The science of microbiomics

A very short post to plug... well, to plug me really, and my very, very small contribution to an article featuring in the Pharmaceutical Journal titled: Microbiomics: its growing significance in the world of medicines testing. The article is only open-access for a short period of time, so if you happen to have stumbled across this post years and years into the future (today is Tuesday 26th February 2013 according to my flux-capacitated DeLorean) sorry.

But just so you don't feel to left out, a few article highlights: yoghurt and C.diff infection, the human microbiome project (HMP), gut bacteria and immune function, dysbiosis, the microbiota-gut-brain axis, fecal transplants (yuck factor 10) and pharmacometabonomics.

Gut microbes and health

I'd like to apologise to my Gutness Gracious Me blog. I've neglected you and your subscribers for quite a few months now and I'm sorry. I have no excuse so please accept my humble apology.

Friends again?

OK. There's been quite a bit of new research come out in the intervening months which I need to catch up on. For this entry I'm going to list a couple of interesting papers showing how, if it was ever needed, gut bacteria really are starting to be taken quite seriously in lots of science circles.

Nature is a good starting point (the journal Nature not nature in general). A whole supplement was recently dedicated to gut bacteria which can be viewed here. Unfortunately the papers aren't open-access but I might draw your attention to two of them in particular:

• Valentina Tremaroli & Fredrik Bäckhed* discuss the "functional interactions between the gut microbiota and host metabolism" and how gut bacteria might, just might have the ability to affect how we derive energy from our food. I suppose this crosses quite a few different issues such as 'is a calorie a calorie' and how overweight and obesity might not just be a simple 'energy in - energy out' relationship. Indeed the concept of gut bacteria potentially regulating metabolism and absorption of things like fatty acids as per this paper by Semova and colleagues** (discussed here) may very well also be relevant.
• The paper by Craig Maynard and colleagues*** highlights another important function of our gut bacteria with regards to immune function and how the communication between the two systems may have the ability to influence our health and ill-health. Other authors have similarly speculated on this process as per this study by Cucchiara and colleagues**** using pediatric inflammatory bowel disease as an example.

Next up is another Nature journal, Nature Neuroscience, which carried an interesting piece by Cryan & Dinan***** on the potential 'mind-altering' effects of gut bacteria and everyone's favourite term: the gut-brain axis. I've kinda done bacteria potentially influencing behaviour before on a sister blog entry (see here) so don't really want to rehash that again. Suffice to say that as well as being home to quite a lot of bacteria, our gut also houses quite a few neurotransmitters and their receptors more traditionally associated with brain, so why would we expect these not to potentially serve functions other than controlling gut motility and the like. Whether there is interaction between these neurotransmitters and gut bacteria.... well I'd speculate there might very well be.

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* Tremaroli V. & Bäckhed F. Functional interactions between the gut microbiota and host metabolism. Nature. 2012; 489: 242-249.

** Semova I. et al. Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish. Cell Host & Microbe. 2012; 12: 277-288.

*** Maynard CL. et al. Reciprocal interactions of the intestinal microbiota and immune system. Nature. 489: 231-241.

**** Cucchiara S. et al. Interactions between intestinal microbiota and innate immune system in pediatric inflammatory bowel disease. Journal of Clinical Gastroenterology. 2012; 46: S64-S66.

***** Cryan JF. & Dinan TG. Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour. Nature Reviews: Neuroscience. September 2012.

Probiotics, probiotics, probiotics

Do you ever have one of those days where a certain word seems to keep cropping up again and again no matter where you turn? Well, today is one of those days for me, and today's word is probiotics. Like a good dose of influenza (if there is such a thing as a good dose), I just can't seem to shake that word today.

So here are the papers with that word:

Delzenne and colleagues* (open-access) report on an interesting relationship between gut bacteria and obesity with a specific focus on studies looking to 'alter' the gut microbiota via pre- and probiotics and the various reported outcomes based on anthropometric and biochemical parameters linked to obesity. I talked about something similar a few months back on a sister blog.

Min Tan and colleagues** (open-access) report on the quite positive effects to patients recovering from traumatic brain injury in intensive care following administration of probiotics. Based on a relatively small patient group, patients (n=52) were randomised into either a nutrition + probiotics group or a nutrition alone group. Feeds were administered via a nasogastric tube initially which then progressed to the 'by mouth' route when patients were well enough. Various serum cytokines and related immune markers were analysed over the course of the study which lasted for 21 days.

Unfortunately some of the patients did not make it following their group allocation as sadly might be expected following a serious brain trauma. Other patients developed complications following their accident which did not seem to differ in quantity statistically between the groups aside from the number of pathogens potentially related to infections: fewer pathogens in the probiotic group. The probiotic group (the probiotic including Bifidobacterium longum, Lactobacillus bulgaricus, and Streptococcus thermophilus) did however show an altered immune profile to the control group in terms of indications of the Th1-Th2 slant to the immune system. Although perhaps a little simplistic, Th1 represents the fighting infection side of the immune system and Th2 is the production of antibodies side of things. The probiotic group showed an immune profile more representative of the Th1 response, speculated to be important for their speedier recovery and their less frequent use of antibiotics.

Although the results were not totally astounding in this study, there is an important clinical lesson from this trial in that patients spent statistically less time in intensive care and relied on fewer antibiotics during their recovery as a result of probiotic administration. For patients and physicians alike, this has got to be a good thing.

Finally, ScienceDaily carries an interesting statement from the Annual Scientific Meeting of the American College of Gastroenterology (ACG) regarding probiotics and the potential anti-inflammatory properties of certain types of probiotic. I like to sound of the collected press conference for the studies listed in this release: "Good, bad and ugly bugs: Mother Nature as a treatment for better health in the GI tract". As per the release there are a few headlines including:

• A meta-analysis of studies looking at the use of probiotics used to reduce cases of antibiotic-associated diarrhoea (diarrhea) concluded that yep, probiotics, and particularly that most lovable to yeasts Saccharomyces boulardii, do a pretty good job at curbing your risk of this quite unpleasant condition.
• The use of Bifidobacterium infantis 35624 for those suffering from recurrent abdominal bloating and discomfort did not fare too well in a new randomised-controlled trial. B.infantis 35624 had previously shown some interesting positive results for those with irritable bowel syndrome (IBS).
• Having said that, it was not all bad news for B.infantis 35624 as per another trial which suggested that the probiotic might have some pretty good anti-inflammatory properties when it comes to those dastardly pro-inflammatory cytokines. Indeed that most common of inflammatory markers, C-reactive protein seemed also to be reduced in cases of psoriasis, ulcerative colitis and even in chronic fatigue patients following probiotic administration.

What then can we assume from these collected studies. Well, at least in the short-term under various controlled conditions, probiotics, various probiotics, might just be able to influence our health and ill-health particularly in certain conditions/states. As per my previous post, our collected gut bacteria is a complicated organism which talks to our immune system in ways we are only starting to understand. Like every married couple, sometime the talk is positive and healthy; other times the talk is slightly less healthy... (not in front of the kids!).

Whether in the longer-term, supplementing with probiotics offers any added benefit, I don't know. Speculation (and it is only that) would perhaps suggest that the way probiotics are delivered (those all important enteric coatings), how our immune system recognise bacteria as 'self' or 'not-self' and good old homeostasis (the body's drive to keep harmony) are all factors potentially affecting the ability to make a more permanent shift in our not-so-good bacterial species to those preferred choices. Indeed this last point on what is good and bad gut bacteria perhaps needs a little more research in terms of the effects of individual species, etc on health and wellbeing.

* Delzeene NM. et al. Targeting gut microbiota in obesity: effects of prebiotics and probiotics. Nature Revs. November 2011.

** Min Tan. et al. Effects of probiotics on serum levels of Th1/Th2-cytokine and clinical outcomes in severe traumatic brain-injured patients: a prospective randomized pilot study. Critical Care. December 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

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

Cytokines and gut motility

A relatively short post this one.

I think most people would understand why gastrointestinal motility is important to our health and wellbeing. Too fast or too slow a transit time is likely to lead to some pretty uncomfortable symptoms and indeed could signal the presence of one of a number of complications.

A recently published review paper on motility in gastrointestinal disorders by Akiho and colleagues* (full-text here) caught my eye. I was interested in this paper because it reviews the association between gastrointestinal motility and the expression of cytokines as a function of which way the immune system might be skewed.

I should perhaps back-up slightly here and provide some commentary on the way the immune system can be poised (according to our current knowledge) and in particular the concepts of Th1 and Th2. A good overview of the T helper cells is here. In brief, it's all to do with different kinds of immunity and how our immune system attempts to strike a balance between cell-mediated immunity (Th1) and humoral immunity (Th2) depending on what particular pathogen the immune system is up against.

The Akiho review paper lists a number of the most common GI disorders currently in the medical dictionary and details what particular types of response and cytokines are tied into the disease state. So for coeliac (celiac) disease and Crohn's disease there is a predominantly Th1 skewed cytokine profile either associated with disease onset or perpetuation. In ulcerative colitis, it is more of a Th2-like response in terms of cytokines associated with the condition. The authors do make mention also about Th17-mediated inflammation (possibly linked to autoimmunity) but this is still very much an emerging area of investigation.

The authors then proceed to review the evidence that Th1-related cytokines seem to show more of an affinity with hypocontractality of inflamed intestinal smooth muscle (slowing down) and Th-2 show a more hypercontractility (speeding up).  This is perhaps too simplistic a view to take, one linked to one but not the other, given the number of cytokines tied into various GI states and the complexity of the whole thing. But their analysis of the current evidence base is an interesting one.

What work like this serves to show is that the our immune system is a fantastic piece of engineering constantly trying to strike a balance between fighting off pathogens and infections and invaders, whilst at the same time keeping the host (us) in working order, trying not to destroy us also. The presentation of GI conditions, many GI conditions, seem to reflect the inner workings (and malfunctions) of the immune system and when establishing how the immune system manifests itself in individual conditions, offers some tantilising insights into potential therapies.

* Akiho H. et al. Cytokine-induced alterations of gastrointestinal motility in gastrointestinal disorders. World J Gastrointest Pathophysiol. October 2011