Evolution of the Hygiene Hypothesis Into Biota

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64 65 1 66 2 Microbes and Infection xx (2017) 1e9 67 3 www.elsevier.com/locate/micinf 68 4 69 5 Review 70 6 71 7 Evolution of the hygiene hypothesis into biota alteration theory: what are the 72 8 73 9 Q4 paradigms and where are the clinical applications? 74 10 75 11 a a a a a 76 12 Q3 Chantal Villeneuve , Henry H. Kou , Henrik Eckermann , Antara Palkar , Lauren G. Anderson , 77 13 Erin A. McKenney b, R. Randal Bollinger a, William Parker a,* 78 14 79 15 a Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA 80 16 b Department of Applied Ecology, North Carolina State University, Raleigh, NC 27607, USA 81 17 82 18 Received 7 August 2017; accepted 2 November 2017 83 ▪▪▪ 19 Available online 84 20 85 21 86 22 87 Abstract 23 88 24 89 25 For thousands of years, changes in human cultures have altered the biota associated with the human body, and those alterations have strongly 90 26 influenced human health. The hygiene hypothesis has evolved over the past 30 years into a nuanced biota alteration theory, but modern medical 91 27 priorities and regulatory policies have resulted in tragic underutilization of the acquired knowledge. 92 28 © 2017 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved. 93 29 94 30 95 31 Keywords: Biota; Biome; Helminth; Hygiene hypothesis; Microbiota 96 32 97 33 98 34 99 35 100 36 1. Hygiene hypothesis: historical views and origins of the infection, the problem was the absence of specific infections 101 37 term during a critical period of immune development. 102 38 Strachan's line of reasoning was at first received with 103 39 The term “hygiene hypothesis” has been used for decades “disdain on grounds of implausibility” [5], but eventually 104 40 105 41 to describe one of the causes of inflammatory disease in moved thinking in the field into a new and productive direc- Western culture. David Barker coined the term in 1988 and tion. The working paradigm has continued to evolve, with the 106 42 107 43 used the term more than once [1,2] that year to explain an more recent scientific literature showing an appreciation for 108 44 increasing incidence of appendicitis in rural communities. the role of broad, culturally-induced changes to the life asso- 109 45 Besides coining a new term, Barker's papers in 1988 provided ciated with the human body, the human biota, in the induction 110 46 a potential explanation for an increased incidence of appen- of inflammatory disease. As Bloomfield et al. noted, “A 111 47 dicitis. Barker's explanation for appendicitis utilized the consensus is beginning to develop round the view that more 112 48 113 49 widely held view in 1988 that the primary problem leading to fundamental changes in lifestyle have led to decreased expo- allergic disease was delayed exposure to infectious agents. sure to certain microbial or other species, such as helminths, 114 50 115 51 According to that model, exposure to infectious agents rela- that are important for the development of immunoregulatory ” 116 52 tively late in life caused immune disease [3,4]. In 1989, David mechanisms [6]. Thus, as Bloomfield and others, including 117 53 Strachan again used the term “hygiene hypothesis”, but Stra- Helmby, Maizels, Shoenfeld, Okada, Yazdanbakhsh and Wills- 118 54 chan changed the paradigm; rather than simply delayed Karp have concluded [7e12], it is not so much a lack of 119 55 infection, as it is dramatic changes in the symbionts normally 120 56 associated with the human body that are connected with in- 121 57 122 58 flammatory related disease. But as Shoenfeld et al. have * 123 59 Corresponding author. Department of Surgery, Duke University Medical pointed out [13], not all infections are created equal, with þ 124 60 Center, Box 2605, USA. Fax: 1 919 684 7263. some infections promoting disease and others preventing E-mail address: [email protected] (W. Parker). 125 61 126 62 127 63 https://doi.org/10.1016/j.micinf.2017.11.001 1286-4579/© 2017 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved. 128

Please cite this article in press as: Villeneuve C, et al., Evolution of the hygiene hypothesis into biota alteration theory: what are the paradigms and where are the clinical applications?, Microbes and Infection (2017), https://doi.org/10.1016/j.micinf.2017.11.001 MICINF4523_proof ■ 14 November 2017 ■ 2/9

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1 disease. Further, work considering the various components of environments leading to vitamin D deficiency [21], changes in 66 2 the biota (e.g., bacteria and helminths) and their relationship to social structure and other factors that lead to chronic psy- 67 3 68 4 inflammatory disease suggests a complex connection between chological stress [22], sedentary lifestyles, and inflammatory 69 5 culture, biota, and human health. In this review, current diets. Further, genetic factors and environmental stimuli also 70 6 thinking regarding this connection between culture, the biota, contribute to inflammatory disease, as shown in Fig. 1. 71 7 and disease will be discussed. 72 8 3. Complexity in the connection between culture, the 73 9 2. The human biota as one factor among several in the human biota, and disease 74 10 context of culture and inflammatory disease 75 11 76 12 Numerous components of modern human culture have 77 13 Alteration of the human biota in modern society has been profoundly altered the array of life associated with the 78 14 linked to an array of hyper-immune related diseases involving ecosystem of the human body, the human biota (Figs. 1 and 2). 79 15 chronic inflammation [14e17]. This phenomenon can be Modification of the biota by culture is not as straight forward 80 16 described by a “biota alteration theory” (or, alternatively, as decreased infections due to current practices of hygiene. 81 17 biome depletion theory), which states that alteration of human Rather, alteration of the biota began approximately 10,000 82 18 biota constituents in post-industrial societies leaves the im- years ago, with the development of agriculture, resulting in 83 19 84 mune system unstable and overly reactive toward harmless and increased population densities and the rise of “crowd in- 20 e ” 85 21 even self-antigens [18 20]. This over-reactivity leads to a fections [23]. Although modern hygiene has alleviated that 86 22 wide range of debilitating conditions that include autoimmu- burden to an extent, most crowd infections either did not exist 87 23 nity, allergy, digestive disorders, cancer, heart disease, and or were extremely rare in the hunteregatherer tribes that 88 24 neuropsychiatric disorders. However, these pandemics of existed prior to the agricultural revolution [23]. Thus, civili- 89 25 inflammation-related problems in modern culture are certainly zation as we know it still has potentially more, not fewer, 90 26 not caused by any one factor alone. That is to say, biota infections than our hunteregatherer ancestors, despite the use 91 27 92 28 alteration theory is not meant to be a stand-alone explanation of modern hygiene practices. The agricultural revolution and 93 29 for the inflammatory diseases of Western culture. Major cul- urbanization also resulted in a dramatic increase in coloniza- 94 30 tural factors, largely independent of biota alteration, that affect tion with various symbionts such as helminths (Fig. 2). Hel- 95 31 pandemics of inflammatory disease include indoor work minths and crowd infections are not the only organisms 96 32 97 33 98 34 99 35 100 36 101 37 102 38 103 39 104 40 105 41 106 42 107 43 108 44 109 45 110 46 111 47 112 48 113 49 114 50 115 51 116 52 117 53 118 54 119 55 120 56 121 57 122 58 123 59 124 60 125 61 126 Fig. 1. Complex relationship between culture, biota alteration, and disease. In this model, biota alteration along with other culture-associated factors such as 62 127 vitamin D deficiency and a sedentary lifestyle are considered to be mediators of inflammatory disease, along with “triggers” of disease (e.g., acute infections or 63 128 environmental antigens) and genetic predisposition. Diet, however, enters the equation in two places, both acting independently of the biota and also being a 64 primary mediator of biota alteration. Modern sanitation also enters the model in two opposing positions, contributing to biota depletion (promoting inflammation) 129 65 and contributing to reduced crowd infections (reducing inflammation). 130

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1 66 2 67 3 68 4 69 5 70 6 71 7 72 8 73 9 74 10 75 11 76 12 77 13 78 14 79 15 80 16 81 17 82 18 83 19 84 20 85 21 86 22 87 23 88 24 89 25 90 26 91 27 92 28 93 29 94 Fig. 2. Alterations of the human biota by Western society and expected approaches to alleviate changes associated with inflammation-related pathology. The 30 95 condition of the human biota is shown in green, with factors causing change in dark blue and approaches to alleviate problems in light blue. Approaches to alleviate 31 96 problems are not intended to return the biota to the hunteregatherer state (>10,000 years ago), but rather to alleviate problems caused by changes to the biota of the 32 97 hunteregatherer state. Although modern medicine is listed as causing primarily acute changes to the microbiota, it is established that some changes induced by 33 98 antibiotics, particularly in a few individuals, can be chronic in nature. Q5 34 99 35 100 36 affected by human culture. Thousands of years after the Similarly, the Westernized, inflammatory diet has no known 101 37 agricultural revolution, additional changes during the indus- effect on helminths, but substantially alters the composition of 102 38 trial revolution altered the microbiota, with infant formulas the microbiota (Fig. 2). With this in mind, it is difficult to 103 39 and modern medical practices in obstetrics profoundly altering conceive of an appropriate term that encompasses only one 104 40 the microbiota in early life [24]. Further, the diversity of the particular aspect of modern culture (e.g., hygiene) and still 105 41 microbiota can be dramatically and chronically altered in describes changes in the biota which affect public health. 106 42 some individuals as a result of the use of antibiotics [25]. Biota alteration is potentially more complex than those 107 43 108 44 However, the largest impact on the microbiota, seen in most changes induced directly by cultural factors. For example, it 109 45 individuals as a result of modernization (Fig. 2), is due pri- now seems likely that microbial adaptation to the disease state 110 46 marily to a diet rich in fats and processed sugars but low in (Fig. 3) may play a role in a vicious cycle connecting culture 111 47 fiber and a diverse array of nutrients [26]. At the same time, and disease. In this model, cultural factors affect the biota, 112 48 advances in sanitation infrastructure, water treatment, and which in turn affects inflammation, and the resulting inflam- 113 49 food preparation technology following the industrial revolu- mation feeds back to further affect the biota (Fig. 4). Although 114 50 tion profoundly reduced the biodiversity of the biota in the an emerging idea that is yet poorly understood, one potential 115 51 116 52 human gut [19,27]. The components of the human biota most mechanism underlying inflammation-induced microbial alter- 117 53 heavily impacted by these factors are helminths and protists ation may involve the selection of particular microbial com- 118 54 [19], which are dramatically reduced in numbers and often munities by the disease state. For example, certain species of 119 55 completely eliminated by modern sanitation and hygiene [28] bacteria that are found in healthy non-human primates which 120 56 (Fig. 2). have naturally occurring short intestinal transit times [29] are 121 57 It is evident that cultural factors affect the biota, which in the same as those enriched in humans with short intestinal 122 58 turn affects the function of the immune system, leading to transit times (e.g., those with diarrheal disease) [30]. Thus, the 123 59 124 inflammatory diseases in Western society (Figs. 1 and 2). It is disease state potentially leads to selection of bacteria that are 60 “ ” 125 61 also apparent that specific elements of modern society do not compatible with and potentially support the disease state 126 62 affect all components of the biota in the same way. For (Fig. 3) in ways that are largely not yet characterized. In 127 63 example, while hygiene and sanitation have a limited impact addition, adaptation of bacteria to the disease state (Fig. 3) 128 64 on the normal gut microbiota [26], they dramatically reduce or rather than simple selection of existing bacteria may be 129 65 even eliminate larger biota, including helminths (Fig. 2). important and perhaps even more damaging. This idea is 130

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1 66 2 67 3 68 4 69 5 70 6 71 7 72 8 73 9 74 10 75 11 76 12 77 13 78 14 79 15 80 16 81 17 82 18 83 19 84 20 85 21 86 22 87 23 88 24 89 25 90 26 91 27 92 28 93 29 94 30 95 31 96 32 Fig. 3. Adaption of the microbiota to the disease state. In this model, microbes potentially adapt to an inflammatory (disease) state and thereby acquire a “biological 97 33 inertia” which supports the disease state and destabilizes the healthy state. 98 34 99 35 100 36 101 37 exemplified in the case of obesity, where it has been postulated is warranted except in a historical context [34,35]. Strachan 102 38 that microbial adaptation to an inflammatory diet has led to an used the phrase originally for its catchy sound much more so 103 39 increased ability of the microbiota to extract absorbable nu- than for any nuanced meaning [5]. Indeed, as explained above, 104 40 trients in some individuals, making those nutrients more the term had already been applied earlier by Barker in a 105 41 available to the host [31]. Applying this principle of microbial different context. However, at present, the term is inaccurate, 106 42 evolution to inflammatory bowel disease (IBD), Hansen and misleading, and potentially detrimental to public health efforts 107 43 108 Vison have postulated that “the environment of the inflamed [34,35]. The term cannot accurately be applied to current 44 “ ” “ 109 45 intestine causes the bacteria to change/evolve to a more thinking regarding biota alteration , or alternatively biome 110 46 aggressive state that contributes to worsening disease and depletion”, since it is not actually hygiene that is currently 111 47 treatment failure” [32]. Studies evaluating the very rapid causing the primary changes in the biota (as discussed above 112 48 evolution of microbes in the mammalian gut support this view. and in Fig. 1). Further, the complex relationship between hy- 113 49 Within a matter of a few years, laboratory bacteria newly giene, culture, biota alteration, and disease precludes the use 114 50 introduced into the gut environment acquire new traits and an of a term that is both accurate and based strictly on hygiene. 115 51 116 52 enhanced ability to live in the gut, while at the same time For example, personal hygiene and the infrastructure associ- 117 53 losing fitness for the laboratory environment [33]. Thus, not ated with the development of hygiene (sewer systems and 118 54 unexpectedly, microbiota have the capacity to adapt to envi- water treatment facilities) were historically some of the major 119 55 ronment of the gut. The mechanisms by which such adaptation drivers of inflammation-induced biota alteration, including 120 56 may provide a “biological inertia” that supports the disease loss of helminth colonization. However, in the current Western 121 57 state and hinders efforts at treating disease (Fig. 3) remain a environment, it would be essentially impossible to acquire 122 58 topic for future study. long term colonization with most helminths that were histor- 123 59 124 60 ically common in humans (e.g., the giant roundworm, hook- 125 61 4. Biota alteration as a more accurate modern worm, human whipworm, or bovine tapeworm) even if an 126 62 replacement for hygiene hypothesis individual completely abandoned all practices of what we 127 63 think of as hygiene, including house cleaning, bathing and 128 64 Our understanding since 1988 has now evolved to the point changing clothes. At the same time, decreased hygiene in the 129 65 that discontinuation of the use of the term hygiene hypothesis current Western environment increases the incidence of crowd 130

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1 66 2 67 3 68 4 69 5 70 6 71 7 72 8 73 9 74 10 75 11 76 12 77 13 78 14 79 15 80 16 81 17 82 18 83 19 84 20 85 21 86 22 87 23 88 24 89 25 90 26 91 27 92 28 93 29 94 30 Fig. 4. Point of impact of various biota-based therapeutics within the disease process. Disease progression moves from root causes on the left to the resulting 95 disease state (downstream result) on the right. The points of impact on the disease process, indicated by the thick arrows, for various biota-based therapeutics as 31 96 well as for “standard” or typical pharmaceutical interventions are shown. The point of impact using fecal material for transplant or therapy depends on whether the 32 97 intervention is aimed at recurrent Clostridium dificile colitis (RCDC) or at inflammatory bowel disease (IBD). The location of the point of impact of most probiotic 33 98 therapies is based on the fact that probiotics are not a naturally occurring component of the biota. 34 99 35 100 5. From hygiene hypothesis to biota alteration theory 36 infections and the abundance of insect-derived antigens, both 101 37 of which can act as drivers for inflammatory disease. Thus, not 102 38 only is hygiene only one factor among several that affect biota Biota Alteration Theory is supported by numerous epide- 103 39 alteration, but the role of hygiene in biota alteration has miologic studies showing that the incidence of hyper-immune 104 40 changed through time. With this in mind, it seems that for the related diseases is drastically higher in populations and in 105 41 sake of accurate communication of current ideas regarding individuals with Westernization-induced biota alteration 106 42 science and medicine, it is appropriate to abandon the term compared to those without such alterations [14,36]. Conclu- 107 43 “ ” 108 44 hygiene hypothesis . Instead, biota alteration is both accurate sive evidence supporting this theory, obtained from direct 109 45 and descriptive, and can account for a wide range of factors experimental evidence in animal models and in humans, shows 110 46 affecting the biota, including those leading to inflammation that restoration of the biota prevents or even treats disease 111 47 and those diminishing it. [37]. Thus, what began as a hypothesis received with disdain 112 48 The hygiene of a century ago resulted in biota changes that has now evolved in terms of both ideas and unequivocal 113 49 can induce inflammatory disease, but hygiene today helps us support. Given the number of studies confirming, for example, 114 50 avoid inflammation-causing factors such as acute crowd in- that multiple sclerosis is attenuated by the presence of hel- 115 51 e 116 52 fections (e.g., the flu), mold, and insect allergens. This brings minths [38 40], it is apparent that biota alteration is indeed 117 53 to the fore the most compelling reason for abandoning the one factor that affects inflammatory disease. At the same time, 118 54 “hygiene hypothesis” as a term used to describe current as pointed out above, the theory is not intended to state that 119 55 thinking in immunology: The idea that hygiene is a driver for biota alteration is the only cultural factor leading to increased 120 56 inflammatory disease in the public consciousness has poten- inflammatory disease. 121 57 tially damaging ramifications for the public health [35], which 122 58 is necessarily dependent to an extent on proper hygiene. This 6. Biota alteration theory and public health: principles of 123 59 124 restoration 60 point has been expounded upon in some detail by Bloomfield, 125 61 Rook et al. [35]. It is counterproductive for scientists to use a 126 62 phrase which is both misleading and dangerous. The fact that The fact that culture-induced biota alteration is an un- 127 63 it is eye catching and recognized publicly is becoming more of derlying cause of inflammation is extremely encouraging 128 64 a disadvantage than an advantage. As Strachan pointed out, the from the perspective of the public health. The underlying 129 65 term is now an “enfant terrible” [5]. problem in this case appears to be vastly more manageable 130

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1 than rapidly mutating pathogenic viruses leading to immune [37]. Thus, these approaches attempt to recapitulate the 66 2 syndromes, or sociopolitical conditions leading to poverty, environment that humans require for health. As such, they are 67 3 68 4 malnutrition, chronic stress, and pollution. Indeed, a very not as prone to adverse side effects that come from blockade 69 5 wide range of relatively benign helminths and protozoans of proximal causes or blockade of symptoms as is typically 70 6 have been put forth as potential agents to reverse the effects accomplished by pharmaceutical intervention [49]. 71 7 of biota alteration [41], and apparently healthy microbiota are Considerable effort and attention has been directed toward 72 8 readily available following routine screening of healthy an obvious half-way point between biota-based therapies and 73 9 donors. traditional pharmaceutical drug discovery/development: The 74 10 Treatment of fundamental causes of disease is preferable to development of symbiont-derived drugs. Efforts directed at 75 11 76 12 treatment of more proximal causes, and offers the hope of developing microbe-based drugs abound. Intriguingly, the 77 13 eliminating disease in an efficient and benign manner. Some development of an isolated and stable helminth-derived 78 14 therapies, including helminth therapy and fecal transplants for molecule is one of the clearest examples of a potential ther- 79 15 recurrent Clostridium difficile colitis [42e47], are designed for apeutic that could, if it works, mimic the beneficial effects of 80 16 replacement of lost components of the biota, and therefore do the naturally occurring organisms while yet holding several 81 17 indeed deal with underlying causes of disease. However, not potential advantages over the organisms themselves. Such a 82 18 all biota-based therapies deal with fundamental causes of hypothetical drug would easily fit into the current drug pipe- 83 19 84 20 disease (Fig. 4). Controlled exposure to soil bacteria [48] line, avoiding the problems that intact therapeutic helminths 85 21 potentially operates based on the same principle of replacing encounter because they do not fit well with current regulatory 86 22 what was lost, although the potential of restoring exposure to policy [49] or with current financial incentives for drug 87 23 soil bacteria for health and treatment of disease has not been development [50]. Further, the stigma associated with all 88 24 explored. Probiotics and some fecal therapies, on the other helminths, widely assumed to be intestinal parasites even if 89 25 hand, operate on a different principle. These therapies gener- they don't induce disease [51,52], can be avoided. We, how- 90 26 ally involve repeated exposures to microbiota in patients ever, have contended that such efforts to develop helminth- 91 27 92 28 whose disease state (e.g., inflammatory bowel disease) was not derived drugs are misguided [19]. Our view is that exqui- 93 29 evidently caused by a loss of their native microbiota. As such, sitely complex interactions between two biological systems 94 30 these therapies do not deal with fundamental causes of disease. cannot be recapitulated by pharmaceutical intervention. 95 31 However, they may interact with the disease process at a level Helminth-derived molecules with specific biochemical targets 96 32 more distal than do typical pharmaceutical interventions may in some cases work as an immunosuppressive drug, 97 33 (Fig. 4). perhaps attenuating the symptoms of a particular disease. 98 34 We argue that several principles should guide our applica- However, no drug can train and modulate immune function as 99 35 e 100 36 tion of biota alteration theory to the public health. The first and do host symbiont interactions [49]. Thus, it is our view that 101 37 foremost principle is to deal with ultimate causes of disease even ideal results from attempts to develop helminth-derived 102 38 when possible, as described above. The second principle that drugs will be disappointing compared to results that can be 103 39 should be considered when applying biota alteration theory to obtained using intact organisms. Further, as we and others 104 40 the public health is to avoid reductionism. While reversing the have maintained [20,53], humankind eventually needs to move 105 41 effects of biota alteration on human immune function must be beyond the idea that helminths are best used as a drug or a 106 42 a high priority, it should be conducted in conjunction with therapy. Rather, we need to embrace the view that helminths 107 43 108 44 effective campaigns to mitigate other fundamental causes of are a necessary component of the ecosystem of a healthy body, 109 45 inflammation. With that in mind, public policy needs to and that helminths should be cultivated for population-wide 110 46 aggressively address not only the root causes of biota alter- biota restoration. Attempts to develop helminth-derived 111 47 ation, but also the factors which drive low levels of vitamin D, drugs are, by intent, designed to treat disease, not to restore 112 48 sedentary lifestyles, chronic psychological stress, and inflam- health to the population. As such, efforts to produce helminth- 113 49 matory diets. derived drugs will not help achieve the long-term goals of 114 50 disease prevention, and may indeed provide a distraction from 115 51 116 7. Shaping therapy around biota alteration theory versus 52 such goals as they divert resources that could be used for 117 53 traditional pharmaceutical-based drug discovery and biota-based restoration and maintenance. 118 54 development. Is there a compromise? 119 55 8. Biota alteration theory and public health: where do we 120 56 The advantage of biota-based therapies over stand? 121 57 pharmaceutical-based approaches is grounded in the ability of 122 58 biota-based therapies to address relatively more distal causes The simplest approach to alleviating inflammatory disease 123 59 124 60 of disease, as described above (Fig. 4). As with effective ex- resulting from biota alteration is relatively straight forward in 125 61 ercise regimens, embracing a healthy diet, and supplementa- design: restore what is lost. Although biota replacement is a 126 62 tion with vitamin D, biota based therapies are typically straightforward approach and is scientifically sound, progress 127 63 directed at restoring a healthy ecosystem to the human body, has been shockingly slow. Perhaps the best characterized 128 64 eliminating “environmental mismatches” that cause disease example of such an approach is the replacement of fecal 129 65 130

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1 bacteria for patients with recurrent C. difficile colitis, a 9. Biota alteration theory and public health: what needs 66 2 debilitating and sometimes deadly disease that occurs when to be done? 67 3 68 4 the microbiota fails to recover after medical use of antibiotics. 69 5 Fecal replacement from a healthy donor was first shown to Biota-based therapies face significant hurdles because they 70 6 effectively rescue patients in 1958 [54] in a study that was do not fit well with current regulatory policy [49]. Our natu- 71 7 ground breaking for Western medicine. In that landmark study, rally occurring symbionts, when used for therapeutic effect, 72 8 Ben Eiseman, founding Chief of Surgery at Denver General occupy a dead zone between human tissue and pharmaceuti- 73 9 Hospital [54], argued that “reintroduction of the bacteria, vi- cals. Attempts to regulate the organisms as pharmaceuticals 74 10 ruses, and bacteriophage normally found in the colon might re- using laws written with a profit-driven pharmaceutical industry 75 11 ” 76 12 establish the balance of nature. Eiseman contended that his in mind are some of the major hurdles at the present time [49]. 77 13 procedure, which would eventually become known as the fecal Current financial incentives for drug development and even for 78 14 transplant, would lead to a decrease in the growth of poten- medical practice are difficult to apply to naturally occurring 79 15 tially harmful and antibiotic-resistant organisms. Eiseman's organisms [50,63]. We have suggested that major legislative 80 16 successes with the fecal transplant were corroborated by correction needs to occur [49]. Laws need to be written which 81 17 several independent hospitals in California in the early 1960s effectively weigh and consider the potential harm of biota- 82 18 [55]. based therapies with the ongoing harm occurring as a result 83 19 84 20 Despite the early success of fecal transplants in resolving of biota alteration. The laws and regulations must take into 85 21 an otherwise deadly disease, fecal transplants are only now account the view that health rather than profit should drive the 86 22 becoming widely accepted. Although the 60-year old pro- biomedical research system [49]. We argue that the goals of 87 23 cedure was named one of the top ten medical innovations for health and profit can be diametrically opposed in biomedical 88 24 2014 by the Cleveland Clinic, the procedure is still not the research, and that this opposition is currently damaging the 89 25 standard of care for patients with recurrent C. difficile colitis, public health [63]. 90 26 and many patients still die of the colitis without being aware 91 27 92 10. Biota alteration theory: research that needs to be 28 that an effective therapy exists. 93 29 Other biota-based therapies have not fared better. Helminth conducted 94 30 exposure was shown in preliminary studies to be effective for 95 31 the treatment of IBD resistant to pharmacological therapy At present, with clinical application of knowledge lagging 96 32 [56,57] and of multiple sclerosis [58] in 2005 and 2007, sometimes decades behind the clinical application of Biota 97 33 respectively. Yet, the follow-up has failed to evaluate the po- Alteration Theory, the scientific community is in danger of 98 34 tential of helminth therapy. Subsequent efforts have been being seen as conducting biomedical research for the sake of 99 35 100 36 primarily limited to the testing of only one helminth, and those science, without the public health in mind. Certainly this is far 101 37 tests were eventually halted, apparently due to technical from reality. Scientists developed the hygiene hypothesis 102 38 problems associated with the storage of the helminth that may almost 30 years ago and are considering Biota Alteration 103 39 have rendered it ineffective [59]. Our own studies suggest that Theory today because we are profoundly interested in atten- 104 40 helminth therapy may be effective for the treatment of Par- uating pandemics of inflammatory disease that afflict Western 105 41 kinson's disease and for such common inflammation- society. Indeed, the basic science of biota alteration theory 106 42 associated conditions as migraine headaches and anxiety dis- would likely receive no attention in the absence of any disease. 107 43 108 44 orders [59,60], but the effects of helminths on these conditions Interest in studying multiple sclerosis would be limited, for 109 45 have not been examined in clinical trials. At present, no hel- example, if everyone was colonized with a benign helminth 110 46 minth is available for approved therapeutic use, and com- and, as predicted, the disease was eradicated. Indeed, a vast 111 47 mercial development of helminths for therapeutic use is array of fascinating phenomena exist in this universe and await 112 48 minimal, despite more than 10 years having passed since the our study, but have largely been put on a back burner for the 113 49 first studies indicated that the organisms may be effective for moment as we study a much less interesting but pressing 114 50 the treatment of diseases that are otherwise difficult to treat or concern: organisms that are unhealthy because their environ- 115 51 116 52 even untreatable. ment has been dramatically altered in readily apparent and 117 53 The origins of the probiotics concept dates back to 1907, easily reversible ways. 118 54 predating helminthic therapy and even fecal transplants [61]. Although we have observed dozens of differences between 119 55 Experiments using Lactobacillus acidophilus as a dietary biota-depleted and biota-enriched animals [64e66], we posit 120 56 supplement were conducted in the 1920s and 30s. However, that the most urgent questions in the field are clinical in nature 121 57 despite this long history, use of probiotics in clinical practice [20] rather than molecular/genetic. Which organisms work 122 58 is not standard of care, even for situations where probiotics are best, which therapies work for treatment, and which ap- 123 59 124 60 known to impart benefit to the patient. For example, even proaches can only be used for prevention? Other questions that 125 61 though certain probiotics are known to attenuate some of the likely need to be addressed include whether genotype affects 126 62 potential adverse effects of antibiotic use [62], co- the need for particular components of the biota. For example, 127 63 administration of probiotics with antibiotics is not the cur- is it possible that groups whose ancestors lived in tropical 128 64 rent standard of care. climates for many millennia have different requirements for 129 65 130

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1 helminths that those whose ancestors lived in temperate, arid, [12] Wills-Karp M, Santeliz J, Karp CL. The germless theory of allergic dis- 66 2 or polar climates? ease: revisiting the hygiene hypothesis. Nat Rev Immunol 2001;1:69e75. 67 3 [13] Kivity S, Agmon-Levin N, Blank M, Shoenfeld Y. Infections and auto- 68 4 immunity e friends or foes? Trends Immunol 2009;30:409e14. 69 5 11. Summary [14] Bach JF. The effect of infections on susceptibility to autoimmune and 70 6 allergic diseases. N Engl J Med 2002;347:911e20. 71 7 In this review, we summarize the evolution of thinking [15] Rook GA, Lowry CA. The hygiene hypothesis and psychiatric disorders. 72 8 surrounding the induction of disease as a result of culturally- Trends Immunol 2008;29:150e8. 73 9 induced biota alteration. The term hygiene hypothesis was [16] Koloski NA, Bret L, Radford-Smith G. Hygiene hypothesis in inflam- 74 10 matory bowel disease: a critical review of the literature. 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