Tuesday, 29 November 2011

Innate immunity and the gut microbial ecosystem

A quick-ish post following the publication of a real fact-finding paper by Larsson and colleagues* (full-text). The aim of the paper was to map out how innate immunity intersects with microbial composition along the length of the gastrointestinal tract in a mouse model.

If you are slightly adverse to mouse research I'm afraid that you won't like this study much, which basically looked at bacterial composition in twelve segments of the mouse gut corresponding to the small intestine, cecum and large intestine correlated with several hundred/thousand genes regulated by the gut microbiota.

I won't lie to you in that this is quite a complicated study to follow. My Mr Men take on it suggested a few important findings were presented:

  • In the small intestine, several thousand genes were regulated by bacterial microbiota. By comparison, fewer genes were regulated in the colon than other areas thought to be due to some shielding in that part of the gut from bacterial exposure.
  • Depending on whether the authors looked at wild or germ-free mice, there were some interesting differences in different parts of the gut for genes related to lipid and fatty acid metabolism and nutrient absorption and metabolism. Genes governing cholesterol biosynthesis seemed to be top of the pile when it comes to being affected by microbiota as a function of whether or not there was a loss of innate immune signalling (Myd88-deficient). 
  • When it came to gut barrier function along various stretches, gut bacteria had some ability to alter the expression of some important genes according to comparisons between germ-free and wide mice. 
  • Myd88-deficient mice showed alterations in the types of bacteria present, some signs of disordered antimicrobial resistance as well as being potentially more susceptible to viral infections such as norovirus.

I can't possibly do justice to the amount of data presented in this paper. Extrapolating from the mouse model to humans, this data suggests that we have an extremely important symbiotic relationship going on in our deepest, darkest recesses. A relationship between self and bacteria; where genes and environment seem to play key roles in how we metabolise our food, how we regulate our ability to take on bacteria and viruses, and ultimately how our health in other organs might just want to make reference to the gut also.

* Larsson E. et al. Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88. Gut. November 2011

Friday, 25 November 2011

Gut bacteria and the immune system

Quite an interesting article by Lamousé-Smith and colleagues* has appeared on the potential gut bacterial requirements of the immune system. The paper is open-access so readers are invited to read it at their leisure.

The basic conclusion reached from this research is that the ability of a mouse (and by proxy a human being) to mount an immune response to a specific pathogen (bacterial or viral) might be to some degree affected by the presence/absence of certain gut bacteria.

In the case of this paper, researchers undertook investigations based on two different scenarios: (a) a mouse model where antibiotics were used to disrupt the normal gastrointestinal (GI) flora and (b) a germ-free mouse model who were subsequently colonised. Under such models, mice were injected with a suspension of ovalbumin (the main protein in egg white) and an immunity stimulator, Freund's complete adjuvant. The authors then looked at the mice ability to mount an immune response to the egg white protein (ova).

They noted a few interesting observations:

  • Administration of antibiotics lead to some interesting changes in the gut microbiota. I should perhaps mention that pregnant mice were given antibiotics in their feed so the changes were noted in both mother and baby mice when born. The specific combination of antibiotics given to pregnant dams - ampicillin, streptomycin and clindamycin -  seemed to particularly deplete Firmicutes and Bacteroidetes bacterial species leaving Enterobacteriaceae to dominate. I don't like the idea of labelling bacterial species as good guys or bad guys because that is a little generalised and unfair. Having said that the Enterobacteriaceae includes things like Salmonella, E.coli, Klebsiella and few more 'pathogenic' species among their lot; if they were people, these would be the ones not to hang around with. 
  • Those offspring mice born to mothers on antibiotics seemed to show similar changes to gut flora. Additionally, antibody titer levels to ovalbumin were lower in this group when compared to a non-antibiotic exposed group when immunised at 7 days. These findings were not replicated when injected at 14 days.
  • Looking at the second mouse model where gut flora was absent, the authors reported consistently lower titer levels across age and when injections were given. This finding was kinda confirmed when germ-free mice (those with no bacterial flora) were colonised via bacteria derived from normal gut flora mice (I guess a sort of bacterial transplant!) thereafter more appropriate antibody titer levels were noted .

Appreciating that these experiments were carried out on mice and quite a small group of mice, there are some interesting things to take from this research. Already on this blog discussions have ranged from gut bacteria and a possible link to coeliac disease to the potential usefulness of bacterial transplantation for certain bowel conditions. Within these pretty diverse areas, a common theme is a potential role for the immune system in terms of clinical outcomes. What this research adds quite nicely, is that our ability to fight infection, develop immunity might be quite a bit more complex than previously thought. Our gut bacteria potentially being a mediator of immunity.

Thinking back to some findings in that other field of interest to me, autism, I do wonder about the implications of this research. On a sister blog, I recently discussed a paper looking at carbohydrate metabolism and dysbiosis in cases of autism. One of the findings from that small-ish study was that levels of Bacteroidetes were in shorter supply. Coincidence or perhaps tied into some interesting data on antibiotic use? Given the various studies suggestive of problems with immunity at least in some people with autism, I wonder if we should be looking at the gut bacteria/immune system relationship a little more closely?

Of course it easy for me to sit here and speculate, compare and contrast. Precisely how our bodies make and utilise immunity is still a source of much research and investigation.

* Lamousé-Smith ES. et al. The intestinal flora is required to support antibody responses to systemic immunization in infant and germ free mice. PLoS ONE. NOvember 2011

Gut bacteria, pesticides and obesity

Although my interest in this blog centres on all things gut-related, within this huge area of research I am particularly interested in how our genetic makeup interacts with our environment and vice-versa. I suppose gastrointestinal (GI) conditions are ideally suited to this complex 'nature-nutrure' relationship as evidenced by conditions like coeliac (celiac) disease, the archetypal gene-environment condition.

An interesting paper has appeared by Hae-Sook Lee and colleagues* suggestive of an interesting 'threesome' between a species of methane gas producing microbe, organochlorine pesticides and obesity. The paper is open-access. A summary of the details:

  • Fecal and blood samples from 83 Korean women were analysed alongside anthropometric (body mass index) measurements.
  • Fecal levels of Methanobacteriales were quantified via qPCR and serum / fecal levels of various organochlorine pesticides (OCPs) were assayed via GC-MS among a selection of participants with detected or non-detected levels of Methanobacteriales.
  • The results: Methanobacteriales were present in about a third of patient stool samples (27/83). Higher Methanobacteriales levels were present in women with a waist circumference above 83cm than below and showed some connection with elevated BMI also. Higher fecal levels of Methanobacteriales were also associated with higher serum levels of the OCPs.

We do need to take a step back from these findings before making too many associations. The sample population is quite small and the numbers of people included for analysis of OCPs for example is even smaller. Bear in mind that just looking at three primary variables is not necessarily grounds for a relationship.

I am however struck by the 'suggestion' that gut bacterial content and obesity might either increase the risk of greater take-up of compounds such as OCPs or that gut bacteria might interact with our chemical environment to potentially predispose to conditions such as obesity. This latter hypothesis: OCP levels determining Methanobacteriales levels which in turn leads to increases in anthropometric measures is the author's preferred interpretation.

The authors discuss the properties of OCPs as being central to the finding i.e. lipophilic (fat or oil loving) and also note that Methanobacteriales are quite often used to biodegrade hydrocarbons such as petroleum. I have to say I have never really thought about industrial waste management being applied to the human model but perhaps should not be so surprised given the current interest in things like industrial biodigestion.

What this study does more than anything is to reaffirm the complexity of conditions such as obesity as well as providing some new targets, environmental and biochemical, which we should perhaps be exploring with a little more assiduity.

* Hae-Sook Lee et al. Associations among organochlorine pesticides, Methanobacteriales, and obesity in Korean women. PLoS ONE. November 2011.

Tuesday, 15 November 2011

Crohn's disease and the LOFFLEX diet

A short post this one following a very interesting series airing here in the UK called the Food Hospital. 'Let food be your medicine' was the mantra of a certain Greek gentleman called Hippocrates (or perhaps according to Bill and Ted, 'Hippo-crates') and that is exactly what this series is suggesting.

In the programmes so far we have seen conditions ranging from migraine to obesity discussed. Tonight's programme featured a particularly brave young woman called Laura who presented with quite a serious case of Crohn's disease. For those who want more information about Crohn's see here. The long and short of it is inflammation, discomfort and quite a few 'peripheral' symptoms; no recognised cure and a life of medication and possibly surgery. Certainly one of the more serious gastrointestinal (GI) conditions.

Anyhow true to the name, the Food Hospital investigated whether it was possible the manage some of the symptoms of Crohn's disease through dietary changes. The plan in question is highlighted here and included a 3-step dietary intervention beginning with a cessation of food intake and reliance instead on a liquid feed containing all the necessary nutrients, followed a few weeks later by the implementation of the LOFFLEX (LOw Fibre, Fat Limited EXclusion) diet finally followed by dietary challenge/rechallenge in the hope of identifying problem foods related to symptoms.

It was interesting to see that some success was reported whilst on the regime in terms of symptom reduction following a flare-up. This is not proof of anything but certainly an interesting case study (n=1). Looking at the scientific literature for the LOFFLEX diet, things seem to be a little bit sparse at the moment. I found this trial from Addenbrookes Hospital which was the first place to look at the diet (I think). I also noted an interesting name on the authorship list, Prof. John Hunter, who is quite an expert on all things gastroenterology and particularly a role for gut bacteria in various bowel conditions.

I await more research on this very interesting regime and its potential applications to other conditions.