Food allergies and our normal microorganisms

Peanuts_with_skinA news article that made the rounds through the popular press this week caught my eye: “Commensal bacteria protect against food allergen sensitization,” which appears in the early access section of the journal of the National Academy of Sciences. I have been a big fan of this type of research for a while now. The basic premise is this: our modern lifestyle has potentially begun to diminish the numbers and variety of microorganisms that live on our bodies in the absence of disease (the normal microbiota), and as a consequence, benefits that these benign organisms can confer to us are being lost. So far, loss of diversity of the normal microbiota have been correlated with a long list of ailments including potentially autism and cancer.

An opinion piece in this week’s Nature warns against drawing too many conclusions from these studies, and suggests that over reporting of some of them by the press reinforces the need to ensure that the public understand the distinction between “correlation” and “causation”–these concepts are frequently confused, and the distinction is sometimes not clear. Indeed, the editorial in Nature suggests that reporting of microbiome analysis and human disease should be tempered by asking 5 questions:

  • Can experiments detect differences that matter? Characterization of microbiomes is generally accomplished by sequencing very highly related genes, and this analysis may hide real differences.
  • Does the study show causation or just correlation? Many of the cases of a disease association with certain microorganisms may be the result of conditions in the body becoming favorable for the microbe, meaning the disease caused the microbes to alter.
  • What is the mechanism? Demonstrating causation is important, however without an explanation of how a change occurs, it is not sufficient.
  • How much do experiments reflect reality? Many of the putative effects of the microbiome on health involve germ free mice; that is mice that have been raised to have no normal microorganisms of their own, as this makes interpreting the effects somewhat easier. However, mice and humans are not the same, and the microorganisms that live on each are not the same.
  • Could anything else explain the results? Many things can cause disease, and other factors should be considered and tested.

With this in mind, I read the article on food allergies linked up at the top. The authors carried out the study to address the hypothesis that the normal microbiota of the gastrointestinal tract are able to guide adaptive immunity at this site. The intestinal tract of animals hosts an incredible variety of organisms in the absence of disease. The immune system needs to be non-responsive to these organisms, as well as to all of the food antigens that enter the digestive tract. Immune cells in lymphoid tissue along the digestive tract modulate signals between the microbiota and the epithelial barrier of the digestive tract, which helps to prevent an ongoing inflammatory response, and thereby promote a homeostatic relationship between the microbiota and the host.

The researchers first experiment was to treat neonatal wild-type mice with an antibiotic regimen prior to weaning to eliminate intestinal microbiota, then sensitized by gastric administration of Peanut Antigen (PN). Three weeks later, the mice were challenged with the antigen and allergic responses were measured a day later by collecting blood. Control mice had essentially undetectable levels of allergic responses, while antibiotic treated mice showed highly elevated levels of IgE. Analysis of the bacteria from feces of mice at the same time intervals also showed that the antibiotic treated mice had lowered levels of fecal bacteria, and greatly diminished diversity of fecal bacteria. Specifically, members of the prokayotic phyla Bacteriodetes and Firmicutes, present under normal conditions, were essentially absent in the antibiotic treated mice. These bacteria were replaced with members of Lactobacilli, a result consistent with another recent report examining changes in the microbiota of antibiotic fed mice. The results outlined above were achieved using outbred mice strains housed in pathogen-free, but not germ free conditions; therefore this study addresses one of the critiques above with the use of outbred mice.

This paper was also significant, in that the authors also propose a mechanism for how the immune modulation occurs. Recolonization of antibiotic fed mice with a group of Firmucutes from genus Clostridium (the major genus of the Firmucutes from normal mice), prevented the allergic response produced by peanuts. Dissection of the intestines from these animals indicated that specific T cells involved in adaptive immune regulation are more prevalent in Clostridia colonized mice. Additionally, mice colonized with Clostridia in comparison to germ free mice and control mice exhibited high levels of an immune cytokine Interleukin 22 (IL-22). The authors propose that IL-22 (induced by the presence of Clostridia) causes the intestinal epithelial barrier to be reinforced, reducing the permeability to dietary proteins. To address this possibility, they then measured the levels of food allergens in the bloodstream after intragastric gavage. Colonization by Clostridia resulted in significantly lower levels of these allergens in comparison to germ free mice, supporting this hypothesis.

The major conclusions of this paper support the important role of the benign normal microbiota in promoting health. Their model argues that tolerance to food antigens is aided by the presence of those antigens along with specific components of the normal microbiota. To translate this work to human therapies, the role of Clostridia needs to be confirmed in humans. Indeed, other work has shown that Clostridia species isolated from human feces do induce the same immune regulatory cells discussed above when transferred to germ free mice, suggesting that they may be playing similar roles in both species.

Update on Zombie Ants



Hello, and welcome to all new/returning YCP students! Additionally, welcome to all new BIO230 students–I hope everyone has had a restful and relaxing summer break. I know I sure did; I had fun during summer Micro, had a week long break, and accomplished some important Science in my spare time. One thing I did not do was update this forum. Looking back, it appears I last opened up WordPress back sometime in April. Let’s see if we can do something about that!

I found a news alert on ASM’s Microbe World site, which gives an update on the Zombie Ant story. It summarized work out of the entomology department at Penn State University, which has been studying a fascinating example of symbiosis between an insect and a fungus called Ophiocordyceps. What is most interesting about this relationship is that infection by the fungus causes behavioral changes in the host. These changes are advantageous for the fungus–the ant moves over a greater range, allowing the spores of the fungus to spread further. Obviously, infection of a colony would be a Bad Thing, leading to this observation on the phenomenon of “Social Immunity”.

Social Immunity has been observed in laboratory settings in a variety of insect species. It prevents the spread of diseases within colonies, however it has not been previously observed in field conditions. In a study published recently in PLOS One, researchers placed ants which had been freshly killed by the fungus inside one of two nests; one nest had live ants, and the second nest had no ants. The fungus-killed ants were rapidly removed from the living nest, and no further fungal infection occurred of that colony. This result suggests that effective reproduction of the fungus requires being outside of the colony.

In an expanded study, researchers examined the dynamics between the appearance of infected dead ants outside of colonies (sources of infection) and the position of foraging trails (future hosts) in several colonies over the course of 20 months. The researchers observed a consistent appearance of 14.5 cadaver ants per month per colony. Based on this low rate of infection and the lack of colony collapse, the researchers proposed that this fungal parasite represents  a “chronic” infection of these colonies. The authors suggest that the removal of corpses from the colony or ants dying in isolation outside the colony may be an essential step in the development of Ophiocordyceps to a stage that enables the fungus to infect a new host.

Potential novel antibiotics under review

Despite my dire announcements regarding the potential challenges in treating infectious diseases in the near future, which are coming about due to a combination of biological and economic reasons, there are some reasons to be somewhat optimistic. Via Microbe, the monthly newsletter from the American Society of Microbiology, an article which summarizes some of the research into novel antibiotics that are currently in clinical trials. The article lists at least 39 potential antibacterial compounds under investigation at present, with 25 of those under what is termed Phase 2 or Phase 3.  In Phase 2 or Phase 3 trials, the compounds have shown promise in in vitro or animal models, have been found to be safe to administer to humans, and therefore are being assessed to see if they show therapeutic promise in humans. Leading the search for new antimicrobials are small biotech companies such as Cubist here in the US, and the large company Hoffman-La Roche from Switzerland.

One of the very interesting targets is an enzyme called DNA topoisomerase, which catalyzes the unwinding of DNA during the process of DNA replication. Many of these compounds are from the quinolone class of antimicrobials, some of which are easily taken up into host cells, thereby allowing them to be effective against intracellular pathogens such as Legionella pneumophilia and Mycoplasma pneumoniae. The target of these compounds are enzymes that are found in all cells, including human cells, however they are able to demonstrate the principle of selective toxicity by inhibiting the prokaryotic enzymes as opposed to eukaryotic enzymes. Some studies have described side effects where the DNA replication of mitochondria can be inhibited as well.

Other important antimicrobial compounds under investigation inhibit protein synthesis, and a number of compounds are currently under intense review for effectiveness. Some of these compounds have been identified by manipulating known antimicrobials (semi-synthetic compounds) or are the result of new compounds identified by screening environmental microorganisms for inhibitory compounds.

One of the major problems due to antibiotic use in appropriate situations is the rise in other infections, which arise as the normal microbial flora are reduced by the use of the antibiotic. Clostridium difficile infections are increasing in frequency at present, and are themselves beginning to demonstrate antibiotic resistance. Several new compounds under investigation appear to target C. difficile infections very specifically, enabling them to be much more effective against the pathogen in question, while having little effect on other microbes. This approach will help to forestall the emergence of other antibiotic resistance microorganisms, at least for a while.

No commentary necessary

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Notes from the Field: Listeria from Soft-ripened cheese


some nice cheese, via

some nice cheese, via

Via the ever helpful Morbidity Mortality Weekly Report, another alert about the dangers of foodborne-illness! The Minnesota Department of Health reported in late July 2013 two cases of invasive listeriosis, for which molecular analysis indicated a sole-source for infection. As an aside, the Minnesota Department of Health seems to be the hardest working state department of health, as evidenced by this alert about Salmonella from Guinea pigs, and this alert about Salmonella from phlebotomy that I found in the BIO230 archives. Way to go, Minnesota Department of Health!

Once the Centers for Disease Control and Prevention were notified, further analysis indicated that the isolate was also identical to an environmental isolate collected from a cheese producer in 2011. With this in place, several other cases were also identified by the CDC in last summer’s outbreak, resulting in one death and one miscarriage. All patients were interviewed to determine their “cheese exposure.” All patients indicated that they had likely eaten one or more of Crave Brothers Farmstead Cheese varieties (Les Frères, Petit Frère, or Petit Frère with truffles) during the likely time frame for infection, at either grocery stores or restaurants in the region. All of the cheeses were shipped as intact wheels to the point of sale, where they were cut and repackaged.

The manufacturer issued a voluntary recall when news of the outbreak was made public. Conjecture by the CDC suggested that the contamination arose during the manufacturing process. The process of pasteurization very effectively eliminates Listeria monocytogenes from milk, however in the cheesemaking process contamination can occur after the original pasteurization. The CDC recommends that strict sanitation and monitoring of contamination steps always be in place for cheesemakers, regardless of whether pasteurized milk is used.

The CDC also reiterated standard precautions to protect against infection by Listeria, which again bear repeating. The organism does not generally pose a significant health risk to the general population, however immunocompromised individuals can become quite seriously ill. Additionally, pregnant women can pass the organism onto the developing baby, and fetal infection due to Listeria is a significant cause of miscarriage. Because of these risks, at risk individuals are strongly advised to avoid any food that carries the potential for infection by Listeria.

Issues in the fight against antibiotic resistance

Development of new antibiotics versus appearance of resistant bacteria

Development of new antibiotics versus appearance of resistant bacteria

I apologize for the slow pace of updates this semester; it has been hectic, and scouring the news for alerts of general microbiological interest to post here has taken a backseat to grading for the past few weeks. However, I came across a review article from the latest issue of Trends In Microbiology that is timely with regards to our current class discussion about antibiotics and their place in modern medicine.

I have painted a less than rosy picture many times in this forum about the future of medicine, primarily as a result of the diminishing utility of antibiotics. The premise is this: the more antibiotics are used to treat infectious disease, the less they are ultimately effective as a result of the acquisition of antibiotic resistance. Indeed, the observation that genes conferring antibiotic resistance to today’s antibiotics have been found in thousands of years old samples of bacteria in permafrost suggests that acquisition of resistance is not a matter of “if it happens,” but rather “when it happens” to antibiotics that haven’t even been developed yet.

In our viewing of the Frontline episode “Hunting the Nightmare Bacteria” in class the other day, one of the most alarming points come out to me was the highlighting of the problem of who is supposed to deal with with looming catastrophe. The majority of the large pharmaceutical companies have pulled out of the antibiotic business due to a simple financial decision–it costs a tremendous amount of money to bring new drugs to market, and by their nature antibiotics give a very poor return on investment. At the same time, it was also clear that there is no national consensus to determine the scope of the problem or what the most appropriate response should be.

The review article takes the following stance; public health officials must be proactive in recognizing the severity of the issue, and governments need to take the lead in prioritizing antibiotic discovery in both academic and industrial settings. Public-Private partnerships (PPPs) have been established in small scale between not-for-profit charities, small biotech companies, and large pharmaceutical firms, however the lack of financial return has limited their effectiveness to date. The model however is valid, and if adopted large scale the financial burden of bringing these critical drugs to market can be distributed broadly between the academic, governmental, and industrial players. Such a model in the current political climate in the United States is difficult, but not impossible to propose. These organizations have successfully come into being in Europe which has traditionally had a more open interaction between government and industry, however the passing in the US of the Prescription Drug User Fee Act (PDUFA V) provides financial incentives for novel antibiotic development in this country. Hopefully, these incentives will allow medicine to stay ahead of antibiotic resistance at least for a little while!


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