Mapping the microscopic
Even though it is such an apparently integral and ancient aspect of human health, scientists are still grasping for better ways to study human microbiota—before it changes beyond historical recognition. Borrowing models from outside of medicine has helped many in the field gain a better understanding of this living world within us. "The important concept is about extinctions," Blaser says. "It's ecology."
Deborah Goldberg, a plant ecologist by trade and professor in the Department of Ecology and Evolutionary Biology at U.M., happened upon the field by chance, but she has found her ecological perspective to be quite "relevant in talking about pathogens," she says. Microbiologists had already begun to apply rudimentary ecological thinking about niches and disturbance to microbial work, she says. But newer developments in the field of ecology—from invasion biology to spatial dynamics and dispersal—have brought new insights, notes Goldberg, who co-authored a 2007 paper with Foxman in Interdisciplinary Perspectives on Infectious Diseases about human microbiota.
For many current research purposes, however, the ecological model can be daunting. "As an overall approach, ecology is hard," Goldberg says. "It's complex systems and highly dimensional."
These challenges have led many to think of human microbiota more as biologists conceptualize organ systems, looking for inputs and outputs and putting aside—for now—what happens in the so-called black box. "It's conceptually easy to think of it as an organ system," Foxman says. "But there are lots of reasons to go into the black box…. Ultimately, we really do need to understand the system."
The first step in understanding these systems is simply taking stock of what archaea, bacteria, fungi, protozoa and viruses are present in healthy individuals. This massive micro undertaking has been ongoing since 2007 through the National Institutes of Health's (NIH) Human Microbiome Project. So far it has turned up some surprisingly rich data, including genetic sequencing for some 205 of the different genera that live on healthy human skin.
Despite the flood of new data, Foxman laughs when asked if there is any hope for a final report from the Human Microbiome Project any time soon. "This is the very, very beginning," she says, comparing this project with the NIH's Human Genome Project, which jump-started a barrage of new genetic research. "There are basic, basic questions that we don't know the answers to," she says, such as how different microbiota are between random individuals or family members; how much microbiota change over time; or how related the microbiota are to each other on or inside a person's body.
Rapid advances in sequencing technology, however, have allowed researchers to accelerate their work by leaps and bounds. "I can do today what I couldn't do six months ago," Foxman says. "It's going to be a wild ride [with] lots of surprises," she adds. "We will be getting in that black box pretty quickly, but we may not like what we find."
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Add CommentSeems to make make sense to me. Hope it's not to late.
Reply | Report Abuse | Link to thisWe need to clean up as much pollution as we can without causing more harm.
This balance is becoming ever more precarious, and with more and more rumors spreading to gullible mothers about what is and what is not "healthy", the children of our country are being put at risk. Might I note that in many European countries, like France, where hygiene isn't taken into so much consideration, children are not suffering so much. In China there are significantly less allergies due to the pollution in the air's affect on the immune system. This brings out even more how too much of a good thing can be bad.
Reply | Report Abuse | Link to thisRemaining competitive from the inside-out: With western culture traditionally praising originality and enterprise, this article is an eye opener, given that collective human behaviour is driven by fear mongering and pressure tactics by contrary political interests touting the positions of patent monoculture pundits for our food chain. Falling face-first in mud is childhood pay dirt for survival. Drinking chlorinated water, for example, raises similar questions for adaptive immune learning capability.
Reply | Report Abuse | Link to thisBugs are much too clever and if you get rid of all the bacteria you're going to get fungi. If you get rid of all the fungi, you're going to get algae. If you get rid of all the algae, you're going to get something worse. (Dr. Sidney M. Finegold, U.C.L.A.)
Reply | Report Abuse | Link to thisMy uncle took Carter's Little Liver pills for 67 years! And, when he died last year, we had to beat his liver to death with a stick.
Reply | Report Abuse | Link to thisThe evolutionary process is observed in all things, and noted changes are inevetable. Humans are no different, and our changes have been slow as yet, but could be in for a major leap
Reply | Report Abuse | Link to thistoward co-habitating with our environment. We are not going to keep the environment just a neat as you wish, but instead have to roll with it. The ability of people with disease to travel widely is a real concern to the health of any area they go to.
Micro-biota is being altered by a science with very limited knowledge other than getting $'s from a large corporation who's only concern is profit. Replentishing the earth can be as easy as utilizing more ecofriendly materials that are natural, organics that do not need to be altered.
Hemp. It is the answer, and it will save the planet, not scientist's ego-centric desires to be innovative.
It's a fertilizer, a natural pesticide, an unequaled soil enhancer, a source of bio-fuel, and it's uses goes on.
Hey, "science", seriously consider, and thouroughly assess this miricle "weed".
"Bugs Inside" twiddles my thoughts about the "bugs" outside. Humans have not only fiddled with internal microbiota but elected to live closely with unnatural external and unhealthy microbiota. Zoonotic diseases for example from domesticated pets.
Reply | Report Abuse | Link to thisVery interesting article. In the Asia Pacific there is a movement towards using a product called Effective Microorganisms in gardening, agriculture, aquaculture, water treatment and animal husbandry. EM is a mixed culture of micro organisms, in three categories: photosynthetic bacteria, lactobbacilus and yeasts. In layman’s terms photosynthetic bacteria fix the sun’s energy into useful acids, sugars and metabolites, lactobbacilus helps suppress some disease inducing microorganisms and pest populations and yeasts promote cell and root division.
Reply | Report Abuse | Link to thisI presume that people who eat food produced from soil that has been treated with EM or eat animals that have been fed hay or herbs/vegetables/water treated with EM would absorb more such micro organisms themselves and be more healthy.
Wow! You mean the obvious, that we are (and always have been) Symbiotes is finally coming to light?
Reply | Report Abuse | Link to thisAmazing! Yes, yes I know - the 'Scientific Process' must be adhered to, and all that; but I still can't believe that this comes as as much of a 'surprise' to so many people and scientists as it seems to be.
I mean, look at your average Cave Man - did they have anti-bacterial soap? NOPE! Sooooo, since we evolved through the process of living that way.......
What they failed to mention is the antibiotics that are being fed to cattle and end up in us. Has this practice altered all of us? In what ways? Is it too late to "go organic"?
Reply | Report Abuse | Link to thisThis article fails to mention the antiobiotics that are introduced into our foods, especially in cattle and poultry. What effect has this practice had on altering humans in the countries that do this? Could that be the reason for the obesity and type 2 diabetes epidemic?
Reply | Report Abuse | Link to thisPerhaps it's time to completely return to organic farming....if there is still time enough to make a difference.
As a French person, I tell you that we take consideration of hygiene!
Reply | Report Abuse | Link to thisPerhaps these observations can explain the ongoing deterioration of our immune systems in various ways, to include higher incidents of Crohns and Ulcerative Colitis disease.
Reply | Report Abuse | Link to thisPerhaps these observations can explain the ongoing deterioration of our immune systems in various ways, to include higher incidents of Crohn’s and Ulcerative Colitis disease.
Reply | Report Abuse | Link to thisThis doesn't come as a surprise to me. We are multicellular microorganisms. What we eat has a direct impact on our gut bacteria and in turn an impact on gene expression. We are what we eat. If that food contains pesticides, biocides or antibiotics this will directly impact on the balance of bacteria in the gut. I think the reduction in diversity of our diets, excessive use of antibacterials and antibiotics and changes in the varieties of wheats and the properties of major carbohydrate food stuffs have led to the increase in disorders such as Crohn's, Ulcerative colitis, allergies, cancer etc.
Reply | Report Abuse | Link to thisAn example: A friend of friend died last year from bowel cancer (in his 20s). An absolute tragedy. Apparently for several years in his teens he refused to eat anything other than white bread and beige foods. By the time he was diagnosed the cancer was so aggressive there was nothing that could have been done. Maybe the prolonged period of white bleached bread monoculture severely changed his gut and led to changes in gene expression of the gut leading to spread of malfunctioning cancerous genes.
Very disappointed to get a push-poll on climate change from Shell when loading this page. They are pushing lies; you can't take their money without doing a disservice to scientific communication.
Reply | Report Abuse | Link to this"Infants may one day be screened for native microbiota and given immunizations to fill in important missing niches." ->shouldn't that be "given innoculations to fill in important missing niches" ? Ie. you would want the infant to be exposed to and to actively cultivate a wider microbiome, not have the immune system wipe out more of them.
Reply | Report Abuse | Link to thisBreast feeding babies, allowing them to explore their environment and minimising exposure to antibiotics, biocides and antibacterials from a young age and eating a varied diet should be enough to cultivate a healthy microbial population.
Reply | Report Abuse | Link to thisI recently read an article that proposed that the appendix, in addition to whatever else it may or may not do, could be a repository or storage niche for our various microbiota, a reserve in times of depletion. I wonder what percentage of people suffering from GERD have had appendectomies (an extremely popular procedure at one time...)?
Reply | Report Abuse | Link to thisClaire: Organic does not = good. Organic farming produces much less per acre. Thus the significantly higher cost for organic foods. The real issue is misuse of chemical pesticides, herbicides and fertilizers. Most farmers use more than is needed and treat large areas. Science is offering a solution with targeted treatment via agrobots that can treat only aflicted plants and avoid spraying an entire field when only a tiny part needs help. Stat-up costs are high but in the long run the savings more than pay for the investment.
Reply | Report Abuse | Link to thisSALuckyLucy: Reduction in diversity of diets??? The average American diet includes food species from 5 continents. Only 100 years ago that was unlikely and 500 years ago it was flat out impossible.
Your second post was completely correct but assumes that a large mortality rate is acceptable. Only 200 years ago over half of people born died before having children that lived to adulthood, in other words, the line died out.
More damage is done by exposure to air "fresheners" and room sprays than people realize. I think I will wait until we know more before getting too worked up about this.
My grandmother was not a germaphobic. She sent us out to play in dirt and mud. We had fun and were healthy. When I had children, I kept them clean. Three have allergies, one has asthma. What can I say? Simplify.
Reply | Report Abuse | Link to thisThe foods may come from 5 continents but they are predominantly a few types, maize, wheat and rice. The genetic diversity of those crops has altered and is much reduced.
Reply | Report Abuse | Link to thisMisuse of chemical pesticides, herbicides and fertilisers are a huge problem and organic is not the answer. Diversification of the varieties available and growing mixed variety crops could provide natural pest management, along with intercropping and rotation based farming systems with precision use of chemicals only when necessary to prevent resistance building up and residues in food.
I agree about chemical air fresheners. Absolutely unnecessary, toxic and can bioacculmulate in body fat upsetting the endocrine system.
Vaccines and antibiotics have saved millions of children and adults from some of the most hideous and deadly diseases. Even if the speculative and likely untrue hypothesis of such advanced treatments causing allergies, etc. were true, such disorders are far superior to the high infant and child death rates of other countries. Who wants to have a portion of their children die horrible deaths, so that maybe their remaining children won't have allergies?
Reply | Report Abuse | Link to thisIt seems that commentors may mistake pure science - the quest for knowledge, from applied science - the application of discoveries to treatments, and making profit from science.
Reply | Report Abuse | Link to thisOn "hideous" disease and technology: Smallpox vaccination antedates knowledge of sterilizing and other treatments for infection as source of illness.
Traditional cultures recognized ourselves and the biosphere as superorganisms - traditional cultures all over the world, many with clear relationships to others that had migrated many thousands of miles. This suggest strongly that human societies knew of our intimate participation in ecological systems far before literacy was invented.
In nature, a high percentage of offspring did not survive. All species have the capacity to overproduce offspring.
Many humans surviving now only do so because of the impossibly determined efforts to save every human, whatever the expense to all other species, and indeed as we begin to see, other complex life in oceans, air, and land.
The "hideous" diseases still occur, and such as malaria have helped vulnerable populations to evolve resistance: immunity in a proportion of individuals.
Hideous is in the eye of the beholder. Evolution will not be denied.
We are living in a period of human overbloom; how long it lasts before the inevitable collapse occurs, remains to be seen.
Bacteria, rabbits, deer, or any other temporarily overgrowing species either depletes its environment of carrying capacity for that particular species, or allows sufficient growth of predators to rebalance the whole.
Science of discovery, studying what organisms vitally evolving with us is appears to be letting us rediscover our relationship with all other life. Should we ignore such a lesson, our destruction of other species and depletion of diversity will cause the resultant collapse to include enough of the world's web of life to send life in utterly new directions, as it appears to have done during other mass extinctions.
Good, the article highlights the intricate dynamics of microbial ecology inside human systems. We need to take every conscious step to least disturb the equilibrium of the microorganisms living inside our digestive system. Antobiotics or probiotics both can counteract to kill native flora.
Reply | Report Abuse | Link to thisthat was a very good article. i wanted to mention that the hook worm plays an important role as well. some day i well get treatment with hook worms, that hopefully will cure my asthma.
Reply | Report Abuse | Link to thisIn reading on the German New Medicine it is mentioned that the tubercular organism is the one that must be in place to dispose of lung cancer tissue when the body is able to stop the neoplastic process on its own. The tumors should then be broken down by these organisms, however, vaccination has eliminated them so the tumors remain...
Reply | Report Abuse | Link to thisIn reading on the German New Medicine it is mentioned that the tubercular organism is the one that must be in place to dispose of lung cancer tissue when the body is able to stop the neoplastic process on its own. The tumors should then be broken down by these organisms, however, vaccination has eliminated them, ... so the tumors remain...
Reply | Report Abuse | Link to thisJust what I've been saying for years. (see www.sustainablemedicine.org.) Traditional diets--raw milk, cream and butter, rare/raw meat and fish, lacto-fermented vegetables, yogurt, kefir, breads made from ancient sourdough cultures, eggs from chickens that browse in the dirt, and barely washed vegetables grown in living organic soil--kept people healthier... and happier. Your vitality is all those microorganisms dancing...
Reply | Report Abuse | Link to thisA metaphor
Reply | Report Abuse | Link to thisLife is a boxing match. Mans opponents are certain parasites and bacteria that we play the game with. In the past, sometimes the bacteria won and at other times man won, but for the most part, man and his adversaries co-evolved to survive one another. Both have survived through constant engagement and millenniums of move and countermove. In boxing, the player is totally engrossed with his opponent and the environment. The boxer is aware of a multitude of strategic factors. Man is focused on his opponent, himself, and his surroundingsaware of each others strengths, weaknesses and strategy. The player is alert to position on the ring, balance, fatigue level, strengths and weaknesses, match duration, etc. In other words, the players are perceptive to the slightest shift in the game.
What has happened in the later part of the last century in Western culture is that man has begun to dominate his opponent, so that his adversary has, in effect been knocked out. That has left man to aimlessly wonder around the ring. As the break in the match continues, man losses his engagement with the game and becomes disoriented. He spies his own trainer on the bench behind him In his confused state, he remembers that he is a boxer and proceeds to pellet punches at his trainer, thinking that he is his boxing sparing partner, when, indeed, they are on his side. So, he attacks his own pancreatic �-cells (type 1 diabetes), myelin (multiple sclerosis), and gut epithelium gut (inflammatory bowl disease). The metaphor is similar to Don Quixote who after a period of excessive reading and dreaming began to think of himself as a knight-errant with a mission to right the wrongs of the world and begins attacking his countrys windmills.
A few years ago I had a "flexible sigmoidoscopy" examination. This is supposed to be a "safe" diagnostic procedure. As a preparation for the examination, I had to drink about 1 Gallon of a solution of polyethylene glycol (PEG) and electrolytes to "clean out" the lower intestinal track (sort of like a powerful laxative).
Reply | Report Abuse | Link to thisMy system never recovered from this supposedly "safe" procedure. The various symptoms:
acid reflux, gas, food sensitivities, ... suggest that the PEG treatment made a permanent change in the intestinal bacteria "ecology" - which "doctors" apparently don't know how to fix. I have tried various "probiotic" solutions, but these didn't fully fix the issue either (but they seemed to help a little).
Thus, antibiotics are not the only "medicines" that can mess up the bacterial balance. Who knows how may cases of things like acid reflux disease (GERD) and other intestinal problems are actually caused by "unintentional consequences of common medical treatments.
science seems to be evolving from cave man like brain now, they are finally learning something useful other then what they always try to learn, which is how to make more and more money or at least the "bad" science. I already knew this, the scientists should have just asked me, seriously.
Reply | Report Abuse | Link to thisYou put it better then even I had.
Reply | Report Abuse | Link to thisHumans are not distinct from the environment. We are very foolish if we think we are. All the organisms on the planet have been evolving for exactly the same amount of time. All are equally evolved, and all have evolved within the matrix of the ecosystem they live in. Their life and health is intimately intertwined with the life, health, and diversity of the ecosystem. We are truly all of one flesh. The loss of any of us harms us all. Wake up humans! Or become extinct.
Reply | Report Abuse | Link to thisHmm,... So I am 10% human and 90% bug. It figures. I always had sympathies for the bug in the Vincent Price movie "The Fly"
Reply | Report Abuse | Link to thisAfter reading this article, two thoughts came to mind -- I have several autoimmune diseases (Behcet's Disease, Sjogrens Syndrome, Raynauds' Phenomenon and guttate psoriasis among other issues which have been treated with many different medications. I often have oral thrush which goes through my system resulting in yeast infections. These have been treated with 10-day 150 mg, twice daily diflucan with questionable results. I have been going through this unending cycle for many years. I told several of my doctors that I thought I had systemic candidiasis but was told that I would be so sick I would be unable to stand in their office, I'd be hospitalized. I also just recently went to an allergist and was told that I had signs of a positive H. pylori. I am under the impression that this was negative as my dad also had this (they thought he had celiac disease) but was "treated" with 2 tough antibiotics and is now able to eat all the things restricted by celiacs?? I am now allergic to most antibiotics, a result I think is from overuse and now the medications are stronger for the more resistant diseases. I have the opportunity to participate in a clinical trial at Northwestern University in a stem cell transplant trial. What are anyone's thoughts on my situation? Would participating be a good idea for someone that already takes forever to heal, I get anything I am subject to as I have been on immuno-suppressant drugs as well as prednisone (low dose) for the last 10 years. I am very much an anti-bacterial soap user and demand my family use it as well. My life went from one of great activity and happiness to now where I have no life except to go to my many dr visits and Remicade infusions every 4 weeks. I have not worked since 2004 when our car was hit head-on by a man driving under the influence of Ambien! I have been rejected 3 times from getting disability from Social Security and am waiting for a judge to be assigned to my ALJ hearing which apparantly takes forever. I told them that I thought they were waiting for me to die so they wouldn't have to pay my backpay and the disability $ I deserve. Thank goodness I have health insurance through my husband but the dr's copays and Rx payments are killing my husband who has been working 2 jobs, HS teacher since 1985 and then he goes to teach at WCSU as an adjunct 3 days a week for night class. The stress is going to kill us both. Please offer your advice of what path I should take? I literally think that "leaky gut" is responsible for many of my problems. Help me please!!
Reply | Report Abuse | Link to thisAfter reading this article, two thoughts came to mind -- I have several autoimmune diseases (Behcet's Disease, Sjogrens Syndrome, Raynauds' Phenomenon and guttate psoriasis among other issues which have been treated with many different medications. I often have oral thrush which goes through my system resulting in yeast infections. These have been treated with 10-day 150 mg, twice daily diflucan with questionable results. I have been going through this unending cycle for many years. I told several of my doctors that I thought I had systemic candidiasis but was told that I would be so sick I would be unable to stand in their office, I'd be hospitalized. I also just recently went to an allergist and was told that I had signs of a positive H. pylori. I am under the impression that this was negative as my dad also had this (they thought he had celiac disease) but was "treated" with 2 tough antibiotics and is now able to eat all the things restricted by celiacs?? I am now allergic to most antibiotics, a result I think is from overuse and now the medications are stronger for the more resistant diseases. I have the opportunity to participate in a clinical trial at Northwestern University in a stem cell transplant trial. What are anyone's thoughts on my situation? Would participating be a good idea for someone that already takes forever to heal, I get anything I am subject to as I have been on immuno-suppressant drugs as well as prednisone (low dose) for the last 10 years. I am very much an anti-bacterial soap user and demand my family use it as well. My life went from one of great activity and happiness to now where I have no life except to go to my many dr visits and Remicade infusions every 4 weeks. I have not worked since 2004 when our car was hit head-on by a man driving under the influence of Ambien! I have been rejected 3 times from getting disability from Social Security and am waiting for a judge to be assigned to my ALJ hearing which apparantly takes forever. I told them that I thought they were waiting for me to die so they wouldn't have to pay my backpay and the disability $ I deserve. Thank goodness I have health insurance through my husband but the dr's copays and Rx payments are killing my husband who has been working 2 jobs, HS teacher since 1985 and then he goes to teach at WCSU as an adjunct 3 days a week for night class. The stress is going to kill us both. Please offer your advice of what path I should take? I literally think that "leaky gut" is responsible for many of my problems. Help me please!!
Reply | Report Abuse | Link to thisthis is bs. bacteria ate my sister,I see no benefit to any.
Reply | Report Abuse | Link to thisInteresting - this had occurred to me recently when I working on biosand filters here in Thailand that use good bacteria to clean the water naturally. I realized that water treatment is like DDT in that it kills the good with the bad. We evolved drinking "untreated" water where we both ingested lots of microbes, many of which are important for digestion etc and I assume we developed immunities too.
Reply | Report Abuse | Link to thisThe doctor was wrong to think C. albicans couldn't be a problem because you were able to stand up and walk... It doesn't have to go fully systemic to be a big problem in the intestinal tract, which can definitely affect sensitivities and allergies (the "leaky gut" theory) and ultimately many other things in the body.
Reply | Report Abuse | Link to thisI would suggest an empirical approach. Look for inexpensive non-prescription approaches to controlling C. albicans and see if they help you. There are books and plenty of information on the net. Remember that M.D.s are only consultants, and some are better than others. Also there are some things they know and many other things they don't know. Many M.D.s are just not broadly trained in areas like nutrition, which has such an impact on chronic and complex disorders. And they often are just not very experimental. They like drugs because it's something concrete they can hand you and the only compliance required is for you to remember to take the pill, plus it's harder to sue them if they can show they were following the current "standard of care" ... :) The prescription drugs are also profitable enough to be run through FDA-approved clinical trials, which are very expensive (although results are murky except at the extremes and my own opinion as a scientist is that they are grossly misusing and misunderstanding statistics), giving an illusion of safety and efficacy (might not be either safe or effective for a particular individual). But you have to be an experimentalist when dealing with anything as inherently complicated as the human body. Trust your own instincts in this. Don't expect so much from the doctors, just use them for the things they do well and work out the rest on your own.
An old book called The Yeast Connection (Dr. William Crook) might be a starting point, although if you're suspecting Candida problems you might already know about it. It was written by an M.D. who took quite a while before he realized that the old approaches weren't working and started listening to his patients about what worked for them in dealing with chronic problems. A followup was the very useful The Yeast Connection Cookbook done with Marjorie Hurt Jones, R.N. who has done a lot of really good books on eating with food allergies (which for many people seem to be a related problem, at least once the yeast is controlled they have fewer problems with food allergies and interestingly enough chemical sensitivities). Just google the title and loads of more recent info will pop up.
Good luck.
"Having evolved along with the human species..."
Reply | Report Abuse | Link to thisYes, however, microbes were here billions of years before we were.
At some point microbes decided to become symbiont, and a symbiotic relationship evolved.
Disruption of the messaging system could have grave consequences for some critical areas of "our brain."
PS: It should become unfashionable to do the "us and them" routine. It is just us once symbiosis develops.
http://powertoxins.blogspot.com/2012/02/microbial-hermeneutics.html
Well said.
Reply | Report Abuse | Link to thisYou can say that again. ;)
Reply | Report Abuse | Link to thisThe number three killer in the U.S. is medial treatment mistakes.
Reply | Report Abuse | Link to thishttp://blogdredd.blogspot.com/2012/02/homeland-terrorism-instability-we-can.html
Time to eliminate GMO for starters! Stop geothermal chemtrail spraying of sea and sky around the world...turn to clean food and water and people will likely regain their health!
Reply | Report Abuse | Link to this