Microbiome
The microbiome is the community of microorganisms that lives in a particular habitat, together with their genes and the conditions they create there. The habitat can be the human gut, a patch of skin, a spoonful of soil or a liter of seawater. The word is often used for the organisms alone, for which the stricter term is microbiota. A human body carries bacteria, archaea, fungi and viruses, most of them in the large intestine, where the community does work the body cannot do for itself: it ferments fibers the human enzymes cannot cut, makes vitamins, and trains the immune system.
Numbers
For decades the textbooks said that bacteria in the body outnumber human cells ten to one. The figure came from an old back-of-the-envelope calculation. In 2016 Sender, Fuchs and Milo redid the count for a reference man of 70 kg and found about 3.8 × 1013 bacteria and 3.0 × 1013 human cells, a ratio of about 1.3 to 1, with a total bacterial mass of about 0.2 kg.[1] Most human cells by count are red blood cells, which carry no nucleus. By gene count the microbes lead by a wide margin: a catalogue of the genes of the gut community, built from the stool of 124 Europeans, held 3.3 million genes, some 150 times the number in the human genome.[2]
Other habitats
Every habitat has one, and the human gut is a small case. In the sea, a review of marine viruses concluded that they are the most numerous biological entities there and that about 1023 viral infections occur each second, a major cause of death among marine organisms.[3] Soil, the skin, a sourdough starter and a hospital sink are others.
History
Antonie van Leeuwenhoek saw the first members of the community in 1683, when he scraped the plaque from his own teeth and from those of others and described the "animalcules" that moved in it in a letter to the Royal Society (see Antonie van Leeuwenhoek).[4] For three centuries the community was studied by growing what could be grown, and most of it could not be. The turn came with sequencing: the gene for the small ribosomal RNA, about 1,500 base pairs long and present in every bacterium, lets a community be counted without culturing it, and shotgun sequencing of all the DNA in a sample reads its genes as well.
The word is older than the field it names. John Whipps and colleagues used microbiome in 1988 for a characteristic microbial community in a well-defined habitat of distinct physical and chemical properties.[5] It spread after Joshua Lederberg and Alexa McCray used it in 2001 in a short essay on the suffix -ome.[6] The United States National Institutes of Health began the Human Microbiome Project in 2007, and in 2012 its consortium reported the healthy community of adults across many body sites, finding wide differences in who was present from one person to the next and a much steadier set of metabolic functions.[7]
Medicine
The community protects the host from infection by taking up the space, and antibiotics that clear it can let an intruder in. Clostridioides difficile is the best-known intruder, and the clearest evidence for treating the microbiome as a whole comes from it. In a Dutch trial of recurrent infection, 13 of 16 patients (81 percent) who received a suspension of donor stool through a tube into the small intestine were free of diarrhea after the first infusion, and the trial was stopped early at an interim analysis.[8]
Sequencing
Nanopore sequencers read DNA molecules whole, and the length of a read matters for a microbial community, because a read that covers the entire 16S gene, and not a short piece of it, separates species that short reads cannot (see MinION and Nanopore sequencing).
In games
Molecular Reality Corporation has planned games around communities of microbes. The memo "Early Releases on Maxine's Quest" lists as the analytes of Raindrop Planet "microbial communities within a 'raindrop planet' micro-incubator accessory". Its last entry, Poop of the Gods, gives its science as "in fimo biology", and its samples as "Poop! From diverse species, irradiated to destroy biohazards in samples we ship".[9] Irradiation kills the organisms and leaves their cells and particles, so the samples would have been a microbiome without the microbes. Neither game was made.
See also
References
- ^ Sender, R.; Fuchs, S.; Milo, R. (2016). "Revised estimates for the number of human and bacteria cells in the body". PLOS Biology 14 (8): e1002533. doi:10.1371/journal.pbio.1002533.
- ^ Qin, J.; et al. (2010). "A human gut microbial gene catalogue established by metagenomic sequencing". Nature 464: 59-65. doi:10.1038/nature08821.
- ^ Suttle, C. A. (2007). "Marine viruses: major players in the global ecosystem". Nature Reviews Microbiology 5 (10): 801-812. doi:10.1038/nrmicro1750.
- ^ Dobell, C. (1932). Antony van Leeuwenhoek and His "Little Animals". Harcourt, Brace and Company.
- ^ Whipps, J.; Lewis, K.; Cooke, R. (1988). "Mycoparasitism and plant disease control". In Burge, M. N. (ed.). Fungi in Biological Control Systems. Manchester University Press.
- ^ Lederberg, J.; McCray, A. T. (2001). "'Ome sweet 'omics: a genealogical treasury of words". The Scientist 15 (7): 8.
- ^ Human Microbiome Project Consortium (2012). "Structure, function and diversity of the healthy human microbiome". Nature 486 (7402): 207-214. doi:10.1038/nature11234.
- ^ van Nood, E.; et al. (2013). "Duodenal infusion of donor feces for recurrent Clostridium difficile". New England Journal of Medicine 368 (5): 407-415. doi:10.1056/NEJMoa1205037.
- ^ "Early Releases on Maxine's Quest". Molecular Reality Corporation. 2022.