Scientists have just discovered 12,000 new species of microbes

Growing microbes in a petri dish is pretty simple – dab just about anything, wipe it on an agar plate, let it sit for a few days in a warm room, and presto! You raised 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 harvested from the swab, only those suitable for the conditions in which you grew them.

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

Now, an international team of researchers has found 12,556 new species of bacteria and archaea that have never been grown in the laboratory, using an incredibly interesting technique called metagenomics.

“We were able to reconstruct thousands of metagenome (MAG) assembled genomes directly from sequenced environmental samples without the need to cultivate the microbes in the laboratory,” said DOE Joint Genome Institute geneticist and first author, Stephen Nayfach.

“What 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 MAG sequenced. (Nayfach et al., Nature Biotechnology, 2020)

The team had access to a huge database of over 10,000 metagenomes, a term meaning all the genetic material of an environmental sample. Any DNA they can extract is cloned and then sequenced using tiny strands of the genome, before they try to assemble these short pieces of DNA again.

It seems like trying to reassemble a puzzle that was put through the blender, but using a technique called ‘binning’, the team was able to piece together 52,515 MAGs from the data, many of them high quality and all over 50 % of their complete genome.

The team isn’t the first to find microbes using metagenomics – in 2018 we wrote about scientists discovering 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 looking to analyze samples from a wide range of areas to fill in some of the gaps we have in our knowledge of microbes.

“We performed metagenomic assembly and binning on 10,450 metagenomes distributed globally from diverse habitats, including ocean and other aquatic environments, human and animal host associated environments, as well as soils and other terrestrial environments, to recover 52,515 MAG, “writes the team in their paper.

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

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

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

“Looking through the tree of life, it’s amazing how many uncultivated lineages are represented only by MAG,” Nayfach said.

“Although these sketches of genomes are imperfect, they can still reveal much about the biology and diversity of wild microbes.”

The research was published in Nature Biotechnology.