Wayne Radinsky (old account)

2025-01-11 04:05:07

"Ten species comprise half of the bacteriology literature, leaving most species unstudied."

"Release 202 of the GTDB database includes 43,409 unique species, and we counted the number of PubMed articles that refer to each species in their title or abstract."

"Almost 74% of all known species have never been the subject of a scientific publication -- these are unstudied bacteria. Even among the species studied (those with at least one publication), 50% of all articles refer to only ten species. More than 90% of all bacteriology articles study fewer than 1% of the species, creating a 'long tail' of understudied microbes."

Those ten species, in case you are wondering, are: 1. Escherichia coli (the famed "E. coli" you see everywhere), 2. Staphyloccus aureus, 3. Pseudomonas aeruginosa, 4. Mycobacterium tuberculosis, 5. Halicobacter pylori, 6. Bacilus subtilis, 7. Klebsiella pneumoniae, 8. Streptococcus pneumoniae, 9. Listeria monocytogenes, and 10. Haemophilus influenzae.

"The scientific enterprise is expanding, and every year scientists publish 4 -- 5% more papers than the previous year. It is tempting to think that the increase in scientific output will overcome the long tail of microbes, that is, scientists will eventually get around to studying every species. Unfortunately, the number of species discovered each year outpaces the increases in scientific output. Between the years 1990 -- 2020, the number of papers published per studied species of bacteria decreased by 60%."

"Our view of bacterial diversity is biased when so much of our understanding comes from so few microbes. Microbiologist Jeffery Gralnick once quipped that 'E. coli is a great model organism -- for E. coli.' Gralnick's comment referenced the discovery of anomalies (relative to E. coli) in the TCA cycle of Shewanella oneidensis."

The TCA cycle they are talking about here is what you may know as the citric acid cycle or Krebs cycle. TCA stands for "here tricarboxylic acid cycle". The TCA cycle uses oxygen to break down food and turn it into energy. More precisely, those molecules such as glucose and other sugars, fatty acids, and proteins, are converted in a previous step to acetyl coenzyme A (acetyl CoA), which is then fed into the TCA cycle, to produce adenosine triphosphate (ATP), the molecule cells actually use to do work, out the other end.

"Although S. oneidensis has 201-fold fewer citations that E. coli, it is arguably not an understudied species. Our analysis ranks it as the 94th most studied bacterium, which is in the top 2.17% of all species. Even the introduction to Gralnick's aforementioned paper refers to S. oneidensis as a 'model environmental organism'. If differences like S. oneidensis' TCA cycle can be found just outside the microbial 2%, imagine the diversity that lies in the other 98% of microbes."

Ten species comprise half of the bacteriology literature, leaving most species unstudied

#discoveries #biology #microbiology #bacteria