Great article! When I was learning microbiology in undergrad (~2016) they taught us a bunch of species names (probably because the pre-meds needed them for the MCAT) but then said nobody cared about species anymore and worked instead with "operational taxonomic units".
I also wanted to provide a bit of clarification on the 32P gels: these are not imaged by X-rays, but rather the radioactive emission of the 32P will expose the film.
Thank you! I wouldn’t go so far as to say nobody cares about species anymore. But use of OTUs has definitely exploded alongside metagenomic sequencing — though the reason is more administrative than scientific. According to the International Committee on Systematics of Prokaryotes (ICSP), bacteria cannot receive an official species name unless they have been isolated in pure culture. But since >99% of bacterial species cannot be cultured and therefore cannot be named, but can be differentiated genomically, they’re referred to by an OTU instead. It’s a controversial choice that’s still hotly debated, but that’s why OTUs are getting so much attention.
And thank you for that corrective note! Yes: the gels were not X-rayed, but X-ray film was used to image the radioactive phorphorus.
Nice read! It appeared just in time for me, exactly while discussing a bacterial taxonomic report manuscript. I have to say, I sometimes wonder if another classification system will arise. It seems to me that the old taxonomic ways still have their use but I do wonder if there might be a way in which the network-y nature of bacterial relatedness could be better adressed instead of the hierarchical taxonomic way. Anyways, I thought this was already hard enough for me until recently, when I started working on viral metagenomics!
The current taxonomic system, with its multicellular-eukaryocentric biases, is for sure incompatible with the evolution of prokayotes in many important ways.
Great article! When I was learning microbiology in undergrad (~2016) they taught us a bunch of species names (probably because the pre-meds needed them for the MCAT) but then said nobody cared about species anymore and worked instead with "operational taxonomic units".
I also wanted to provide a bit of clarification on the 32P gels: these are not imaged by X-rays, but rather the radioactive emission of the 32P will expose the film.
Thank you! I wouldn’t go so far as to say nobody cares about species anymore. But use of OTUs has definitely exploded alongside metagenomic sequencing — though the reason is more administrative than scientific. According to the International Committee on Systematics of Prokaryotes (ICSP), bacteria cannot receive an official species name unless they have been isolated in pure culture. But since >99% of bacterial species cannot be cultured and therefore cannot be named, but can be differentiated genomically, they’re referred to by an OTU instead. It’s a controversial choice that’s still hotly debated, but that’s why OTUs are getting so much attention.
And thank you for that corrective note! Yes: the gels were not X-rayed, but X-ray film was used to image the radioactive phorphorus.
Nice read! It appeared just in time for me, exactly while discussing a bacterial taxonomic report manuscript. I have to say, I sometimes wonder if another classification system will arise. It seems to me that the old taxonomic ways still have their use but I do wonder if there might be a way in which the network-y nature of bacterial relatedness could be better adressed instead of the hierarchical taxonomic way. Anyways, I thought this was already hard enough for me until recently, when I started working on viral metagenomics!
The current taxonomic system, with its multicellular-eukaryocentric biases, is for sure incompatible with the evolution of prokayotes in many important ways.