The Tiny Shiny was originally published in hardcopy in 2011.
Geneticists have long used twins to study the relative role of nature versus nurture and how each affects human disease, behavior, and health. A new field is emerging where twins are being used to understand what shapes the human microbiome -the collection of microbes living in and on our bodies. Our bodies contain 10 times more microbial cells than human cells, and 100 times more microbial genes than human genes. We are thus a complex system comprised of multiple organisms—a 'supraorganism'—and the interactions among our human and microbe components influence our health and well-being .
Several studies have used comparisons between identical and fraternal twins to quantify the heritability of the gut microbiome ,  . The gut features prominently in human microbiome research because it harbors our largest collection of microbes, exceeding 1011 cells per milliliter of colonic content. The gut microbial ecosystem serves numerous functions, including protection against pathogens, nutrient processing, and the regulation of fat storage. Human microbiome research is a relatively new field, and the effect of host genotype on the gut microbiome remains unclear. To date, twin studies suggest that host genetic factors and environmental exposures are both important drivers of gut microbial community composition .
Viruses are the most abundant organisms on the planet, and can be found as parasites in all types of organisms. Derived from the Greek word for “devour”, the bacteriophage, or phage, is a virus that specifically preys on bacteria. Virulent phages attack by attaching to the surface of bacteria, drilling a hole through the bacterial cell wall, and injecting their DNA into the cell.
Bacteria are greatly outnumbered by phages in many environments, and are under constant threat of phage predation. Bacteria have thus evolved mechanisms to evade phage infection and killing, and in turn phage have evolved ways to continue infecting and killing resistant bacteria. This bacteria-phage co-evolution has been described as an evolutionary arms race. The influence of this arms race is thought to be far reaching, impacting global climate and the evolution of virulence in human pathogens .
Once phage DNA is inside the host cell, the phage commandeers the machinery of the host cell and thousands of new phages are created. The bacterium then bursts open and dies, and the newly formed phages are released. These released phages infect other susceptible bacterial cells in the vicinity, and the viral multiplication cycle is repeated.
Doubling is a characteristic feature of microbial life. Most single-celled microbes such as Bacteria and Archaea reproduce by a doubling process called binary fission. Unlike sexual reproduction, binary fission is an asexual process by which offspring arise from a single parent, and inherit the genes of that parent only. The mother cell grows and divides in half, creating two daughter cells, which can loosely be thought of as the mother dying at childbirth while having twins.
The time required for a cell population to double is a key life history trait of microbes, because it can influence how rapidly the population colonizes a new environment. Vibrio parahaemolyticus, a bacterium that causes seafood poisoning, has a doubling time as short as eight minutes under ideal conditions. Gone unchecked, this rate of growth will result in more than one million cells borne from one parent cell in less than three hours.
The mouth is a complex microbial ecosystem housing a myriad of habitats including teeth, tongue, cheek, lip, and saliva. Microbes are abundant in the mouth, with densities ranging from 108 -1011 bacterial cells/cm3 in saliva and dental plaque, respectively . The mouth is also diverse, harboring thousands and possibly tens of thousands of distinct bacterial species . Because the mouth is a major gateway for microbes into the human body, oral health and general health are intimately linked.
Saliva is a significant mode of transport for microbes to move from the mouth to other parts of the body, such as the gut. A person’s average daily flow of saliva ranges between 1 – 1.5 liters, and more than 1011 salivary bacteria may be swallowed daily.
Scientists are beginning to explore the salivary microbiome, and how microbial community composition in spit varies from person to person. The results are surprising. Although there is high diversity in the salivary microbiome within and among individuals, there is little geographic structure. In other words, your neighbor’s spit is just as likely to be as similar to yours as the spit of someone on the other side of the globe .
Fingerprints have been used as a means of personal identification for thousands of years. Every human has a unique pattern of ridges, whorls and valleys on the tips of their fingers that leave a mark on nearly everything they touch; this forms the basis of forensic fingerprinting.
In recent years scientists have been exploring the concept of forensic microbial fingerprinting. Studies of skin-associated microbes suggest that humans harbor a personally unique microbial community on their hands, and that these hand-associated collections of microbes are not easily disturbed (e.g. by hand washing) .
Further, data show that humans leave a “trail” of their fingertip-associated microbes on the objects that they touch . Although still in the development phase, it is feasible that microbial fingerprinting will be a standard forensics tool accompanying human fingerprint and DNA analyses.
Advances in DNA sequencing technology have radically shifted our understanding of microbial biodiversity. Most microorganisms cannot be identified morphologically and, until recently, could only be identified using culture-based methods in the laboratory. But only a small fraction of microbial life – some say less than 1% - can be detected using culturing techniques. Scientists are now using genes as a yardstick to quantify the evolutionary relatedness among Earth’s organisms (the “Tree of Life”). This approach entails comparing the differences in DNA sequences of specific genes (the order of the nucleotide bases adenine (A), cytosine (C), guanine (G), and thymine (T)) between pairs of organisms to quantify the evolutionary distance among the organisms.
The ribosomal RNA gene-based Tree of Life significantly differs from the 5-kingdom model taught in high school not long ago, which was comprised of Animals, Plants, Fungi, Protists, and Monera. Rather, it groups organisms into three major branches, or domains: Eukarya (including plants and animals) and the single celled organisms Bacteria and Archaea. This molecular perspective shows that most of the genetic diversity on Earth is comprised of microbes organisms invisible to the naked eye . Recent research by microbiologists stalking the dark matter of the biological universe suggests there may be a fourth domain in the Tree of Life, although its existence remains uncertain.
Illustrations by Steve Green
- Turnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C., Knight, R., & Gordon, J. I. (2007). The human microbiome project: exploring the microbial part of ourselves in a changing world. Nature, 449(7164), 804.
- Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., … others. (2009). A core gut microbiome in obese and lean twins. Nature, 457(7228), 480.
- Hansen, E. E., Lozupone, C. A., Rey, F. E., Wu, M., Guruge, J. L., Narra, A., … Gordon, J. I. (2011). Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins. Proceedings of the National Academy of Sciences, 108(Supplement_1), 4599–4606. https://doi.org/10.1073/pnas.1000071108
- Spor, A., Koren, O., & Ley, R. (2011). Unravelling the effects of the environment and host genotype on the gut microbiome. Nature Reviews Microbiology, 9(4), 279–290. https://doi.org/10.1038/nrmicro2540
- Stern, A., & Sorek, R. (2010). The phage-host arms race: Shaping the evolution of microbes. BioEssays, 33(1), 43–51. https://doi.org/10.1002/bies.201000071
- Lazarevic, V., Whiteson, K., Hernandez, D., Francois, P., & Schrenzel, J. (2010). Study of inter- and intra-individual variations in the salivary microbiota. BMC Genomics, 11(1), 523. https://doi.org/10.1186/1471-2164-11-523
- Lazarevic, V., Whiteson, K., Huse, S., Hernandez, D., Farinelli, L., Østerås, M., … François, P. (2009). Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. Journal of Microbiological Methods, 79(3), 266–271. https://doi.org/10.1016/j.mimet.2009.09.012
- Nasidze, I., Li, J., Quinque, D., Tang, K., & Stoneking, M. (2009). Global diversity in the human salivary microbiome. Genome Research, 19(4), 636–643. https://doi.org/10.1101/gr.084616.108
- Fierer, N., Hamady, M., Lauber, C. L., & Knight, R. (2008). The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proceedings of the National Academy of Sciences, 105(46), 17994–17999. https://doi.org/10.1073/pnas.0807920105
- Fierer, N., Lauber, C. L., Zhou, N., McDonald, D., Costello, E. K., & Knight, R. (2010). Forensic identification using skin bacterial communities. Proceedings of the National Academy of Sciences, 107(14), 6477–6481. https://doi.org/10.1073/pnas.1000162107
- Pace, N. R. (1997). A molecular view of microbial diversity and the biosphere. Science, 276(5313), 734–740.