Rick Robinson

Mar 12th 2021

A World of Microbes Revealed by Metagenomics


Microbes (also called microorganisms) are not only all around us — they are also inside us. Vast colonies of microorganisms inhabit our digestive system and other tissues, where their activity is vital to our life and health.

Though invisible to the naked eye, and never even imagined until the microscope revealed them, microorganisms are not only ubiquitous but often easily cultivated. As ScienceAlert explains, wipe down practically any surface, dab the wipe in a Petri dish, keep the Petri dish warm and cozy for a few days, and you will cultivate colonies of microorganisms to show off to your friends with a handy microscope.

The ease of finding and cultivating microorganisms is good news for microbiologists: They have no shortage of microbes to study. They’ve also been able to apply tools such as genomics to examine the genetic material of microorganisms, sequencing their DNA in the same way as geneticists who study the human genome or those of other plants and animals.

Examining in the Wild

There is a hitch: Not all microorganisms thrive equally well in the artificial environment of a Petri dish. Thus, the gathering process outlined above, even in sophisticated versions, does not give us a cross section of microbes but only those that thrive in a lab.

As a result, according to the National Center for Biotechnology Information (NCBI), traditional methods of microorganism cultivation and study tend to give us “laboratory knowledge” of these microscopic creatures. Even in our microscopes, we see them only in highly artificial conditions, not living and acting within their natural ecosystem.

This is a serious limitation, rather like trying to understand the behavior and ecology of tigers, if the only tigers you could study were in a zoo.

When Genomics Goes Meta

To get around this limitation, microbiologists have devised an approach called metagenomics, which examines the gene sequences not of individual specimens but of entire ecological communities. And, per ScienceAlert, this technique has begun to yield spectacular results — most recently the discovery of 12,000 species of microbes that had never been observed in a lab.

Such a large-scale discovery was possible because more than ten thousand metagenomes, or group samples, were collected from all parts of the world, across land and sea, providing researchers with an unmatched range and variety of ecosystems.

According to the National Human Genome Research Institute, the term “metagenomics” combines “genomics,” a.k.a. the study of gene sequencing and effects, with “meta”, which denotes multiplicity. (In various contexts it can also mean “more,” “beyond,” or “transcending.”)

Separately, the NCBI notes that metagenomics is “both a set of research techniques, comprising many related approaches and methods, and a research field” — the branch of microbiology that uses those techniques to microbe ecosystems rather than only at individual microorganisms.

Putting a Jigsaw Puzzle Through a Blender

All of this has its own challenges. As Jacinta Bowler of ScienceAlert rather vividly puts it, the process “sounds like trying to reassemble a jigsaw puzzle that’s been put through the blender.”

But this is not the first time that scientists have confronted similar problems. From dinosaurs to our own hominid ancestors, animal species have been reconstructed from scattered bone fragments. Similar achievements abound across scientific disciplines. What scientists in all field do when confronted with a mass of scattered bits of evidence is look for patterns and use them to group the finds. In metagenomics, this pattern-matching process is known as “binning.”

Metagenomics is in the process of transforming microbiology, which through the 20th century worked primarily with cultured microorganisms. Only gradually did microbiologists fully grasp the degree to which the natural environment is dominated by microbes never found in the lab.

A review from the American Society for Microbiology describes this transformation as a “culture divide” between studying “wild” versus culture-grown microbes.

But in the big picture this “culture divide” reflects not just the development of new technologies but also a growing understanding that living organisms and systems can only be understood in an ecological context shaped by their interactions with one another.