Nearly Three-Quarters of All Known Bacterial Species Have Never Been Studied

Nearly three-quarters of all known bacterial species have never been studied in scientific literature, while just 10 species account for half of all published research, according to a new analysis published on bioRxiv.

The study of over 43,000 bacterial species found that E. coli dominates with 21% of all publications, followed by human pathogens like Staphylococcus aureus. Microbes crucial for human health and Earth's ecosystems remain largely unexplored, University of Michigan biologist Paul Jensen reported.

A new $1-million project by non-profit Align to Innovate aims to help close this gap by studying 1,000 microbes under varying conditions.

How are they Known?

[Roger W Moore]

Nearly three-quarters of all known bacterial species have never been studied in scientific literature

How are they known if they have _never_ been studied? This sounds like more than a bit of an exaggeration since presumably they must have been studied wnough to determine that they are a new species.

It's also a daft metric. We want researchers to spend their time studiying interesting and relevant bacteria like those that cause disease not to start picking species at random. While it is certainly possible that some unexpected discoveries may result from that the problem is that you have to spend a huge

Re:How are they Known?

[OrangeTide]

Old Rummy said it best:
“As we know, there are known knowns; there are things we know we know. We also know there are known unknowns; that is to say we know there are some things we do not know. But there are also unknown unknowns — the ones we don’t know we don’t know.

Re:How are they Known?

[Gilgaron]

I didn't read the article but you can sequence bacteria via PCR that you cannot culture (e.g. archaea species), so while you may discover dozens of species this way you can't learn much about them other than that they exist in specific environments.

Re:How are they Known?

[MilliMicro]

More or less. The paper looked at bacteria which are present in the Genome Taxonomy DataBase, which uses a range of marker genes/proteins in a genome to identify the species the genome is from and to build a tree of life based on that data. This includes a lot of shotgun sequencing data which produces DNA data from across the genome, compared to a PCR-based technique which normally focuses on a specific part of a genome. The environmental samples (soil, water etc.) this is done on will contain many different microbes, and a very large proportion of microbes in that data will never have been cultured or specifically studied. They just happened to be in the area when someone took a quick survey of the local microbial community. Even if a microbe has had a paper published on it, we probably know next to nothing about it. It is common for people to isolate a microbe, deposit it in a culture collection so other people can buy samples of it, and then publish a paper with a very high-level, general description of it. We'd still know next to nothing about the organism, or how it interacts with the world. Many organisms in culture collections have publicly accessible genome sequences, which can be helpful, but even that isn't a guarantee of anything. DNA is genetic potential, but there's a whole load of factors which control whether or not that DNA is actually expressed. This is why culturing hasn't been made obsolete by sequencing, and why you really need culture-based papers studying specific microbes to understand them rather than just a genome sequence.

Re:

[Roger W Moore]

I didn't read the article but you can sequence bacteria via PCR that you cannot culture (e.g. archaea species), so while you may discover dozens of species this way you can't learn much about them

Well in my book sequencing the DNA counts as studying them so they have been studied.

Re:

[RockDoctor]

Well in my book sequencing the DNA counts as studying them so they have been studied.

That's a fair enough semantic point, but I'm not sure it addresses the situation here.

The "restriction enzymes" used to slice up the environmental DNA into chunks that standard automated lab tech can turn into a (partial) sequence can be chosen completely at random. or even chosen looking for a specific type of bacterium (say, to pick on soil samples in particular) you use restriction enzymes that work well on strains of T

Re:

[Geoffrey.landis]

Nearly three-quarters of all known bacterial species have never been studied in scientific literature

How are they known if they have _never_ been studied?

You can know something exists without having studied it.

Re:

[Geoffrey.landis]

It all depends on what the defintion of "knowing" and "studied" means

These are defined in the article. A bacterium is "known" if it has been named. A bacterium has been "studied" if there exists at least one paper with the name of the bacterium in the title or in the abstract.

Re:

[Roger W Moore]

You can know something exists without having studied it.

In completely general terms that's a possibility. However, in this situation you need to know that a particular bacterium is of a species that has not been seen before and I can't think of any way you can possibly know that without some level of study of it.

Re:

[ZipNada]

I assume you didn't read the article. Nowhere was it suggested that uninteresting bacteria be studied.

"many organisms important to human health that Segata and others have found haven’t even been named, let alone studied"

Re:

[Roger W Moore]

Nowhere was it suggested that uninteresting bacteria be studied.

Not directly no, but by picking a metric of "number of species studied" that the article implies is too low means that researchers should switch from studying the species they currently are to studying a different species that presumably they are much less interested in. So perhaps "uninteresting" is going too far, but definitely less interesting.

Re:

[ZipNada]

As the article said, most of the bacteria in the "top 10 with the most published studies" are human pathogens, and therefor interesting.

"microbes abundant in healthy human microbiomes don’t crack the list of the 50 best studied" which is understandable.

Came hear for the Your Mom jokes...

[greytree]

Leaving disappointed, but clean.

Re:

[nightflameauto]

Your mom didn't leave disappointed *OR* clean.

Also,

[JustAnotherOldGuy]

Also, studies show that only 10% of microfleems are subradiant.

Re:

[Tablizer]

Your flux is capacitating.

Species?

[Tablizer]

Does "species" even apply to bacteria? They are asexual so that the reproductive test used for animals wouldn't apply. Seems a fuzzy guess.

Re:

[RockDoctor]

It's a fine distinction in a complex field where normal human intuition just isn't a good guide.

If that means "fuzzy guess" to you, then I'd have to ask - who is being fuzzy? The scientists writing their paper. or the (likely non-scientists) writing the press release at their employing institution? Or the journalists at Nature?

How good a fit is the human concept of "species" for "bacteria" (meaning what? - there are at least 3 different meanings to that term) which have at least three different types of "

Resources

[Retired Chemist]

There are a gigantic number of species of single-celled organisms and a limited number of researchers, so of course most of the species have never been studied. Yes, a great deal of work has been done on a few species such as E. coli. It is often more useful to understand one species in great detail than to have looked at many superficially. Bacteria particularly change so rapidly that is unlikely we will ever study most of them in enough depth to obtain any real understanding of their place in the ecosy

Re:

[bugs2squash]

what are the odds that much of the research was dedicated to weaponizing them

Re:

[Retired Chemist]

Very small. Biological warfare is tricky at best. Diseases have a nasty tendency not to distinguish which side you are on. Most biological warfare involves biotoxins rather than the use of living organisms.