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

Antimicrobial Resistance – Links to papers /resources

*** For any stewardship/education sessions – this post will serve as a resource for links to the evidence quoted- I’ll try and keep it up-to-date as I can***

“Hi, I’d really like an overview on where we are with antibiotic resistance!”  – recommend the CDC overview- colorful, diagramatic, comprehensive

“Hi, tell me about Carbapenem-Resistant Enterobacteriaceae (CRE)  and why everyone thinks this is seriously bad stuff” – great review in the Mayo Clinic Proceedings – Vasoo et al 2015

****Selection and transmission of resistance*****

Sub-lethal doses of antibiotic can select for resistance (eg wastewater…)  Gulberg  2011
Sublethal doses of biocide can select for resistance Forbes 2014
Resistance spread by the bacteriophage network – Modi 2013
Rapid spread of carbapenem resistance between multiple species (Klebsiella, Enterobacter, Serratia, E.coli… )  caused by jump of plasmid to multiple species – Mathers 2011, Conlan 2012 and  then jumping to high-fitness strains, evolving and spreading further.
Nepal MDR Klebsiella outbreak featuring horizontal gene transfer –Chung 2015
Antibiotic levels in wastewater above serum therapeutic levels –Larsson 2007
The widely-quoted correlation between antibiotic use on a population level and antibiotic resistance –Albrich 2004
Antibiotic resistance genes in cave microbiome Bhullar 2012
Is there a link between resistance in food-animals and resistance in humans? Examples:
Lazarus2015 Systematic review– plenty of studies saying probably, yes
More under the cut….

Continue reading

Methods, artistic and scientific

A couple of months ago I started trying to create some cool effects with chromogenic agar on cloth, inspired by Anna Dumitriu’s bioart. Not wanting to take up resources or paid time, I remember at 6pm embarking with glee upon my project, armed with past-expiry-date agar, and lab equipment discards, and exclaiming to myself “Oh Great! Now I’m doing Art, I can be free, and no longer shall I need to be careful and spend ages documenting!”.  (Anyone who has ever been with me in a lab will attribute to my almost pathological inability to follow slow, systematic instructions to the letter, and magnetic attraction to messing around…)

Continue reading