genetic engineering of space travelers

Video - Twilight Zone Episode Third From the Sun

LiveScience | NASA's human spaceflight program might take some giant leaps forward if the agency embraces genetic engineering techniques more fully, according to genomics pioneer J. Craig Venter.

The biologist, who established the J. Craig Venter Institute that created the world's first synthetic organism earlier this year, told a crowd here Saturday (Oct. 30) that human space exploration could benefit from more genetic screening and genetic engineering. Such efforts could help better identify individuals most suited for long space missions, as well as make space travel safer and more efficient, he said.

"I think this could change the shape of what NASA does, if you make the commitment to do it," said Venter, who led a team that decoded the human genome a decade ago. Venter spoke to a group of scientists and engineers who gathered at NASA's Ames Research Center for two different meetings: a synthetic biology workshop put on by NASA, and Space Manufacturing 14: Critical Technologies for Space Settlement, organized by the nonprofit Space Studies Institute.

Astronauts with the right (genetic) stuff

Genetics techniques could come in extremely handy during NASA's astronaut selection process, Venter said. The space agency could screen candidates for certain genes that help make good spaceflyers — once those genes are identified, he added.

Genes that encode robust bone regeneration, for example, would be a plus, helping astronauts on long spaceflights battle the bone loss that is typically a major side effect of living in microgravity. Also a plus for any prospective astronaut: genes that code for rapid repair of DNA, which can be damaged by the high radiation levels in space.

Genetic screening would be a natural extension of what NASA already does — it would just add a level of precision, according to Venter.

"NASA's been doing genetic selection for a long time," he said. "You just don't call it that."

Last summer, the agency chose just nine astronaut candidates — out of a pool of 3,500 — for its rigorous astronaut training program based on a series of established spaceflight requirements and in-depth interviews.

A new microbiome
At some point down the road, NASA could also take advantage of genetic engineering techniques to make long space journeys more efficient and easier on astronauts, Venter said.

As an example, he cited the human microbiome, the teeming mass of microbes that live on and inside every one of us. Every human body hosts about 100 trillion microbes — meaning the bugs outnumber our own cells by a factor of at least 10 to one.

While humans only have about 20,000 genes, our microbiome boasts a collective 10 million or so, Venter said. These microbes provide a lot of services, from helping us digest our food to keeping our immune system's inflammation response from going overboard.

With some tailoring, the microbiome could help us out even more, according to Venter.

"Why not come up with a synthetic microbiome?" he asked.

Theoretically, scientists could engineer gut microbes that help astronauts take up nutrients more efficiently. A synthetic microbiome could also eliminate some pathogens, such as certain bacteria that can cause dental disease. Other tweaks could improve astronauts' living conditions, and perhaps their ability to get along with each other in close quarters.

Body odor is primarily caused by microbes, Venter said. A synthetic microbiome could get rid of the offenders, as well as many gut microbes responsible for excessive sulfur or methane production. Fist tap Nana.

Human Microbiome Project

Now I know that before I even get started here, nobody read the Oxygen Wars, nobody read Gould's Planet of the Bacteria - and nobody read Wizardology 101 so the noodle-baking I really want to put on you - is only going to come out half-baked - if it gets baked any at all.

Be that as it may, I will continue scattering bread crumbs in hopes that somebody attending to this peculiar web log will connect them all up and go AHHH!!!!!

At the end of the day - all it is - is a different angle of approach or perspective from which to view and consider the affairs in which it is broadly and uncritically believed and accepted that we are the agents. What pipsqueak arrogance leads us to conclude, believe, and act as if it were natural and theological law that we are the fundamental units of selection, the sine qua non and center of the implicate order of creation?

Gut Reaction;

For the first time, scientists have defined the collective genome of the human gut, or colon. Up to 100 trillion microbes, representing more than 1,000 species, make up a motley "microbiome" that allows humans to digest much of what we eat, including some vitamins, sugars, and fiber.

In a study published in the June 2 issue of Science, scientists at The Institute for Genomic Research (TIGR) and their colleagues describe and analyze the colon microbiome, which includes more than 60,000 genes--twice as many as found in the human genome. Some of these microbial genes code for enzymes that humans need to digest food, suggesting that bacteria in the colon co-evolved with their human host, to mutual benefit.

"The GI tract has the most abundant, diverse population of bacteria in the human body," remarks lead author Steven Gill, a molecular biologist formerly at TIGR and now at the State University of New York in Buffalo. "We're entirely dependent on this microbial population for our well-being. A shift within this population, often leading to the absence or presence of beneficial microbes, can trigger defects in metabolism and development of diseases such as inflammatory bowel disease."

The Human Microbiome Project;

Within the body of a healthy adult, microbial cells are estimated to outnumber human cells by a factor of ten to one. These communities, however, remain largely unstudied, leaving almost entirely unknown their influence upon human development, physiology, immunity, and nutrition. To take advantage of recent technological advances and to develop new ones, the NIH Roadmap has initiated the Human Microbiome Project (HMP) with the mission of generating resources enabling comprehensive characterization of the human microbiota and analysis of its role in human health and disease.

Traditional microbiology has focused on the study of individual species as isolated units. However many, if not most, have never been successfully isolated as viable specimens for analysis, presumably because their growth is dependant upon a specific microenvironment that has not been, or cannot be, reproduced experimentally. Among those species that have been isolated, analyses of genetic makeup, gene expression patterns, and metabolic physiologies have rarely extended to inter-species interactions or microbe-host interactions. Advances in DNA sequencing technologies have created a new field of research, called metagenomics, allowing comprehensive examination of microbial communities, even those comprised of uncultivable organisms. Instead of examining the genome of an individual bacterial strain that has been grown in a laboratory, the metagenomic approach allows analysis of genetic material derived from complete microbial communities harvested from natural environments. In the HMP, this method will complement genetic analyses of known isolated strains, providing unprecedented information about the complexity of human microbial communities.

By leveraging both the metagenomic and traditional approach to genomic DNA sequencing, the Human Microbiome Project will lay the foundation for further studies of human-associated microbial communities.

Just a little food for thought...., are you thinking about it yet? (the picture accompanying this post is of a polished stromatolite in the shape of an egg)

medical ecology

NYTimes | For a century, doctors have waged war against bacteria, using antibiotics as their weapons. But that relationship is changing as scientists become more familiar with the 100 trillion microbes that call us home — collectively known as the microbiome.

“I would like to lose the language of warfare,” said Julie Segre, a senior investigator at the National Human Genome Research Institute. “It does a disservice to all the bacteria that have co-evolved with us and are maintaining the health of our bodies.”

This new approach to health is known as medical ecology. Rather than conducting indiscriminate slaughter, Dr. Segre and like-minded scientists want to be microbial wildlife managers.

No one wants to abandon antibiotics outright. But by nurturing the invisible ecosystem in and on our bodies, doctors may be able to find other ways to fight infectious diseases, and with less harmful side effects. Tending the microbiome may also help in the treatment of disorders that may not seem to have anything to do with bacteria, including obesity and diabetes.

“I cannot wait for this to become a big area of science,” said Michael A. Fischbach, a microbiologist at the University of California, San Francisco, and an author of a medical ecology manifesto published this month in the journal Science Translational Medicine.

Judging from a flood of recent findings about our inner ecosystem, that appears to be happening. Last week, Dr. Segre and about 200 other scientists published the most ambitious survey of the human microbiome yet. Known as the Human Microbiome Project, it is based on examinations of 242 healthy people tracked over two years. The scientists sequenced the genetic material of bacteria recovered from 15 or more sites on their subjects’ bodies, recovering more than five million genes.

The project and other studies like it are revealing some of the ways in which our invisible residents shape our lives, from birth to death.

A number of recent reports shed light on how mothers promote the health of their children by shaping their microbiomes. In a study published last week in the journal PLoS One, Dr. Kjersti Aagaard-Tillery, an obstetrician at Baylor College of Medicine, and her colleagues described the vaginal microbiome in pregnant women. Before she started the study, Dr. Aagaard-Tillery expected this microbiome to be no different from that of women who weren’t pregnant.

“In fact, what we found is the exact opposite,” she said.

ideas of the microbiome and the virome...,

Sciencemag | Humans have been doing battle with bacteria since the 1800s, thwarting disease with antibiotics, vaccines, and good hygiene with mixed success. But in 2000, Nobel laureate Joshua Lederberg called for an end to the “We good; they evil” thinking that has fueled our war against microbes. “We should think of each host and its parasites as a superorganism with the respective genomes yoked into a chimera of sorts,” he wrote in Science in 2000.

His comments were prescient. This past decade has seen a shift in how we see the microbes and viruses in and on our bodies. There is increasing acceptance that they are us, and for good reason. Nine in 10 of the cells in the body are microbial. In the gut alone, as many as 1000 species bring to the body 100 times as many genes as our own DNA carries. A few microbes make us sick, but most are commensal and just call the human body home. Collectively, they are known as the human microbiome. Likewise, some viruses take up residence in the body, creating a virome whose influence on health and disease is just beginning to be studied.

Their genes and ours make up a metagenome that keeps the body functioning. This past decade we've begun to see how microbial genes affect how much energy we absorb from our foods and how microbes and viruses help to prime the immune system. Viewing the human and its microbial and viral components as intimately intertwined has broad implications. As one immunologist put it, such a shift “is not dissimilar philosophically from the recognition that the Earth is not the center of the solar system.”

This appreciation has dawned gradually, as part of a growing recognition of the key role microbes play in the world. Microbiologists sequencing DNA from soil, seawater, and other environments have discovered vast numbers of previously undetected species. Other genomics research has brought to light incredible intimacies between microbes and their hosts—such as a bacterium called Buchnera and the aphids inside which it lives. A study in 2000 found that each organism has what the other lacks, creating a metabolic interdependency.

One of the first inklings that microbiologists were missing out on the body's microbial world came in 1999, when David Relman of Stanford University in Palo Alto, California, and colleagues found that previous studies of bacteria cultured from human gums had seriously undercounted the diversity there. Turning to samples taken from the gut and from stools, the researchers identified 395 types of bacteria, two-thirds of them new to science.

In 2006, Steven Gill of the University at Buffalo in New York and colleagues did a metagenomics study of the gut, analyzing all the genes they could find in the 78 million bases sequenced. They found metabolic genes that complemented the human genome, including ones that break down dietary fiber, amino acids, or drugs, and others that produce methane or vitamins. This and a more comprehensive survey in 2010 by Jun Wang of BGI-Shenzhen in China and colleagues provided support for the concept of the microbe-human superorganism, with a vast genetic repertoire. Now, large-scale studies have surveyed the microflora in the gut, skin, mouth, nose, and female urogenital tract. The Human Microbiome Project has sequenced 500 relevant microbial genomes out of a planned 3000.

Some of these microbes may play important roles in metabolic processes. In 2004, a team led by Jeffrey Gordon of Washington University School of Medicine in St. Louis, Missouri, found that germ-free mice gained weight after they were supplied with gut bacteria—evidence that these bacteria helped the body harvest more energy from digested foods. Later studies showed that both obese mice and obese people harbored fewer Bacteroidetes bacteria than their normal-weight counterparts.

The microbiome is also proving critical in many aspects of health. The immune system needs it to develop properly. What's more, to protect themselves inside the body, commensal bacteria can interact with immune cell receptors or even induce the production of certain immune system cells. One abundant gut bacterium, Faecalibacterium prausnitzii, proved to have anti-inflammatory properties, and its abundance seems to help protect against the recurrence of Crohn's disease. Likewise, Sarkis Mazmanian of the California Institute of Technology in Pasadena showed that the human symbiont Bacteroides fragilis kept mice from getting colitis. And inserting bacteria isolated from healthy guts restored the microbial communities, curing chronic diarrhea in a patient infected with Clostridium difficile.

Herbert Virgin of Washington University School of Medicine finds a similar role for the virome. In mice, his team found that dormant herpesviruses revved up the immune system just enough to make the mice less susceptible to certain bacterial infections.

The ideas of a microbiome and a virome didn't even exist a decade ago. But now researchers have reason to hope they may one day manipulate the body's viral and microbial inhabitants to improve health and fight sickness.

the body's ecosystem

thescientist |  The human body is teeming with microbes—trillions of them. The commensal bacteria and fungi that live on and inside us outnumber our own cells 10-to-1, and the viruses that teem inside those cells and ours may add another order of magnitude. Genetic analyses of samples from different body regions have revealed the diverse and dynamic communities of microbes that inhabit not just the gut and areas directly exposed to the outside world, but also parts of the body that were long assumed to be microbe-free, such as the placenta, which turns out to harbor bacteria most closely akin to those in the mouth. The mouth microbiome is also suspected of influencing bacterial communities in the lungs. Researchers are also examining the basic biology of the microbiomes of the penis, the vagina, and the skin.

“No tissue in the human body is sterile, including reproductive tissues and, for that matter, the unborn child,” Seth Bordenstein, a biologist at Vanderbilt University, says in an e-mail to The Scientist.

Altogether, the members of the human body’s microbial ecosystem make up anywhere from two to six pounds of a 200-pound adult’s total body weight, according to estimates from the Human Microbiome Project, launched in 2007 by the National Institutes of Health (NIH). The gastrointestinal tract is home to an overwhelming majority of these microbes, and, correspondingly, has attracted the most interest from the research community. But scientists are learning ever more about the microbiomes that inhabit parts of the body outside the gut, and they’re finding that these communities are likely just as important. Strong patterns, along with high diversity and variation across and within individuals, are recurring themes in microbiome research. While surveys of the body’s microbial communities continue, the field is also entering a second stage of inquiry: a quest to understand how the human microbiome promotes health or permits disease.

“None of us in the field—and this is true for the gut, this is true for the skin—none of us can actually tell how our experimental observations really relate to human disease, but we’re getting closer to mechanistic insights,” says immunologist Yasmine Belkaid, chief of mucosal immunology at the National Institute of Allergy and Infectious Disease.

the business model consists in fleecing credulous geeks with more money than sense...,

discovermagazine |  Full disclosure, I didn’t pay $89 for my sample analysis kit. But if I had, I would have been disappointed. And if I had paid $399 for the five-site kit, I would have been even more so. The amount of readily available information provided little enlightenment about what my internal lurkers meant about me.

To be fair, this is not totally uBiome’s fault, and it’s something they disclose explicitly in the terms of service. We don’t know enough about the microbiome to say, “Too many of X and too little of Y mean Z,” or, “Firmicutes make you fat.” I knew that, and uBiome made very clear that no human should use their service to diagnose themselves or predict their future, and that knowledge of the microbiome is nascent and evolving. But I did expect the comparison tools to have more flexibility.

I could check out how my bacteria’s phyla stood up to those of vegans, paleos, vegetarians, heavy drinkers, weight losers, weight gainers, those on antibiotics, men, and women. But not women on antibiotics. Or vegetarian women who are in their 30s. And I couldn’t compare a level beneath phylum.

My microbiome doesn’t look like vegans’, paleos’, vegetarians’, lushes’, or any of the other groups’, which makes sense given that I’m an individual and don’t strictly fit within those categories. 

However, it also means that my data didn’t provide me much insight. I could download my own raw data and manipulate it, but then I was looking at it in a vacuum, without a set to compare to, so the analysis amounts mostly to, “Hey, look. I have this many of those bacteria. Neat?”

Beyond that, I could see a list of all my bacteria and what percentage of the population they were; which were “most enriched” compared to the aggregate; and which were “most depleted” compared to the aggregate. For some, I could click on their name — digging down from phylum to genus — and learn more about their lives and the effect they might have on mine.

However, many — more than half, if you go all the way to genus — don’t have entries. That’s because science hasn’t figured them out yet. And science will almost certainly figure them out in the future… By which time, however, my microbiome will probably have changed.

Bio Business Model

uBiome bills itself primarily as a citizen science project—your guts in your hands!

missing microbes: conspicuously obvious once the man points it out...,

martinblaser |   From Missing Microbes by Martin J. Blaser, MD. Blaser, former chair of medicine at NYU and president of the Infectious Diseases Society of America, is one of a growing number of medical practitioners and researchers who believe that we are experiencing a growing array of "modern plagues," and that the cause of these plagues is rooted in our "disappearing microbiota":

"Within the past few decades, amid all of [our] medical advances, something has gone terribly wrong. In many different ways we appear to be getting sicker. You can see the headlines every day. We are suffering from a mysterious array of what I call 'modern plagues': obesity, childhood diabetes, asthma, hay fever, food allergies, esophageal reflux and cancer, celiac disease, Crohn's disease, ulcerative colitis, autism, eczema. In all likelihood you or someone in your family or someone you know is afflicted. Unlike most lethal plagues of the past that struck relatively fast and hard, these are chronic conditions that diminish and degrade their victims' quality of life for decades. ...

"The autoimmune form of diabetes that begins in childhood and requires insulin injections (juvenile or Type I diabetes) has been doubling in incidence about every twenty years across the industrialized world. In Finland, where record keeping is meticulous, the incidence has risen 550 percent since 1950. ... But the disease itself has not changed; something in us has changed. Type I diabetes is also striking younger children. The average age of diagnosis used to be about nine. Now it is around six, and some children are becoming diabetic when they are three.

"The recent rise in asthma, a chronic inflammation of the airways, is similarly alarming. One in twelve people (about 25 million or 8 percent of the U.S. population) had asthma in 2009, compared with one in fourteen a decade earlier. Ten percent of American children suffer wheezing, breathlessness, chest tightness, and coughing; black children have it worst: one in six has the disease. Their rate increased by 50 percent from 2001 through 2009. But the rise in asthma has not spared any ethnicity: the rates were initially different in various groups, and all have been rising. ... No economic or social class has been spared.

"Food allergies are everywhere. A generation ago, peanut allergies were extremely rare. ... Ten percent of children suffer from hay fever. Eczema, a chronic skin inflammation, affects more than 15 percent of children and 2 percent of adults in the United States. In industrialized nations, the number of kids with eczema has tripled in the past thirty years. ...

"Why are all of these maladies rapidly rising at the same time across the developed world and spilling over into the developing world as it becomes more Westernized? Can it be a mere coincidenc

e? If there are ten of these modern plagues, are there ten separate causes? That seems unlikely.

"Or could there be one underlying cause fueling all these parallel increases? A single cause is easier to grasp; it is simpler, more parsimonious. But what cause could be grand enough to encompass asthma, obesity, esophageal reflux, juvenile diabetes, and allergies to specific foods, among all of the others? Eating too many calories could explain obesity but not asthma; many of the children who suffer from asthma are slim. Air pollution could explain asthma but not food allergies. ...

"The most popular explanation for the rise in childhood illness is the so-called hygiene hypothesis. The idea is that modern plagues are happening because we have made our world too clean. The result is that our children's immune systems have become quiescent and are therefore prone to false alarms and friendly fire. ...

"We need to look closely at the microorganisms that make a living in and on our bodies, massive assemblages of competing and cooperating microbes known collectively as the microbiome. ... Each of us hosts a ... diverse ecology of microbes that has coevolved with our species over millennia. They thrive in the mouth, gut, nasal passages, ear canal, and on the skin. In women, they coat the vagina. The microbes that constitute your microbiome are generally acquired early in life; surprisingly, by the age of three, the populations within children resemble those of adults. Together, they play a critical role in your immunity as well as your ability to combat disease. In short, it is your microbiome that keeps you healthy. And parts of it are disappearing.

"The reasons for this disaster are all around you, including overuse of antibiotics in humans and animals, Cesarean sections, and the widespread use of sanitizers and antiseptics, to name just a few. ...

"The loss of diversity within our microbiome is far more pernicious [than the overuse of antibiotics and resulting antibiotic resistance]. Its loss changes development itself, affecting our metabolism, immunity, and cognition.

"I have called this process the 'disappearing microbiota.' It's a funny term that does not immediately roll off your tongue, but I believe it is correct. For a number of reasons, we are losing our ancient microbes. This quandary is the central theme of this book. The loss of microbial diversity on and within our bodies is exacting a terrible price. I predict it will be worse in the future. Just as the internal combustion engine, the splitting of the atom, and pesticides all have had unanticipated effects, so too does the abuse of antibiotics and other medical or quasi-medical practices (e.g., sanitizer use).

"An even worse scenario is headed our way if we don't change our behavior. It is one so bleak, like a blizzard roaring over a frozen landscape, that I call it 'antibiotic winter.'"

oops, they forgot the breastesses...,

kurzweilai | Some 200 members of the Human Microbiome Project (HMP) Consortium from nearly 80 universities and scientific institutions, organized by the National Institutes of Health, have mapped the normal microbial makeup of healthy humans, producing numerous insights and even a few surprises.

The report on on their five years of research was published Thusday June 14, 2012, in a series of coordinated scientific reports in Nature the PLoS.

Researchers found, for example, that nearly everyone routinely carries pathogens, microorganisms known to cause illnesses.

In healthy individuals, however, pathogens cause no disease; they simply coexist with their host and the rest of the human microbiome, the collection of all microorganisms living in the human body.

Researchers must now figure out why some pathogens turn deadly and under what conditions, likely revising current concepts of how microorganisms cause disease.

“Like 15th century explorers describing the outline of a new continent, HMP researchers employed a new technological strategy to define, for the first time, the normal microbial makeup of the human body,” said NIH Director Francis S. Collins, M.D., Ph.D.

“HMP created a remarkable reference database by using genome sequencing techniques to detect microbes in healthy volunteers. This lays the foundation for accelerating infectious disease research previously impossible without this community resource.”

To define the normal human microbiome, HMP researchers sampled 242 healthy U.S. volunteers (129 male, 113 female), collecting tissues from 15 body sites in men and 18 body sites in women.

Researchers collected up to three samples from each volunteer at sites such as the mouth, nose, skin (two behind each ear and each inner elbow), and lower intestine (stool), and three vaginal sites in women; each body site can be inhabited by organisms as different as those in the Amazon Rainforest and the Sahara Desert.

Historically, doctors studied microorganisms in their patients by isolating pathogens and growing them in culture. This painstaking process typically identifies only a few microbial species, as they are hard to grow in the laboratory. In HMP, researchers purified all human and microbial DNA in each of more than 5,000 samples and analyzed them with DNA sequencing machines.

transhumans about the bidnis of enginnering biomes, as well...,

MIT |  No matter where you are, you are surrounded by your microbiome—the complex biological system of more than 100 trillion microorganisms on the human body, in airwaves, and in every environment.

“You may not know it, but you’re walking around with two pounds of microbes on you,” says Bernat Olle SM ’05, MBA ’07, PhD ’07. “But only recently have scientists discovered how important and how useful they can be.”

Research in the field of the microbiome is still in its early stages, but it has already shown that microbes play important roles in metabolism, digestion, and even mood. And Olle is one of a growing group of engineers focusing on this area.

“Modern habits have been to clean up and sterilize everything—make it clean as possible,” he says. “But we’re starting to find out this might not be a good idea—and we’re abusing anti-microbial chemicals. These microbial exposures can help develop key human functions.”

Olle is co-founder and COO of Vedanta Biosciences, a Boston-based startup that researches interactions between the human microbiome and the immune system. He spoke to Slice of MIT at the 2015 South by Southwest (SXSW) Interactive, where he was part of a three-person panel that discussed the benefits of microbes and the impact they could have on medicine in the future.

biota, diet, brains, power...,

bbc |  I have some startling news: you are not human. At least, by some counts. While you are indeed made up of billions of human cells working in remarkable concert, these are easily outnumbered by the bacterial cells that live on and in you – your microbiome. There are ten of them for every one of your own cells, and they add an extra two kilograms (4.4lbs) to your body. 

Far from being freeloading passengers, many of these microbes actively help digest food and prevent infection. And now evidence is emerging that these tiny organisms may also have a profound impact on the brain too. They are a living augmentation of your body – and like any enhancement, this means they could, in principle, be upgraded. So, could you hack your microbiome to make yourself healthier, happier, and smarter too?

According to John Cryan, this isn’t as far-fetched as it sounds. As a professor of anatomy and neuroscience at University College Cork, he specialises in the relationship between the brain and the gut. One of his early experiments showed the diversity of bacteria living in the gut was greatly diminished in mice suffering from early life stress. This finding inspired him to investigate the connection between the microbiome and the brain.

The bacterial microbiota in the gut helps normal brain development, says Cryan. “If you don’t have microbiota you have major changes in brain structure and function, and then also in behaviour.” In a pioneering study, a Japanese research team showed that mice raised without any gut bacteria had an exaggerated physical response to stress, releasing more hormone than mice that had a full complement of bacteria. However, this effect could be reduced in bacteria-free mice by repopulating their gut with Bifidobacterium infantis, one of the major symbiotic bacteria found in the gut. Cryan’s team built on this finding, showing that this effect could be reproduced even in healthy mice. “We took healthy mice and fed them Lactobacillus [another common gut bacteria), and we showed that these animals had a reduced stress response and reduced anxiety-related behaviours.” Fist tap Dale.

do you ever wonder what your anthropocene antics look like from the bacterial apex?

pnas |  In most ecosystems, microbes are the dominant consumers, commandeering much of the heterotrophic biomass circulating through food webs. Characterizing functional diversity within the microbiome, therefore, is critical to understanding ecosystem functioning, particularly in an era of global biodiversity loss. Using isotopic fingerprinting, we investigated the trophic positions of a broad diversity of heterotrophic organisms. Specifically, we examined the naturally occurring stable isotopes of nitrogen (¹⁵N:¹⁴N) within amino acids extracted from proteobacteria, actinomycetes, ascomycetes, and basidiomycetes, as well as from vertebrate and invertebrate macrofauna (crustaceans, fish, insects, and mammals). Here, we report that patterns of intertrophic ¹⁵N-discrimination were remarkably similar among bacteria, fungi, and animals, which permitted unambiguous measurement of consumer trophic position, independent of phylogeny or ecosystem type. The observed similarities among bacterial, fungal, and animal consumers suggest that within a trophic hierarchy, microbiota are equivalent to, and can be interdigitated with, macrobiota. To further test the universality of this finding, we examined Neotropical fungus gardens, communities in which bacteria, fungi, and animals are entwined in an ancient, quadripartite symbiosis. We reveal that this symbiosis is a discrete four-level food chain, wherein bacteria function as the apex carnivores, animals and fungi are meso-consumers, and the sole herbivores are fungi. Together, our findings demonstrate that bacteria, fungi, and animals can be integrated within a food chain, effectively uniting the macro- and microbiome in food web ecology and facilitating greater inclusion of the microbiome in studies of functional diversity.

N-1 a literal diseased state?

biologydirect |  The variety of parasites that can affect host behavior suggests that the phenomena of parasitic host control might be more common in nature than currently established and could have been overlooked in humans. This warrants a detailed search for parasitic organisms that affect human behavior. One approach to search for “invisible” microbes that influence behavior is by comparing the microbiomes of control subjects and humans that consistently engage in irrational ritualistic behavioral activities, which contribute to the spreading of parasites and infections.

The modern anthropological view on religion is that it is a cultural meme that replicates through social communication [44]. While the meme itself may influence behavior, religious icons are known to be vectors of infectious diseases [45]. Most major religions have rituals that are likely to promote the transmission of infections. This includes circumcision [46], Christian common communion chalice [46], the Hindu ‘side-roll’[46] and Islamic ritual ablution [46] as well as the Hajj congregation in Mecca [47]. For example, the latter is specifically associated with outbreaks of meningococcal disease [48].

Also many religions are centered on sacred relics that are worshiped and frequently kissed by multiple people and thereby can act as vessels for microbial transmission. Crosses, icons, Bible covers are kissed in some denominations of the Christian tradition, the Black Stone (the eastern cornerstone of the Kaaba) is a relic that is kissed by millions of Muslims, kissing of the Wailing Wall is a religious tradition for the Jewish. It is unlikely, but possible that the rejection of condom use, vaccination and use of antibiotics present in some religious cultures, as well as the sacred status of specific domestic animals (possible definitive hosts to the parasites) may also be related to microbial host control. Finally, it has been noted that many parasites eliminate their hosts reproductive potential as they channel all available resources to maximize their own reproductive success [18]. Coincidentally celibacy is commonplace for holy individuals that are most devoted to their faith such as monks or nuns.

Thus it is possible that various religious practices could represent biomemes: manifestations of a symbiosis between informational memes [54] and biological organisms. This concept is somewhat similar to the fictional midichlorians of the Jedi Order from the popular series “Star Wars”[55].

Two particular parts of the human body seem to be most promising for the search of  behavior-altering parasites. First of all, the human gut microbiome may be of interest in light of the microbiome-gut-brain axis concept. Another promising area to search for behavioraltering parasites is the human brain. Several organisms that can bypass the mammalian blood–brain barrier and produce a latent infection without obvious symptoms are currently known. In mice with latent toxoplasmosis, Toxoplasma gondii cysts can be found in various regions of the brain, especially in the olfactory bulb, the entorhinal, somatosensory, motor and orbital, frontal association and visual cortices, the hippocampus and the amygdala [56]. In humans the brain also appears to be an important site for Toxoplasma gondii cyst formation and the parasite is capable of infecting a variety of brain cells, including astrocytes and neurons [57-59].

subreality mainstreamed?

NYTimes | This week, the 40th anniversary of the first moon landing, there’s much talk of exploring other worlds. Which is exciting and grand; such is the stuff that dreams are made on. Yet we don’t need to go abroad to find amazing new life forms. We just need to look at the palms of our hands, the tips of our fingers, the contents of our guts.

The typical human is home to a vast array of microbes. If you were to count them, you’d find that microbial cells outnumber your own by a factor of 10. On a cell-by-cell basis, then, you are only 10 percent human. For the rest, you are microbial. (Why don’t you see this when you look in the mirror? Because most of the microbes are bacteria, and bacterial cells are generally much smaller than animal cells. They may make up 90 percent of the cells, but they’re not 90 percent of your bulk.)

This much has been known for a long time. Yet it’s only now, with the revolution in biotechnology, that we’re able to do detailed studies of which microbes are there, which genes they have, and what they’re doing. We’re just at the start, and there are far more questions than answers. But already, the results are astonishing, and the implications profound.

Even on your skin, the diversity of bacteria is prodigious. If you were to have your hands sampled, you’d probably find that each fingertip has a distinct set of residents; your palms probably also differ markedly from each other, each home to more than 150 species, but with fewer than 20 percent of the species the same. And if you’re a woman, odds are you’ll have more species than the man next to you. Why should this be? So far, no one knows.

But it’s the bacteria in the digestive tract, especially the gut, that intrigue me most. Many of these appear to be true symbionts: they have evolved to live in guts and (as far as we know) are not found elsewhere. In providing their habitat — a constant temperature, some protection from hostile lifeforms and regular influxes of food — we are as essential to them as they are to us.

And they definitely are essential to us. Gut bacteria play crucial roles in digesting food and modulating the immune system. They make small molecules that we need in order for our enzymes to work properly. They interact with us, altering which of our genes get turned on and off in cells in the intestinal walls. Some evidence suggests that they are essential for the building of a normal heart. Finally, it seems likely that gut bacteria will turn out to affect appetite, as well as other aspects of our behavior, though no one has shown this yet. (Imagine the plea: I’m sorry, sir, my microbes made me do it.)

Together, your gut microbes provide you with a pool of genes far larger than that found in the human genome. Indeed, the gut “microbiome,” as it is known, is thought to contain at least 100 times more genes than the human genome. Moreover, whereas humans are extremely similar to one another at the level of the genome, the microbiome appears to differ markedly from one person to the next.

What determines these differences? Good question. Diet has some effect: a diet rich in sugars and fats reduces the diversity of gut bacteria, and shifts the balance towards those that are more efficient at extracting energy. Start eating more plants and you can shift the balance back, and increase the diversity of your gut microbes. Your own genetic background may play a role as well, though we are far from understanding how, or how much. It probably also matters which other microbes are present: as in any ecosystem, relationships among different inhabitants are likely to be complex.

(At this point, I’d like to introduce a caveat. We know that the diversity of microbial species differs between your gut and mine, and that the less related we are, the more that will be true. Family members tend to have more similar gut microbes than nonrelatives, and preliminary evidence suggests that geography matters, too. So the gut microbes of people in China are different from those of people in the United States — though whether this is due to diet, human genes or geography is entirely unknown. But despite this variation at the species level, we don’t yet know how much variation there is at the genetic level. It may be that different sets of gut microbes provide broadly equivalent sets of genes.)

Naturally, a huge effort is now under way to see whether differences in gut bacteria are responsible for differences in health. But what interests me most about all this is that it suggests another mode of human evolution. Bacteria evolve quickly: they can go through many thousands of generations for every human one.

This has two potential consequences. First, during your lifetime, your bacteria can change their genes even though you cannot change yours. (You do have some flexibility: your immune system has a built-in capacity to change.) It may be that gut bacteria evolve in response to short-term changes in the environment, especially exposure to food-borne diseases. They may thus act as an evolving supplement to the immune system.

The second potential consequence is further reaching. Because bacteria can evolve so fast, it may be that some of what we think of as human evolution — like the ability to digest new diets that accompanied the invention of agriculture — is actually bacterial evolution. We know that hostile bacteria — those that cause diseases in ourselves and our domestic plants and animals — have undergone dramatic genetic changes in the last 10,000 years. Perhaps our friendly bacteria have, too.

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gut harbors antibiotic resistance

The Scientist | The millions of microbes that crowd the human intestinal tract are teeming with new antibiotic resistance genes that could jump to disease-causing pathogens, according to researchers from Harvard University.

They found more than 90 undiscovered bacterial genes capable of conferring antibiotic resistance hiding in microbes harvested from two healthy adults. They report their findings in Science today (August 27).

"I thought this was an incredibly cool story," Gerry Wright, McMaster University chemical biologist, told The Scientist. "It tells you just how ignorant we are of microbial ecology."

Wright, director of McMaster's Michael G. DeGroote Institute for Infectious Disease Research, said that the findings raise several key questions. "If there's so much resistance out there, how come [antibiotics] work at all?" asked Wright, who was not involved with the study. "It either means that we really don't understand how antibiotics work or we really don't understand how microbes work."

This lack of understanding is underscored by the fact that humans have exposed their bodies to a potentially dangerous flood of antibiotics -- directly in medicines and indirectly through agriculture and cleaning products -- for decades. This exposure has likely selected for the newly discovered antibiotic resistance genes in our internal microbiome, according to lead author Morten Sommer, a postdoc in Harvard geneticist George Church's lab. "And that could be a problem when the microbiome interacts with disease-causing microbes," he told The Scientist.

the quantified microbiome visualization looks strangely like an appflow visualization...,

nationalgeographic |  Some of my friends are sporting wristbands these days that keep track of their bodies. Little computers nestled in these device inside record the steps they take each day, the beats of their heart, the length of their slumbers. At the end of each day, they can sit down at a computer and look at their data arrayed across a screen like a seismogram of flesh.

I got one of these devices as a gift recently. But as much as I enjoy wasting time with technology, I just didn’t care enough to put it on my wrist. I already know that I should run more, walk more, stand more, and avoid sitting in front of monitors more. I don’t need granular data to remind me of that.

But as I read the journal Genome Biology today, I decided that someday I might surrender to the Quantified Self movement. I’ll just have to wait till I can track my trillions of microbes from one day to the next.

Thanks to the falling cost of sequencing DNA, it’s now possible for us to survey the thousands of species that live in our bodies. A couple years ago, for example, I found out that I have 58 species in my bellybutton. But all I knew was that there were 58 species in my bellybutton at one point in time–that moment I swiped a Q-tip around my navel. But everything we know about bacteria tells us that our inner ecosystems can change swiftly. My bellybutton may be remarkably different today than it was when I put a Q-tip in it.

Eric Alm, a biologist at MIT, and a graduate student of his named Lawrence David decided to plumb this change by tracking a year in the life of their microbiomes. Each day, they saved some of their stool, and later, they extracted DNA from it to figure out which species of bacteria were living in their guts. David also spat some of his saliva into a tube each day so that he could compare how his microbiome changed in his gut compared to his mouth.

Even though their study only involved two people, it was still very much a Big Data project. And one of the major challenges of any Big Data project is to visualize the results in a useful way. A number on a wrist watch won’t cut it. Between Alm and David, they and their colleagues identified thousands of species of microbes. Most were rare, while a few hundred made up the majority of bugs in their bodies. Some species showed up briefly and vanished; others lingered all year.

Here’s one way to look at their microbiomes. It shows David’s saliva. Each band represents one of the dominant species (or operational taxonomic units). Species belonging to the same lineage (a phylum) have different shades of the same color.  Fist tap Dale.

gut bacteria are what we eat

The Scientist | Japanese people regularly consume sushi wrapped in seaweed, which carries with it marine bacteria that produce porphyranases. "It was directly obvious for us that this was horizontal gene transfer from the ocean to the Japanese gut," Hehemann said. "As far as I know, there has not before been an example of horizontal gene transfer between different ecosystems."

In a commentary accompanying the study, Sonnenburg compared the gene transfer event to giving human gut bacteria a "new set of utensils" -- likely providing them the ability to digest specific foods prevalent in different regional diets. "I think there's a good bet that you'll see diet match microbiota functionality over and over and over again," he said. "That's exactly what we see in this study."

But the food purification and sterilization techniques commonly used throughout the industrialized world might affect the environmental tuning of the human gut biome function suggested by the study, Sonnenburg added. Removing many harmful bacteria from foods has dramatically reduced food-borne diseases in recent decades, he said, "but I think there's a likely cost -- the loss of microbes that are not harmful." Such microbes may transfer seemingly beneficial genes to the gut biome, increasing its ability to adapt to changes in diet, as well as fine-tune the immune system, such that "if you begin to eradicate microbes with which we have coevolved, that has the potential [to disrupt] homeostasis," Sonnenburg said.

"It shows how we rely on biodiversity that is surrounding us," Hehemann agreed. "Maybe that's the natural way -- that there is a frequent update of our gut microbiome [through] gene transfer to increase gene diversity. Obviously when we eat these highly processed foods, that's not going to happen."

How exactly this gene transfer helps the host, however, is still unclear, said Hehemann, who is currently looking into the benefits porphyranase genes provide gut bacteria in his new lab at the University of Victoria in British Columbia, Canada. It's possible that when the bacteria break down marine algae polysaccharides, it benefits the host through the production of short chain fatty acids, the end product of bacterial metabolism, which can be taken up by the host in the form of calories, Sonnenburg said. "Those are calories that, in the absence of this capability, go totally unrealized."

are we organisms or living ecosystems?

SeedMagazine | To find a biological answer to the question “Who are we?” we might look to the human genome. Certainly, when the Human Genome Project first produced a draft of the 3 billion-base-pair sequence, it was touted as a blueprint for human life. Less than a decade later, however, most experts recognize that our genomes capture only a part of who we are. Researchers have become aware, for example, of the influence of epigenetic phenomena — imprinting, maternal effects, and gene silencing, among others — in determining how genetic material is ultimately expressed. Now comes the notion that the genomes of microbes within us must also be considered. Our bodies are, after all, composites of human and bacterial cells, with microbes together contributing at least 1,000 times more genes to the whole. As we discover more and more roles that microbes play, it has become impossible to ignore the contribution of bacteria to the pool of genes we define as ourselves. Indeed, several scientists have begun to refer to the human body as a “superorganism” whose complexity extends far beyond what is encoded in a single genome.

The physiology of a superorganism would likely look very different from traditional human physiology. There has been a great deal of research into the dynamics of communities among plants, insect colonies, and even in human society. What new insights could we gain by applying some of that knowledge to the workings of communities in our own bodies? Certain body functions could be the result of negotiations between several partners, and diseases the result of small changes in group dynamics — or of a breakdown in communication between symbiotic partners.

Recently, for instance, evidence has surfaced that obesity may well include a microbial component. In ongoing work that is part of the Human Microbiome Project, researchers in Jeffrey Gordon’s lab at the Washington University School of Medicine in St. Louis showed that lean and obese mice have different proportions of microbes in their digestive systems. Bacteria in the plumper rodents, it seemed, were better able to extract energy from food, because when these bacteria were transferred into lean mice, the mice gained weight. The same is apparently true for humans: In December Gordon’s team published findings that lean and obese twins — whether identical or fraternal — harbor strikingly different bacterial communities. And these bacteria, they discovered, are not just helping to process food directly; they actually influence whether that energy is ultimately stored as fat in the body.

Even confined in their designated body parts, microbes exert their effects by churning out chemical signals for our cells to receive. Jeremy Nicholson, a chemist at Imperial College of London, has become a champion of the idea that the extent of this microbial signaling goes vastly underappreciated. Nicholson had been looking at the metabolites in human blood and urine with the hope of developing personalized drugs when he found that our bodily fluids are filled with metabolites produced by our intestinal bacteria. He now believes that the influence of gut microbes ranges from the ways in which we metabolize drugs and food to the subtle workings of our brain chemistry.

Scientists originally expected that the communication between animals and their symbiotic bacteria would form its own molecular language. But McFall-Ngai, an expert on animal-microbe symbiosis, says that she and other scientists have instead found beneficial relationships involving some of the same chemical messages that had been discovered previously in pathogens. Many bacterial products that had been termed “virulence factors” or “toxins” turn out to not be inherently offensive signals; they are just part of the conversation between microbe and host. The difference between our interaction with harmful and helpful bacteria, she says, is not so much like separate languages as it is a change in tone: “It’s the difference between an argument and a civil conversation.” We are in constant communication with our microbes, and the messages are broadcast throughout the human body.

microbial colonization...,

thescientist |  Infants start out mostly microbe-free but quickly acquire gut bacteria, which take root in three successive groups. First, Bacilli dominate. Then Gammaproteobacteria surge, followed by Clostridia. But the pace at which these bacterial groups colonize the gastrointestinal tract depends on the time since the babies were conceived, not since when they were born. And time since conception appears to have more of an influence on the infant gut microbiome than other factors, such as exposure to antibiotics, whether babies were born vaginally or by cesarean section, and if they were breastfed. These are a few of the findings from a survey of 922 fecal samples collected from 58 premature babies, published today (August 11) in PNAS.

“It is an interesting study that provides useful data regarding temporal changes in microbial composition in the infant gut that can be mined further,” Shyamal Peddada, a biostatistician at the National Institute of Environmental Health Sciences who was not involved in the study, wrote in an e-mail to The Scientist.

“I think the paper does a nice job of showing that premature babies develop differently from full-term babies . . . it is not just a function of colonization after birth,” Rob Knight from the University of Colorado, Boulder, told The Scientist in an e-mail. “Differences in gut physiology or in the infant immune system could explain this pattern.”

Researchers at the Washington University School of Medicine in St. Louis embarked on this survey in an effort to better understand the role of the microbiota in the development of gut disorders common in premature infants, such as necrotizing enterocolitis. Without first defining the premature infant gut in the absence of gastrointestinal issues, the researchers struggled to identify potentially pathogenic bacterial patterns.

The researchers collected stool samples each time the babies defecated until they were thirty days old, and sampled every third elimination after that. They then sequenced 16S ribosomal RNA genes to identify the bacterial composition of each sample.

Viruses Modulate the Function and Evolution of All Living Things

NYTimes |  High in the Sierra Nevada mountains of Spain, an international team of researchers set out four buckets to gather a shower of viruses falling from the sky.

Scientists have surmised there is a stream of viruses circling the planet, above the planet’s weather systems but below the level of airline travel. Very little is known about this realm, and that’s why the number of deposited viruses stunned the team in Spain. Each day, they calculated, some 800 million viruses cascade onto every square meter of the planet.

Most of the globe-trotting viruses are swept into the air by sea spray, and lesser numbers arrive in dust storms.

“Unimpeded by friction with the surface of the Earth, you can travel great distances, and so intercontinental travel is quite easy” for viruses, said Curtis Suttle, a marine virologist at the University of British Columbia. “It wouldn’t be unusual to find things swept up in Africa being deposited in North America.”

The study by Dr. Suttle and his colleagues, published earlier this year in the International Society of Microbial Ecology Journal, was the first to count the number of viruses falling onto the planet. The research, though, is not designed to study influenza or other illnesses, but to get a better sense of the “virosphere,” the world of viruses on the planet.

Generally it’s assumed these viruses originate on the planet and are swept upward, but some researchers theorize that viruses actually may originate in the atmosphere. (There is a small group of researchers who believe viruses may even have come here from outer space, an idea known as panspermia.)

Whatever the case, viruses are the most abundant entities on the planet by far. While Dr. Suttle’s team found hundreds of millions of viruses in a square meter, they counted tens of millions of bacteria in the same space.

Mostly thought of as infectious agents, viruses are much more than that. It’s hard to overstate the central role that viruses play in the world: They’re essential to everything from our immune system to our gut microbiome, to the ecosystems on land and sea, to climate regulation and the evolution of all species. Viruses contain a vast diverse array of unknown genes — and spread them to other species.

Last year, three experts called for a new initiative to better understand viral ecology, especially as the planet changes. “Viruses modulate the function and evolution of all living things,” wrote Matthew B. Sullivan of Ohio State, Joshua Weitz of Georgia Tech, and Steven W. Wilhelm of the University of Tennessee. “But to what extent remains a mystery.”