From Science Alert:
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. More.
They won’t be easy to isolate because apparently, 99% of microbes cannot be grown under lab conditions. Many have specific requirements and grow slowly.
Here’s the abstract:
Background Microbial genetic diversity is often investigated via the comparison of relatively similar 16S molecules through multiple alignments between reference sequences and novel environmental samples using phylogenetic trees, direct BLAST matches, or phylotypes counts. However, are we missing novel lineages in the microbial dark universe by relying on standard phylogenetic and BLAST methods? If so, how can we probe that universe using alternative approaches? We performed a novel type of multi-marker analysis of genetic diversity exploiting the topology of inclusive sequence similarity networks.
Results Our protocol identified 86 ancient gene families, well distributed and rarely transferred across the 3 domains of life, and retrieved their environmental homologs among 10 million predicted ORFs from human gut samples and other metagenomic projects. Numerous highly divergent environmental homologs were observed in gut samples, although the most divergent genes were over-represented in non-gut environments. In our networks, most divergent environmental genes grouped exclusively with uncultured relatives, in maximal cliques. Sequences within these groups were under strong purifying selection and presented a range of genetic variation comparable to that of a prokaryotic domain.
Conclusions Many genes families included environmental homologs that were highly divergent from cultured homologs: in 79 gene families (including 18 ribosomal proteins), Bacteria and Archaea were less divergent than some groups of environmental sequences were to any cultured or viral homologs. Moreover, some groups of environmental homologs branched very deeply in phylogenetic trees of life, when they were not too divergent to be aligned. 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. Open access – Philippe Lopez, Sébastien Halary, and Eric Bapteste, Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life, Biology Direct
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