Hygiene Hypothesis

SLIDE: Hygiene Hypothesis Definition

The hygiene hypothesis states a lack of early childhood exposure to infectious agents, symbiotic microorganisms, and parasites increase susceptibility to allergic disease by suppressing the natural development of the immune system (1,2).
In 1989 David Strachan first articulated the concept now widely known as the Hygiene Hypothesis. He proposed that the rapid post-Industrial Revolution rise in allergic diseases, such as asthma and hay fever, were due to a lack of early childhood infection (3). Since then, thousands of studies, from epidemiology to randomized-clinical studies have supported that early life microbial exposure protects against eczema, allergic rhinitis, and asthma (4,5,6,7,8). It has also been extended to explain food allergies (9), and as research into the microbiome across species grows, we are finding evidence that early life exposure to diverse microbes plays an important part in training the immune system to recognize and respond appropriately to its environment.
Semantics:

Some scientists have become averse to the term, “hygiene hypothesis,’ as they believe the public may misconstrue this to mean one shouldn’t participate in basic hygiene practice and call for new terms to describe this phenomenon (10).
These are:
Biome Depletion Theory
“Lost Fiends’ Hypothesis
“Old Friends” Hypothesis
Biodiversity Hypothesis
Where emphasis on early exposure to diverse microbes (prenatal and up to 3 years in humans; 3 weeks in mice; prior to 6 months in dogs) is necessary to train the immune system to act appropriately to stimuli (11, 12,13,14,15,16, 17).

Hologenomes and Holobionts:

It is widely accepted that humans and other mammals did not evolve as a single species, but rather have co-evolved with microbes as a “super-organism” or “holobiont.” The co-evolution over millennia has created outsourcing of immune-mediated responses to the microbial symbionts (2). In 1992, Lynn Margulis first described Holobionts as the host and its microbial symbionts that include transient and stable members (3). We will be discussing the bulk of research in human studies and controlled lab animals. The concept of superorganisms applies to all mammals with varying microbial makeup.

SLIDE Get Dirty

Basically, our obsession with sanitation is creating an epidemic of allergic and immune disorders (18, 19). In contrast, children who grow up exposed to more dirt and microbes tend to have more robust immune systems and fewer allergies (20).
SLIDE: Epidemiological studies
These graphs illustrate the question about modern society that is relatively free of infectious diseases, a major cause of inflammation yet are prone to inflammatory, allergic, and autoimmune diseases (1). A similar inverse relationship is found in countries that are free of helminths (worms) have a higher incidence of autoimmune disease (2).

SLIDE: Western Disease Allergic Trends

Hay fever began with what was known as the rich person’s disease as wealthy people tended to sneeze while poorer and rural counterparts were immune to pollen. The distinct timeline and swift introduction of these three types of allergic diseases indicate that it is likely different environmental, behavioral, or socioeconomic factors that influence them (1, 2, 3, 4, 5).

SLIDE: Companion Animals Chronic Disease

While we don’t have published data on companion animals that mimics the epidemiological graphs showing an inverse relationship between infectious disease and allergic disease, we can extrapolate the data from insurance reports and veterinary data. These tables clearly show that pet parents are visiting the vet for similar ’western’ chronic disease that the human owners' experience (1,2). Pets are also exposed to a similar environment, more processed diet, and more chemical antimicrobials than their human guardians.

SLIDE: Factors that influence Allergies under the Hygiene Hypothesis

We introduce the most common factors that influence the development of allergic disease under the Hygiene Hypothesis. These include; family size, helminth (worm) exposure, early exposure to infections, antibiotic exposure, farming exposure which all converge in having an effect on the diversity of the microbiome through microbial exposure (1, 2).

SLIDE: Canine studies

The research for the Hygiene hypothesis has few canine studies. We will discuss the specific canine studies and implications of the support from epidemiological and controlled animal studies on current health and wellness practices suggested by the veterinarians in future videos.
Future videos (insert links when made)

SLIDE: Family Size

The frequency of allergic disease is strongly correlated to family size, where younger siblings are less likely to develop allergic disease than their older siblings (1-3). This has been attributed to younger siblings being exposed to more infections and pathogens from older siblings. However, more recent research also indicated maternal IgE decreases with birth order making younger siblings less prone to allergy (4) indicating other factors may contribute in family size. At the same time, unrelated children exposed to a greater number of people, such as in daycare, show a protective effect against allergies (5,6). Other benefits from older siblings include early inoculation with beneficial bacteria such as Faecalibacterium prausnitzii which are associated with the prevention of Atopic Dermatitis (AD) (7).

Mechanism of Action:
It is suggested that larger family size increases microbial exposure at a young age and trains the immune system to deal with these microbes in the future, thereby lessening allergic response. This includes induction of regulatory T-cells (Treg) through diverse exposure to helminths, saprophytic mycobacteria, and diverse microbes (8, 9, 10) and maternal alterations with subsequent children (4).

SLIDE: Helminths

Helminth is defined as a parasitic worm; a fluke, tapeworm, or nematode (1). It may seem foreign that helminths could be used in the treatment of allergic disease, but humans have turned maggots, leeches, and bacteria into medical tools (2,3). Moreover, all mammalian species have evolved with worms. No doubt worm infestation or damaging parasitic worms is a global health concern that can create severe illness. In the last century, mass deworming initiatives have taken place in developing countries with some unintended consequences (4, 5) Their sudden eradication from humans (and pets) are being correlated with increased allergic disease (6,7).

Examination of 520 Gabonese schoolchildren found that those with blood flukes and filarial worms measured least allergic to antigens (8). A follow up randomized, double-blind, placebo-controlled study where 317 children were dewormed found that the posttreatment allergic response by the dewormed group was dramatically enhanced. After losing their parasites, children were 2 and a half times more likely to respond to dust mites (9). Similar studies show a consistent inverse relationship between deworming and allergic response (7,10).

Helminths can prevent colitis in mice and improve established colitis in mice (11, 12). Prevent brain and spinal inflammation in mice (13). Similarly, a small human study of 12 multiple sclerosis patient found that patients with worms had less nerve damage over time. However, when 4 of these patients were dewormed their multiple sclerosis symptoms got worse. Also, those with parasite had more regulatory T cells recognizing a protein, myelin basic protein that triggers the attack of neural tissue which is why they have less nerve damage (14).

Dr. Graham Rook, from the University College London, a pioneer in the “old friends’ hypothesis, explains how our coevolution with helminths has led to codependence. His explanation of this phenomenon is aptly described with the analogy of Vitamin C and primates. Dr. Rook explains that vitamin C is so essential for cellular processes that the majority of animals process their own. However, at some point in primate evolutionary history, the extended opportunity to gorge on a vitamin-C-rich diet made this internal function redundant. In an environment with an abundance of Vitamin C, the genes that manufactured Vitamin C became obsolete and bore no cost to lose this ability. At that time, the primate ancestry outsourced vitamin C production to plants. In much the same way, humans and many other mammals have outsourced their immune regulation to helminths (7).

Variability in the success of helminth for different types of allergies and chronic disease include;
1. Timing. Initial infection and duration of infection along with early and long-lasting infections are more efficient in down-regulating the disease.
2. Intensity. Meta-analysis shows that heavy parasite burden induces immune suppression where mild infections tend to promote allergy
3. Genetics. The ability to induce immune regulation may be due to variation in genetics such as NOD2 mice and humans below.
4. Types of Helminth. Meta-analyses show treatment results vary based on which helminth is used for which disease. Hookworm and Schistosoma’s lessen allergen skin test reactivity. Hookworm lessens asthma. Porcine whipworm reduces Crohn’s disease, and ulcerative colitis and N. americanus reduce Crohn’s and asthma. While other helminths can increase allergy response.
(15, 16, 17).

Helminth research in humans is so profound that major Universities are now conducting clinical trials with helminths and allergic disease. There are few studies in dogs. One pilot study administered helminth eggs (Trichuris vulpis) to Atopic Dermatitis (AD) dogs. Helminth treated dogs showed improvement in pruritus and Canine Atopic Dermatitis Extent and Severity Index scores, but, histological inflammation was not changed. A follow-up placebo-controlled study did not show a significant difference between the placebo and helminth treated dogs (18). However, much like the documented underground worm therapy for humans in Velasquez-Manoff’s book, “The Epidemic of Absence (7)”, there is a growing group of people already experimenting with helminth therapy in allergic pets (19). It would be safer to question the overuse of anti-helminth protocols in the current veterinary model than blindly infecting our companion animals (20). Much like the “antimicrobial stewardship” movement, there may be a need for judicious use of dewormers in our companion animals (21, 22). For example, much like the dilemma of antibiotic-resistant microbes, we are seeing anti-helminth resistant parasites that no longer respond to deworming treatment. One particular parasite that is no longer responding to anthelminthic medications is the roundworm Mansonella, which can cause lethargy.
Interestingly, the mode of elimination is by targeting the parasite’s symbionts in its hologenome. Specifically, scientists are killing the symbiotic microbe living in the parasite with antibiotics. The antibiotic, doxycycline, does not destroy the parasite; instead, it kills the symbiont that is involved in molting and thereby kills the holobiont (23).

MECHANISM OF ACTION:
A specific mechanism of action is best described from this quote, “Helminth infections typically produce a type 2 immune response, characterized by the production of interleukin -4 (IL-4), IL-5, IL-9, and IL-13 from T2 innate lymphoid cells (ILC2) and T helper 2 (Th2) cells, and the recruitment of eosinophils, mast cells, basophils, and alternatively activated macrophages (24)” Basically, some helminths calm the immune system by releasing anti-inflammatory signals so the body doesn’t go overboard trying to kill the worms. At the same time, they are also reducing inflammation that leads to autoimmune conditions, and the overreaction to allergens. Helminths also induce the production of regulatory T cells which recognize parts of the body that might trigger inflammation and down-regulate the response. These cells keep the immune system from staying in attack mode after the invaders are dead and from reacting to benign antigens such as pollen or chicken. Moreover, helminth has been shown to use and create beneficial metabolites such as the short-chain fatty acids (SCFA); butyrate, acetate, and propionate. SCFA can increase mucin production which helps prevent leaky gut, and they can inhibit the release of inflammatory cytokines through inhibition of NF-kB. Helminth producing acetate has been shown to protect against E. coli infection (25, 26, 27, 28, and 29). Helminths have also induced goblet cells to increase mucin production in gene mutations of NOD2 mice and humans preventing IBD (30) and induce regulatory T cells (31).
What does all this mean?
Worms keep the body from freaking out over benign antigens, create beneficial products and counter intestinal inflammation by changing the gut microbiome, and create an unfavorable environment for other pathogens.

SLIDE: Infections

A more controversial aspect of the Hygiene Hypothesis is that early exposure to certain childhood infections prevents allergies and more pathogenic disease. Some people claim that people will use this concept to promote anti-vaccination and so it should not be considered as part of the hygiene hypothesis there are attempts to remove this aspect from the hypothesis. However, there is scientific evidence that some infections can have a protective effect from more pathogenic infections and this may be mediated by genetics, single-nucleotide polymorphisms (SNPs), the timing of infection and co-infections. Awareness of these factors could modify the timing of vaccinations and even the mode of delivery (intestinal/olfactory vaccination where the microbes receive pathogen as it has on an evolutionary basis) (1, 2, 3).

Mumps: Individuals who had mumps in childhood have half the chance of developing ovarian cancer in adulthood. The initial study was an association. However, later studies showed the mechanism of action. There is a similar antigen in mumps that is similar in ovarian cancer cells. In this way, the virus trains the immune system to identify and attack ovarian cancer cells later in life. MOA: Specifically, the immune recognition of a tumor-associated form of MUC1 found in mumps and ovarian cancer. (4).
Measles: Individuals who are exposed to a wild form of childhood measles have a decreased risk of various cancer (5). Measles virus is being injected into hard to treat cancers and has been found to decimate these cancers (6). Childhood measles has also been shown to have a protective effect against atopic disorders (7, 8).
Helicobacter Pylori (H. pylori): H. pylori infections in humans cause gastric disorders on the one hand and are inversely associated with allergies and chronic inflammatory conditions on the other (9). One interesting caveat is that H. pylori increase the risk of one form of cancer noncardia gastric cancer (NCGC) at the same time decreases the risk of another form of cancer esophageal adenocarcinoma (EAC) along with allergic diseases (atopy, rhinitis, asthma). The former cancer appears to be mediated by the timing of exposure (early exposure decreases cancer risk) along with coinfection (helminths coinfection also reduce cancer risk) (10, 11).
Mechanism of action: Reduced inflammation through regT cells and altered composition of diversity and keystone strains in the microbiome (10, 11, 12).
Murine Norovirus (MNV): This concept covers a more general understanding of infections and specifically viruses. Finally, viruses may be able to step in and modulate the immune system when bacteria is compromised. For example, germ-free and antibiotic-treated mice were given a benign virus (murine norovirus, MNV), and the virus took over for the bacteria. The microbiome continued to function without a hitch (13).

Mechanism of Action:
Basically, viral infection was able to take over the essential functions of the microbiome in the absence of bacteria that was decimated. When the holobiont becomes deficient in bacterial microbes, the virome can step in to ensure proper function on the gut to maintain life (13).

SLIDE: Antibiotics

Antibiotics have undoubtedly saved millions of lives since their inception. However, the scientific community is alerting the public to the dangers of the over-use of antimicrobials in everything from agriculture to prescriptions and hand sanitizers, calling for “antimicrobial stewardship” (1). Antibiotic-resistant pathogens have become such a widespread problem that the Centers for Disease Control and Prevention (CDC) states it is one of the world’s most pressing public health problems (2). In addition to superbugs that are resistant to antibiotics, the unintended consequences to the microbiome appear to be far-reaching (3, 4). Antibiotics not only wipe out the pathogenic bacteria (which constitutes about 2% of all bacteria) it also decimates beneficial bacteria (5). The worst damage appears when administered prior to the onset of an adult microbiome (6, 7, 8, 9, 10, 11). Antibiotics administered during pregnancy and infancy increase the probability of allergic disease (12). Antibiotics prior to the age of one can permanently decrease the diversity of the microbiome (13). The overuse of antibiotics is creating superbugs that no longer respond to current drugs (14). Antibiotics can permanently alter the diversity of the microbiome (15).

Mechanism of action:
Antibiotics are shown to decrease the diversity of both beneficial and pathogenic bacteria. They increase gut permeability, susceptibility to yeast overgrowth, and damage the mitochondria — all factors in allergy development (16, 17, 18).

SLIDE: Farm Effect

The Farm Effect states that children exposed to traditional farms are less likely than other children to develop asthma, allergies and other gut-related disorders (1). Studies have discovered that a lower incidence of atopic conditions and asthma in children who are raised in rural environments and exposed to what is called “the farm effect.” This difference is seen even after adjusting for other environmental exposures and lifestyle differences (2). For example, a 2011 study in the New England Journal of Medicine reported that children who grew up on traditional farms were 50% less likely than other children to develop asthma and atopy (3). A 2018 study concluded, “Clustering of farms within a neighborhood of 100m is strongly associated with the protective effect on asthma and may represent a more traditional style of farming with broader microbial exposure (4).”
In terms of diverse microbial exposure, scientists were able to predict the likelihood of allergy from the number of endotoxins identified on the pregnant mother’s mattress with a higher endotoxin count being inversely related to the child acquiring allergic disease (5).

It should be noted that industrial farming does not have the same protective effect as traditional farming and may even increase allergic response (6, 7, 8).
Mechanism of Action:
While farming homes and urban homes have the same amount of bacteria, farming homes have a vastly larger DIVERSITY of natural microbes. It is suggested that exposure to diverse microbes from the natural evolutionary environment trains the mammalian immune system to recognize the difference between benign and pathogenic microbes. Also, maternal exposure to farming affected the quality and function of neonatal Tregs when confronted with endotoxins. Finally, decreased level of grass IgE. (3, 9, 10, 11).

SLIDE: Microbiome Diverse and Early Exposure

Ultimately, all signs converse to a diverse microbiome.
1. Siblings: exposing younger kids to more microbial diversity from older kids.
2. Helminths: some commensal helminths create a more diverse microbial environment.
3. Infections: early exposure train the immune system to handle later disease, like cancer.
4. Antibiotics: destroy microbial diversity.
5. Farm Effect: early exposure to rich and diverse microbial environment associated with health.
See extensively cited videos on the microbiome and diversity

Canine microbiome: https://www.facebook.com/PawsitivelyPrimal/videos/1634890073272457/

Diversity: https://www.facebook.com/PawsitivelyPrimal/videos/1619908298154017/

SLIDE: Summary of Hygiene Hypothesis

SLIDE: Timing of microbial exposure

As noted previously, the timing of exposure to diverse microbes, virus, and parasites may be a significant factor on the protective effects of those modalities.

SLIDE: Other Mediating Factors

The hygiene hypothesis stresses the importance of early life exposure to diverse microbes. Other factors later in life and prior to birth also impact the health outcomes.
Oher mediating factors are cited in the introduction to the canine microbiome: Canine microbiome: https://www.facebook.com/PawsitivelyPrimal/videos/1634890073272457/

References:
SLIDE: Hygiene Hypothesis Definition
1. Villeneuve, C., Kou, H. H., Eckermann, H., Palkar, A., Anderson, L. G., McKenney, E. A., ... & Parker, W. (2017). Evolution of the hygiene hypothesis into biota alteration theory: what are the paradigms and where are the clinical applications?. Microbes and infection.
2. Parker, W. (2010). Reconstituting the depleted biome to prevent immune disorders. Evolution and Medicine Review.
3. Strachan, D. P. (2000). Family size, infection and atopy: the first decade of the ‘hygiene hypothesis'. Thorax, 55(Suppl 1), S2.
4. Krämer, U., Heinrich, J., Wjst, M., & Wichmann, H. E. (1999). Age of entry to day nursery and allergy in later childhood. The Lancet, 353(9151), 450-454.
5. Ball, T. M., Castro-Rodriguez, J. A., Griffith, K. A., Holberg, C. J., Martinez, F. D., & Wright, A. L. (2000). Siblings, day-care attendance, and the risk of asthma and wheezing during childhood. New England journal of medicine, 343(8), 538-543.
6. Ownby, D. R., Johnson, C. C., & Peterson, E. L. (2002). Exposure to dogs and cats in the first year of life and risk of allergic sensitization at 6 to 7 years of age. Jama, 288(8), 963-972.
7. Braun-Fahrländer, C., Riedler, J., Herz, U., Eder, W., Waser, M., Grize, L., ... & Lauener, R. P. (2002). Environmental exposure to endotoxin and its relation to asthma in school-age children. New England Journal of Medicine, 347(12), 869-877.
8. Ege, M. J., Mayer, M., Normand, A. C., Genuneit, J., Cookson, W. O., Braun-Fahrländer, C., ... & von Mutius, E. (2011). Exposure to environmental microorganisms and childhood asthma. New England Journal of Medicine, 364(8), 701-709.
9. Lack, G. (2008). Epidemiologic risks for food allergy. Journal of Allergy and Clinical Immunology, 121(6), 1331-1336.

Semantics:
10. Bloomfield, S. F., Rook, G. A., Scott, E. A., Shanahan, F., Stanwell-Smith, R., & Turner, P. (2016). Time to abandon the hygiene hypothesis: new perspectives on allergic disease, the human microbiome, infectious disease prevention and the role of targeted hygiene. Perspectives in public health, 136(4), 213-224.
11. Mueller, N. T., Bakacs, E., Combellick, J., Grigoryan, Z., & Dominguez-Bello, M. G. (2015). The infant microbiome development: mom matters. Trends in molecular medicine, 21(2), 109-117.
12. Haahtela, T., Holgate, S., Pawankar, R., Akdis, C. A., Benjaponpitak, S., Caraballo, L., ... & von Hertzen, L. (2013). The biodiversity hypothesis and allergic disease: world allergy organization position statement. World Allergy Organization Journal, 6(1), 1.
13. Langille, M. G., Meehan, C. J., Koenig, J. E., Dhanani, A. S., Rose, R. A., Howlett, S. E., & Beiko, R. G. (2014). Microbial shifts in the aging mouse gut. Microbiome, 2(1), 50.
14. Burton, E. N., O'Connor, E., Ericsson, A. C., & Franklin, C. L. (2016). Evaluation of fecal microbiota transfer as treatment for postweaning diarrhea in research-colony puppies. Journal of the American Association for Laboratory Animal Science, 55(5), 582-587.
15. Guard, B. C., Mila, H., Steiner, J. M., Mariani, C., Suchodolski, J. S., & Chastant-Maillard, S. (2017). Characterization of the fecal microbiome during neonatal and early pediatric development in puppies. PloS one, 12(4), e0175718.
16. Conversation with Holly Ganz 2018 at AnimalBiome on the age at which puppies are likely to reach a stable “adult-like” microbiome. Only 2 studies follow puppy microbiomes and how high variability post-weaning,
17. Scudellari, M. (2017). News Feature: Cleaning up the hygiene hypothesis. Proceedings of the National Academy of Sciences, 114(7), 1433-1436.
Holobionts:
18. Margulis, L., & Fester, R. (Eds.). (1991). Symbiosis as a source of evolutionary innovation: speciation and morphogenesis. Mit Press.
SLIDE: Get Dirty
19. Callahan, G. N. (2003). Eating dirt. Emerging infectious diseases, 9(8), 1016.
20. Bloomfield, S. F., Stanwell‐Smith, R., Crevel, R. W. R., & Pickup, J. (2006). Too clean, or not too clean: the hygiene hypothesis and home hygiene. Clinical & Experimental Allergy, 36(4), 402-425.
21. Gilbert, J., & Knight, R. (2017). Dirt is Good: The Advantage of Germs for Your Child's Developing Immune System. St. Martin's Press.

SLIDE: Epidemiological studies
(1) Bach, J. F. (2002). The effect of infections on susceptibility to autoimmune and allergic diseases. New England journal of medicine, 347(12), 911-920.
(2) Joel Weinstock, MD., Tufts Medical Center, Boston

SLIDE: Western Disease Allergic Trends
(1) Umetsu, D. T., McIntire, J. J., Akbari, O., Macaubas, C., & DeKruyff, R. H. (2002). Asthma: an epidemic of dysregulated immunity. Nature immunology, 3(8), 715.
(2) Bach, J. F. (2002). The effect of infections on susceptibility to autoimmune and allergic diseases. New England journal of medicine, 347(12), 911-920.
(3) Platts-Mills, T. A. (2015). The allergy epidemics: 1870-2010. Journal of Allergy and Clinical Immunology, 136(1), 3-13.
(4) Sicherer, S. H., Muñoz-Furlong, A., Godbold, J. H., & Sampson, H. A. (2010). US prevalence of self-reported peanut, tree nut, and sesame allergy: 11-year follow-up. Journal of Allergy and Clinical Immunology, 125(6), 1322-1326.
(5) Lack, G. (2008). Epidemiologic risks for food allergy. Journal of Allergy and Clinical Immunology, 121(6), 1331-1336.

SLIDE: Companion Animals Chronic Disease
(1) Nationwide. Top 10 reasons Pets Visit Vets. 2016. https://phz8.petinsurance.com/…/top-10-reasons-pets-visit-v…
(2) Veterinary Practice News. Top 10 reasons why pets see a veterinarian. October 25,2018. https://www.veterinarypracticenews.com/top-10-reasons-why-…/

SLIDE: Factors that influence Allergies under the Hygiene Hypothesis
(1) Bloomfield, S. F., Stanwell-Smith, R., Crevel, R. W., & Pickup, J. (2006). Too clean, or not too clean: the hygiene hypothesis and home hygiene. Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology, 36(4), 402-25.
(2) Okada, H., Kuhn, C., Feillet, H., & Bach, J. F. (2010). The 'hygiene hypothesis' for autoimmune and allergic diseases: an update. Clinical and experimental immunology, 160(1), 1-9.
SLIDE: Canine studies

SLIDE: Family Size
(1) Strachan, D. P. (1989). Hay fever, hygiene, and household size. BMJ : British Medical Journal, 299(6710), 1259–1260.
(2) Strachan, D. P., Aït-Khaled, N., Foliaki, S., Mallol, J., Odhiambo, J., Pearce, N., & Williams, H. C. (2015). Siblings, asthma, rhinoconjunctivitis and eczema: a worldwide perspective from the International Study of Asthma and Allergies in Childhood. Clinical and Experimental Allergy, 45(1), 126–136. http://doi.org/10.1111/cea.12349
(3) Bodner, C., Godden, D., & Seaton, A. (1998). Family size, childhood infections and atopic diseases. The Aberdeen WHEASE Group. Thorax, 53(1), 28-32.
(4) Karmaus, W., Arshad, S. H., Sadeghnejad, A., & Twiselton, R. (2004). Does maternal immunoglobulin E decrease with increasing order of live offspring? Investigation into maternal immune tolerance. Clinical & Experimental Allergy, 34(6), 853-859.
(5) Ball, T. M., Castro-Rodriguez, J. A., Griffith, K. A., Holberg, C. J., Martinez, F. D., & Wright, A. L. (2000). Siblings, day-care attendance, and the risk of asthma and wheezing during childhood. New England journal of medicine, 343(8), 538-543.
(6) Krämer, U., Heinrich, J., Wjst, M., & Wichmann, H. E. (1999). Age of entry to day nursery and allergy in later childhood. The Lancet, 353(9151), 450-454.
(7) Laursen, M. F., Laursen, R. P., Larnkjær, A., Mølgaard, C., Michaelsen, K. F., Frøkiær, H., ... & Licht, T. R. (2017). Faecalibacterium Gut Colonization Is Accelerated by Presence of Older Siblings. Msphere, 2(6), e00448-17.
(8) Guarner, F., Bourdet-Sicard, R., Brandtzaeg, P., Gill, H. S., McGuirk, P., Van Eden, W., ... & Rook, G. A. (2006). Mechanisms of disease: the hygiene hypothesis revisited. Nature Reviews Gastroenterology and Hepatology, 3(5), 275.
(9) Penders, J., Gerhold, K., Thijs, C., Zimmermann, K., Wahn, U., Lau, S., & Hamelmann, E. (2014). New insights into the hygiene hypothesis in allergic diseases: mediation of sibling and birth mode effects by the gut microbiota. Gut microbes, 5(2), 239-244.

SLIDE: Helminths
(1) Castro, G. A. (1996). Helminths: structure, classification, growth, and development.
(2) Salzet, M. (2005). Neuropeptide-derived antimicrobial peptides from invertebrates for biomedical applications. Current medicinal chemistry, 12(26), 3055-3061.
(3) Whitaker, I. S., Twine, C., Whitaker, M. J., Welck, M., Brown, C. S., & Shandall, A. (2007). Larval therapy from antiquity to the present day: mechanisms of action, clinical applications and future potential. Postgraduate medical journal, 83(980), 409-413.
(4) Ismail, M. (2007). Preventive chemotherapy in human helminthiasis, Coordinating use of anthelminthic drugs in control interventions: A manual for health professionals and programme managers. Indian Journal of Medical Research, 126(3), 235.
(5) Humphries, D., Nguyen, S., Boakye, D., Wilson, M., & Cappello, M. (2012). The promise and pitfalls of mass drug administration to control intestinal helminth infections. Current opinion in infectious diseases, 25(5), 584-589.
(6) Velasquez-Manoff, M. (2012). An epidemic of absence: a new way of understanding allergies and autoimmune diseases. Simon and Schuster
(7) Afifi, M. A., Jiman-Fatani, A. A., El Saadany, S., & Fouad, M. A. (2015). Parasites–allergy paradox: Disease mediators or therapeutic modulators. Journal of microscopy and ultrastructure, 3(2), 53-61.
(8) van den Biggelaar, A. H., van Ree, R., Rodrigues, L. C., Lell, B., Deelder, A. M., Kremsner, P. G., & Yazdanbakhsh, M. (2000). Decreased atopy in children infected with Schistosoma haematobium: a role for parasite-induced interleukin-10. The Lancet, 356(9243), 1723-1727.
(9) van den Biggelaar, A. H., Rodrigues, L. C., van Ree, R., van der Zee, J. S., Hoeksma-Kruize, Y. C., Souverijn, J. H., ... & Yazdanbakhsh, M. (2004). Long-term treatment of intestinal helminths increases mite skin-test reactivity in Gabonese schoolchildren. Journal of Infectious Diseases, 189(5), 892-900.
(10) Flohr, C., Tuyen, L. N., Lewis, S., Quinnell, R., Minh, T. T., Liem, H. T., ... & Williams, H. (2006). Poor sanitation and helminth infection protect against skin sensitization in Vietnamese children: a cross-sectional study. Journal of allergy and clinical immunology, 118(6), 1305-1311.
(11) Weinstock, J. V. (2006). Helminths and mucosal immune modulation. Annals of the New York Academy of Sciences, 1072(1), 356-364.
(12) Weinstock, J. V., Summers, R. W., & Elliott, D. E. (2005, June). Role of helminths in regulating mucosal inflammation. In Springer seminars in immunopathology (Vol. 27, No. 2, pp. 249-271). Springer-Verlag.
(13) Smallwood, T. B., Giacomin, P. R., Loukas, A., Mulvenna, J. P., Clark, R. J., & Miles, J. J. (2017). Helminth immunomodulation in autoimmune disease. Frontiers in immunology, 8, 453.
(14) Correale, J., & Farez, M. (2007). Association between parasite infection and immune responses in multiple sclerosis. Annals of Neurology: Official Journal of the American Neurological Association and the Child Neurology Society, 61(2), 97-108.
(15) Yazdanbakhsh, M., Kremsner, P. G., & Van Ree, R. (2002). Allergy, parasites, and the hygiene hypothesis. Science, 296(5567), 490-494.
(16) Smits, H. H., Everts, B., Hartgers, F. C., & Yazdanbakhsh, M. (2010). Chronic helminth infections protect against allergic diseases by active regulatory processes. Current allergy and asthma reports, 10(1), 3-12.
(17) Ruyssers, N. E., De Winter, B. Y., De Man, J. G., Loukas, A., Herman, A. G., Pelckmans, P. A., & Moreels, T. G. (2008). Worms and the treatment of inflammatory bowel disease: are molecules the answer?. Clinical & developmental immunology, 2008, 567314.
(18) Mueller, R. S., Specht, L., Helmer, M., Epe, C., Wolken, S., Denk, D., ... & Sauter-Luis, C. (2011). The effect of nematode administration on canine atopic dermatitis. Veterinary parasitology, 181(2-4), 203-209.
(19) https://helminthictherapywiki.org/…/Helminthic_therapy_for_…
(20) Veterinary Information Network. Could Pet Deworming Regimen Fuel Parasite Resistance?” Jan. 29, 2013. Christy Corp-Mminamiji, DVM
(21) Hardefeldt, L. Y., Gilkerson, J. R., Billman-Jacobe, H., Stevenson, M. A., Thursky, K., Bailey, K. E., & Browning, G. F. (2018). Barriers to and enablers of implementing antimicrobial stewardship programs in veterinary practices. Journal of veterinary internal medicine, 32(3), 1092-1099.
(22) https://apic.org/…/Practice-Resou…/Antimicrobial-Stewardship
(23) Ta-Tang, T. H., Crainey, J. L., Post, R. J., Luz, S. L., & Rubio, J. M. (2018). Mansonellosis: current perspectives. Research and reports in tropical medicine, 9, 9-24. doi:10.2147/RRTM.S125750
(24) Brosschot, T. P., & Reynolds, L. A. (2018). The impact of a helminth-modified microbiome on host immunity. Mucosal immunology, 1.
(25) Grencis, R. K. (2015). Immunity to helminths: resistance, regulation, and susceptibility to gastrointestinal nematodes. Annual review of immunology, 33, 201-225
(26) Zaiss, M. M., Rapin, A., Lebon, L., Dubey, L. K., Mosconi, I., Sarter, K., ... & Paerewijck, O. (2015). The intestinal microbiota contributes to the ability of helminths to modulate allergic inflammation. Immunity, 43(5), 998-1010.
(27) Tielens, A. G., van Grinsven, K. W., Henze, K., van Hellemond, J. J., & Martin, W. (2010). Acetate formation in the energy metabolism of parasitic helminths and protists. International journal for parasitology, 40(4), 387-397.
(28) Thorburn, A. N., Macia, L., & Mackay, C. R. (2014). Diet, metabolites, and “western-lifestyle” inflammatory diseases. Immunity, 40(6), 833-842.
(29) Fukuda, S., Toh, H., Hase, K., Oshima, K., Nakanishi, Y., Yoshimura, K., ... & Taylor, T. D. (2011). Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature, 469(7331), 54 3.
(30) Ramanan, D., Bowcutt, R., Lee, S. C., San Tang, M., Kurtz, Z. D., Ding, Y., ... & Lim, Y. A. (2016). Helminth infection promotes colonization resistance via type 2 immunity. Science, 352(6285), 608-612.
(31) Guarner, F., Bourdet-Sicard, R., Brandtzaeg, P., Gill, H. S., McGuirk, P., Van Eden, W., ... & Rook, G. A. (2006). Mechanisms of disease: the hygiene hypothesis revisited. Nature Reviews Gastroenterology and Hepatology, 3(5), 275.
(32) Mueller, R. S., Specht, L., Helmer, M., Epe, C., Wolken, S., Denk, D., ... & Sauter-Luis, C. (2011). The effect of nematode administration on canine atopic dermatitis. Veterinary parasitology, 181(2-4), 203-209.
(33) Ramanan, D., Bowcutt, R., Lee, S. C., San Tang, M., Kurtz, Z. D., Ding, Y., ... & Lim, Y. A. (2016). Helminth infection promotes colonization resistance via type 2 immunity. Science, 352(6285), 608-612.

SLIDE: Infections
(1) Cann, S. A. H., Van Netten, J. P., & Van Netten, C. (2006). Acute infections as a means of cancer prevention: Opposing effects to chronic infections?. Cancer detection and prevention, 30(1), 83-93.Cramer, D. W., Vitonis, A. F., Pinheiro, S. P., McKolanis, J. R., Fichorova, R. N., Brown, K. E., ... & Finn, O. J. (2010). Mumps and ovarian cancer: modern interpretation of an historic association. Cancer Causes & Control, 21(8), 1193-1201.
(2) Albonico, H. U., Bräker, H. U., & Hüsler, J. (1998). Febrile infectious childhood diseases in the history of cancer patients and matched control. Medical hypotheses, 51(4), 315-320.
(3) Bach, J. F. (2002). The effect of infections on susceptibility to autoimmune and allergic diseases. New England journal of medicine, 347(12), 911-920.
(4) Anderson, B. D., Nakamura, T., Russell, S. J., & Peng, K. W. (2004). High CD46 receptor density determines preferential killing of tumor cells by oncolytic measles virus. Cancer research, 64(14), 4919-4926.
(5) Kyburz, A., Fallegger, A., Zhang, X., Altobelli, A., Artola-Boran, M., Borbet, T., ... & Huehn, J. (2018). Transmaternal Helicobacter pylori exposure reduces allergic airway inflammation in offspring through regulatory T cells. Journal of Allergy and Clinical Immunology.
(6) Galanis, E., Hartmann, L. C., Cliby, W. A., Long, H. J., Peethambaram, P. P., Barrette, B. A., ... & Sloan, J. A. (2010). Phase I trial of intraperitoneal administration of an oncolytic measles virus strain engineered to express carcinoembryonic antigen for recurrent ovarian cancer. Cancer research, 0008-5472.
(7) Kucukosmanoglu, E., Cetinkaya, F., Akcay, F., & Pekun, F. (2006). Frequency of allergic diseases following measles. Allergologia et immunopathologia, 34(4), 146-149.
(8) Rosenlund, H., Bergström, A., Alm, J. S., Swartz, J., Scheynius, A., van Hage, M., ... & Riedler, J. (2009). Allergic disease and atopic sensitization in children in relation to measles vaccination and measles infection. Pediatrics, 123(3), 771-778.
(9) Shaheen, S. O., Barker, D. J. P., Heyes, C. B., Shiell, A. W., Aaby, P., Hall, A. J., & Goudiaby, A. (1996). Measles and atopy in Guinea-Bissau. The Lancet, 347(9018), 1792-1796.
(10) Blaser, M. J. Disappearing microbiota: Helicobacter pylori protection against esophageal adenocarcinoma. Cancer Prev. Res. (Phila. Pa) 1, 308–311 (2008).
(11) Kienesberger, S., Cox, L. M., Livanos, A., Zhang, X. S., Chung, J., Perez-Perez, G. I., ... & Blaser, M. J. (2016). Gastric Helicobacter pylori infection affects local and distant microbial populations and host responses. Cell reports, 14(6), 1395-1407.
(12) Blaser, M. J. (2014). Missing microbes: how the overuse of antibiotics is fueling our modern plagues. Macmillan.
(13) Kernbauer, E., Ding, Y., & Cadwell, K. (2014). An enteric virus can replace the beneficial function of commensal bacteria. Nature, 516(7529), 94.

SLIDE: Antibiotics
(1) Li, D. X., & Cosgrove, S. E. (2017). Antimicrobial Stewardship: Efficacy and Implementation of Strategies to Address Antimicrobial Overuse and Resistance. Antimicrobial Stewardship, 2, 13.
(2) Centers for Disease Control and Prevention. (2018) National Antimicrobial Resistance Monitoring System for Enteric Bacteria (NARMS). https://www.cdc.gov/narms/faq.html
(3) Blaser, M. J. (2014). Missing microbes: how the overuse of antibiotics is fueling our modern plagues. Macmillan.
(4) Bisgaard, H., Li, N., Bonnelykke, K., Chawes, B. L. K., Skov, T., Paludan-Müller, G., ... & Krogfelt, K. A. (2011). Reduced diversity of the intestinal microbiota during infancy is associated with increased risk of allergic disease at school age. Journal of Allergy and Clinical Immunology, 128(3), 646-652.
(5) Langdon, A., Crook, N., & Dantas, G. (2016). The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome medicine, 8(1), 39.
(6) Jordan, S., Storey, M., & Morgan, G. (2008). Antibiotics and allergic disorders in childhood. The open nursing journal, 2, 48.
(7) Love, B. L., Mann, J. R., Hardin, J. W., Lu, Z. K., Cox, C., & Amrol, D. J. (2016). Antibiotic prescription and food allergy in young children. Allergy, Asthma & Clinical Immunology, 12(1), 41.
(8) Mitre, E., Susi, A., Kropp, L. E., Schwartz, D. J., Gorman, G. H., & Nylund, C. M. (2018). Association Between Use of Acid-Suppressive Medications and Antibiotics During Infancy and Allergic Diseases in Early Childhood. JAMA pediatrics, 172(6), e180315-e180315.
(9) Kozyrskyj, A. L. (2015). Can we predict future allergies from our infant gut microbiota?.
(10) Abrahamsson, T. R., Jakobsson, H. E., Andersson, A. F., Björkstén, B., Engstrand, L., & Jenmalm, M. C. (2012). Low diversity of the gut microbiota in infants with atopic eczema. Journal of allergy and clinical immunology, 129(2), 434-440.
(11) Wang, M., Karlsson, C., Olsson, C., Adlerberth, I., Wold, A. E., Strachan, D. P., ... & Coates, A. R. (2008). Reduced diversity in the early fecal microbiota of infants with atopic eczema. Journal of Allergy and Clinical Immunology, 121(1), 129-134.
(12) Tamburini, S., Shen, N., Wu, H. C., & Clemente, J. C. (2016). The microbiome in early life: implications for health outcomes. Nature medicine, 22(7), 713.
(13) Hirsch, A. G., Pollak, J., Glass, T. A., Poulsen, M. N., Bailey‐Davis, L., Mowery, J., & Schwartz, B. S. (2017). Early‐life antibiotic use and subsequent diagnosis of food allergy and allergic diseases. Clinical & Experimental Allergy, 47(2), 236-244.
(14) Ramya, K., & Sankar, P. (2018). Antimicrobial Resistance: Alarming Universal Concern.
(15) Blaser, M. J. (2016). Antibiotic use and its consequences for the normal microbiome. Science, 352(6285), 544-545.
(16) Kalghatgi, S., Spina, C. S., Costello, J. C., Liesa, M., Morones-Ramirez, J. R., Slomovic, S., ... & Collins, J. J. (2013). Bactericidal antibiotics induce mitochondrial dysfunction and oxidative damage in mammalian cells. Science translational medicine, 5(192), 192ra85-192ra85.
(17) Tulstrup, M. V. L., Christensen, E. G., Carvalho, V., Linninge, C., Ahrné, S., Højberg, O., ... & Bahl, M. I. (2015). Antibiotic treatment affects intestinal permeability and gut microbial composition in Wistar rats dependent on antibiotic class. PLoS One, 10(12), e0144854.
(18) Becattini, S., Taur, Y., & Pamer, E. G. (2016). Antibiotic-induced changes in the intestinal microbiota and disease. Trends in molecular medicine, 22(6), 458-478.

SLIDE: Farm Effect
(1) Wlasiuk, G., & Vercelli, D. (2012). The farm effect, or: when, what and how a farming environment protects from asthma and allergic disease. Current opinion in allergy and clinical immunology, 12(5), 461-466.
(2) Lewis, M. C., Inman, C. F., Patel, D., Schmidt, B., Mulder, I., Miller, B., ... & Bailey, M. (2012). Direct experimental evidence that early‐life farm environment influences regulation of immune responses. Pediatric Allergy and Immunology, 23(3), 265-269.
(3) Ege, M. J., Mayer, M., Normand, A. C., Genuneit, J., Cookson, W. O., Braun-Fahrländer, C., ... & von Mutius, E. (2011). Exposure to environmental microorganisms and childhood asthma. New England Journal of Medicine, 364(8), 701-709.
(4) Müller‐Rompa, S. E. K., Markevych, I., Hose, A. J., Loss, G., Wouters, I. M., Genuneit, J., ... & von Mutius, E. (2018). An approach to the asthma‐protective farm effect by geocoding: Good farms and better farms. Pediatric Allergy and Immunology, 29(3), 275-282.
(5) Yu, J., Liu, X., Li, Y., Meng, S., Wu, F., Yan, B., ... & Liu, J. (2018). Maternal exposure to farming environment protects offspring against allergic diseases by modulating the neonatal TLR-Tregs-Th axis. Clinical and translational allergy, 8(1), 34.
(6) Vuitton, D. A., & Dalphin, J. C. (2017). From Farming to Engineering: The Microbiota and Allergic Diseases. Engineering, 3(1), 98-109.
(7) Tantoco, J. C., Bontrager, J. E., Zhao, Q., DeLine, J., & Seroogy, C. M. (2018). The Amish have decreased asthma and allergic diseases compared with old order Mennonites. Annals of Allergy, Asthma & Immunology, 121(2), 252-253.
(8) Stein, M. M., Hrusch, C. L., Gozdz, J., Igartua, C., Pivniouk, V., Murray, S. E., ... & Neilson, J. W. (2016). Innate immunity and asthma risk in Amish and Hutterite farm children. New England Journal of Medicine, 375(5), 411-421.
(9) Vuitton, D. A., & Dalphin, J. C. (2017). From Farming to Engineering: The Microbiota and Allergic Diseases. Engineering, 3(1), 98-109.
(10) Schaub, B., Liu, J., Höppler, S., Schleich, I., Huehn, J., Olek, S., ... & von Mutius, E. (2009). Maternal farm exposure modulates neonatal immune mechanisms through regulatory T cells. Journal of Allergy and Clinical Immunology, 123(4), 774-782.
(11) Ege, M. J., Herzum, I., Büchele, G., Krauss-Etschmann, S., Lauener, R. P., Roponen, M., ... & Dalphin, J. C. (2008). Prenatal exposure to a farm environment modifies atopic sensitization at birth. Journal of allergy and clinical immunology, 122(2), 407-412.
SLIDE: Microbiome Diverse and Early Exposure

(1) Ege, M. J., Mayer, M., Normand, A. C., Genuneit, J., Cookson, W. O., Braun-Fahrländer, C., ... & von Mutius, E. (2011). Exposure to environmental microorganisms and childhood asthma. New England Journal of Medicine, 364(8), 701-709
SLIDE: Summary of Hygiene Hypothesis
SLIDE: Timing of microbial exposure
SLIDE: Other Mediating Factors

References:
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