Scientists have just discovered 12,000 new species of microbes

Growing microbes in a Petri dish is pretty straightforward – dab almost anything, wipe it down on an agar plate, let it sit for a few days in a warm room and voila! You have grown new furry friends.

But the microbial species you can grow in a petri dish are only a tiny fraction of the bacteria, archaea, and other microorganisms that would have been picked up by the swab – only those that are suitable for the conditions you grew them under. .

The vast majority of them do not like the environments we can provide and therefore will not grow obediently in a Petri dish.

Today, an international team of researchers have discovered 12,556 new species of bacteria and archaea that have never been cultured in the lab, using an incredibly cool technique called metagenomics.

“We have been able to reconstruct thousands of metagenome-assembled genomes (MAG) directly from sequenced environmental samples without the need to grow the microbes in the lab,” said Stephen Nayfach, geneticist and lead author of the DOE Joint Genome Institute.

“What really sets this study apart from previous efforts is the remarkable environmental diversity of the samples we analyzed.”

A map of the locations and types of MAGs sequenced. (Nayfach et al., Nature Biotechnology, 2020)

The team had access to a huge database of more than 10,000 metagenomes – a term for all the genetic material in an environmental sample. Any DNA they can extract is cloned, then sequenced using tiny strands of genome, before they try to readjust those tiny pieces of DNA.

It looks like trying to reassemble a puzzle that was put in the blender, but using a technique called ‘binning’ the team were able to piece together 52515 MAG from the data – many of them high quality, and all having more than 50 percent. of their complete genome.

The team isn’t the first to find microbes using metagenomics – in 2018 we wrote about scientists finding 16 giant viruses, while in 2017 scientists found 20 new evolutionary branches in the tree of life using these methods.

But in this new work, the researchers were attempting to analyze samples from a wide range of fields to fill in some of the gaping holes we have in our knowledge about microbes.

“We performed metagenomic assembly and binning on 10,450 metagenomes distributed around the world from a variety of habitats, including ocean and other aquatic environments, human and animal environments associated with hosts, as well as soils. and other terrestrial environments, to recover 52,515 MAG, ”the team wrote in their paper.

“The catalog expands the known phylogenetic diversity of bacteria and archaea by 44 percent.”

When the team checked the genomes of isolates, MAGs from previous studies, and the genomes of individual cells, they found that 12,556 of the 50,000 MAG had never been sequenced before.

Now, it’s important to note that these genomes aren’t as good as the ones you would get by growing bacteria and archaea in a lab and then sequencing them. The grouping process can mix up some pieces of the genome between bacterial species, and pieces of the genome will often be missing; but without the ability to cultivate these particular species in a lab, it’s still an amazing way to discover microbes in the world around us.

“Looking through the tree of life, it is striking how many uncultivated lines are represented only by MAG,” said Nayfach.

“While these genome projects are imperfect, they can still reveal a lot about the biology and diversity of uncultivated microbes.”

The research was published in Biotechnology of nature.