Man and his microbiome
Excerpt from the book
Turney J. I am a superorganism! Man and his microbiome (Jon Turney. I, Superorganism: Learning to Love Your Inner Ecosystem). – M.: Laboratory of Knowledge, 2016. Translated from English by Alexey Kapanadze.
The book was published in the Universum series (lead editor – Irina Opimakh).
There are many bacteria and viruses living in each of us – in the mouth, on the skin, in the intestines. They help to digest food and absorb medications, affect our hormonal and immune systems and, moreover, even the brain!
Scientists have called this whole community of microorganisms a microbiome. John Turney talks about the latest research on the microbiome, its origin, growth and role in the development of various diseases (allergies, diabetes, gastrointestinal disorders, cancer and schizophrenia).
Small does not mean simple
Why are bacteria so important? To begin with, these are microbes, that is, very, very small creatures. The length of a typical bacterium along the longest axis is from one to several thousandths of a millimeter. Which means they're easy to miss. Almost all the time of our own (relatively brief) stay on the planet, we had no idea that they even existed. Judging by quite reliable estimates, there are about !!!!1030 (million trillion trillion) bacteria. However, there are large groups among them, about which we know almost nothing. Perhaps we will never establish not only the total number of microorganisms on Earth, but even the total number of their species.
On the other hand, since we are aware of their existence, the small size and rapid growth of these creatures make some of them suitable objects for research – one species at a time. Therefore, with relatively scant information about the global bacteriosphere, scientists have managed to study some microorganisms in incredible detail, especially the universal laboratory favorite – E. coli.
It is enough to get to know her at least a little, and even if you don't recognize all the bacteria in the world, you will be imbued with considerable respect for what bacteria are capable of. Well, yes, they can grow and multiply, that's what makes them alive. They have a complete set of tiny nanodevices for creating copies of their own DNA, reading the information that it stores in itself, and for transmitting it to protein molecules. They are able to digest food molecules, extract energy when they split and use the resulting fragments of molecules to create new ones.
Most of what we know about these processes – from the details of the genetic code (the same in all organisms on Earth) to the network of chemical transformations that serve as the basis of metabolism– we learned from experiments on countless E. coli colonies in laboratory cups. But the contribution of this microorganism to science is far from being limited to this. Further experiments, often conducted in conditions closer to life in nature than to existence in a laboratory cup, and having no competitors in this cup, showed that bacteria are capable of much more.
At the molecular level, they have some kind of sensory organs. No, they can't see or hear, but E. coli and other microbes can detect changes in the concentration of significant molecules around them. They can move independently, using an actively rotating miniature flagellum as a kind of super-mobile tail. They change course to get closer to the molecules they like (i.e. food), or to move away from the molecules they don't like. They adapt to the environment by noticing its changes (for example, temperature changes or the level of availability of certain nutrients). The reaction to changing conditions leads to the activation (or deactivation) of certain genes, and such activation (deactivation) is organized using complex biochemical chains, where molecules arranged in a special way bind to each other. Unicellular cells react to the presence of other cells due to the so-called "quorum sensing", which manifests itself in the fact that certain functions are activated only when the density of the cellular population reaches a given threshold value.
Some bacteria wage chemical wars with others or establish close metabolic relations with them, in which one species devours molecular food that has already been partially processed by another in the process of consumption. They often combine into huge cellular ensembles. This is not yet multicellular life, but something very similar to it in function. Bacteria produce sticky molecules that create a single mucous "biofilm" that holds the ensemble together. Such films often cover surfaces that represent a habitable ecological niche (say, your teeth), and support the existence of a long-lasting bacterial system with a sophisticated mechanism for the division of biochemical labor.
Moreover; as Joshua Lederberg showed in the works of the 1940s that won him the Nobel Prize, they have sex. Actually, to be honest, E. coli and other bacteria are perfectly able to reproduce without the help of anything even remotely resembling sex: they can create clones of genetically identical cells (although mutations occasionally occur). But bacteria do not dismiss other options. From time to time, two bacterial cells connect, and DNA is transferred from one to the other. Thanks to this exchange of genes, the microbial world looks completely different compared to the world of multicellular eukaryotic organisms with their clear differentiation into species. In the world of microbes, genetic fragments are constantly exchanged through the transfer of pieces of the bacterial chromosome or the movement of small DNA rings (plasmids) present in most bacteria, or with the help of bacterial viruses. If nothing like this happens, the bacterium can even capture free DNA from the surrounding space and include some part of it in its chromosome (this process is called transformation).
In addition, with mutation, bacterial DNA usually changes faster than DNA in the chromosomes of other organisms, and not only because of the high rate of reproduction. Microbes in stressful situations (for example, when there is little food) copy DNA less accurately and repair it worse. Is it just a side effect of stress, or is it a clever evolutionary trick that allows you to quickly give a variety of possible answers to the problem that has arisen? Biologists continue to argue about this, but in any case, such hypermutation allows for rapid changes.
Human-like bacteria, bacterial-like people
So, bacteria are more complicated than they seem at first glance. They have adaptability and ingenuity, as befits a life form that somehow manages to survive for three to four billion years. The life and evolutionary history of these ancestors of ours (and now our contemporaries) are intertwined with our own life and evolutionary history, connected with them by countless connections, which we have only recently begun to understand.
Take at least an inconvenient fact for someone that prompted me to write this book: they live inside us. And here Escherichia coli is no exception. The first samples of this bacterium were isolated back in 1885 by Theodor Escherich – from the first feces of newborn infants. These bacteria have proven to be easier to isolate than most other gut bacteria because they live in both the presence and absence of oxygen. A number of the most innocent strains of E. coli live in our colon. They have perfectly adapted to life in the intestines of warm-blooded creatures. On the other hand, there is an equally diverse set of E. coli strains that cause unpleasant symptoms – food poisoning or something worse.
There is also a much stranger form of cohabitation, in which scientists have refused to believe for many years. We know that the basis of the entire biosphere is unicellular prokaryotes. And more complex life forms like you and me, with all the "additions" that came with the advent of the eukaryotic cell endowed with a nucleus, carry the descendants of ancient bacteria.
Our highly organized, large-volume eukaryotic cells have a much greater energy supply compared to prokaryotes, even if we recalculate the energy by their size. A radically new look at the evolution of cells helps to understand how this could happen.
Apparently, the very appearance of complex cells is a highly unlikely event, since bacteria have been the only living organisms on Earth for two billion years. Why did the chemical and physical processes that shaped the energy of cellular evolution make the emergence of eukaryotic complexity so unlikely? This question is explained in Nick Lane's wonderfully reasoned book, The Vital Question (Nick Lane, The Vital Question. — New York: WW Norton & Company, 2015)
Eukaryotes receive energy from intracellular "power plants" – mitochondria. Mitochondria are somewhat similar to bacteria. Why? Because that's what bacteria are. More precisely, they were once bacteria. They have long lost the ability to exist independently, but they still have a small genome of their own, encoding (among other things) DNA copying and information reading apparatus; this is more like bacterial mechanisms, and not those macromolecular miracles that are very different from them, which perform the same work in the cell nucleus.
The explanation was offered by the outstanding American biologist Lynn Margulies (1938-2011) back in the 1960s. In her opinion, some bacterial flirtation billions of years ago led to a symbiosis in which one bacterium began to live inside another. The inner colonist then adapted to the new conditions: he receives everything necessary for life from the surrounding cell in exchange for the energy that he released by chemically breaking down sugars with oxygen. The result was the appearance of a specialized organelle (a "very small organ") in a real, fully-fledged eukaryotic cell. This organelle, the mitochondria, acted as a kind of miniature power plant. What was once a bacterium first became an intracellular parasite, and then a simpler-structured pouch of folded membranes designed to generate energy.
Margulis considered this irreversible cooperation (endosymbiosis) as one of the key evolutionary mechanisms and believed that some other parts of eukaryotic cells have the same origin. The hypothesis is still considered controversial, but now few people argue with the fact that both mitochondria and chloroplasts (performing similar tasks in plants) arose in this way. It's strange to think that all our cells contain these ancient remains. Sometimes the number of such relics reaches thousands. They are still dividing and reproducing independently. We are all still alive thanks to this colossal collection of degraded bacteria.
Finally, there are bacterial remains that perform other important work in all other types of cells. In essence, this is simply a consequence of the course of the history of life and evolution in a downward direction. All of Darwin's "infinite most beautiful forms of life" have a common ancestor; he probably looked very much like some bacteria that still exist today. This ancient ancestor of ours has already managed to acquire many necessary genes and many important functions that proteins perform in cells; this means that proteins, and therefore the genes where information for their synthesis is stored, change very little during evolution. When proteins are already active, any changes that occur through DNA mutations tend to worsen their work, so that this change disappears in the course of natural selection, relentlessly screening out unsuitable new ideas.
In principle, we all knew this, but the recent exploits of gene decoders, which gave us the opportunity to study entire genomes of large and small organisms, showed how important these factors are and how closely interconnected all the inhabitants of our planet are. Compare the genetic chains and you will find that 37% of human genes are very similar to bacterial genes. This means that these genes have already appeared in our common ancestor more than two billion years ago. Meanwhile, we share 28% of genes with other eukaryotes, 16% of genes with other animals, and only 6% with other primates (we also have a corresponding common ancestor) (McFall-Ngai et al., 2013). So whatever contribution the bacteria cohabiting with us make to our lives today, in an evolutionary sense, more than a third of our genes (among other gifts) are provided to us by bacteria.
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23.09.2016