Metagenomics analyses simultaneously the genomes of everything in a sample—be it of soil, water, leaf litter or a mashed up part of a plant or animal. That can lead to some illuminating discoveries
Look at it another way, though, and you arrive at a figure roughly twice as large. That adds in the archaean, bacterial, fungal and protist cells which occupy the mouth, gut, skin, lungs and almost every other surface, nook and cranny of the human body. These cells contribute only about 0.3% to a person’s body weight. But being, on the whole, much smaller than “proper” human cells, they are almost equally numerous.
Dr Bell and his colleagues are looking, in particular, at insects, amphibians and plants. Besides being eukaryotes—meaning their cells have proper nuclei and contain complex structures called organelles—these have little enough in common, evolutionarily speaking. Each group was picked for study because viewing its members as holobionts rather than individual creatures is illuminating.
Plants find themselves in the centre’s crosshairs because most are accompanied by a “rhizosphere” of bacteria and fungi attached to, or even penetrating their roots. The rhizosphere’s biochemical pathways increase the range of nutrients available to the holobiont as a whole. The rhizosphere is sustained in turn by carbohydrates and other nutrients synthesised by the holobiont’s plant component.Work like Dr Bell’s means the idea of holobionts as a meaningful category is catching on .
Sometimes, as with bark beetles and their mycangia, the evolutionary integration of primary host and microbiome is obvious even without a genetic analysis., an Australian termite, relies on gut microbes to break the tough wood it eats into molecules which the holobiont’s animal part can metabolise., one of those fibre-digesting components, is itself a composite of a protist and four types of bacteria.
The gut microbiome is thus deeply integrated with the mammalian part of the human holobiont—as can be seen when that integration goes wrong. Dysbiosis, as this is known, is at least associated with, and in many cases probably helps cause, obesity, diabetes, high blood pressure, atherosclerosis, asthma, inflammatory bowel disease, some liver diseases, various cancers, autism, Parkinson’s disease and depression. And this is not an exhaustive list.
Jean-Michel Ané of the University of Wisconsin-Madison, who is, inter alia, a scientific adviser to Pivot, has two other nitrogen-fixing ideas up his sleeve. One, observing that legumes grow special root nodules to house nitrogen-fixing bacteria, is to reshape the roots of cereals so that they grow similar nodules. He and his colleagues have identified two leguminous genes that, when transplanted to poplars cause them to grow nodules too.
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