the microbes. Except for the paper I attached, no other geochip papers have drawn the similar conclusion.
Hi Fang,
It is a really difficult question. We beleved that have proved HGT by MLST analysis in some Xanthomonas strains, but complete genome sequecing revealed that different hypothesys is more probable (natural selection). So, I think that not all the data obtained by your probes can be confirmed by other methods. It would be useful to confirm at least part of them by other methods.
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