Antibiotics and resistance – there is a problem, but it’s not my fault!


When I talk to my hospital colleagues, and my patients,  about antibiotics, overuse, and resistance, there is certainly no lack of awareness. Unprompted I frequently get told exactly what the problem is.


There’s one answer I rarely get.

“I’m probably part of the problem, and I am changing what I am doing, to do my bit”.


Is this reflected in what is said online? 

Continue reading

Probiotics -seeds of change, or unnecessary chimpanzees?

AKA What I say when people ask me about Yakult.


“Probiotics -what do you think of them?” 

I get asked this quite a lot, when I talk about antibiotics, gut bacteria, and our own microbial community, or ‘microbiome’,  in general.

So first up, let’s just say, I love Microbiomes. I think the whole area is fascinating, I’m lucky enough to work in the area,  and I firmly believe a better understanding will transform how we see health, and how we treat our patients.

I think…we’re not quite there yet.

As I’ve heard it described many times, Microbiome science is generally still in the ‘cataloguing’ stage. We’ve just been given the tools for the first time to go and explore these incredibly complex ecosystems, previously hidden from our eyes. And we’re going into Amazon rainforest, Appalachian plains, and snowy mountains, and we’re cataloguing and counting everything we find there.  It’s a wonderfully exciting time.


We’re finding that some people have incredibly diverse guts, full of  rarely-seen species – (Amazon rainforest guts) – and others maybe have guts more like Siberian tundra – more sparse, fewer different species (that we can see).

Some scientists are finding they can correlate the presence of certain species with health conditions. You might say guts of patients with diabetes are less likely to contain oak trees, or guts of obese patients have far more monkeys than ants, compared to those of normal bodyweight.   Great.  This is all interesting stuff.

What can we do with this, and how does it relate to probiotics? 

Continue reading

The wild garden of the gut bacteria 

This is an entry for the  American Society of Microbiology Agar Art competition, and yes, it’s created using poop! Or more correctly, bacteria from poop.

You can see more of the agar art at:

Update: We’ve now got a full gallery of  our art at


Photography is by Chris Wood, of Oxford Medical Illustration, whose awesome work is all over this blog. The images are photographed over a lightbox, to bring out the colors and transparency of the agar.



There’s a lot more behind it than I could fit into 200 words! So I  so here’s the longer description.

What’s the science behind this? 


We often talk about bacteria as harmful things. Images in the media, advertising, even Doctors and Scientists, portray a healthy, desirable world as one free of bacteria- sterile, washed and scrubbed clean.  It’s becoming increasingly clear that this isn’t true. Recent advances in scientific research have enabled us to study bacteria in new ways, helping us realise that we wouldn’t be able to survive in this world without bacteria – we live together, and often help one another.  One of the most important places this happens is in our partnership with the bacteria in the gut. We provide them with food and habitat. They, in return, help protect us from harmful bacteria, help regulate the immune system so it fights infections but doesn’t get over-reactive (which may stimulate auto-immune diseases), and also affect our metabolism, or hormones, even possibly our mood…

Some people have compared the bacteria that live in our gut to a ‘garden’ – a healthy gut is one that is populated with many different types of bacteria, living together – in this setting, bacteria are desirable and beautiful.  Some bacteria are almost always beneficial, some are harmless, and some can be harmful. They all interact with one another, forming an ecosystem- they compete for nutrients, interact and communicate with one another.  But much like a garden, some types of bacteria can get out of control and cause damage if the careful balance between human and bacterial community is disrupted. For instance, previously harmless gut bacteria can sometimes escape the gut and enter our bloodstream if our immune system isn’t working well, or if our gut wall is damaged. Perhaps, rather than partnership, we should consider the relationship between our bacteria as a mutually-beneficial truce, occasionally broken by both sides when circumstances change.

You can see the techniques used here:

Thanks to That’s Oxford TV!

What’s going on in the images? 

Continue reading

“Protect your good bacteria” a comic proposal from Med Student Educational Module

So, this is what happens if you set a Medical Student the task of creating something that communicates an important message in how antibiotics are used….


(And if you’re interested – this isn’t just a fart joke…it’s an evidence-based piece of targeted work!

Poster presented FIS conference, Glasgow, 2015

For the literature behind the comic, read on…)

Continue reading

Microbiological Phrases for the short of memory

So despite years of trying to learn tables of resistance profiles and antibiotic mechanisms (and trying to teach them this way) I’ve written down the way I’ve managed to remember something about antibiotic – little pearls of wisdom that microbiologists/seniors have trotted out at opportune times at the bedside/wardround, which, when uttered, earn a small nod of acknowledgement.  eg. “Hmm… should we add in metronidazole?” “Well, co-amoxiclav has decent anaerobic cover, but metronidazole will get into any abscess better”.  Funny, as mostly I’m a diagrams sort of person

Continue reading