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Scientists think a whole new type of life form could be living in our microbiome.

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We are only now just beginning to understand the life forms in the microbiome.

Our digestive system is home to a weird and wonderful collection of bacteria, and we're only just beginning to understand how these unique populations are not just having an effect how we digest our food, but potentially even how we think and behave.

And now new research has found that the situation in our guts is even stranger than we thought, with biologists suggesting that we may need to define a whole new type of life form to describe these tiny residents.

A team from the Pierre and Marie Curie University in Paris, France has been attempting to redefine the way we classify the organisms living inside our colons. By studying 86 different gene families, they've discovered DNA sequences that are different enough to suggest they're beyond the three forms of life that we currently recognise.

Those forms are classified as bacteria, archaea, and eukaryotes. Archaea were once bundled with bacteria, but have a different biochemical make-up and can survive in more extreme conditions, whereas eukaryotes refers to fungi, plants, and animals.

What the Paris team, led by Philippe Lopez and Eric Bapteste, found makes the case for a fourth type being added to that list, but it's important not to get ahead of ourselves - it might also mean that the existing types are more genetically diverse than we thought.

New Scientist explains the findings, published in the journal Biology Direct.

"They analysed microbiome samples, recovering about 230,000 DNA sequences that are related to known sequences in those 86 gene families. They then used these sequences as the starting point for a second analysis - a little like digging deeper into your ancestry by using your parents' DNA rather than your own to guide the search. This revealed an additional 80,000 stretches of microbial DNA that belonged in the 86 gene families.

But the sequence of bases was highly unusual in about one-third of the DNA - it shared just 60 percent or less of its identity with any known gene sequences. That degree of difference is what you might expect to separate different domains of life, such as bacteria and archaea." 

But before a fourth domain can be added, scientists will need to isolate and study these organisms in a lab environment, and that's no easy task. Right now, around 99 percent of microbes can't be grown in the lab, which is why there's still so much we don't know about these basic forms of life. Plus many genes are swapped around between microbes, further adding to the confusion, which is one of the reasons why this research focuses on gene families that don't often cross over.

"These results underline how limited our understanding of the most diverse elements of the microbial world remains, and encourage a deeper exploration of natural communities and their genetic resources, hinting at the possibility that still unknown yet major divisions of life have yet to be discovered," concludes the report.

Peer-reviewed ("Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life") :

Redditor mccavity explains like I'm five:

We're just beginning to really delve into the world of the microscopic creatures in our gut. Most of them can't be grown or isolated, so genetic analysis is our best tool. It's like trying to reassemble a library after a hurricane. We copy all the text from the pages lying around, and try to use context and books from other libraries to put it all back in order.

All life evolved from a common ancestor, so they all share some DNA in common. Typically, the more two species, families, genera, etc share DNA sequences, the closer related they are.

We use this information to classify life by relatedness. Humans had a more recent common ancestor with whales than with trout, which has a more recent common ancestor than corn, and this is reflected in the DNA. A change that happened way back in the common ancestor with corn will be present in all four branches, but a change in the common ancestor with whales will only be shared between us, whales, and anything else that branched from that creature. We use this to build a classification system showing how life branched out.

The highest level of classification are the domains. The three domains are prokaryotes (bacteria,) archaea (originally considered bacteria, but reclassified as their own domain because they're so genetically different) and eukaryotes (plants, animals, fungi, amoebae, anything with nuclei and organelles).

These researchers are saying that they found sequences that are as genetically different from the known domains as the domains are from each other. That could mean that there's a type of microscopic living creature that's as different from known life as a bacterial cell is from an animal cell. That's a huge level of difference.

But it isn't that simple. How you compare DNA sequences can affect the level of difference. Back to the library metaphor, are you counting letters, words, or sentences as a difference? If you change one sentence, that can be one change or many. Add in that many organisms, especially microscopic ones, can "swap" DNA with other species not closely related to them, and it gets complicated. So DNA evidence alone isn't proof that a new domain has been discovered. We need to figure out what's carrying this DNA, and why it's so different.

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