Growing germs in a Petri dish is pretty simple – wipe anything with a cotton swab, leave it in a warm room for a few days and you're done! You've made some new furry friends.
But the types of microbes that you can culture in a petri dish are just a tiny fraction of bacteria, archaea, and other microorganisms that have settled on the swab – only those that are suitable for the conditions in which you grew them.
The vast majority of them do not like the environment that we can provide and therefore will not obediently grow in a petri dish.
Now, an international team of researchers has discovered 12,556 new species of bacteria and archaea that have never been grown in a laboratory using a new technique called metagenomics.
“We were able to reconstruct thousands of metagenome-derived genomes (MAG) directly from sequenced environmental samples without the need for microbial cultivation in a laboratory,” said Stephen Knifach, geneticist and study author at the US Department of Energy's Joint Genome Institute.
“What really sets this study apart from previous ones is the remarkable ecological diversity of the samples we analyzed.”
The team had access to a huge database of more than 10,000 metagenomes – a term for all genetic material from environmental samples. Any DNA they can extract is cloned and then sequenced using tiny strands of the genome before scientists try to put those short DNA fragments back together.
It's like trying to piece together a jigsaw puzzle that has been blended, but using a technique called 'binning', the team was able to piece together 52,515 MAGs from the data – many of them are of high quality, and all have over 50 percent of the genome complete.
It is not the first time that scientists have discovered microbes using metagenomics – they discovered 16 giant viruses in 2018, and in 2017, using new methods, they discovered 20 new evolutionary branches on the tree of life.
But in this new work, researchers have tried to analyze samples from a huge range of areas to fill some of the gaps in our knowledge of microbes.
Consistent map of location and MAG types. (Naifach et al., Nature Biotechnology, 2020).
'We performed metagenomic assembly and binning on 10,450 globally distributed metagenomes from various habitats, including the ocean and other aquatic environments, environments associated with humans and animals, as well as soils and other terrestrial environments, to restore 52,515 MAG,' genetics.
'The catalog expands the known phylogenetic diversity of bacteria and archaea by 44 percent.'
When the scientists examined the genomes of the isolates, the MAGs from previous studies, and the genomes from individual 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 are not as good as what you would get from growing bacteria and archaea in a laboratory and then sequencing them. The fusion process can mix parts of the genome between bacterial species, and fragments of the genome will often be missing; without the ability to grow such species in a laboratory, but it's still a great way to detect microbes in the world around us.
The study was published in Nature Biotechnology.
Sources: Photo: (Rodolfo Parulan Jr / Getty Images)
