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Holobionts: a new Paradigm to Understand the Role of Humankind in the Ecosystem

You are a holobiont, I am a holobiont, we are all holobionts. "Holobiont" means, literally, "whole living creature." It ...

Wednesday, August 12, 2020

Longevity secrets of a 100-year old holobiont

 

These four holobionts are related by vertical gene transmission through their female organisms. Among other things, their mitochondria have all the same DNA. The oldest of the three, Liliana, is 100 year old. There follow Grazia (68), Donata (31) and Aurora (1). Photo taken in July 2020

When my mother-in-law, Liliana, turned 100 last month, several people asked me what is the secret of her longevity. Not only it is not usual to reach that age, but to reach it in relatively good conditions. Liliana surely has problems: she walks very slowly and she tends to forget things. But her mind still works and, the day of her birthday, she categorically refused to be carried to the garden where we were having the celebration. She insisted to walk there by her own, even climbing the steps of the stairs leading there. It took her a lot of time, but she made it.

As you know, there is an entire field of research that studies centenarians. In particular, the gut microbiota of centenarians seem to age together with the main organism, but we don't know exactly how longevity is related to these modifications. So, here I'll just tell you something about Liliana and you may make your own deductions on what may be the ways to reach a very old age, still healthy.

First of all, Liliana was born in 1920 and she was young in a world that was very different from ours. The kind of diet, the way of living, the ways of seeing the world -- she might as well have been born on another planet. Imagine a world where there is no central heating, no TV, no telephone, where women still washed clothes by hand and hung them to dry out of the windows. A world without showers, only bathtubs where the water had to be heated by a wood fire. In the morning, there were standalone washbasins in the bedrooms where you could wash your face when you woke up. In winter, it was not uncommon to find that the water had frozen solid in the basin. 

It was a world where cars were rare and reserved for the rich: life was mainly within the area that could be reached on foot. And when a boy wanted to woo a girl, he would normally use a method already described by Boccaccio in his "Decameron" (14th century), that is making "passes" on foot under the windows of his beloved. Liliana confirmed to me that this was the way her future husband courted her, in the late 1930s. 

Coming of age in Italy during the 1930s meant a very different kind of life for women. Liliana never learned to drive a car and she can't even ride a bicycle. She completed he middle school curriculum ("scuola media" in Italian), but even for a middle-class girl, as she was, it would have been considered a little weird to continue her studies. She was supposed to become a housewife, and she did: she never had a salaried job during all of her life, although she worked occasionally as a seamstress. But her life was far from being easy. She went through the ordeal of WW2 when she survived the bombings and the shelling of Florence. Her boyfriend was drafted in the Italian army and he barely survived the war in North Africa, then he was wounded in the Italian civil war in 1944. The war may have been a watershed for many people alive today: those who survived it were especially resilient people. 

So, Liliana had an eventful life. One reason was her decision to marry a Sicilian man, something that was considered a scandal in his family. In the 1940s it was like, say, if today a middle-class American girl were to decide to marry a poor boy from Afghanistan. For Liliana, that implied several adventures but she was stubborn. She wanted that boy and she had it. Eventually she settled with her husband in the house that her grandfather had bought for the whole family in Florence and where she is still living today. She had three children, all born at home. Right now, she has four grand-children and two great-grand children.

As you can imagine from what I just told you, Liliana could be, and still is, a rather stubborn character. But I can also say that she is not very aggressive, she has always been flexible and friendly to everybody. A positive character in many ways, I have never seen her truly angry or mad at someone. Maybe this easygoing character was a help for her in getting old so gracefully. 

How about Liliana's diet? I can tell you that if you want to have some idea of what Liliana eats today, you can find it in books such as  "A Room with a View" (1908) by E.M. Forster and "Etruscan Places" (1932) by D.H. Lawrence. Incredible as it may sound, there was a time when the British would complain about Italian cuisine: the tasteless soups, the hard-to-chew boiled meat, the uninspiring kind of cheese made from sheep milk, and the mysterious castagnaccio that, according to Forster, tasted "partly of the paper in which it was wrapped, partly of hair oil, partly of the great unknown." And I have a feeling that Forster really wanted to write "the great unwashed." 

Today, Liliana still eats those thin soups that Lawrence hated and that nobody would want anymore in Florence. She eats cheese, eggs, and a little meat, not much but she is not vegetarian. She likes cooked vegetables, she seems to be a little wary of raw greens and she never cultivated anything edible in her garden -- she was a housewife, not a peasant. She is not fond of pizza, but occasionally she eats it. She never went to a Chinese restaurant in her life, she knows what a "hamburger" is (she can make them at home) but she has no idea of what a McDonald's restaurant might look like. She doesn't drink wine and she has never tasted beer in all her life. One characteristic that may be relevant to her longevity is how she tends to eat slowly. And she never-ever was overweight.

Then, how about Liliana's microbiota? We have no analysis of it, but I can tell you that she had flatworms in her gut for a long time. Some people say that flatworms are part of our biome and that they are good for health. On this point, I can't say much, but surely flatworms didn't harm Liliana. Then, I can also tell you that she never took a shower in her life and she never washed her hair with soap. On this, she seems to have been extremely modern, following the advice we are receiving today from James Hamblin in his recent book "Clean." Hamblin has not been taking showers for 5 years, not much in comparison to Liliana who has been shower-less for much longer. In both cases, anyway, the effect on preserving one's skin's microbiota seems to have been good. At 100, Liliana still has thick, white hair. 

What else? Liliana told me that once she took a bath in the sea. She didn't like it and she never wanted to repeat the experience. She hated the sunshine and she would never dream of sunbathing. She never took an airplane flight, her longest trip ever was from Florence to Sicily, for her honeymoon. It was just after the war and the trip took two days by an old, chugging steam train.

Among other things, Liliana always maintained a deep distrust in medical doctors and in medicines. For most of her life she succeeded in not seeing doctors and avoiding pills of any kind. Now, of course, she needs various pills everyday, but not so many. Ah... and of course she never smoke cigarettes nor indulged in any kind of what we call today "recreational drugs." She did like coffee, though, although she can't drink it anymore.

So, where is Liliana's secret of longevity? Hard to say. Maybe we could conclude that it consists in not taking too many showers, eating a little of everything, and slowly. Maybe eating thin soups helps, just as having survived a major world war. And a little coffee won't harm you. But maybe the main point is to stand by one's ideas but also take life as it comes. We are all holobionts, just passengers of the ecosystem of this planet that's engaged in an immense journey that has been ongoing for billions of years. And onward we go, fellow holobionts!


Monday, August 10, 2020

The Virome: Viruses are an essential part of the human holobiont

 

 
 
 
Eradicating viruses and bacteria may not be so easy as some people think. We are surrounded by viruses, we eat viruses, we drink viruses, we breathe viruses. And the "virome" is an essential part of the human holobiont.

From "Half-Earth" by E. O. Wilson (p. 125).
 
"Although recognized only in 1988, Prochlorococcus are far from rare. They are in fact the most abundant organism in tropical and subtropical seas around the world. They live in waters as deep as two hundred meters and reach local densities of more than a hundred thousand per millimeter. Because the tiny cells account for 20 to 40 percent of the biomass of all photosynthetic organisms present between 40 N and 40 S in the open ocean, they are responsible for up to half the local net primary production.
 
Yet, if Prochlorococcus along with a second superabundant bacterium, Pelagibacter, are the most important organisms, might they be the prey of viruses that are even smaller? Experts used to think that such micro-predators are at best relatively rare. In 2013, however, new methods in the fast-moving field of ultramicroscopic research revealed the presence of viruses on an averaged of billions per liter of seawater, all are bacteriophages (literally, eaters of bacteria), of which one HTVC010P is the most abundant... it must be classified as the most abundant known species on Earth.

Thursday, August 6, 2020

But what is a "superorganism," in the end?

What is a superorganism, exactly?

I was mulling over this question and I came up with the classic example: the ant colony is supposed to be a superorganism in the sense that all the organisms in it share the same genome, just like in a human beings all cells have the same DNA (except mitochondria, of course).

But no, wait! That cannot be: ants are sisters, not clones. They may even have different fathers. For a quirk of the genetic setup of male ants, ant sisters share 75% of their genes, not 50% as human siblings do. But they are not clones. So an ant colony is not a superorganism, but a kind of tightly knit holobiont.

But then, a discovery: that's not true, either! As reported in this paper, there are ant colonies where all the ants are clones of each other! Unbelievably, some ants have discover tricks to completely eliminate the need of males: yes, no males and no queens. They reproduce by parthenogenesis. These colonies are true superorganisms, not holobionts. And I keep discovering new things: one that starts to be very common is that males seem to be obnoxious and useless in all species!




Saturday, August 1, 2020

The Earth Goddess According to Jenny Jinya






Jenny Jinya is a phenomenal German artist who knows something about empathy, the fundamental element that keeps together the multiform creatures we call "holobionts."

For a taste of her awesome work, you may start from this one. (be careful, this is powerful stuff -- it may make you cry like a child).

In the most recent comic strip by Jenny Jinya, we even see appearing the Goddess of life herself, mistress of all the holobionts of Earth. You can find it here. Enjoy the good ending!





Wednesday, July 29, 2020

A happy holobiont is a holobiont that takes care of its microbiome


An obviously unhappy holobiont engaged in exterminating its own microbiome. Bad idea.

The epidemic of biophobia is still raging worldwide, with people still washing their hands with poisonous substances, convinced to do something good, or forced by law to do so.

Not a good idea. You skin microbiome is precious to you, among other things it is the first true barrier against infections. Some people are recognizing the problem, as it is described in a recent article on "The Guardian"

Just an excerpt:
Hand-washing aside, James Hamblin has not used soap for five years. He warns that our obsession with being clean is harming the microbiome that keeps us healthy
Take care of your microbiome, and be a happy holobiont!



(h/t Miguel Martinez)

Tuesday, July 21, 2020

Sex and Death among Holobionts and Organisms

My mother in law, Liliana, turns 100 today. Happy Birthday, Liliana!

Both holobionts and organisms have to fight entropic decay. Holobionts do that by continuously changing their hologenome in a horizontal exchange of information. Organisms do the same by the vertical mixing of their genome in the process called sexual reproduction. Both methods are driven by natural selection.
The second strategy, sexual reproduction, brings the need of eliminating the old genomes by the process of aging. True holobionts never die (think of a forest), but organisms do. Too bad for organisms, but it is a choice (and a lot of fun, too!). 
Liliana turned out to be a successful and resilient organism. So far, she has three daughters, a son, three grandsons, one grand-daughter and, recently, two great-grand daughters. Not bad!

Saturday, July 18, 2020

The March of the Holobots




I am just back from a scientific meeting held in a small city in the mountains, you know, like things were.... when? Was it the Pleistocene, when people met in person to discuss things? Or was it before the PETM, during the Paleocene? Anyway, you learn things while having discussions at dinner with the other attendees. And I had a very interesting dinner with a group of roboticists. Many, many ideas. One I came up with is that of the "Holobot" -- the solid state equivalent of the holobiont! 

Bots are not based on cells, and they have no genetic code, either. So they are born holobionts.We are witnessing the birth of a new ecosystem that we might describe with the words of a recent article on Quanta Magazine (h/t Chuck Pezeshky): 


"Within this theory, individuals can be cells, tissues, organisms, colonies, companies, political institutions, online groups, artificial intelligence or cities — even ideas or theories, according to Krakauer. “What we’re trying to do is discover a whole zoo of life forms that extend far beyond what we have conventionally called living,”
So, the bots we are building can be seen as individuals and they do fulfill this extended definition of "life" -- a dynamic phenomenon that extends in time, not being just limited in space. It is just that they are not the same kind of life as ours. And so, onward, fellow holobots!





This subject is also being discussed on the Facebook group "The Proud Holobionts"