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Metagenomics: Exploring Microbiomes at Nature’s New Frontiers

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What is Metagenomics? 

“Metagenomics is the study of microbial communities via DNA extracted from the whole population rather than looking at the individual organisms within it,” says Professor Penny Hirsch, Research Scientist at Rothamsted Research.

The technique can help uncover what microorganisms are present in a sample, determine their relative abundances and get a handle on their biochemical pathways.

“It gives you a global view of what’s happening in a complex microbial community in a way that is technically quite straightforward,” says Professor Mark Pallen, Research Leader at the Quadram Institute.

It’s a powerful approach that’s enabling scientists to explore microbial life in environments that are challenging to study, including in soil or the human gut.

Soil Metagenomics: Opening the Black Box

Traditionally, microbiology has relied upon isolating and cultivating individual species in the laboratory. But this has left many organisms out of reach – as they are too difficult to grow under standard culture techniques.

“Soil is the best example because it’s a kind of black box and we know can only culture around 1% of the organisms that live in it,” explains Hirsch.

But metagenomics is now enabling scientists to study soil ecosystems in extraordinary detail, helping them unpick the role of microorganisms in nutrient cycles or in suppressing plant pathogens.

“We need to be able to understand soils so we can manage them more efficiently – so, for instance, we can optimize their release of things like greenhouse gases,” explains Hirsch.

The approach can also help detect potential sources of antibiotic resistance genes and track their spread through the environment. Conversely, it could also offer a rich new source of potential new antibiotics.

Soil is packed full of microorganisms which cannot be cultured in the lab, but metagenomics is helping bring them into the light. 

A Quantum Leap in Metagenomic Sequencing

A key enabler of metagenomics was the rapid and dramatic improvements in DNA sequencing technologies that happened around a decade ago.

“It would have been completely impossible to sequence something like DNA extracted from soil, it was far too complex,” explains Hirsch.

But as the cost went down and the throughput went up, it became feasible to sequence at the required depth of coverage – and this happened in tandem with key advances in bioinformatics.

“You need a big database and the ability to match sequences against it – without it you wouldn’t know what things are,” says Hirsch.

And big collaborative projects like CLIMB (Cloud Infrastructure for Microbial Bioinformatics) are also providing support with data analysis.

“I think all those things running in parallel – the advances in sequencing, bioinformatics and the infrastructure around it are all making this a lot more tractable than it would have been a few years ago,” says Pallen.

Exploring Microbial ‘Dark Matter’

Metagenomics is providing new and unparalleled insights into microbial communities, uncovering a wealth of new biodiversity.

“We’re discovering so much hidden biology, there’s hidden taxonomy and there are many organisms we didn’t even know were there,” says Pallen. “For example, we did some metagenomics of the chicken gut and many of the organisms we discovered were previously unknown species, new to science.”

In fact, there has been such an explosion in the discovery of new microbial species that this has led to an expansion of the tree of life known as the Candidate Phyla Radiation that represents more than 15% of all bacterial diversity.

“They’ve got dozens of new bacterial phyla and they have discovered all these weird things that people just didn’t even know were out there,” says Pallen.

Evolutionary Origins

Metagenomics is also finding organisms in unexpected places. An example is the archaea, primitive single-celled organisms that were thought to live only in extreme environments like oceanic vents or acid mines.

“But we now know they are in soils everywhere – and are relatively common, about 1% of the total community – and they’re actually quite important in nitrogen cycling,” says Hirsch.

Studying the genomes of archaea is also helping explore one of science’s biggest questions, the origins of the big evolutionary lineages within the tree of life.

“At first the archaea looked like bacteria, but their DNA sequence tells us they are very different –more different than we are from trees, for example,” says Hirsch.

Due to these dramatic differences, archaea are now classified in a separate domain to bacteria. And questions are now arising about the origin of eukaryotes, which were previously thought to have derived from bacteria.

“It’s now clear from metagenomics studies that many of the archaea have innovations that were thought to be purely eukaryotic,” says Pallen.

This suggests that eukaryotes actually evolved from the archaeal lineage, rather than bacteria.

Using Metagenomics to Explore the Human Microbiome

Metagenomics is also enabling the study of the billions of microorganisms that live in and on our bodies.

Around a decade ago the Human Microbiome Project set out to perform a census of our resident microorganisms in our gut and other organs. Other efforts are examining those of animals including chickens, pigs and ruminants.

“Within the gut microbiome, there was a hit list of things that nobody’s ever been able to culture. Many of those organisms have been chased down now and people are now getting to the next stage – working out what might be contributing to various disease states,” says Pallen.

Changes to the gut microbiome have been implicated in many conditions from inflammatory bowel disease to diabetes, allergies, obesity and even autism. The hope is that by understanding this, we may able to find ways to reverse the changes or even prevent people from getting those illnesses in the first place.

“And there’s the comparative aspect as well as it turns out there isn’t a single or conserved gut microbiome, but instead an extraordinary diversity between healthy individuals – so we’re also looking at the potential impact of these variations,” explains Pallen.

Overcoming Challenges in Shotgun Metagenomics

Metagenomics relies on next-generation (or shotgun) sequencing, which can detect what genes and what organisms are present in a population. But because it only gives short pieces of DNA, reconstructing whole genomes from individual organisms remains a challenge.

“It’s a bit like doing a jigsaw, but it’s actually worse than that, it’s like if you take 100 jigsaws and then throw them all into one box and then tried to solve them,” explains Pallen.

But hope is on the horizon with the development of long-read sequencing technologies that will enable researchers to see which genes occur together in the same organism.

“So instead of having lots of short bits of maybe up to 500 base pairs, we think it will be possible to extract very long sequences which will give you big chunks of microbial chromosomes,” explains Hirsch.

Another challenge is with the bioinformatics, with the sheer expense on computing time to analyze the huge volumes of data and a lack of clarity on the optimal approach for analysis.

“It’s a constraint, it’s held us back a bit, not just the time it takes to process but the way you interpret things, there hasn’t been a complete consensus on the way you do this yet, which the bioinformaticians need to solve,” says Hirsch.

Metagenomics Analysis: A Powerful Tool of Discovery 

Metagenomics is enabling researchers to dissect out communities living in a range of environments in more detail than ever before.

“It’s kind of a new frontier in a way. It allows you to discover the ‘unknown unknown’ – the things that you didn’t even suspect were out there,” says Pallen.

From studies so far, what’s clear is that is still so much more to discover – what we thought we knew about the living world and the biosphere is only a small part of what’s out there.

“I think it will improve the way that we manage certain environments, whether that be our guts or soils, or our rivers. It will help us to understand what we should or shouldn’t do and what we have to be careful about,” says Hirsch.