Tuesday, November 27, 2018

 ‘Lava-Lamp’ Proteins May Help Cells Cheat Death
With proteins that reversibly self-assemble into droplets, cells may control their metabolism — and harden themselves against harsh conditions.

Hibernating animals put themselves into a largely inert state to survive a hostile winter. Individual cells may do something similar to cope with stressful conditions by solidifying and lowering their metabolism with the help of phase-shifting proteins.
Rachel Suggs for Quanta Magazine

November 26, 2018

“If you make a discovery and at first people tell you that it can’t be right, and then they eventually switch to telling you ‘we knew that all along,’ then you are probably on to something.” It’s a quip that has stuck in Clifford Brangwynne’s mind. For the biophysicist at Princeton University, that is “exactly what happened with our findings on intracellular liquid phases.”
Think of liquids with different properties that don’t really mix but, under specific circumstances, cluster and separate like the shifting blobs in a lava lamp. That phenomenon, also known as liquid-liquid phase separation, was once considered to be an exclusively chemical process. But less than a decade ago, Brangwynne became one of the first to observe it happening inside cells as well, and ever since then, biologists have been trying to learn its significance.
Now scientists are beginning to understand that evolution has tuned certain proteins to act in aggregate like liquids. Through phase separation, they spontaneously self-assemble into dynamic, membrane-free, dropletlike structures that can perform needed tasks in cells.
In this ‘solidified’ state, a cell can survive starvation.
Vasily Zaburdaev, Max Planck Institute for the Physics of Complex Systems
“Somehow, no one thought that this kind of ability of molecules could be harnessed by evolution to achieve functionality or regulate functions,” said Simon Alberti, a biologist at the Max Planck Institute of Molecular Cell Biology and Genetics (MPICBG) in Dresden, Germany. “The focus was on the individual molecule and not on the collective.”
The breakthrough has big implications for our understanding of cellular organization and function, said Vasily Zaburdaev, a biophysicist at the Max Planck Institute for the Physics of Complex Systems, also in Dresden. One of the latest findings is that phase separation allows certain types of cells to cheat death when they are deprived of nutrients or otherwise put under stress. Phase separation enables the cells to turn a large part of their cytoplasm from a liquid to a solid — essentially putting themselves into a hardy condition of stasis until the nutrients return.
Organelles Without Membranes
Nineteenth-century cell biologists coined the term organelle (“little organ” in Latin) to describe the tiny components they saw inside cells. Even then, pioneers in the field such as the American cell biologist Edmund Beecher Wilson suspected that the jellylike cytoplasm filling cells might hold various liquids “like suspended drops … of different chemical nature.” That early insight found little purchase in biology for almost a century, however: Researchers simply assumed that any droplet-shaped cellular organelles must have an encapsulating lipid membrane to prevent their contents from remixing with the cytoplasm.
Still, electron microscopy by researchers such as L. Dennis Smith of the University of California, Irvine, and Edward Mitchell Eddy of the National Institute of Environmental Health Sciences in the 1960s and early 1970s showed that some organelles simply didn’t seem to have any membrane at all. More membraneless structures continued to be found, such as the nucleolus, a dense structure in the cell nucleus. Yet until 2009, how and why they were forming wasn’t clear.

While studying the distribution of membraneless organelles called P granules (green) in the cells of a roundworm, Clifford Brangwynne and his colleagues discovered that they were liquid droplets of protein, not solid masses.
Courtesy of Clifford Brangwynne/Science
That year, when Brangwynne was a young postdoc at MPICBG, he, his colleague Christian Eckmann and his supervisor Tony Hyman saw something unexpected. They were looking at the uneven and inconsistent distribution of organelles called P granules inside cells of the roundworm Caenorhabditis elegans. P granules were widely assumed to be dense pellets of RNA and protein. But Brangwynne, Eckmann and Hyman saw that the granules were not solid at all. Instead, they appeared to be droplets of liquid that were coalescingat times to form bigger drops, like oil in a well-shaken vinaigrette.
“It was a serendipitous discovery,” Brangwynne said. “When we discovered that they were liquids, a number of quantitative measurements that we had been taking suddenly made perfect sense.” It also changed biologists’ understanding of how cells work.
That initial work by Brangwynne, Eckmann and Hyman triggered an avalanche of papers investigating the assembly and dispersal of various cytoplasmic proteins under various conditions. The evidence was getting stronger that cells had evolved a fine-tuned mechanism for organizing some of their internal structure and processes through phase separation — that is, letting proteins self-assemble into structures that could perform distinct functions.
Michael Rosen, a structural biologist and chairman of the biophysics department at the University of Texas Southwestern Medical Center in Dallas, was the first to reproduce this kind of phase separation in the lab with certain proteins and RNA molecules that could coalesce into droplets. Phase separation seemed to give proteins a reversible way to align and separate again when conditions were right.
In some instances, however, researchers are learning that the process is not reversible — and that this failure represents a malfunction of proteins associated with a broad range of diseases, including neurodegenerative disorders and cancer. For example, Zaburdaev observed that several mutant forms of a protein linked to certain diseases showed abnormal phase-separation behavior.  “Instead of forming nice drops, they form very strange hedgehog structures,” he said.
Solidifying for Survival
Intrigued, Zaburdaev and several of his colleagues, including Alberti, decided to check what happens to proteins when cells are subjected to stresses such as falling temperatures and the sudden disappearance of nutrients. The surprising result they uncovered was that phase separation can be part of a cell’s survival mechanism.
The cells’ behavior could be likened to hibernation for bears. The animal lays still in a dormant state for weeks, minimizing its expenditure of energy. At a cellular level, phase separation helps the gelatinous cytoplasm make a protective transition into something more solid. “In this ‘solidified’ state, a cell can survive starvation,” Zaburdaev said.

Clifford Brangwynne, a biophysicist at Princeton University, was named a MacArthur Fellow in 2018 for his pioneering work on identifying the role that phase separation plays in cell regulation.
The researchers studied this phenomenon by depriving yeast and amoebas of nutrients. No nutrients means no energy, and yeast cells need energy to pump protons out of their cytoplasm to maintain the neutral pH essential for their biochemistry. “By starving, cells acidified,” Zaburdaev said. Under the more acidic conditions, proteins readily went from a dissolved state to a more condensed and solid one, and the well-mixed cytoplasm separated into clusters of gelatinous blobs.
Simply by varying the acidity of the cells’ environment, the scientists could induce them to switch into this survival state, even without taking away the cells’ nutrients. The cells could rest this way for hours or even days. “We found that the cells are so rigid that they keep their shape” instead of being deformable, Alberti said. They “transition into a completely different material state.”
When their normal pH was later restored, the cells returned to normal, “dividing and living happily,” Zaburdaev said.
The scientists found that they could also trigger phase separation and solidification by completely dehydrating the yeast through osmosis. Different types of stresses seem to induce slightly different solid states, however. Exactly how that works is “something we don’t yet understand,” Alberti said.
Nevertheless, the survival mechanism that the experiments revealed was very simple, Alberti said: When there is stress, extensive phase separation leads to the rigidification of the entire cytoplasm, and the cell turns off its metabolism, like a hibernating bear settling down for the winter.
The comparison to hibernation may be more than figurative. “The cells of hibernating mammals may also solidify inside,” Alberti said. “It’s a perfect way of dealing with these kinds of environmental changes because solidification comes for free. The energy comes out of the temperature change or the drop in pH.” However, the hypothesis that phase separation is involved still needs to be tested, he said.
Immobilized for Metabolic Control
Most recently, Alberti’s team has been probing the phase-separation response of cytoplasmic proteins to stress at the molecular level. Their particular interest is in how it relates to control over cellular metabolism.
The perfect way to turn something off, Alberti said, is to put it into a solid material that can reversibly immobilize it until it’s needed again. “It’s a way of protecting molecules from damage, but also turning them off, storing them for later use.”
The team found that when a protein has a certain identifiable domain or region, the protein will form easily reversible gels. In the absence of this domain, the protein forms an irreversible type of assembly — permanently removing it from further use.
It’s a way of protecting molecules from damage, but also turning them off, storing them for later use.
Simon Alberti, Max Planck Institute of Molecular Cell Biology and Genetics
In effect, this domain modifies the protein’s phase behavior and keeps it reusable. “The domain provides a new possibility, for that protein to assemble into a benign kind of gel and not something from which you cannot come back,” Alberti said.
In one test-tube experiment, the researchers took a solution containing a single type of protein and lowered its pH. They saw molecules of the protein phase-separate from the solution and form gel-like blobs. Then they brought the pH back to neutral, getting the gels to dissolve, “showing exactly what we saw in cells,” Alberti said.
Such results imply that nature has designed the domain sequences to tune the proteins’ material properties. That’s very beneficial, said Dustin Updike, a biologist at the MDI Biological Laboratory in Bar Harbor, Maine, because it gives cells “a mechanism to respond to abrupt stress, such as heat shock, pH or osmotic stress.” Regulatory mechanisms in cells often work at the genetic level, he explained, meaning that they depend on signals reaching the nucleus, initiating gene transcription and the manufacture of an appropriate enzyme. But those events take time. In contrast, phase separations are very rapid — and can provide an almost immediate response to stress.
Does It Really Matter?
Understanding the precise mechanism and effects of phase separation in cells could be highly relevant for a whole range of big biological challenges — from organ preservation and aging research all the way to space travel, according to Zaburdaev.
Recently, for example, the neuroscientist Pietro De Camilli at Yale University and his colleagues found evidence that phase separation might be involved in the controlled release of neurotransmitters at synapses. It had been observed that vesicles containing neurotransmitters routinely hover in clusters near the presynaptic membrane until they are needed. De Camilli’s team showed that a scaffolding protein called synapsin 1 condenses into a liquid phase, along with other proteins, to bind the vesicles into these clusters. When the synapsin is phosphorylated, the droplet rapidly dissipates and the vesicles are freed to spill the neurotransmitters into the synapse.

Lucy Reading-Ikkanda/Quanta Magazine
It’s still early days, though. When Brangwynne and his colleagues published their paper a decade ago, biologists reacted with either total incredulity or hope for a brand-new direction of research. As Updike noted, it can be hard for cell biologists to go from thinking about a phenomenon in terms of protein aggregation to the more complex problem of liquid phase separation, which requires fluid dynamics to describe.
“To me, Cliff’s work was a huge advance that better described the nature of P granules and what we were seeing,” Updike said, in part because it also explained why P granules had evaded biochemical purification for over two decades. “You can purify a granule, but purifying something more similar to an oil droplet is much more of a challenge.”
As ever more scientific papers back up the concept of phase separation as a cellular mechanism, the number of skeptics keeps on dropping, according to Updike and Brangwynne. Questions still remain, though.
When we discovered that [the P granules] were liquids, a number of quantitative measurements that we had been taking suddenly made perfect sense.
Clifford Brangwynne, Princeton University
“One of the criticisms is that some people say every protein can do this,” Alberti said. It’s common knowledge in science that concentrating proteins under various conditions can sometimes make them solidify or liquefy. “But there was never this idea that this could actually be used by cells, that evolution would actually act and use this ability of biomolecules to achieve a functional change such as down-regulating metabolism.”
Susan Wegmann, a biologist at the German Center for Neurodegenerative Diseases (DZNE), said, “So far it has not been shown that phase separation of proteins actually occurs in a living multicellular organism.” The relevance of phase separation in cells to complex problems in neuroscience and other areas is therefore uncertain. “We and others are trying to make that link, but it is of course very difficult and technically challenging. And if it turns out that protein condensation is linked to human diseases such as neurodegeneration, then we have to find smart ways to interfere in a specific manner with it.”
Tim Mitchison, a professor of systems biology at Harvard Medical School, is skeptical about whether phase separation is a generally important concept in biology. “I haven’t seen much evidence for phase separation in the cytoplasm of cells except for a few specific examples, like stress granules,” he said. The concept has seemingly not found much of an audience outside of cell biology: Many researchers either have not yet heard of phase separation or are ignoring the research.
 “Maybe [they’re] waiting until there is more functional evidence,” Mitchison said. He noted that with enough of the right solvent, almost any protein or RNA can be made to phase separate. “But it’s not clear how much of this is physiologically relevant. I’m totally convinced phase separation is a thing, perhaps especially in RNA-protein biology,” he said. “I’m less clear how general it is.”
Brangwynne seems unperturbed by that reservation. He thinks that some skeptics “are asking very valid questions about what this all means for cell function and dysfunction, which is still not well understood.” Others might still be warming up to the idea of predictive quantitative models, he said, “but that is the future of biology.”

Thursday, November 22, 2018

Last week, Israeli media reported of rioting Haredim onboard an El Al plane. The true story turned out to be very different, and deeply revealing.
November 21, 2018 • 12:00 AM

Last Thursday, as New York was struggling with the obstacles presented by 5 mighty inches of snow, El Al Flight 002 to Tel Aviv, scheduled to depart at 6:30 p.m., was delayed. It finally took off at 11:45 p.m., which, ordinarily, is hardly the stuff of front page news. Except that shortly after its landing, the flight became not only the subject of explosive nationwide controversy but also a perfect metaphor for so much that is wrong—and so much that is right—with Israeli society.
The first accounts of Flight 002, appearing in the Israeli press on Saturday, were grim. The snowstorm, in this version of events, caused an inevitable delay, and when the Haredi passengers on board learned that the flight would arrive in Israel only an hour or so before Shabbat, they began to riot. A poorly lit, grainy video was produced, taken onboard the flight, showing religious men flailing their arms and shouting. And a famous passenger—Shimon Sheves, the former director of the Prime Minister’s Office under the late Yitzhak Rabin—posted a widely quoted account of the flight on Facebook featuring “hands raised in the air,” as Sheves described it, “hitting stewardesses, who, in turn, burst out crying.” El Al’s official statement said bluntly that the company will pursue legal charges, “with determination and without compromise,” against any passenger behaving violently.
For 24 hours, the impudence of the Orthodox was all many Israelis heard about, online, on air, and in print. But then Shabbat ended, and the religious passengers on board Flight 002 returned from Athens—where the flight eventually made a pit stop to allow those who wished to observe Shabbat to deplane—with a very different story.
So what really happened en route from New York to Tel Aviv? As we now know, three noteworthy things: First, the delay was caused because the crew arrived at the airport three hours late. Sure, it was snowing, and the roads were a slushy hellscape, but virtually all of the flight’s 400 passengers realized that and had the good sense to allow plenty of time for travel. The professionals of El Al weren’t quite as attentive or wise.
Even more maddening, once the passengers, still on the ground and growing irate, learned that the flight would not land in Israel in time for Shabbat, many asked to return to the gate so that they could leave the plane and spend the weekend stateside before making other travel arrangements. The flight’s captain asked everyone to sit down and buckle up, promising his passengers that he was merely taxiing back to the gate. Instead, without providing any further updates, without adhering to the requisite safety protocols, and in blatant violation of his promise, he simply took off for Israel.
Under the circumstances, you’d understand why the passengers, having been disrespected and lied to, might be upset. But the best was yet to come: When Yehuda Schlesinger, a passenger aboard Flight 002 and a reporter for Yisrael Hayom, returned home from Athens, he saw the viral video that allegedly documented those rascally Haredi men flexing their muscles and threatening violence. He recognized the clip, because he had shot it with his smartphone on Thursday night and shared it on social media. There was only one small problem: The video Schlesinger took was of Haredi men singing and dancing to cheer each other up under difficult circumstances; the video shown on Israeli TV was edited and given a radically different soundtrack, one featuring men shouting in a menacing fashion. When Schlesinger, incensed, pointed this out to Israel’s Channel 10, they apologized and claimed that the soundtrack was swapped due to technical trouble. The term for that in Yiddish is fake news.
But while Israel’s national airline proved to be incompetent, its media mendacious, and its mandarins seething with contempt for their observant brothers and sisters, there’s another side to the story of Flight 002 that deserves to be heard. Far from being uniformly Haredi, as early press reports insisted, the passengers who rushed against the clock in Greece were a wildly diverse bunch: black hatters and wearers of knitted kippot, Ashkenazim and Sephardim, men and women from all across Israel with nothing much in common save for the tradition that has bound us all for millennia. Welcomed by Rav Mendel and Rebbetzin Nechama Hendel, the local Chabad emissaries, these stranded passengers, according to their own accounts, passed a joyous Shabbat, enjoying each other’s company and the spirit of the holy day despite being separated from their luggage and their loved ones waiting at home.
If Israelis are indeed slouching toward elections—as of this week, the government is still teetering on the brink of collapse—you need only look to Flight 002 to discover the nation’s real divides. With the Israeli left having eroded into irrelevance by insisting that only further concessions can stop the surge of terror, voters aren’t divided by significant ideological differences. Instead, Israelis, like Americans, fall squarely into the two camps visible on board the Boeing that snowy night last week. In one corner are those who keep their faith, who come together in times of crisis, and who expect the conversation to remain respectful and those in power to remain accountable. If you’re wondering about their values, just watch Schlesinger’s undoctored video and ask yourself when was the last time you reacted to a major inconvenience by finding some stream of inner happiness and bursting into song in public.
The group in the other corner, sadly, isn’t quite so cheerful. A former senior government official, news reporters and editors, a major airline: All could’ve returned quietly to their homes, taken a long shower, brushed off the ordeals of their ill-fated flight and gone on with their lives. Instead, they felt a need to concoct a sickening little story of the religious behaving badly, drawing on very little evidence and a lot of animosity toward the deplorables who dare expect that the national carrier of the world’s only Jewish state might show some consideration when it comes to observing Shabbat. There’s a term in Yiddish for that, too: It’s prejudice.
One group sang songs and broke bread together, grateful for the gift of community. The other wasted not a moment before taking to the media and portraying their fellow passengers as a benighted mob disdainful of all that is enlightened and good.
If you’ve been paying any attention at all to politics anywhere in the world, you already know which group is likely to prevail in the long run: In Tel Aviv, in Tampa, in Tottenham, and elsewhere, cataclysmic coalitions of tired citizens are coming together, forming movements that are as much personal as they are political. Often, these movements are composed of folks who have no real coherent agenda except the pain of yet again turning on the TV and seeing themselves cast as the butt of the joke, listening to the news and hearing themselves blamed for all ills, reading the paper and learning that their self-appointed moral and intellectual betters have again dug up an opportunity to scorn them. They’ve had enough, and when they vote, they often just vote against that well-dressed person in the emergency exit seat who gently shook her head at the mere sight of a beard and sidelocks or a covered head.
That’s the troubling news. The good news is that while the aircraft of Israeli statehood may, like Flight 002, suffer some occasional turbulence, it always lands safely, and there’s plenty of room onboard for anyone, of any denomination or disposition, capable of coexistence and respect.

Wednesday, November 21, 2018

Should Evolution Treat Our Microbes as Part of Us?
How does evolution select the fittest “individuals” when they are ecosystems made up of hosts and their microbiomes? Biologists debate the need to revise theories.

Microbiome science has revealed the deep interdependencies of animals and plants on their microbial partners, prompting calls for an expansion of evolutionary theory.
Andrew Rae for Quanta Magazine

November 20, 2018

Twilight falls on the Tanzanian plain. As the sky turns a deeper purple, a solitary spotted hyena awakens. She trots along the border of her clan’s territory, marking the boundary with a sour paste from under her tail. She sniffs a passing breeze for hints of itinerant males interested in mating, giving little attention to her stomach’s rumbling over the remnants of the previous night’s hunt or the itch on her flank. The lone hyena chooses what she will do next to make her living.
Except she is not alone. That paste she secretes is produced not by her own cells but by billions of bacteria housed within her scent glands. The scents on the breeze from potential mates also come from unique microbial concoctions. A diverse array of bacteria that line her gut are helping to break down her meal. Others assist her immune system in fending off the hordes of parasites and pathogens trying to invade her skin and other tissues.
Who precisely is it, then, trying to survive on the Tanzanian plain? Can we consider the fates of the hyena and the microbes within her independently? Or does their interaction form something new, greater than each part alone?
“We’ve underestimated the potential contribution of microbes to traits we’ve been studying for decades or centuries,” said Kevin Theis, a microbiologist at Wayne State University who studies the paste-making microbes of the hyena. “If the genes for these important traits are actually in the microbiome and not the animal itself, then we need to take a systems-level approach and look at the host-microbe system as a whole.”

Kevin Theis, a microbiologist at Wayne State University, believes that evolutionary science needs to look at host-microbe systems as a whole.
Courtesy of Kevin Theis
Look closely enough at any plant or animal and you will discover a riot of bacteria, fungi and viruses forming a complex and interconnected ecosystem. A recent explosion of research reveals how deeply we rely on our microbial patterns to keep our bodies functioning, raising profound questions about what it means to be an individual.
Vital functions like digestion and immunity were long assumed to be under the purview of individual organisms, as capabilities developed and were refined through evolution by natural selection — the differential survival and reproduction of individuals. But if our bodies are less an autocracy of identical cells and more a coalition of multitudes, how can we explain their evolution?
Some biologists are calling for a radical upgrade of evolutionary theory, arguing that prevailing ideas, developed from the study of bigger, more easily understood organisms, don’t fit nicely into this new world. Others contend that existing theory just needs to be applied more carefully. All agree that the micro and macro worlds are inescapably interdependent, and that biologists must explore the frontier of their interconnections.
Never Alone
We have never been individuals,” proclaimed a 2012 paper in The Quarterly Review of Biology by Scott Gilbert, a developmental biologist at Swarthmore College, and his colleagues. This bold assertion echoed previous calls for a reconceptualization of complex organisms as new kinds of individuals — holobionts. The term holobiont encompasses a host animal or plant and all its constituent microbes. All genes within a holobiont, belonging to host or microbes, constitute the “hologenome.”
Holobionts and hologenomes are “incontrovertible realities of nature,” wrote Theis and his colleagues in the journal mSystems. Hologenomes contain vastly more genes than the host genome alone, and since at least a fraction of the microbial genes have significant bearing on the survival and reproduction of the host, we need to consider the hologenome as a possible unit of selection if we want to understand the evolution of the holobiont.
“First and foremost, I think of the holobiont and hologenome as structural definitions,” said Seth Bordenstein, an evolutionary biologist at Vanderbilt University. Along with other researchers, Bordenstein argues that fresh language is needed to refer to this entity, given the ubiquity of host-associated microbes in nature. “We accept the chromosome or the genome as structures. The next level up is the hologenome,” he said.

Seth Bordenstein, an evolutionary biologist at Vanderbilt University, argues that the ubiquity of host-associated microbes in nature suggests that “holobionts” need to be recognized as meaningful units.
Courtesy of Seth Bordenstein/Vanderbilt University
“The secondary question is: Does the hologenome matter?” he continued. No one knows what proportion of the microbiome will influence host fitness; many are surely just along for the ride. But if there is some degree of cooperation — for instance, if the host provides shelter or nutrients for some microbes that in return metabolize products the host can’t make on its own — then they are more than just two organisms occupying the same space. They are, to a degree, functionally integrated. And that raises the question of whether the hologenome might also matter evolutionarily.
The tighter the integration, the more closely intertwined the fates of host and microbe become. For such holobionts, Bordenstein says, you can’t understand the evolution of either the host genome or the microbial genomes in isolation because the community of organisms as a whole shapes the traits of the individual. “We need to understand what the microbes make, what the host makes and potentially how those products work together,” he said. The holobiont, he argues, adds up to more than the sum of the host and microbes. Out of their interaction emerges a coherent entity that natural selection might act on alongside other units of selection, like the individual or a gene.
Proponents of this hologenomic concept of evolution argue that if there is a fidelity across generations between hosts and microbes, then the holobiont embodies a coming together of numerous, disparate evolutionary lineages into a singular being, a coalition of many that contributes to the functional integrity of the whole. Only when considering the holobiont as a single entity capable of being shaped as a unit by natural selection can we make sense of its complexities.
Variation and Heritability
What might it mean for a holobiont to evolve through natural selection? How can traits emerging from the holobiont as a whole rather than from any individual line of cells in it be “chosen” by nature and spread in the population? The classic recipe for evolution by natural selection begins with a population of individuals with varying characteristics that affect the number of viable offspring they are likely to have. Those characteristics must be inheritable — that is, passed on with some fidelity from generation to generation. A trait could hypothetically double some lucky individual’s lifespan and number of offspring, but unless that trait gets passed on, it’s an evolutionary dead end.

Lucy Reading-Ikkanda/Quanta Magazine
Do holobionts meet those criteria for evolving entities? Microbes and host genomes can interact in ways that profoundly affect host fitness. But whether we inherit our microbiome in something like the way we inherit our genome remains a point of contention.
Parents do pass along microbes to their offspring. For example, females of some species of stink bug nestle a fecal pellet near freshly laid eggs to serve as the larvae’s first meal, thereby inoculating them with their mother’s gut microbiome. Typically, human babies not born by cesarean section acquire their mother’s vaginal microbes en route to the outside world. Mom’s microbes also rub off on a baby through close contact and breastfeeding. Although eventually the microbial community changes as the child moves more freely through the world, these early microbes play an outsize role in immune system development.
Not all of the microbiome is transferred from parent to offspring, but according to Bordenstein, it doesn’t have to be. “Nobody I know expects the microbiome to be inherited in its entirety, faithfully,” said Bordenstein. But if a significant portion of it is, he and others argue that those interactions and their evolution might be understood as a unit of selection.
Poking Holes in Hologenomes
Other researchers think the hologenome concept of evolution stretches the notion of a selectable unit to the point of incoherence. “Just because the microbes are there with one organism at one time does not mean they are a unit of selection, especially if they are not passed on vertically,” said Joan Strassmann, an evolutionary biologist at Washington University in St. Louis who studies microbes.
“I don’t want to make the strong claim that vertical transmission is absolutely necessary, but it’s certainly the most likely mechanism to lead to the cumulative evolution of the partnership as a whole,” said Derek Skillings, a philosopher of biology at the University of Pennsylvania and the City College of New York.
Skillings and other critics argue that there just isn’t enough evidence of vertical transmission of symbionts to allow for the holobiont to be a coherent evolutionary individual. Many of a host’s microbes are acquired from the outside environment, not from its parents. Even when the environment is shared, there is little reason to assume that a parent’s microbes will make it to its offspring. Even if they’re the same sorts of microbes, the direct line of vertical transmission is still necessary to form an evolutionary individual.
Just because the microbes are there with one organism at one time does not mean they are a unit of selection …
Joan Strassmann, Washington University in St. Louis
Skillings further argues that the repeated co-occurrence of species in nature does not imply that they have shared interests. Consider a host and a parasite locked in perpetual conflict: Every generation, they come together and attempt to subvert each other. You could even imagine a familial line of hosts being infected by the same familial line of parasites. Nevertheless, persistent as this relationship is, Skillings argues that you’re only going to understand it by considering each lineage’s interests separately. Proponents of the hologenome concept acknowledge that cooperation, conflict and even neutrality can influence the evolution of the holobiont, making the disagreement less about the facts of the matter, and more about how to approach them.
Strassmann argues that focusing solely on what’s happening in the holobiont misses much of the microbes’ story. Many host-associated microbes spend significant chunks of their lives outside their host, in an environment where they’re subject to very different selection pressures. The holobiont idea, she says, puts blinders on our understanding of the evolution of these microbes, focusing attention on the host environment and neglecting other habitats that could shape a microbe’s character.
Critics of holobiont-centered theories are not discounting the importance of studying the interconnections between microbes and hosts, but they think the holobiont framework is almost always misleading. They envision the holobiont as an ecological community, not an evolutionary individual. The knowledge that symbiotic relationships with microbes are important “doesn’t mean we have to completely forget what we know about how evolution and natural selection operate,” Strassmann said.
But translating existing ecological and evolutionary theory to this new microbial world is more easily said than done, cautions Britt Koskella, a biologist at the University of California, Berkeley. Many of these theories were built to explain how plants and animals interact and coexist, and “there are well-understood aspects of microbial ecology that just don’t fit here,” she said.

Joan Strassmann, an evolutionary biologist at Washington University in St. Louis, thinks that a hologenome concept of evolution pushes the idea of selectable units too far.
Joe Angeles/Washington University
Take ecological succession, a framework for evaluating how a community assembles over time. The state of a plant community on a new island, for example, may depend much more on the order in which species arrived and the niches they filled than on the local evolution of the plants, because evolution is usually so much slower.
But bacteria evolve much faster than plants and animals, and they can swap genes instantaneously via horizontal gene transfer. “Now you have to consider the possibility that a microbe could arrive and, whether by mutation or horizontal transfer, fill all available niches before anyone else shows up,” Koskella said. Bacterial succession might work in different, counterintuitive ways from traditional succession.
Other differences to consider, according to Koskella, include the influence of a host’s immune system over its microbiome and microbes’ ability to dynamically alter their environment. She argues that theoreticians need to think through basic assumptions made by their models and consider whether they apply equally well to microbes, and empiricists need to test the predictions of those models. “Cross-talk between empiricists and theoreticians is really important,” Koskella said. “The data are just so complex, and we’re very quickly moving beyond intuition.”
Settling empirical questions, such as how often a substantial portion of the holobiont is inherited, and how stable communities are across generations, will help sharpen intuition and inform theoretical work. “We can keep just asking questions and getting data, but without theory, you don’t really know how to begin interpreting or testing all this complexity,” Koskella said.
It’s the Song, Not the Singer
One radical idea seeks to forge a third way forward by turning the problem on its head. Forget about the particulars of which microbes are doing the interacting or whether they’re vertically or horizontally transmitted, its proponents say — just focus on the interactions, the stable metabolic processes enacted by various microbial players.
It’s the song, not the singer,” said W. Ford Doolittle, an evolutionary biologist at Dalhousie University in Nova Scotia. He and his former Dalhousie colleague Austin Booth originated this idea and gave it its name, abbreviated ITSNTS, by inverting the title of a Rolling Stones song. They argue that it captures what’s so compelling about the idea of holobionts, namely the stable networks of interaction patterns among disparate lineages, without ascribing a special evolutionary identity to them. Instead, the processes themselves form a sort of evolutionary lineage.

W. Ford Doolittle, an evolutionary biologist at Dalhousie University in Nova Scotia, is one of the authors of a new evolutionary concept in which stable patterns of metabolic interactions among hosts and microbes — but not necessarily the organisms themselves — might serve as a unit of selection.
Courtesy of Ford Doolittle
Doolittle and Booth begin from the observation that gut microbiomes contain a wide diversity of species and strains across many bacterial taxonomic groups but exhibit a remarkable conservation of core functions performed by those organisms. These networks of different players participate in metabolic cycles, in which a set of bacteria converts nutrients to metabolites, which get picked up by other bacteria to produce a different metabolite, which gets used by the host, and the cycle continues. Many of these functional steps can be carried out by myriad strains present in the gut, making any given strain potentially redundant. But the cycle itself continues, regardless of which cells are enacting it.
Doolittle illustrates the idea using the nitrogen cycle. Atmospheric nitrogen gets churned through a series of chemical states by a diverse assortment of bacteria, plants and decomposers like fungi performing different reactions. Each step in the cycle can be carried out by innumerable species that all belong to a kind of “functional guild,” but the process itself remains remarkably stable.
Once these networks exist, they create a niche for other microbes to occupy. The cycle becomes a sort of structure for various lineages to grab onto, a way for them to make a living. “If you make the leap and think of these interaction networks … as populations of entities, you can begin to understand them as units of selection,” Booth said. “It turns traditional ways of thinking about evolution on its head. The materialistic basis of lineages takes a back seat.”
Doolittle and Booth liken this to the way songs perpetuate themselves as cultural entities. “There are songs which have lasted for a long time basically because a lot of people were happy to sing them,” Doolittle said. Individual singers come and go, but even in cultures where written and recorded music don’t exist, the songs survive by recruiting appropriate talent in new generations. Similarly, once a metabolic network exists, diverse lineages of organisms can evolve to perform some of the interactions and processes that define it — and evolution can support that association because it is selfishly advantageous for the individuals, or genes, within the various lineages to do so.
Processes being selected via differential persistence is certainly an unusual idea, but not unprecedented. Cultural evolution of ideas in the form of “memes,” while controversial, is seen by many as at least plausible (the meme concept was itself inspired by the biological concept of genes). In this case, the idea or meme is the metabolic interaction, and it persists based on its ability to recruit microbes to carry it out.
It remains to be seen how useful this framework might be for studying the holobiont, and significant kinks remain to be ironed out. The notion that differential persistence is analogous to differential reproduction might seem strange to many evolutionary biologists, and it’s still far from clear how to define a metabolic network.
Fertile Ground
Spirited argument over how evolution fundamentally works is nothing new. “Evolution, if you look at the history of the idea, has always been beset with these kinds of debates,” Booth said, referring to early debates about whether evolution proceeded gradually or in fits and starts.
“It’s safe to say that the microbial revolution has been impactful in that it throws so many of the traditional ideas out, or at least casts them in a new light,” Booth said.
 “I think we’re just beginning a field here,” Bordenstein said. He points to the early days of genetics. “Those early questions were so basic — what is a gene? How are genes inherited?” Biologists are just starting to get a handle on the basic questions of microbe-host interactions. “Who’s there? What is the complexity of the holobiont and how do its parts function together? We have a century’s worth of work ahead of us to figure this out.”
Strassmann agrees. “It’s really important that we keep talking to each other. We have so much exploring to do.”