Microbes have just received 12,000 new species as members of the family.

We all know that anyone can grow microbes in a petri dish. The process is very simple. Just take a swab of anything, rub it on an agar plate and let it sit for a few days in a warm environment. You will soon have grown your own batch of microbes. However, the cultivated microbial species will be a small fraction of the great microbial realm. This happens as only those microbes will grow that find the surrounding environment suitable for them.

Use of metagenomics to find new microbes

Larger species of microbes generally do not grow in a petri dish. Hence, a team of international researchers used a fascinating technique called metagenomics. They discovered a whopping 12,556 species of microbes that had never previously been grown in a controlled environment. DOE Joint Genome Institute geneticist and first author Stephen Nayfach said, Our team was able to remodel numerous metagenome-assembled (MAG) genomes directly from sequenced environmental samples. We didn’t need the microbes to be grown in the lab. ”

The new study differs from the previous ones for the significant environmental variation detected by the analyzed samples. The research team used a huge collection of nearly 10,000 metagenomes. Any extractable DNA is cloned and subsequently constructed using small genomic strands, before fitting these short pieces of DNA again. It is very similar to reassembling a puzzle that has been put in a blender.

The team, however, used a method called “binning” to piece together 52,515 MAGs from the data, with high quality and nearly 50% of the complete genome. This team isn’t the first to use metagenomics to discover new microbes. In 2018, scientists found 16 huge viruses, and in 2017, scientists discovered 20 new evolutionary branches in the tree of life using an identical method.

Not as good as lab grown ones

In the new study, the research team was looking to study microbial samples from a wide range to plug holes in our understanding of the microbial world. We performed metagenomic collection and binning on 10,450 metagenomes transported internationally from assorted living spaces, including the ocean and other marine environments, just like soils and other terrestrial environments, to recover 52,515 MAG, “the group wrote in their article.

The new discoveries have expanded the catalog of the kingdom of bacteria and archaea known to us by a whopping 44%. When the team analyzed them against isolates, MAGs from previous studies, and single cell genomes, they found that 12,556 of the 50,000 MAGs were never sequenced. One thing to note is the fact that the new genomes are not as good quality as those grown in the laboratory and subsequently sequenced. The binning process can cause pieces of the genome to mix between species of microbes, and large genomic pieces will often be missing.

Despite this, it is still an incredible method of finding the microbial species that surround us. The research was published in Nature Biotechnology.