Uncultured Microbial Cells Dominate Earth Microbiomes

[Weird]

https://msystems.asm.org/content/3/5/e00055-18

To describe a microbe’s physiology, including its metabolism, environmental roles, and growth characteristics, it must be grown in a laboratory culture. Unfortunately, many phylogenetically novel groups have never been cultured, so their physiologies have only been inferred from genomics and environmental characteristics. Although the diversity, or number of different taxonomic groups, of uncultured clades has been studied well, their global abundances, or numbers of cells in any given environment, have not been assessed. We quantified the degree of similarity of 16S rRNA gene sequences from diverse environments in publicly available metagenome and metatranscriptome databases, which we show have far less of the culture bias present in primer-amplified 16S rRNA gene surveys, to those of their nearest cultured relatives. Whether normalized to scaffold read depths or not, the highest abundances of metagenomic 16S rRNA gene sequences belong to phylogenetically novel uncultured groups in seawater, freshwater, terrestrial subsurface, soil, hypersaline environments, marine sediment, hot springs, hydrothermal vents, nonhuman hosts, snow, and bioreactors (22% to 87% uncultured genera to classes and 0% to 64% uncultured phyla). The exceptions were human and human-associated environments, which were dominated by cultured genera (45% to 97%). We estimate that uncultured genera and phyla could comprise 7.3 × 1029 (81%) and 2.2 × 1029 (25%) of microbial cells, respectively. Uncultured phyla were overrepresented in metatranscriptomes relative to metagenomes (46% to 84% of sequences in a given environment), suggesting that they are viable. Therefore, uncultured microbes, often from deeply phylogenetically divergent groups, dominate nonhuman environments on Earth, and their undiscovered physiologies may matter for Earth systems.


IMPORTANCE In the past few decades, it has become apparent that most of the microbial diversity on Earth has never been characterized in laboratory cultures. We show that these unknown microbes, sometimes called “microbial dark matter,” are numerically dominant in all major environments on Earth, with the exception of the human body, where most of the microbes have been cultured. We also estimate that about one-quarter of the population of microbial cells on Earth belong to phyla with no cultured relatives, suggesting that these never-before-studied organisms may be important for ecosystem functions.

 

[CosmicGiggle]

Think of alla the potential knowledge lurking in those unknown microbes, funny how we humans mostly concentrate on the ones causing disease.

 

[mean mr.mustard]

Now now....

I think we are better off with the six days of creation/Adam named everything story.

It's written down and everything...

Plus I don't have to do any free thinking, so I have time to go find out what others want me to buy and buy it.

I'm often amazed that we sense ourselves as all one us...

When we are a roving pile of various communities of microbes and separate functioning parts, being conscious of only a "me" seems absurd.

I consider that scale of difference to point at the Earth as being an organism.

We are tiny dust mites on a huge critter.

 

[Water-]

Think of alla the potential knowledge lurking in those unknown microbes, funny how we humans mostly concentrate on the ones causing disease.

true.

and not just the ones causing disease, its the diseases they can make money off of treating that matter.

there are countless children dying everyday in third world countries from diseases that are not being studied at all because there is no profit in saving poor children.

 

[CosmicGiggle]

Microbiomes are interesting, more so now that we can identify all of them without having to try to culture organisms that refuse to grow outside their natural environment.

For anyone interested in 1 tiny microbiome niche, here's an interesting read on what's potentially living inside your belly button:

The Belly Button Biodiversity Project, North Carolina State University, 2011:
http://robdunnlab.com/projects/belly-button-biodiversity/

 

[Water-]

when i clicked on the link, a page came up that said it was unsafe and that hackers might be stealing my info!!

 

[CosmicGiggle]

that's weird, I get the message now but not before, sorry about that!

 

[Cvh]

I did not understand a single word from that article.

(Remove the S from the HTTPS to remove the warning).

 

[troutman]

Imagine the microbiome is a seagull's stomach.

 

[Weird]

basically we know very little about the microbiology throughout the world outside of our human body and they equate the foot print of microbiology on earth to empty space in earth, vast yet intangible to our senses.

 

[Water-]

.