We are living in a bacterial world, and it's impacting us more than previously thought

Feb 15, 2013 by Lisa Zyga feature
The percentage of the human genome that arose at a series of stages in evolution. 37% of human genes originated in bacteria. Credit: Margaret McFall-Ngai, et al. ©2013 PNAS

(Phys.org)—Throughout her career, the famous biologist Lynn Margulis (1938-2011) argued that the world of microorganisms has a much larger impact on the entire biosphere—the world of all living things—than scientists typically recognize. Now a team of scientists from universities around the world has collected and compiled the results of hundreds of studies, most from within the past decade, on animal-bacterial interactions, and have shown that Margulis was right. The combined results suggest that the evidence supporting Margulis' view has reached a tipping point, demanding that scientists reexamine some of the fundamental features of life through the lens of the complex, codependent relationships among bacteria and other very different life forms.

The project to review the current research on animal-bacterial interactions began when some scientists recognized the importance of in their own fields of study. For Michael Hadfield, Professor of Biology at the University of Hawaii at Manoa, the recognition grew over many years while studying the metamorphosis of . He found that certain bacteria influence marine larvae to settle to particular places on the , where they transform into juveniles and live out the rest of their lives.

"Once we determined that specific biofilm bacteria provide an essential and unique ligand to stimulate the larvae of one globally distributed , our research naturally progressed to a study of the portion of the responsible for the signaling, and to other species, where we found the same genes involved," Hadfield told Phys.org. "Coming from different perspectives on the study of animal-bacterial interactions, and recognizing many more, Margaret McFall-Ngai [Professor of Medical Microbiology and Immunology at the University of Wisconsin, Madison] and I discussed the current situation extensively and then decided to attempt to draw together a significant number of experts on various approaches to the study of bacterial-animal interactions to draft a paper such as the one you have in hand. We proposed a 'catalysis meeting' on the subject to the National Science Foundation's National Evolutionary Synthesis Center (NESCent), which was funded, and the project took off."

Bacteria surround us

In many respects, it's easy to see the prominent role that bacteria play in the world. Bacteria were one of the first life forms to appear on Earth, about 3.8 billion years ago, and they will most likely survive long after humans are gone. In the current tree of life, they occupy one of the three main branches (the other two are Archaea and Eucarya, with animals belonging to the latter). Although bacteria are extremely diverse and live nearly everywhere on Earth, from the bottom of the ocean to the inside of our intestines, they have a few things in common. They are similar in size (a few micrometers), they are usually made of either a single cell or a few cells, and their cells don't have nuclei.

Although scientists have known for many years that animals serve as a host for bacteria, which live especially in the gut/intestines, in the mouth, and on the skin, recent research has uncovered just how numerous these microbes are. Studies have shown that humans have about 10 times more bacterial cells in our bodies than we have human cells. (However, the total bacteria weigh less than half a pound because bacterial cells are much smaller than human cells.)

While some of these bacteria simply live side-by-side with animals, not interacting much, some of them interact a lot. We often associate bacteria with disease-causing "germs" or pathogens, and bacteria are responsible for many diseases, such as tuberculosis, bubonic plague, and MRSA infections. But bacteria do many good things, too, and the recent research underlines the fact that animal life would not be the same without them.

"The true number of bacterial species in the world is staggeringly huge, including bacteria now found circling the Earth in the most upper layers of our atmosphere and in the rocks deep below the sea floor," Hadfield said. "Then add all of those from all of the possible environments you can think of, from cesspools to hot springs, and all over on and in virtually every living organism. Therefore, the proportion of all bacterial species that is pathogenic to plants and animals is surely small. I suspect that the proportion that is beneficial/necessary to plants and animals is likewise small relative to the total number of bacteria present in the universe, and surely most bacteria, in this perspective, are 'neutral.' However, I am also convinced that the number of beneficial microbes, even very necessary microbes, is much, much greater than the number of pathogens."

Animal origins and coevolution

From our humble beginnings, bacteria may have played an important role by assisting in the origins of multicellular organisms (about 1-2 billion years ago) and in the origins of animals (about 700 million years ago). Researchers have recently discovered that one of the closest living relatives of multicellular animals, a single-celled choanoflagellate, responds to signals from one of its prey bacterium. These signals cause dividing choanoflagellate cells to retain connections, leading to the formation of well-coordinated colonies that may have become multicellular organisms. However, such questions of origin have been subjects of intense debate, and scientists have many hypotheses about how these life forms emerged. A bacterial role in these processes does not exclude other perspectives but adds an additional consideration.

Bacteria in an animal’s microbiota, such as those in the gut, in the mouth, and on the skin, communicate among themselves and exchange signals with the animal’s organ systems. Some of the chemical signals are noted in this illustration. Credit: Margaret McFall-Ngai, et al. ©2013 PNAS

After helping get animals started, bacteria also played an important role in helping them along their evolutionary path. While animal development is traditionally thought to be directed primarily by the animal's own genome in response to environmental factors, recent research has shown that animal development may be better thought of as an orchestration among the animal, the environment, and the coevolution of numerous microbial species. One example of this coevolution may have occurred when mammals evolved endothermy, or the ability to maintain a constant temperature of approximately 40 °C (100 °F) by metabolic means. This is also the temperature at which mammals' bacterial partners work at optimum efficiency, providing energy for the mammals and reducing their food requirement. This finding suggests that bacteria's preferred temperature may have placed a selection pressure on the evolution of genes associated with endothermy.

Bacterial signaling

Evidence for a deep-rooted alliance between animals and bacteria also emerges in both groups' genomes. Researchers estimate that about 37% of the 23,000 human genes have homologs with bacteria and Archaea, i.e., they are related to genes found in bacteria and Archaea that were derived from a common ancestor.

Many of these homologous genes enable signaling between animals and bacteria, which suggests that they have been able to communicate and influence each other's development. One example is Hadfield and his group's discovery that bacterial signaling plays an essential role in inducing metamorphosis in some marine invertebrate larvae, where the bacteria produce cues associated with particular environmental factors. Other studies have found that bacterial signaling influences normal brain development in mammals, affects reproductive behavior in both vertebrates and invertebrates, and activates the immune system in tsetse flies. The olfactory chemicals that attract some animals (including humans) to their prospective mates are also produced by the animals' resident bacteria.

Bacterial signaling is not only essential for development, it also helps animals maintain homeostasis, keeping us healthy and happy. As research has shown, bacteria in the gut can communicate with the brain through the central nervous system. Studies have found that mice without certain bacteria have defects in brain regions that control anxiety and depression-like behavior. Bacterial signaling also plays an essential role in guarding an animal's immune system. Disturbing these bacterial signaling pathways can lead to diseases such as diabetes, inflammatory bowel disease, and infections. Studies also suggest that many of the pathogens that cause disease in animals have "hijacked" these bacterial communication channels that originally evolved to maintain a balance between the animal and hundreds of beneficial bacterial species.

Signaling also appears in the larger arena of ecosystems. For example, bacteria in flower nectar can change the chemical properties of the nectar, influencing the way pollinators interact with plants. Human infants who are born vaginally have different gut bacteria than those delivered by Caesarean section, which may have long-lasting effects. And bacteria feeding on dead animals can repel animal scavengers—organisms 10,000 times their size—by producing noxious odors that signal the scavengers to stay away.

In the gut

In the earliest animals, gut bacteria played an important role in nutrition by helping animals digest their food, and may have influenced the development of other nearby organ systems, such as the respiratory and urogenital systems. Likewise, animal evolution likely drove the evolution of the bacteria, sometimes into highly specialized niches. For example, 90% of the bacterial species in termite guts are not found anywhere else. Such specialization also means that the extinction of every animal species results in the extinction of an unknown number of bacterial lineages that have evolved along with it.

Scientists have also discovered that bacteria in the human gut adapts to changing diets. For example, most Americans have a gut microbiome that is optimized for digesting a high-fat, high-protein diet, while people in rural Amazonas, Venezuela, have gut microbes better suited for breaking down complex carbohydrates. Some people in Japan even have a gut bacterium that can digest seaweed. Researchers think the gut microbiome adapts in two ways: by adding or removing certain bacteria species, and by transferring the desired genes from one bacterium to another through horizontal gene transfer. Both host and bacteria benefit from this kind of symbiotic relationship, which researchers think is much more widespread than previously thought.

The big picture

Altogether, the recent studies have shown that animals and bacteria have histories that are deeply intertwined, and depend on each other for their own health and well-being as well as that of their environments. Although the researchers focused exclusively on animal-bacteria interactions, they expect that similar trends of codependency and symbiosis are universal among and between other groups, such as Archaea, fungi, plants, and animals. Once considered an exception, such intermingling is now becoming recognized as the rule—just as Margulis predicted many decades ago. Due to these symbiotic relationships, the scientists here propose that the very definitions of an organism, an environment, a population, and a genome have become blurred and should be reviewed. It may be, for instance, that animals are better viewed as host-microbe ecosystems than as individuals.

An insect (1 mm) living in a forest canopy (10 m) illustrates the effects animal-bacterial interactions across multiple scales. Bacteria (1 micrometer) residing in the animal’s gut (0.1 mm) are essential to the insect’s nutrition, and insects often make up a majority of the animal biomass in forest canopies. Credit: Margaret McFall-Ngai, et al. ©2013 PNAS

In addition, the scientists predict that the recent findings on animal-bacteria interactions will likely require biologists to significantly alter their view of the fundamental nature of the entire biosphere. Along these lines, large-scale research projects such as the Human Microbiome Project and the Earth Microbiome Project are already underway to investigate the wide range of bacteria in the individual and global systems, and to see what happens when the bacteria are disturbed.

In the end, the scientists hope that the results will promote more cross-disciplinary collaboration among scientists and engineers from different fields to explore the new microbial frontier. They argue that these discoveries should revolutionize the way that biology is taught from the high school level on up, by focusing more on the relationships between bacteria, their animal partners, and all other life forms.

"It is hard to summarize a single 'most important conclusion,' other than the admonition to biologists studying animals, from behavior to physiology and ecology to molecular biology, that no matter what process you think you are studying, you must look for and consider a major role for bacteria," Hadfield said. "In many cases, this may require partnerships across traditional boundaries of research, meaning that zoologists must collaborate with microbiologists to advance their research, that molecular biologists must collaborate with whole-organism biologists, etc. We want badly for the message in 'Animals in a bacterial world,' to be a call for the necessary disappearance of the old boundaries between life science departments (e.g., Depts of Zoology, Botany, Microbiology, etc.) in universities, and societies (e.g., the American Society for Microbiology, etc.). We also want the message disseminated in college and university classes from introductory biology to advanced courses in the various topic areas of our paper."

The results will profoundly change the way that the scientists of this collaboration continue with their own areas of research, Hadfield said.

"Each of the authors of our paper conducts basic research in one or more areas of animal-bacterial interactions discussed in the paper, and each will continue to focus on her/his own speciality, I'm sure," he said. "However, I'm also certain that the interactions developed during the composition and writing of the paper (starting with our NESCent meeting in October 2011, when most of us met for the first time) will impact our own research and cause us to establish new collaborations with other laboratories. That has already occurred for me; I have a new collaboration with Dianne Newman's group at CalTech, an outstanding group of bacteriologists who are helping us do a much more in-depth investigation of the bacterial gene-products responsible for larval development."

Explore further: Scientists create mouse model to accelerate research on Ebola vaccines, treatments

More information: Margaret McFall-Ngai, et al. "Animals in a bacterial world, a new imperative for the life sciences." PNAS Early Edition. DOI: 10.1073/pnas.1218525110

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PPihkala
3.7 / 5 (6) Feb 15, 2013
For doctors meeting an ill patient this again calls for holistic approach. They should consider the whole person, including any bacteria he/she crries with himself. If possible even the biomes his/her parents had.
NikFromNYC
2.2 / 5 (12) Feb 15, 2013
Practically every day this very site posts headlines about global warming catastrophe whose certainty of tone relies on super computer models that not only leave out shadow casting cloud dynamics but the entire micro microbiosphere that is responsible for carbon cycle feedbacks, most of them obviously and logically negative.
JVK
1.8 / 5 (5) Feb 15, 2013
Re: "The olfactory chemicals that attract some animals (including humans) to their prospective mates are also produced by the animals' resident bacteria."

From Kohl (2012) http://dx.doi.org...i0.17338
"...reproduction began with an active nutrient uptake mechanism in heterospecifics and that the mechanism evolved to become symbiogenesis in the conspecifics of asexual organisms (Margulis, 1998). In yeasts, epigenetic changes driven by nutrition might then have led to the creation of novel cell types, which are required at evolutionary advent of sexual reproduction (Jin et al., 2011). These epigenetic changes probably occur across the evolutionary continuum that includes both nutrition-dependent reproduction in unicellular organisms and sexual reproduction in mammals."

"Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans."
JVK
1.8 / 5 (5) Feb 16, 2013
"It is hard to summarize a single 'most important conclusion,' other than the admonition to biologists studying animals, from behavior to physiology and ecology to molecular biology, that no matter what process you think you are studying, you must look for and consider a major role for bacteria," Hadfield said.

Kohl (2012) concluded: "Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans." http://dx.doi.org...i0.17338
It was not summarize this single most important conclusion because the molecular mechanisms are common to all species.

We see in the diagram: "The percentage of the human genome that arose at a series of stages in evolution. 37% of human genes originated in bacteria." The stages of adaptive evolution are, of course, nutrient-dependent and pheromone-controlled. Thus, adaptive evolution clearly does not result from random mutations (a ridiculous theory, if ever there was one).
ryggesogn2
1 / 5 (3) Feb 16, 2013
"Demonstrating that even in medicine, "one man's trash is another man's treasure," patients with debilitating diarrhea are finding relief, if not cures, after receiving bacteria-rich stool from the guts of healthy donors, usually close relatives. "
http://abcnews.go...13601702
Torbjorn_Larsson_OM
5 / 5 (3) Feb 16, 2013
The same coevolution is also prominent vs virus, for example the immuno-modifying viral genes that placental mammals like humans and sheep have usurped in the germline to make a more tight placental embedding. It may predict why humans can grow in utero so long, and be responsible for our ability to grow relatively large brains.

"bacteria may have played an important role by assisting in the origins of multicellular organisms (about 1-2 billion years ago)".

Multicellularity is ubiquitous among clades, and the first terminally differentiated multicellulars were cyanobacterial. In fact, "Evolution of multicellularity coincided with increased diversification of cyanobacteria and the Great Oxidation Event" [Schirrmeister et al, PNAS Early Edition 2012.]
Torbjorn_Larsson_OM
5 / 5 (2) Feb 16, 2013
[cont] That eukaryotes adopted, and could adopt, a high energy density lifestyle by mitochondrial endosymbiosis were a consequence of that, but also likely prompted by the differentiated biomats that along the similarly differentiated stromatolites were a product of oxygenation and differentiated photosynthesis (anoxic _and_ oxygenating). Oxygen gradients would have promoted multicellular movement to better utilize the mats as food source, as opposed to unicellular surface grazers.

@PPIhkala: Certainly not "holistic" methods, as it is the methods consistent with medicine that has uncovered these complexities. It calls for more and deeper informed medicine, certainly.

@NikFromNYC: Now you are just trolling. But as much as climate science is vital, it headlines the current AGW regime and the problems that ushers in, not a "catastrophe".
TheGhostofOtto1923
1 / 5 (1) Feb 16, 2013
The biota we acquire from our mothers is irreplaceable and essential to our growth and development. And until they figure out what to replace and how to replace it, antibiotics should not be given to children for any reason.
aroc91
5 / 5 (1) Feb 16, 2013
The biota we acquire from our mothers is irreplaceable and essential to our growth and development. And until they figure out what to replace and how to replace it, antibiotics should not be given to children for any reason.


You'd rather have children die from curable infections? The benefits of probiotics have been clearly shown. Just because we don't know everything about our microbiota doesn't mean we don't know enough to administer probiotics to get it back to where it needs to be.

Worst case, they get some gastric distress and need fluids until they eat some yogurt and everything's hunky-dory. It's not as mysterious as you're making it out to be.
Mandan
1 / 5 (1) Feb 16, 2013
This is excellent news.

But what about the other half of Margulis' revolutionary contributions-- endosymbiosis? The fact that besides the mitochondrion and the chloroplast having their origins as formerly independent-living organisms which are now organelles, every other cell in a so-called "complex" organism is descended from previously independent-living single--celled organisms as well, which have, over time, given up autonomy in order to enter into symbiotic cooperation at the microbiochemical level, and now hide inside us as nerve cells, muscle cells, red blood cells, the various components of immune systems, and form the structure of every one of our specialized organs as well, including our brains.

It's too bad that like Wegener and so many other great scientific minds through the ages who were scorned and ridiculed during life, her vindication will only be forthcoming after her death.
TheGhostofOtto1923
1 / 5 (1) Feb 16, 2013
You'd rather have children die from curable infections?
There are many other ways than by using wide spectrum antibiotics and killing everything.
The benefits of probiotics have been clearly shown.
No,

"...a growing body of scientific evidence suggests that you can treat and even prevent some illnesses"

-In other words, 'maybe' and 'quite possibly' some.
Just because we don't know everything about our microbiota doesn't mean we don't know enough to administer probiotics to get it back to where it needs to be.
Get 'it' back to where 'it' needs to be? We have no idea what the body needs of this stuff or when.

We only know that we have evolved in symbiotic relationship with it, that it appears to be essential in the development of critical functions and organs, INCLUDING the brain, and that these drugs kill off a lot of it.

Thats ALL we know. Eating some supplements which may or may not benefit the gut, is no answer. Killing everything is most obviously reckless.
rfw
not rated yet Feb 16, 2013
So I love it!!! Statistically speaking Humans are Bacterial colonies with legs. :-)
aroc91
5 / 5 (1) Feb 16, 2013
There are many other ways than by using wide spectrum antibiotics and killing everything.


Yeah, we can use targeted antibiotics. Besides that, what?

No,

"...a growing body of scientific evidence suggests that you can treat and even prevent some illnesses"

-In other words, 'maybe' and 'quite possibly' some.


Lactobacillus administration after antibiotics has been known to be beneficial for years. http://www.ncbi.n...11148433

Get 'it' back to where 'it' needs to be? We have no idea what the body needs of this stuff or when.


There has been a ton of recent research characterizing the gut microbiome. We know it contributes to digestion and even synthesizes vitamins for us.

Thats ALL we know.


We know what it's composed of, what it does, and how to get it back to baseline. Sure sounds like a hell of a lot to me. Of course there's more to discover, but again, it's not as mysterious as you're making it out to be.
RealScience
5 / 5 (2) Feb 17, 2013

Thus, adaptive evolution clearly does not result from random mutations (a ridiculous theory, if ever there was one).


@JVK - it has been pointed out to you numerous times (for example, in http://phys.org/n...s.html), that mutations are a PART of evolution and provide variety that natural selection acts on.

In spite of making more than 100 posts in that thread you failed to provide any evidence that evolution does not use mutations (other than trying to claim that simultaneous mutations would be needed, which was shown to be false).
And you also failed to refute examples of natural selection selecting FOR mutations, such as the sickle-cell example.

Stick to epigenetics, where you at least understand the basics, and to pheromones, where you are correct that mainstream biologist have greatly underestimated their effects mammals, and where you have actually written good papers.
TheGhostofOtto1923
1 / 5 (1) Feb 17, 2013
Yeah, we can use targeted antibiotics. Besides that, what?
Antibiotics are often not needed.

"Official guidelines by the American Heart Association for dental antibiotic prophylaxis call for the administration of antibiotics to prevent infective endocarditis. Though the current (2007) guidelines dictate more restricted antibiotic use, many dentists and dental patients follow the 1997 guidelines instead, leading to overuse of antibiotics"
http://en.wikiped...c_misuse
Lactobacillus administration after antibiotics
"Bacteria make up most of the flora in the colon and up to 60% of the dry mass of feces. Somewhere between 300 and 1000 different species live in the gut with most estimates at about 500. However, it is probable that 99% of the bacteria come from about 30 or 40 species. Fungi and protozoa also make up a part of the gut flora, but little is known about their activities."

-Which do you kill? Which do you replace?
TheGhostofOtto1923
1 / 5 (1) Feb 17, 2013
We know what it's composed of, what it does
Per your recent research and the article above, no we dont yet know what it is composed of, what it does, or what happens if we kill it. Especially in children.
http://en.wikiped..._infants
Sure sounds like a hell of a lot to me.
"the evidence supporting Margulis' view has reached a tipping point, demanding that scientists reexamine some of the fundamental features of life through the lens of the complex, codependent relationships among bacteria and other very different life forms."

-Try (re)reading the article.
Skepticus
1.7 / 5 (6) Feb 17, 2013
The egoistic, individualistic view that there are such thing as "me" and "the others" was refuted as far as 2500 years ago. Our bodies incorporate substances that had been our ancestor's wastes, or decayed bodies through the food chain etc, our bodies are colonies of living cells that just happen to cooperate to make us, which most of the time we can't tell or command what they are doing. As long as there are interrelated lives, there is no such thing as standalone "me" or "you".
aroc91
5 / 5 (1) Feb 17, 2013
Antibiotics are often not needed


You're putting words in my mouth. I'm talking about the cases where they ARE needed. Our immune systems can't handle everything.

Per your recent research and the article above, no we dont yet know what it is composed of, what it does, or what happens if we kill it. Especially in children.


Did you even read the wiki article you cited?

All infants are initially colonized by large numbers of E. coli and streptococci ... subsequent bacterial succession of strict anaerobic species mainly belonging to the genera Bifidobacterium, Bacteroides, Clostridium, and Ruminococcus.[23] Breast-fed babies become dominated by bifidobacteria... In contrast, the microbiota of formula-fed infants is more diverse, with high numbers of Enterobacteriaceae, enterococci, bifidobacteria, Bacteroides, and clostridia


I'd call that well characterized and those are based off of studies in the early 2000s. There have been many more since then.

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