More tired children

Brain, Guts, and Skin – No, This Isn’t a Blog Post for Zombies

In every place in the world, mental illnesses like depression and anxiety and skin problems like acne have probably affected everyone at some point in their lives. But, how are these related? And what can we do about them?

Scientists have discovered a link between metal illness and acne — a long time ago. It’s not really breaking news anymore, but in the 1930s, researchers John Stokes and Donald Pillsbury came up with the brain-gut-skin theory. While it’s less-than-eloquently titled and sounds as if perhaps a zombie scientist came up with it, it’s actually very important – for living humans. The brain-gut-skin theory states that an negative emotional state (like depression or anxiety) changes the levels of the necessary, important bacteria living in harmony inside your gut, which leaves you susceptible to skin inflammation problems (like acne). The fix? Stokes and Pillsbury gave these people a a very important bacteria naturally found in your gut called Lactobacillus acidophilus, which is a super-common probiotic – in fact, it’s probably one of the key bacteria listed on the side of almost all probiotic supplements sold at your nearest drugstore. Probiotics help maintain the levels of healthy, good bacteria in your gut so your  body stays balanced inside [1]. Indeed, for Stokes and Pillsbury’s subjects suffering from emotional stress, messed-up levels of gut bacteria, and skin problems, Lactobacillus acidophilus helped restore the levels of good, natural bacteria in the gut which in turn cleared up skin issues and helped resolve some mental illness. However, what Stokes and Pillsbury hadn’t figured out was how the brain-gut-skin theory actually worked within the body.


A plethora of bacteria live within your gut to help to keep your body and mind healthy [2].

Recently, this old theory was re-investigated to help us out today. A review by Powe and Logan 2011 has found many instances of strong evidence that the brain-gut-skin theory still holds true [3]. For example, a group of people on medications to help prevent heartburn developed a condition called SIBO, or small intestinal bacterial overgrowth. This means that while these medications were stopping heartburn, they were causing way too much bacteria to build up in the gut. In turn, SIBO-sufferers’s bodies had trouble taking in and absorbing all the nutrients in their diet they needed to live, and suffered from depression and/or skin problems, too. So, scientists gave these sufferers probiotics and the SIBO decreased, along with the depression and acne. In another study, more than half (66%) of acne patients showed that they had bacterial issues inside their guts as well, further proving a link between gut and skin.

People have shown that a variety of psychological and physical stress can hurt the healthy levels of intestinal bacteria, with the most harmful reductions coming from Lactobacillus and a species of bacteria called Bifidobacteria. However, it was found that until now, few studies really sought to prove that fact – the studies were either way too small or conducted in an entirely different language. A doctor studied 300 patients who were given probiotic containing a mixture of bacterias L. acidophilus and L. bulgaricus, and found that  that 80% of those 300 people with acne had improvement, and that the probiotic was actually most valuable in cases of painful, inflammatory acne. Similar results have been found in studies in countries throughout the world. But, probiotics helping clear skin issues by doesn’t just stop at ingesting the probiotic – in fact, topical probiotics, or ones rubbed on acne-affected skin, were proven to be very helpful as well.

A lot of testing was done on the gut-skin link, but not a lot was done on the correlation between brain-gut until now. The first study of the mental health benefits of probiotics in humans involved 132 adults affected with depression. After weeks of taking a probiotic drink containing Lactobacillus casei, the mood scores of these people improved. Probiotics have also shown to be significantly helpful in decreasing anxiety in people. In an even more recent French study, people who had been given probiotics Lactobacillus helveticus and Bifidobacterium longum for a month showed decreased levels of depression, anxiety, anger, and stress inside the body and out. In fact, rats were then given probiotics with their food, too, and their levels of anxiety decreased.


Within the past 10 years, not only has much evidence been found to support the brain-gut-skin theory, but scientists think they have finally discovered how it works. There are currently two explanations for how keeping healthy levels of gut bacteria leads to better mental health and clearer skin. Simply stated, one explanation says that probiotics increase toughness of nerve cells in the brain, fending off depression, and help keep cells alive and healthy during times of stress, fending off both depression on the inside and skin problems on the outside. The addition of probiotic also increases the levels of omega-3 fatty acids in the body, which contribute to healthy moods as well as prevent inflammation, like in the skin. The second explanation for the brain-gut-skin theory states that probiotics might work directly to regulate levels of blood sugar, preventing blood sugar from becoming too high or too low. If blood sugar becomes too high or low, it could lead to unhealthy medical conditions, including but not limited to depression and acne. This explanation further states that an incorporation of a healthy diet – one low in saturated fats and excess carbohydrates – in addition to probiotics has been shown to help you fend off unhealthy blood sugar levels, which keeps you happier and keeps your skin clearer.


The brain-skin-gut theory shows links between the three, as well as how an unhealthy diet can harm your gut, skin, and mind [3].

Though some studies since the dawn of the brain-gut-skin theory until now have claimed their results showed that probiotics did not help improve mood and/or skin, these studies are few and far between, and were deemed questionable or inaccurate due to their methods of measuring these conditions. For the most part, the brain-gut-skin theory has shown that a link between healthy gut bacteria and a better mental state does exist, and even more overwhelming evidence shows that and acne is a disease triggered by unhealthy levels of bacteria in the gut, and these have been proven true in countless studies throughout decades. Mechanisms behind how this theory works have even been uncovered. Soon, perhaps more mechanisms will be proposed, and we can discover new bodily pathways and ways to better care for ourselves inside and out, body and mind. What links will we discover next?


Goldin, Barry R., and Sherwood L. Gorbach. “Probiotics for humans.” Probiotics. Springer Netherlands, 1992. 355-376. [1] [2]

Bowe, Whitney P., and Alan C. Logan. “Acne vulgaris, probiotics and the gut-brain-skin axis-back to the future?.” Gut pathogens 3.1 (2011): 1. doi:10.1186/1757-4749-3-1 [3]


The Power of Your Poo: Transplant of donor feces more effective at treating C. diff infection than antibiotics

Even though “fecal transplantation” and “duodenal infusion of donor feces” sound sort of scientific, it is exactly what you are thinking–poop from one person is transplanted into another person’s gut. Yes, this proposed treatment for Clostridium difficile,  a bacterial infection that causes diarrhea, fever and abdominal pain, has an ‘ew’ factor, but researchers have found that it is highly effective in treating recurrent infections–much more effective than the traditional antibiotic regimen (1).



Typically, C. difficile or ‘C. diff‘ infections are treated with a standard vancomycin regimen. This regimen works fairly well against an initial C. diff infection (about 60% efficacy), but works very poorly against recurrent infections (2). But because there is no effective treatment for these returning infections, patients are just given repeated courses of the antibiotics and their prognosis is poor (3). That was the case until researchers found a promising treatment from an unlikely source–healthy donor feces.

To oppose the unappealing nature of this treatment and doctors’ reluctance to perform it, van Nood et al. (2013) completed a controlled, randomized trial to prove the huge benefits of fecal transplantation. All patients included in the study had confirmed relapsed C. diff infections after at least one course of antibiotic therapy. 16 patients received a shortened regimen of vancomycin (4 days), follows by bowel lavage (flushing) and infusion of donor feces through a nasoduodenal tube (enters the nose and ends at the beginning of the small intestine). One control group of 12 patients received the standard vancomycin treatment (14 days) only and another control of 13 received the standard vancomycin treatment plus a bowel lavage on day 4 or 5. The second control confirmed that bowel lavage was not curing the infection (1).

Successful treatment was defined by cure (no C. diff related diarrhea and three consecutive negative tests for C. diff toxin) without relapse for ten weeks after the start of treatment. Doctors unaware of study group assignments observed patients and decided which were cured. Also, the fecal microbiota of patients before and after treatment and of donors was analyzed for bacterial diversity (1).



Figure 1. A higher percentage of patients were cured after treatment with infusion of donor feces compared to vancomycin or vancomycin with bowel lavage controls (van Nood et al. 2013).

After the first infusion of donor feces, 13 of 16 (81%) patients were cured! The three remaining patients received a second infusion and 2 of them were cured. Overall, the success of this treatment was staggering–94% of patients with a recurring C. diff infection were cured by donor feces. In the vancomycin group, only 31% of patients were cured and of those who were treated with vancomycin and bowel lavage, 23% were cured. Therefore, donor feces infusion was significantly more effective than the vancomycin control treatments. Fecal transplant was so successful in curing C. diff infections that researchers stopped the study and performed the treatment on the eighteen patients who had relapsed after the failed vancomycin treatments. Of these 18, 15 (83%) were cured by donor feces infusion (1).


Figure 2. Fecal microbiota diversity of donors and C. diff patients before and after donor feces infusion (van Nood et al. 2013).

Fecal microbiota diversity was evaluated using  Simpson’s Reciprocal Index of Diversity, which measures the species richness and evenness of a community (on a scale from 1 to 250, with higher values indicating greater diversity). Microbiota diversity in C. diff infected patients before donor feces infusion was consistently low, but increased within two weeks after treatment to levels that were the same as the donors. Relevant groups of intestinal bacteria were also quantified. It was found that after donor-feces infusion, numbers of Bracteriodetes and Firmicutes increased, while Proteobacteria decreased to levels consistent with a healthy person (1). These results suggest that donor-feces infusion is effective due to the reestablishment of normal microbiota which allows for a host defense against C. diff. The improved microbial diversity that was established through infusion was found to persist over time, and likely contributed to the absence of recurrent infection.

Overall, this study has shown that infusion of donor feces is an effective treatment strategy against recurrent C. diff infection. Because this study was designed for patients with relapsed infection and because antibiotic therapy decreases its effectiveness with each recurrence, the efficacy of vancomycin seen here was lower than in studies in which vancomycin was used to treat initial infections (1). Because of the decent efficacy of vancomycin on the first occurrence of C. diff, it is reasonable to only treat recurrent infections with a donor-feces infusion. Although, these results would be strengthened if treatments were tested on patients with initial infections. Additional investigation into donor feces infusion alone (without the abbreviated vancomycin regimen) would also prove beneficial and may eliminate the need for antibiotic use at all.

The bottom line is, don’t be turned off by the unappealing nature of fecal transplants–THEY WORK! Maybe your dog that eats poop is smarter than you think….



(1) van Nood E, Vrieze A, Nieuwdorp M, et al. 2013. Duodenal Infusion of Donor Feces for Recurrent Clostridium difficileN Engl J Med. 368(5): 407-415.

(2) Pépin J, Routhier S, Gagnon S, Brazeau I. 2006. Management and outcomes of a first recurrence of Clostridium difficile-associated disease in Quebec, CanadaClin Infect Dis. 42:758-764.

(3) Bartlett JG. 2008. The case for vancomycin as the preferred drug for treatment of Clostridium difficile infectionClin Infect Dis. 46:1489-1492.

For the Love of Gluten

The Role of the Microbiome in Celiac Disease and the Effects of Treatment with Probiotics

Imagine you are out to dinner. First, you order the mozzarella sticks. Then, you choose a pizza with all your favorite toppings. For dessert,  you decide on the homemade chocolate cake. Now, imagine you are told that you can never eat those things again, along with bread, pasta, crackers, cereals, cookies and a seemingly never ending list of gluten filled foods. Oh, and if you accidentally slip up, you can be sick for days. This is what happens to people who develop Celiac Disease (CD). CD is an autoimmune disease that effects about 1% of the population. Different from gluten intolerance, the partial digestion of gluten to gliadin results in an immune response that causes some cells to become activated and attack the cells in your intestinal lining leading to the desctruction of the small intestine. Not only are cramps, vomiting, and diarrhea common symptoms, those with CD have a greater risk for certain cancers, such as lymphoma and adenocarcinoma. There is a strong genetic component and the genes involved are known. However, they alone do not cause CD. It is also influenced by a variety of environmental factors (2).


In patients with CD, the presence of gluten causes an inmmune response in which cells are activated to kill cells in the intestinal lining leading to villous atrophy and crypt hyperplasia (2).

As of now, the only treatment for CD is a strict adherence to a gluten free diet (GFD). However, due to peer pressures, cost of the food, palatability of the food, dining out of the home, and a lack of education, it is difficult to remain on a completely GFD (2). With the increased interest of the importance of the microbiome in other autoimmune diseases, significant research has been devoted to the role of the microbiome in CD and as a potential target for treatment. The microbiome is the collection of bacteria living inside you. Many bacteria are mutualistic and important as barriers for colonization of pathogens, for vitamin synthesis, and for simulation of the immune system. Although there is no one typical microbiome for patients with CD, their microbiome is often characterized by decreased diversity including the reduction of Gram Positive bacteria. Quagliariello et al. targeted this dysbiosis, or disturbance in the microbiome composition, as method for treatment by administrating probiotics (1).

Quagliariello et al. looked at strains of Bifidobacterium, which have shown  promising results, such as the prevention of gliadin generation during in vitro digestion. However, only a few studies have looked at the effectiveness of the bacteria in vivo (1). One study by Smecuol et al. studied of the effect B. infantis NLS on untreated CD subjects, or patients who did not adhere to a GFD. They found that, although the bacteria does not modify inflammatory protein abnormalities, they may help improve symptoms (3). Quagliareillo et al. decided to use B. breve, a strain that has been successful in trials regarding other diseases such as necrotizing enterocolitis. The reserachers’ two main goals were to determine the effect of probiotics on the gut microbiota composition of those with CD on a GFD and to evaluate the effects of maintaining a GFD for several years on the gut microbiota compared to healthy individuals (1).

After enrollment, the researchers divided the subjects, ages 1 to 19, into 3 groups. They had 16 healthy children, 20 CD subjects that were given a placebo, and 20 CD subjects that were given the probiotics. The experiment was double-blind, meaning that within the CD groups neither the researchers or subjects knew to what group the subjects were randomly assigned. The placebo group was used as a control to show that the effects were from the bacteria themselves, not what they were administered in. The bacteria strains were


Overview of selection of participants included in the study. Exclusion criteria (4) were acute or chronic diseases, permanent use of medication, and ingestion of antibiotics at least 1 month prior to study (1).

administered in a powder taken with breakfast each morning for three months. Fecal samples were taken once from the healthy subjects at the time of enrollment and twice for CD subjects, once at enrollment (T0) and once after three months of probiotic administration (T1) . The fecal samples were analyzed using metagenome analysis and qPCR. Metagenome analysis amplifies a certain region of bacterial RNA called 16S rRNA to determine the strains present while qPCR amplifies the DNA in order to quantify the amount of each type of bacteria present. This method only analyzes colony forming units (CFU), which includes only viable bacteria (bacteria capable of reproducing) (1).


Alpha diversity indices measure the species richness in a specific habitat. In order to confirm there was no significant difference between the healthy children and the children with CD, the researchers performed three different calculations (1).



Using the results from the metagenome analysis, Quagliareillo et al. determined the alpha diversity indeces for the different treatment groups.The alpha diversity index is a mathematical formula that measures the mean species diversity, or species richness, on a local scale.They computed three different versions of the alpha index diversity, which are simply different variations of the mathematical formula. Each method showed the same result. There was no significant difference in diversity between the control and CD subjects although they expected to see an extreme dysbiosis in diversity. They believed that the adherence to a strict GFD helped to restore the diversity (1).


The hiearchally clustered heat map shows the differences between the healthy individuals and those with CD. The Probiotic Time1 was seen as intermediate between those with and with out CD indicating that probiotics helped to restore their microbiota (1).

Although the overall diversity between the three groups was similar, they still noticed a dysbiosis when looking at the phyla and classes represented. A hierarchally clustered heat map was created showing the six phyla that made up more than 1% of the microbiome. According to the hierachial clustering, the probiotic T1 was an intermediate between the control and other CD subjects. This indicates the probiotic treatment helped to partially restore the gut microbiome. The phyla Firmicutes and Bacteriodetes made up the majority of the gut microbiome. Firmicutes are Gram Positive baceteria and had a higher abundance in healthy subjects while Bacteriodetes are Gram Negative bacteria and had a higher abundance in CD subjects (1). This supports the previous findings that CD subjects have a reduction in Gram Postitive bacteria (2). The researchers then compared the ratio of the two strains. There was an increase in the ratio in the probiotic treatment, reflecting the increase in Firmicutes after the probiotic treatment (1).


Although probiotic treatments partially restored the microbiata of CD subjects, some phyla, such as Euyarchaeota, were still extremely imbalanced in CD subjects after administration of probiotics (1).







They also compared three individual phyla: Firmicutes, Actinobacteria, and Euryarchaeota. For the Firmicutes and Actinobacteria, the probiotic treatment partially restored these species in CD subjects. However, the probiotics seemed to have no effect on Euryarchaeota, which were found in very low levels in CD subjects. Since these bacteria are involved in polysaccharide degradation and gluten is a main source of polysaccharides in the human diet, they hypothesize that the reduction in this phylum is due to the strict adherence to the GFD (1).


Within the phylum Firmicutes, there was still differences in the microbiota of healthy and CD subjects. Only Lactobacillaceae seemed to be restored to the control (1).


They then looked at four families within Firmicutes. They found similar findings in which the abundance of some bacteria, such as Lactobacillaceae, were made more similar to the healthy subjects while others, such as Methanobacteriaceae, were not affected by the probiotic treatment. They also found that Gracilibacteraceae and Deltaproteobacteria were found in higher abundance after probiotic treatment (1).



Finally, they used qPCR to quantify the amount of CFU per g of feces. They performed this


The log of the colony forming unit (CFU) is used to measure the viable amount of bacteria present per gram of feces. There was a significant difference between many of the species in the healthy and CD subjects (1).

analysis on Bifidobacterium, Lactobacillus, B. fragilis, Enterobacteria, and Clostridium sensu stricto. As expected, adding the Bifidobacterium breve, slightly increased the amount of Bifidobacterium. The Lactobacillus were more abundant in healthy subjects while the B. fragilis were more abundant in CD subjects. Probiotics did not significantly affect the abundance of these bacteria. Enterobacteria were more abundant in the healthy subjects, and the probiotics did slightly decrease their abundance in CD sujects. Lastly, there was no significant difference between healthy and CD subjects in Clostridium sensu stricto (1).

Overall, Quagliariello et al. described some of the differences in the microbiome of CD subjects compared to healthy subjects including differences that have yet to be reported in literature. Some of the findings did support previous research, such as that with CD subjects there was an increase in Gram Negative bacteria at the expense of Gram Postive bacteria. They also found that the GFD did partially restore the diversity in CD subjects’ microbiome. Furthermore, the probiotics did seem to partially restore the dysbiosis in the CD subjects’ microbiome. However, many changes were not significant and no major changes occurred. This could be due to the short duration of time that they probiotics were administered (1).

Since research of probiotics as a treatment method is still in the early stages, I believe studies such as the one done by Quagliariello et al. are extremely important. With the vast complexity of the gut microbiome, they help to pinpoint which strains seemto be the most affected by the disease. From there, future research may be able to determine the mechanisms behind CD. I believe that Quagliariello et al. should include whether the probiotics had an effect on the healthy individuals, explore different strains of Bifidobacterium, and administer the probiotics for a longer period of time. Futhermore, they could repeat the experiment with CD subjects not adhering to a GFD to determine if probiotics help to alleviate symptoms.

While those with CD may not be able to eat that pizza today, research may one day find a treatment simply by altering the commensal bacteria that live inside their gut.


 1Quagliariello, A., Aloisio, I., Bozzi Cionci, N., Luiselli, D., D’Auria, G., Martinez-Priego, L., Pérez-Villarroya, D., Langerholc, T., Primec, M., Mičetić-Turk, D. and Di Gioia, D., 2016. Effect of Bifidobacterium breve on the Intestinal Microbiota of Coeliac Children on a Gluten Free Diet: A Pilot Study. Nutrients, 8(10), p.660. doi:10.3390/nu8100660

2Green, P.H. and Cellier, C., 2007. Celiac disease. New England Journal of Medicine, 357(17), pp.1731-1743. DOI: 10.1056/NEJMra071600

3Smecuol, E., Hwang, H.J., Sugai, E., Corso, L., Chernavsky, A.C., Bellavite, F.P., Gonzalez, A., Vodanovich, F., Moreno, M.L., Vazquez, H. and Lozano, G., 2013. Exploratory, randomized, double-blind, placebo-controlled study on the effects of Bifidobacterium infantis natren life start strain super strain in active celiac disease. Journal of clinical gastroenterology, 47(2), pp.139-147. DOI: 10.1097/MCG.0b013e31827759ac

4Klemenak, M.; Dolinšek, J.; Langerholc, T.; Di Gioia, D.; Micˇetic ́-Turk, D. Administration of Bifidobacterium breve Decreases the Production of TNF-↵ in Children with Celiac Disease. Dig. Dis. Sci. 2015, 60, 3386–3392.



Don’t Take my Microbes!

An investigation of early exposure to microbes as protection from immune-related diseases.

The adaptive immune system is one branch of the immune system designed to specifically target invading pathogens [3]. In contrast to this, the innate immune system is less specific, but responds immediately at the first sign of distress. Normally, cells that play a role in immunity are categorized as belonging to one of these two systems, but there are a few exceptions [4]. One exception is the invariant natural killer T cell, or iNKT, which is super cool because it expresses cell surface receptors of both natural killer cells and T lymphocytes [4]. Why is this cool? What is a “killer” cell? Who cares about lymphocytes?


The majestic lymphocyte [5].

First of all, everyone should care about lymphocytes because they are the warrior cells that protect us from toxins, viruses, and cancer cells every single day [3]. Lymphocytes are broken into two main categories – B cells and T cells – and work as part of the adaptive immune system to recognize and eliminate particular invading microbes [3]. Natural killer cells belong to the innate immune system and are far less picky in what they destroy [3]. Whereas T lymphocytes require special cell-surface proteins called the major histocompatibility complex (MHC) to display fragments of a foreign invader (antigen) in order to signify what needs to be destroyed, natural killer cells simply eradicate any cell that does not possess an MHC native to the host individual [3]. Our super cool iNKT cells are essentially a hybrid of these two cell types, meaning they function as both part of the innate immune system and the adaptive immune system [4]. Unfortunately, the activation of these super-fighters can sometimes be a false alarm.

Asthma and inflammatory bowel disease are both the result of a hyperactive immune system leading to unnecessary inflammation [3]. The inflammation is triggered by an accumulation of T cells in either the bronchioles or intestine. Why would our super-fighters be congregating to such an extent as to lead to this hyperactive immune response? The researchers of this paper believe the accumulation is the result of a lack of exposure to microorganisms at an early stage of development [1].  Exposure to microorganisms at a young age leads to the establishment of the microbiome, an entire community of microorganisms living inside of you right now and helping to keep you healthy [2].

The researchers used mice to investigate the concentration of iNKT cells in association with the age of mice and completeness of their microbiomes [1]. The scientists compared the amount of iNKT cells present in mice without a microbiome, called germ-free mice, to the amount of iNKT cells present in mice with a modified microbiome, called specific pathogen-free mice [1]. In doing so, they found that germ-free mice had increased numbers of iNKT cells compared to specific-pathogen free mice [1].


Figure 1C. A comparison of the number of iNKT cells accumulated in the colon of germ-free mice (GF) as compared to specific-pathogen free mice (SPF). Number of cells was counted using flow cytometry, a technique that counts individual particles by identifying their physical properties [1][6].

Not only was the iNKT cell number increased, but it remained high throughout the lives of the germ-free mice [1]. This was then associated with some unfortunate consequences. The germ-free mice turned out to be more susceptible to colitis, an inflammation of the intestine induced by the drug oxazolone [1]. However, the scientists found that blocking the MHC that presents antigens to T cells decreased the mortality of germ-free mice because the iNKT cells were no longer being recruited to the same extent [1]. This held true in both adult and newborn mice [1]. Just as in the adults, when MHC was blocked there were fewer iNKT cells recruited to the area and a decreased susceptibility to colitis later in life [1]. This further confirmed the role of the MHC in recruiting iNKT cells and the correlation between increased iNKT cell levels and immune-related diseases.


Figure 2A. Survival percentage of germ-free (GF) mice compared to specific-pathogen free (SPF) mice when treated with the receptor blockade (19G11). Isotope IGG2b served as the control [1]. Mice that had the MHC receptor blocked had a higher percentage of survival [1].

To determine whether a microbiota could be established in a germ-free mouse and possibly turn their little lives around, the researchers exposed adult and neonatal germ-free mice to microorganisms [1]. The adult mice were unable to restore their iNKT cells to a normal level, but the baby mice successfully established microbiomes that persisted into adulthood [1]. This demonstrated the importance of establishing a microbiome early in development [1].


Figure 2D. Percentage of iNKT cells as measured with flow cytology in the colon of SPF mice as compared to GF mice, GF mice exposed to a microbial environment as adults (GF/a), and GF mice exposed to a microbial environment as pups (GF/n) [1]. GF/a mice were unable to establish a microbiome and retained high levels of iNKT cells [1].

By now our researchers had it pretty well established that not having a microbiome is correlated with high levels of iNKT cells and that a high level of iNKT cells is correlated with an increased risk for immune-related diseases. How is the microbiome connected to iNKT cell levels? The researchers looked toward the ligand CXCL16, a molecule expressed at high levels during inflammation [1]. CXCL16 is important for maintaining the balance of iNKT cells, and when expressed at high levels leads to the accumulation of these cells [1]. The researchers postulate that the microbiome determines the level at which CXCL16 is expressed to prevent the over-accumulation of iNKT cells [1].


Figure 4A. Concentration of ligand CXCL16 in specific-pathogen free mice (SPF), germ-free mice (GF), germ-free mice introduced to a microbial environment as adults (GF/a), and germ-free mice introduced to a microbial environment as pups (GF/n) [1]. Concentrations were greatest in GF and GF/a mice [1].

Humans and mice have very similar MHC and iNKT cell systems, meaning the findings of these researchers can be applied to people as well as rodents [1]. Although the method by which the microbiome regulates CXCL16 expression and therefore iNKT cell accumulation is still ambiguous, it is clear that we should all hold onto our microbiomes.


Works Cited

[1] Olszak, T., D. An, S. Zeissig, M. P. Vera, J. Richter, A. Franke, J. N. Glickman, R. Siebert, R. M. Baron, D. L. Kasper, and R. S. Blumberg. “Microbial Exposure During Early Life Has Persistent Effects on Natural Killer T Cell Function.” Science 336.6080 (2012): 489-93. NIH Public Access. Web. 13 Nov. 2016.

[2] Guinane, Caitriona M., and Paul D. Cotter. “Role of the Gut Microbiota in Health and Chronic Gastrointestinal Disease: Understanding a Hidden Metabolic Organ.” Therapeutic Advances in Gastroenterology 6.4 (2013): 295–308. PMC. Web. 14 Nov. 2016.

[3] Marieb, Elaine Nicpon, and Katja Hoehn. Human Anatomy & Physiology. 10th ed. Boston: Pearson, 2016. Print.


[4] Van Kaer, Luc, Vrajesh V. Parekh, and Lan Wu. “Invariant Natural Killer T Cells: Bridging Innate and Adaptive Immunity.” Cell and tissue research 343.1 (2011): 43–55. PMC. Web. 13 Nov. 2016.

[6] Robertson, Sally. “What Is Flow Cytometry?” N.p., 2014. Web. 14 Nov. 2016.



[Microbe] Self-Acceptance

Did you know that your body is a 1:1 ratio (at least) of bacterial cells and your own cells?? You’re as much bacteria as you are human! But before you start panicking about how unsanitary you are, just know this: many of these bacterial cells are actually helping you stay healthy.

To understand how this works, you’ll need a brief background on innate immunity, Microbe-associated molecular patterns (MAMPs), and Pattern-recognition receptors (PRRs). Your immune system is incredible and multifaceted. You’re born with your innate immune system: it is non-specific, widespread, and quick to the punch (1). As a matter of fact, your innate immune system can get moving within hours of infection!

innateimmunityFigure 1. The main components of the innate immune system- critical for fighting microbes at the site of infection (2).

Molecular-associated molecular patterns, previously recognized as Pathogen-associated molecular patterns, are molecules that can be found on all microbes (3). It was recently recognized that the molecules are highly conserved across all bacteria – pathogenic or non-pathogenic – therefore resulting in the name change. These MAMPs are what your immune system recognizes to detect a foreign entity. This recognition occurs thanks to host pattern-recognition receptors (PRRs).

Pattern recognition receptors sense microbial molecules during infection and initiate inflammatory responses (4). PRRs produce signals that are extremely important in protection against pathogens. Pathogens are the bad bacteria that you don’t want to colonize in your body. But remember earlier when I mentioned that a lot of you are bacteria? Those good ones are called commensal bacteria. And they express MAMPs that signal PRRs as well. So why isn’t your body constantly producing an immune response?

The researchers Chu and Mazmanian (5) were interested in elucidating this complicated conundrum: how do your immune system and PRRs tell the difference between commensal bacteria and pathogenic infections? One proposed idea is the surrounding environment when the PRRs recognize a MAMP. For example, a MAMP that belongs to a pathogen would most likely be accompanied by other cell damage from the infection, while a MAMP belonging to a symbiotic bacterium would not be accompanied by any host damage. Chu and Mazmanian reviewed recognition of MAMPs by PRRs in “steady-state” conditions in various models.

There were a ton of proteins, receptors, and pathways reviewed here. I’ll keep it as simple as I can, so bear with me! To begin, Chu and Mazmanian explored five models: Drosophila melanogaster (fruit fly), Hydra, squid-Vibrio, zebrafish, and mice. These models were picked for good reason, not just by chance!

D. melanogaster is a model system for genetics with rapid lifespans. Hydra species are members of the second oldest phylum (they’re really old!!) and are a simple system to use for understanding the evolution of commensalisms. The squid-Vibrio symbiosis is one of the longest studied and most well understood symbiotic relationships to date, offering a wealth of background information. Zebrafish have recently been appreciated as a model vertebrate system thanks to their ease of genetic manipulation, capability for germ-free conditions, and they physiologically resemble mammals! Mice are mammals often used for scientific experiments, since we don’t want to be doing these experiments on humans!


Figure 2. The five models explored. Key (Top to bottom, left to right): Zebrafish: Danio rerio, Mouse: Mus musculus, D. melanogaster, Hydra species, squid-Vibrio: E. scolopes. Edited from Chu and Mazmanian (5).

Between the five models, an important factor in immune response to bacteria is the Toll-like receptor family (TLRs). The first PRR identified was Toll, discovered in D. melanogaster. Also important – particularly for D. melanogaster, squid-Vibrio, and mice – are Peptidoglycan recognition proteins (PGRPs). These recognize peptidoglycan, a major component of both gram positive and gram negative bacteria (6). In almost all of these models, signaling occurs through an adaptive protein called MyD88. The important piece to know is that this signaling often results in the production of antimicrobial peptides that limit host immune response to symbiotic bacteria.

While those were a lot of biochemical processes thrown at you- you can still walk away with a good idea of what this review has brought to light. TLRs are needed to mediate immune responses that protect the host, such as you. Microbes can mediate TLR signaling, indicating a deeply rooted co-evolutionary symbiosis that allows for “molecular conversations” between host and microbes with the PRR system. Their exploration also suggests that a host (you) is not “hard-wired” to differentiate between commensal vs. pathogenic bacteria. Rather, the commensal bacteria have specific ligands that have evolved to actively allow for a mutualism with their host. That is INCREDIBLE! Think about all your gut bacteria- they have evolved, so that they will not harm you, but help you! Your immune system does not simply ignore symbiotic bacteria, but the microbes directly interact with your immune system to benefit immune responses!

The importance of your gut microbiota is just recently coming to light. It is being implicated for a many facets of human health and disease, such as inflammatory bowel disease, obesity, and cardiovascular disease, just to name a few! The frontier is wide-open for possible areas of research and medical applications. And in regards to Chu and Mazmanian’s review: there’s still plenty to understand about personal ‘microbe self-acceptance.’



  1. Innate Immune System. Oct. 27, 2016. In Wikipedia, the Free Encyclopedia. Retrieved Nov. 11, 2016, from
  2. The innate and adaptive immune systems. Patrick Fisher, University of California at San Francisco. Retrieved Nov. 11, 2016 from
  3. Pathogen-associated molecular pattern. Nov. 1, 2016. In Wikipedia, the Free Encyclopedia. Retrieved Nov. 11, 2016 from
  4. Pattern recognition receptor. Oct. 22, 2016. In Wikipedia, the Free Encyclopedia. Retrieved Nov. 11, 2016 from
  5. Chu H, Mazmanian SK. 2013. Innate immune recognition of the microbiota promotes host-microbial symbiosis. Nat Immunol. 14(7): 668-675. Doi: 10.1038/ni.2653.
  6. Oct. 20, 2016. In Wikipedia, the Free Encyclopedia. Retrieved Nov. 13, 2016 from


Don’t be a Wormophobe!



Journal of Tropical Diseases & Public Health. Helminths.

In the recent past, there has been an explosion of allergic, autoimmune, and other inflammation-associated diseases. Whether it is as small as an allergy in the spring or inflammatory bowel disorder or even as serious as lupus or multiple sclerosis (1), everyone knows someone who has been affected. These diseases are caused by your normal immune system being too sensitive. Normally the immune system recognizes harmful objects in the body and eliminates them. When it is being overly sensitive, it can attack non-harmful cells like pollen and even your own cells. This isn’t a huge problem in rural areas and developing countries, but these kinds of diseases are much more common in countries that have modern medical care, sanitation practices, and water treatment- all of which are largely products of post-industrial societies (2).


Autoimmune Disease: When our immune system goes haywire.


We didn’t used to have all these problems. The occurrence of diseases associated with overactive immune systems has increased hugely in the recent past.  So what changed? The answer is in the worms!

The most common theory that explains why there has been an increase in the occurrence of these diseases is called The Biome Depletion Theory. This states that “a profound depletion of components from the ecosystem of the human body, the human biome, in post-industrial society has left our immune systems profoundly over-reactive, with a strong propensity to react against a wide range of non-pathogenic self and non-self antigens” (2).

So what does that mean? First, we have to establish a few things. We as humans are not entirely independent entities. Actually, we have about as many bacterial cells in our body as we have human cells! All of these bacterial cells make up what is called the human biome. A really important subset of these bacterial cells is called the gut microbiome. The gut microbiome is made up of bacterial cells that live in our digestive tract. We have known for a while that they help us digest our food, but we have recently started learning that they do a lot more! These bacterial cells have been linked to development, mood, and even our immune systems (2).


Knowing this, we can look at the Biome Depletion Theory. Essentially, it says that the changes we have made to society have changed our human biome. With the increased focus on sanitation and a widespread use of antibiotics, we have killed a lot of the bacteria that used to live in our guts. We now know that this can have huge effects on our immune systems, changing immune development and function. The immune system has largely been thought of as a defensive wall against the outside world. What we are coming to realize is that this is not the case. Our immune system is a connection between our bodies and the environment (3). When we change the environment, we change that interaction also.

A soybean cyst nematode and egg.

Speaking of changing our environment, there is one change that stands out to scientists: our contact with helminths. Helminths are small worms that inhabit the guts of all vertebrate species (4). These worms have found a home in vertebrates for over 100 million years, and this includes humans! Humans and helminths have even coevolved, meaning that they changed together in response to changing environments. But recently, humans changed the environment too much for this relationship to continue. With sanitation, water treatment, antibiotic use, the prevalence of Caesarian sections, and even the use of formula over breast milk, we have created an environment where the helminths can’t possibly survive (2). Now, humans living in a post-industrial society have no helminths.


Modified logo of International Year of Sanitation, used in the UN Drive to 2015 campaign logo.

To most people, getting rid of parasitic worm infections might wound like a great thing, but evidence connecting increased allergies with decreased levels of helminths suggests otherwise. Helminths secrete molecules that make the immune system less sensitive (4). They do this out of selfish reasons- they are worms living in the human gut and they don’t want to be kicked out! However, over a long period of coevolution, humans adapted to this less sensitive immune system. The helminths not only decreased the strength of the immune system, but they also took the focus of the immune system away from human cells, helping it from being too sensitive and causing allergies and autoimmune diseases (2). Now, we don’t have helminths to tone down our immune system and this has been tied to the increase in allergies and autoimmune diseases that we see today. And the effects aren’t over! The impact on the immune system was delayed and is increasing with time.


A hookworm attached to the intestine of a dog.

Allergic disorders are serious. In fact, in a year 150-200 people die from allergic reactions and over 3000 people die from asthma. Additionally, 1 in 300 people will have their life negatively affected by lupus, multiple sclerosis, or type 1 diabetes. Biome depletion is even being looked at for links to autism, schizophrenia, Alzheimer’s, and depression (2). And it could still be getting worse! Believe it or not, researchers are looking into reintroducing helminths to our bodies as a solution. Although it may seem kind of gross to think about a worm inside of you, science has shown that this type of treatment may be very promising. In animals, researchers have already seen that restoring the helminths to the organisms’ biomes both treats and prevents diseases associated with over-reactive immune systems. Even in humans, researchers have seen improvements with multiple sclerosis and Inflammatory Bowel Disease (2).


Paragordius tricuspidatus(Nematomorpha).

Some pharmaceutical companies are trying to make a helminth inspired drug (2). Researchers believe that allowing live helminths into our systems would be an even better for us since that is how we evolved. More research is being done in the hopes that this can be a treatment in the near future. Until then, it is time to get over the idea of being a wormophobe!



  1. Genuis SJ. 2010. Sensitivity-related illness: the escalating pandemic of allergy, food intolerance and chemical sensitivity. Sci Total Environ 408: 6047–61.
  2. Bilbo, S., Wray, G., Perkins, S., Parker, W. Reconstitution of the human biome as the most reasonable solution for epidemics of allergic and autoimmune diseases. Medical Hypotheses 77: 494-504.
  3. Parker W, Thomas AD. 2010. Cultivation of epithelial-associated microbiota by the immune system. Future Microbiol 5: 1483–1492.
  4. Rook G. 2009. Review series on helminths, immune modulation and the hygiene hypothesis: the broader implications of the hygiene hypothesis. Immunology 126: 3–11.