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Asperger Syndrome, Barry Marshall: ulcers, Berlin Wall, biofilm, clean water, correlation does not imply causation, David Strachan, discovery of penicillin, Drosophila, Fall of the Berlin Wall, friendly fire, germ theory of disease, hygiene hypothesis, Ignaz Semmelweis: hand washing, illegal immigration, John Snow's cholera map, Louis Pasteur, Maui Hawaii, meta analysis, meta-analysis, microbiome, phenotype, placebo effect, the scientific method
Quickly dubbed the ‘hygiene hypothesis’, Strachan’s idea was supported by the fact that the rise in allergies was matched by improvements in hygiene standards over time. A weekly wash before church in a lukewarm bath became a daily shower in steaming hot water. Food was refrigerated or frozen rather than pickled and fermented. Family sizes were shrinking, and life was becoming more and more urban and refined. The hygiene hypothesis just made sense, especially as in developing countries with high rates of infectious disease, allergies were still rare. It seemed that in Europe and North America, people were simply too clean for their own good, and their immune systems were champing at the bit, desperate to attack even harmless particles like pollen. Although the hygiene hypothesis represented a new paradigm for immunologists, it quickly gained scientific favour.
What’s more, they are extremely similar to the very creatures that cause the immune system so much trouble – the pathogenic varieties of bacteria, viruses and fungi. Members of the microbiota even have the same type of give-away molecules coating their surfaces that the immune system uses to detect pathogens. But something about these microbes tells the immune system not to attack. David Strachan’s original hygiene hypothesis was an excellent one, but it now faces an overhaul. He suggested that more infections in childhood meant a lower chance of allergies. The trouble is, the evidence doesn’t support the idea, and the mechanisms don’t quite work. But in some sense the rethink the hygiene hypothesis is undergoing is a subtle one. Although it does not cause disease, the microbiota is, in some sense, a vast infection. These microbes are intruders, but they have been intruding for such a long time, and they bring such great benefit, that the immune system has learnt to accommodate them.
But the researchers accounted for this by calculating the likelihoods again, this time excluding any child who had suffered from wheeze before the age of eighteen months. The link remained strong. Of course, taking antibiotics is all about ridding the body of infection, so the hygiene hypothesis stands up in light of the link between them and allergies. But the paradox remains: why would the immune system attack harmless allergens in preference to the apparently more alarming threat from the body’s microbes? And if the rise in allergies were connected to the drop in infections, why wouldn’t those of us who had had fewer infections be the ones who had more allergies? Professor Agnes Wold of the University of Gothenburg in Sweden was the first to provide an alternative to the hygiene hypothesis, in 1998. Research into the importance of the microbiota was just beginning to pick up steam, and the lack of correlation between infections and allergy had started to challenge Strachan’s idea.
The Microbiome Solution by Robynne Chutkan M.D.
Strachan’s initial paper, titled “Hay Fever, Hygiene and Household Size,” was published in the British Medical Journal in 1989 and laid the foundation for the “hygiene hypothesis,” which challenged the idea of germs as something to be avoided and posited the importance of early microbial exposure for preventing disease later in life. In 2003 Graham Rook, MD, emeritus professor of medical microbiology and immunology at University College London, expanded on this concept with his “Old Friends” hypothesis, suggesting that a lack of exposure to ancient organisms like parasites that coevolved with our ancestors, not just the absence of relatively new germs like influenza, was responsible for the emergence of these modern plagues. If we look at a map of the world today, one of the striking observations is that illnesses like Crohn’s disease are common in more developed countries and rare in less developed ones. The hygiene hypothesis accounts for this uneven distribution by suggesting that less childhood exposure to bacteria and parasites in affluent societies like the United States and Europe actually increases susceptibility to disease by suppressing the natural development of the immune system.
Version_1 To my parents, Winston and Noelle— Thanks for a dirty childhood Eat a peck of dirt before you die. Contents Title Page Copyright Dedication Epigraph Acknowledgments Introduction: Live Dirty, Eat Clean part 1 • Getting to Know Your Gut Bacteria Chapter 1. The Zoo Inside You Chapter 2. Microbes: Your Worker Bees part 2 • Messing Up the Microbiome Chapter 3. The Hygiene Hypothesis and Our Modern Plagues Chapter 4. Pharmageddon and the Antibiotic Paradox Chapter 5. Dysbiosis—Do You Have It? Chapter 6. Are Our Bacteria Making Us Fat? Chapter 7. Modern Microbial Disruptors part 3 • Rewilding Ourselves Chapter 8. Introducing the Live Dirty, Eat Clean Plan Chapter 9. The Live Dirty, Eat Clean Diet Chapter 10. The Live Dirty Lifestyle Chapter 11.
The other essential step is recognizing what threatens your gut garden’s growth. Being aware of the interlopers and inclement conditions that will reduce your victory garden to an overgrown or blighted plot is key. In the next part of this book we’ll explore in detail how the microbiome gets messed up, and what you can do to preserve yours. part 2 MESSING UP THE MICROBIOME CHAPTER 3 |||||||||||||||||||||||||||||||||||||||||| The Hygiene Hypothesis and Our Modern Plagues MANY OF US were brought up to believe that it’s better to be clean than dirty. But evidence is mounting to show that if you start from that premise, you will arrive at the wrong destination as far as human health is concerned. The microbial communities established in our bodies at birth, during infancy, and in early childhood mold our health as we grow and help determine whether or not we develop illness.
Food Allergy: Adverse Reactions to Foods and Food Additives by Dean D. Metcalfe
active measures, Albert Einstein, bioinformatics, epigenetics, hygiene hypothesis, impulse control, life extension, meta analysis, meta-analysis, mouse model, pattern recognition, phenotype, placebo effect, randomized controlled trial, selection bias, statistical model, stem cell
Another category of environmental factors that show overwhelming inverse association with atopy are infections, vaccinations, absence of antibiotic treatment, traditional farming environments, older siblings, day care attendance, and pet ownership [60–62]. These findings lead to the “hygiene hypothesis” which proposes that reduced exposure to particular microbiological stimuli , which decrease with improved living standards and higher personal hygiene, might result in an increased risk of developing allergy. Indeed, perinatal treatment (mothers prenatal and infants 6-month postnatal) with the probiotic Lacobacillus GG strain significantly reduced the development of allergies up to the age of 4 years . Although the “hygiene hypothesis” is widely accepted, the underlying mechanisms are controversial. In particular, the molecular link between environmental stimuli and immune hyperresponsiveness is far from being understood.
Annu Rev Immunol 2005;23:749–86. 59 Eder W, Klimecki W, Yu L, et al. Association between exposure to farming, allergies and genetic variation in CARD4/NOD1. Allergy 2006;61:1117–24. 77 Gilfillan AM, Tkaczyk C. Integrated signalling pathways for mast-cell activation. Nat Rev Immunol 2006;6:218–30. 60 Vercelli D. Mechanisms of the hygiene hypothesis – molecular and otherwise. Curr Opin Immunol 2006;18:733–7. 61 Yazdanbakhsh M, Kremsner PG, van RR. Allergy, parasites, and the hygiene hypothesis. Science 2002;296:490–4. 62 de MG, Janssen NA, Brunekreef B. Early childhood environment related to microbial exposure and the occurrence of atopic disease at school age. Allergy 2005;60:619–25. 63 Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system.
Although subcutaneous immunotherapy has been successful in treating allergic rhinitis, it has, unfortunately, resulted in increased adverse systemic reactions and has proven unacceptable for the treatment of food allergy [5,6]. However, in the advent of the “hygiene hypothesis,” there have been various novel approaches to the treatment Food Allergy: Adverse Reactions to Foods and Food Additives, 4th edition Edited by Dean D. Metcalfe, Hugh A. Sampson, and Ronald A. Simon © 2008 Blackwell Publishing, ISBN: 978-1-405-15129-0 of atopic disorders. The “hygiene hypothesis” postulates that increased hygiene and the lack of immunostimulatory pathogens early in childhood have resulted in a skewing of the Th1 and Th2 response . Consequently, due to an increased persistent Th2 immune response, there is a growing prevalence of allergic disorders.
Cooked: A Natural History of Transformation by Michael Pollan
biofilm, bioinformatics, Columbian Exchange, correlation does not imply causation, creative destruction, dematerialisation, Drosophila, energy security, Gary Taubes, Hernando de Soto, hygiene hypothesis, Louis Pasteur, Mason jar, microbiome, peak oil, Ralph Waldo Emerson, Steven Pinker, women in the workforce
Children born by Cesarean section, a far more hygienic process, take much longer to populate their intestinal tract, and never acquire quite the same assortment of bugs. Some researchers believe this could help explain the higher rates of allergies, asthma, and obesity observed in children born by Cesarean. The sanitized environment in which we try to surround our children is probably also taking its toll on their microbiota. Now widely accepted, the “hygiene hypothesis” holds that children need to be exposed to more bacteria, not fewer, in order to properly develop their immune system, so that it can learn to accurately distinguish between good and bad microbes. Without that training, the theory goes, the body is apt to mistake benign proteins, such as those in certain foods, for mortal threats, and react accordingly. The hypothesis explains escalating rates of allergy, asthma, and autoimmune disease in the developed world, as well as the curious fact that children reared in the microbially rich—some would say perilous—environment of a farm have fewer allergies and generally more robust immune systems.* The average child in the developed world has also received between ten and twenty courses of antibiotics before his or her eighteenth birthday, an assault on the microflora the implications of which researchers are just beginning to reckon.* Like the pesticides applied to a farm field, antibiotics “work,” at least in the short term.
Milk and cheese can be contaminated after pasteurization, and often are. Also, the cleanliness of dairying has only gotten worse under the regime of pasteurization; since dairy farmers know their milk will be sterilized after it leaves the farm and gets mixed with milk from countless other farms, they have less incentive to be scrupulous about hygiene. Nowadays, the post-Pasteurians can cite in their support the hygiene hypothesis. This is perhaps their most devastating argument, though it, too, has unacknowledged weaknesses. According to the argument, the problem is not so much with the bacteria in the milk, which they’re prepared to concede, but with the compromised immune systems of us milk drinkers—compromised (need it be said?) by years of misrule by the Pasteurians themselves, with their antibiotics, sterilized food, and sanitized child-rearing regimes.
The Diet Myth: The Real Science Behind What We Eat by Tim Spector
biofilm, British Empire, Colonization of Mars, cuban missile crisis, David Strachan, double helix, Drosophila, epigenetics, hygiene hypothesis, life extension, Mahatma Gandhi, meta analysis, meta-analysis, microbiome, phenotype, randomized controlled trial, Steve Jobs
A study recently found that babies who had their rubber dummies sucked clean by a parent then popped back into their mouths had considerably fewer allergies than those with parents dutifully replacing hygienic sterile dummies.12 The old-fashioned practice of mothers pre-chewing their baby’s food, which is rare in the West nowadays, served both to break down tough starchy foods and meats and to transmit a wide range of helpful microbes via saliva. Licking babies is common in most mammals and in some human cultures, and of course kissing is pretty universal. The Hygiene Hypothesis is an idea you may have heard of. It was developed by a colleague I trained with in epidemiology, David Strachan, whose interest was sparked when he was looking at the national data of children followed up from birth for asthma and eczema. He found a correlation between damp housing conditions and allergy in the UK.13 But the link was not what we might intuitively have expected: the damp, poor conditions and overcrowded families were actually protective, even after adjusting for other possible sources of bias.
Researchers from Indiana who studied the local Amish found only 7 per cent of Amish children had positive results from skin-prick tests, which is six times fewer than genetically similar Swiss children.14 The Amish way of living hasn’t changed much since they left Berne in Switzerland in the seventeenth century. All kids are raised communally and taught to walk and milk cows in dusty barns full of hay, straw, animal hair and manure. The workers that do most of the farming possess the most diverse sets of gut microbes, with large amounts of some species like Prevotella which, as we have seen, are rare in the rest of America but common in Africa.15 The Hygiene Hypothesis has stood the test of time so far, but now has to be adapted to our new knowledge of the importance of microbes. We need to remember that our gut microbes play a key role in training our immune systems. They do this via communication with the Treg cells in the gut walls, which are the main communicators and thermostats between what we eat and how our immune systems react.16 High Treg levels are generally healthy as they suppress the immune system.
Bad Science by Ben Goldacre
Asperger Syndrome, correlation does not imply causation, experimental subject, hygiene hypothesis, Ignaz Semmelweis: hand washing, John Snow's cholera map, Louis Pasteur, meta analysis, meta-analysis, offshore financial centre, p-value, placebo effect, publication bias, Richard Feynman, Richard Feynman, risk tolerance, Ronald Reagan, selection bias, selective serotonin reuptake inhibitor (SSRI), the scientific method, urban planning
The Times, for example, covered an experiment which showed that having younger siblings was associated with a lower incidence of multiple sclerosis. MS is caused by the immune system turning on the body. ‘This is more likely to happen if a child at a key stage of development is not exposed to infections from younger siblings, says the study.’ That’s what The Times said. But it’s wrong. That’s the ‘hygiene hypothesis’, that’s the theory, the framework into which the evidence might fit, but it’s not what the study showed: the study just found that having younger siblings seemed to be somewhat protective against MS. It didn’t say what the mechanism was, it couldn’t say why there was a relationship, such as whether it happened through greater exposure to infections. It was just an observation. The Times confused the evidence with hypothesis, and I am very glad to have got that little gripe out of my system.
Microtrends: The Small Forces Behind Tomorrow's Big Changes by Mark Penn, E. Kinney Zalesne
affirmative action, Albert Einstein, Ayatollah Khomeini, Berlin Wall, big-box store, call centre, corporate governance, David Brooks, Donald Trump, extreme commuting, Exxon Valdez, feminist movement, glass ceiling, God and Mammon, Gordon Gekko, haute couture, hygiene hypothesis, illegal immigration, immigration reform, index card, Isaac Newton, job satisfaction, labor-force participation, late fees, life extension, low skilled workers, mobile money, new economy, RAND corporation, Renaissance Technologies, Ronald Reagan, Rosa Parks, Rubik’s Cube, stem cell, Stephen Hawking, Steve Jobs, Superbowl ad, the payments system, Thomas L Friedman, upwardly mobile, uranium enrichment, urban renewal, War on Poverty, white picket fence, women in the workforce, Y2K
They said sloppiness allows for the qualities critical to greatness—like improvisation, adaptability, and serendipity. (If Alexander Fleming hadn’t been sloppy enough to leave dirty Petri dishes lying around his desk, he would never have discovered penicillin.) They even said that messy people make better parents—focused as they are on warmth and hominess, rather than stacked-up toys and ring-free coffee tables. They even hinted that clean is killing us. Doctors are now starting to credit the “hygiene hypothesis”—the idea that the sharp rise in childhood asthma and allergies today is attributable to the lack of exposure to certain germs. Chlorine bleach, which erases all mistakes one can make in clothing, is said to poison hundreds of kids a year, and may be linked to breast cancer in women and reproductive problems in men. Pesticides, those cure-alls for green trimmed lawns, have been linked to diminution of short-term memory, hand-eye coordination, and drawing ability in children.
Antifragile: Things That Gain From Disorder by Nassim Nicholas Taleb
Air France Flight 447, Andrei Shleifer, banking crisis, Benoit Mandelbrot, Berlin Wall, Black Swan, Chuck Templeton: OpenTable, commoditize, creative destruction, credit crunch, Daniel Kahneman / Amos Tversky, David Ricardo: comparative advantage, discrete time, double entry bookkeeping, Emanuel Derman, epigenetics, financial independence, Flash crash, Gary Taubes, George Santayana, Gini coefficient, Henri Poincaré, high net worth, hygiene hypothesis, Ignaz Semmelweis: hand washing, informal economy, invention of the wheel, invisible hand, Isaac Newton, James Hargreaves, Jane Jacobs, joint-stock company, joint-stock limited liability company, Joseph Schumpeter, Kenneth Arrow, knowledge economy, Lao Tzu, Long Term Capital Management, loss aversion, Louis Pasteur, mandelbrot fractal, Marc Andreessen, meta analysis, meta-analysis, microbiome, money market fund, moral hazard, mouse model, Myron Scholes, Norbert Wiener, pattern recognition, Paul Samuelson, placebo effect, Ponzi scheme, principal–agent problem, purchasing power parity, quantitative trading / quantitative ﬁnance, Ralph Nader, random walk, Ray Kurzweil, rent control, Republic of Letters, Ronald Reagan, Rory Sutherland, selection bias, Silicon Valley, six sigma, spinning jenny, statistical model, Steve Jobs, Steven Pinker, Stewart Brand, stochastic process, stochastic volatility, The Great Moderation, the new new thing, The Wealth of Nations by Adam Smith, Thomas Bayes, Thomas Malthus, too big to fail, transaction costs, urban planning, Vilfredo Pareto, Yogi Berra, Zipf's Law
Thuman, 2002, “Extrapair Paternity in Birds: A Review of Interspecific Variation and Adaptive Function.” Molecular Ecology 11: 2195–212. Grob, Gerald N., 2002, The Deadly Truth: A History of Disease in America. Cambridge, Mass.: Harvard University Press. Guadalupe-Grau, A., T. Fuentes, B. Guerra, and J. Calbet, 2009, “Exercise and Bone Mass in Adults.” Sports Medicine 39(6): 439–468. Guarner, F., R. Bourdet-Sicard, et al., 2006, “Mechanisms of Disease: the Hygiene Hypothesis Revisited.” Nature Clinical Practice Gastroenterology & Hepatology 3(5): 275–284. Guidone, C., et al., 2006, “Mechanisms of Recovery from Type 2 Diabetes After Malabsorptive Bariatric Surgery.” Diabetes 55: 2025–2031. Hacking, Ian, 1984, The Emergence of Probability: A Philosophical Study of Early Ideas About Probability, Induction and Statistical Inference. Cambridge: Cambridge University Press.