Your microbiome and you (part I): Gut

This post was chosen as an Editor's Selection for ResearchBlogging.orgYOU probably think that your body has things pretty much under control, being the finely evolved machine that it is, it knows where its at, and does a generally good job of looking after itself. You’d be right of course, but it doesn’t do this without a little help.

Some of this help comes in the form of your microbiome.

I have written previously about the exciting concept of the human microbiome in which I described how the number of bacterial cells on your body out number your own cells 10 to one, and asked to what degree you consider yourself to be human? The vast majority of these co-residents of you are organised into defined communities, the structure and diversity of which vary depending on where on the body they’re found: your mouth, your nose, various areas of your skin, your gut and urogenital tract. By understanding the interactions between each of these communities and our body, we can better understand their role in health and disease.*

In this the first of two posts on your microbiome, we’ll take a look at your gut.

The gut

probiotics-good-bacteriaMost people are undoubtedly familiar with the idea of ‘good bacteria’, in particular those of your gut, which we are encouraged to top-up on a daily basis with sickly sweet probiotic supplements containing various species of Lactococcus and/or Bifidobacterium. One can only imagine how on Earth we’ve coped throughout the course of evolutionary history without our daily supplement of Yakult.

The general scientific consensus on probiotics is that they don’t do any particular harm to most people, except perhaps your wallet, but occasionally the claims made by the manufacturers are often circumstantial, based on studies with poor methodologies, or are based solely upon observations from a petri dish or mouse model. Furthermore, when reliable evidence is documented, it is invariably for a very specific strain, thus there can be little confidence that is is a general property of the bacterial species as a whole.

Where the use of probiotics moves away from a general supplementation to being part of an active treatment for a condition, there is some evidence to suggest they may be of benefit, but on the whole, evidence is lacking and more research is certainly warranted. A Cochrane review (an international not-for-profit organization, providing up-to-date information about the effects of health care) in 2004, concluded:

“Probiotics appear to be a useful adjunct to rehydration therapy in treating acute, infectious diarrhoea in adults and children. More research is needed to inform the use of particular probiotic regimens in specific patient groups.”

However, in general there are insufficient data for the use of probiotics, over current standard therapies, in conditions such as eczema, Crohn’s disease, bacterial vaginosis and a slew of others. This is probably not helped by the fact that there is a good chance that the little pot of living bacterial joy you are consuming doesn’t actually contain any live bacteria of the type you think you’re getting.

A study published last month in the International Journal of Food Microbiology by an Italian team based the Istituto Superiore di Sanità in Rome, described a survey of such probiotics in Italy between 2005-6, seeking to identify and enumerate bacteria in commercially available supplements 1. A whopping 87% of samples showed evidence of not conforming to the Italian guidelines.

“Even though most labelled supplements (25 samples) indicated the presence of Bifidobacterium bifidum, this organism was only detected sporadically and always as dead cells.”

They also noted contaminants such as the food-poisoning pathogen Bacillus cereus, yikes.

Continue reading “Your microbiome and you (part I): Gut”

The ‘negatome’ – a database of negative information…

Research bloggingWE researchers often joke that no-one ever publishes negative results, but that doesn’t mean to say that negative results aren’t extremely useful. On one level, knowledge of such negative results can prevent you repeating the same mistakes that countless other researchers, in other labs, have undoubtedly made over the years. On the other hand, they can provide a valuable dataset with which to generate new and useful information. One such example is the ‘Negatome Database‘, which has been reported by Smialowski et al.1 in Nucleic Acids Research advance access (November 17, 2009).

The Negatome is a collection of protein and domain (functional units of proteins) pairs that are unlikely to be engaged in direct physical interactions. But why on Earth would we want to know about proteins that don’t interact with each other; in fact, why do we need to know about proteins that interact at all?

Macromolecular machineResearchers recognize that that a cell doesn’t function purely by the action of individual proteins, but instead by large macromolecular complexes mediated by many interacting proteins.  The image to the left indicates an example macromolecular ‘machine’, in this case those involved in signal processing at the neuronal synapses (and which are likely to be working quite hard right now!).

Continue reading “The ‘negatome’ – a database of negative information…”

Windshield splatter analysis…

rb1A few years ago I took part in an RSPB survey called the Big Bug Count, which sought to quantitate what had hitherto been anecdotal accounts that the number of insect splats on car windscreens had decreased in recent years. Essentially it was a sticky pad of define area that was placed on the front registration plate of your car. Following a car journey (I drove the 20 miles from from Keswick to Windermere), the number of bugs splats were counted and the results submitted.

Some suggested that the dwindling insect splats may in fact be due to cars being more aerodynamic, and not the tin boxes of previous decades. However, even I had noticed that I was swallowing fewer bugs on my bike rides around Cumbria than my childhood years, but hardly scientifically rigorous data – I do after all scream with glee less now than I used to.

Unfortunately, because the ‘bug splat’ survey, as it became known, was the the first such study by the RSPB, they could draw no conclusions as to whether the insect population was dwindling (despite what some press articles claimed) until subsequent seasonal surveys, over multiple years, were performed.

Of course, what some of you may have noticed is that the RSBP doesn’t seem to have followed up with any further surveys – at least none that I’ve been able to find in 30 mins of googling and scouring their website. Shame, so we had a baseline, of sorts, against which nothing further has been measured.

But assessing species diversity is an important task, as I’m sure anyone can appreciate. Changes in biodiversity act as markers of climate change or pollution, and have knock on effects on the food chain, such as bird life.

Continue reading “Windshield splatter analysis…”

Stand up for research…

I’VE had a bit of an axe to grind recently about the government’s proposed policy on requiring such a large proportion of research funding to be allocated on the basis of economic and social impact. The University & College Union (UCU) is curently hosting a petition, signed against the statement that I’ve copied from their site below.

Sign it if you care to.

From the UCU’s website:

The latest proposal by the higher education funding councils is for 25% of the new Research Excellence Framework (REF) to be assessed according to ‘economic and social impact’. As academics, researchers and higher education professionals we believe that it is counter-productive to make funding for the best research conditional on its perceived economic and social benefits.

The REF proposals are founded on a lack of understanding of how knowledge advances. It is often difficult to predict which research will create the greatest practical impact. History shows us that in many instances it is curiosity-driven research that has led to major scientific and cultural advances. If implemented, these proposals risk undermining support for basic research across all disciplines and may well lead to an academic brain drain to countries such as the United States that continue to value fundamental research.

Universities must continue to be spaces in which the spirit of adventure thrives and where researchers enjoy academic freedom to push back the boundaries of knowledge in their disciplines.

We, therefore, call on the UK funding councils to withdraw the current REF proposals and to work with academics and researchers on creating a funding regime which supports and fosters basic research in our universities and colleges rather than discourages it.

[12,007 signatures at 11:43, 16 Nov 2009]

Sign the petition here.

Food for thought…

FINALLY, some lectures that don’t require a trip to London. Some big names are coming all the way up North, way up to the provinces, to give lectures as part of a celebration of 150 years of On the Origin of Species:

24th November 2009

2pm: Dr Gordon Chancellor
Charles Darwin, his life and his science
Dr Gordon Chancellor is from the UK Data Archive at the University of Essex. He is an Associate Editor of darwin-online.org.uk which hosts the largest online resource in the world relating to Charles Darwin.

2.45pm: Professor Steve Jones
Is human evolution over?
Professor Steve Jones is Professor of Genetics at University College London and is one of the best known contemporary popular writers on evolution. He is a television science presenter and writes a science column in the Daily Telegraph.

3.30 – 4pm: Interval

4pm: Professor Sydney Brenner
The Reconstruction of the Past: Reading the Human Genome
Professor Sydney Brenner opened the JIF building in 2007, now known as the Wellcome Trust Brenner building. Sydney was awarded the Nobel Prize for Physiology or Medicine in 2002 for his seminal work on discoveries of organ development and programmed cell death.

4.45pm: Professor Sir Alec Jeffreys
DNA fingerprinting and the turbulent genome
Professor Sir Alec Jeffreys is Royal Society Wolfson Professor at Leicester University. He discovered DNA fingerprinting 25 years ago. Among other important aspects of this method is that it allows identification of people by detecting variations in their genomes and has altered forensic science world wide.

5.30pm: Close

It’s going to be popular. Off to try and get a ticket, otherwise I’ll be sweating it out in a lecture teatre watching a live video feed instead.

Holes in the ice…

Research bloggingCRYOCONITE (‘ice dust’) holes are small pock-like depressions that are strewn over the surface of glaciers, looking much like a pristine snow drift after you’ve thrown a handful of gravel at it. Such melt-holes have been documented on glaciers at both poles, and on other glaciated regions such as Iceland, Greenland, Canada and the Himalayas. According to one account, at least, cryoconite holes  have been a bane to scientists working on the Greenland ice sheet, the holes being typically full of slushy ice, and big enough to step in by accident. However, cryoconite holes have been the subject of much debate in recent years; a debate centring on their role as contributors to glacial melting. Continue reading “Holes in the ice…”