I found Nowak’s commentary to be very helpful in understanding the larger Fleichmann paper. The diagram from Nowak’s paper alone really summarized the whole gene random sequencing talked about in the paper well. Additionally, the diagram really highlighted how overexpression of genes versus knocking out of a genes was used in the context of gene sequencing.
Something I found interesting regarding genome science during its early days was the greater emphisis on identifying what unknown genes did. This makes sense because today we have fairly expansive gene libraries that can tell us the function of a gene and if a novel sequence is a potential relative with a similar function. However, somebody had to actually make these libraries so the greater emphisis is reasonable. In class, I almost felt like figuring out what a gene did via culturing was an afterthought, but perhaps this is because of the current expansive gene libraries making this a rarer occurrence. Additionally, our focus for much of the class what ecological 16S community rRNA sequencing, not determining the function of novel genes so perhaps the focus of the class is biasing my perception of modern-day gene sequencing.
From my current standpoint, I would not have thought that genome sequencing from ~25 years ago would have been able to annotate a genome in as much detail as Fleichmann was able too. I wouldn’t have thought their libraries would have been complete enough to give the level of detail they did but clearly, this was a misconception.
I also thought it was interesting how in neither the article nor the commentary they talked about unculturable bacteria. In their diagram, it seemed as if culturing the bacterium was seen as important for both applications (antibiotic, vaccine, and industrial enzyme production) and for understanding the role of genes. For most bacteria we cannot culture, a major benefit to sequencing is that it gives information regarding phylogeny and related characteristics. However, maybe this also has to do with the gene libraries. Sequencing can give us lots of info on unculturable bacteria because of gene libraries but if these weren’t built up enough yet then it does make sense for them to focus on the culturable bacteria. I was just very surprised they did not even use the word “unculturable” at any point during either the commentary or the paper because the relationship between sequencing and unculturable bacteria is emphasized so heavily in class.
