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? 

There are multiple stories woven into this ‘conversation piece’ about one’s gut bacteria, and antibiotics. It is designed on a very simple level to be visually attractive and intriguing, encouraging a passing viewer to look closer and find out more.

Things you might notice:

1)      The gut bacteria are portrayed using organic, biological motifs  to invoke the ‘garden’ allegory of the gut bacteria, similar to the plants we live alongside -sometime friend, sometime adversary. The motif is meant to carry an element of beauty, but also a slightly alien edge, like vines or ivy – trying to avoid simplistic ‘gut bacteria are good and beautiful’ – when clearly, sometimes, they’re not…


2)      The piece is made from a mixture of three common gut bacteria – purple *E.coli, turquoise Citrobacter, and a tiny, tiny amount of dark blue Klebsiella (over 500 times less than the other bacteria). The bacteria were stamped onto the agar, and then left to grow overnight. Each small round ‘dot’ represents a bacterial colony (which may in itself contain a few million individual bacteria, growing together) – you may need to click on the pictures to see these in detail.  Mostly the bacterial colonies are so close, they merge together. You can see that generally the more numerous purple and turquoise bacteria can out-compete the dark blue Klebsiella, so that the Klebsiella colonies can only grow as big as pinpricks. This is similar to what happens in the gut, where ‘beneficial’ bacteria can out-compete more harmful ones and keep them under control.

3)      The discs around the edge have antibiotics in them, which enter into the agar and spread out, forming a ‘halo’ of antibiotic where bacteria find it harder, or impossible to grow.  ‘AMC’ represents Co-Amoxiclav, an antibiotic used very commonly in hospitals, and one I used to prescribe all the time.  You can see that it kills the purple E.coli.


The plate a few hours earlier – the more numerous purple E.coli are much more obvious, and the ‘halo’ around the AMC/Co-Amoxiclav disc is more visible. Later on, the dark blue Klebsiella really catch up and take over a bit, and you can’t see the halo as well.

For me, this tells me to remember that the antibiotics I prescribe can sometimes cause unintended harm to gut bacteria that are helping to keep my patient healthy, and I should be careful not to use antibiotics where they’re not needed.   A lot of the time, if my patient has a healthy, robust gut, the antibiotic doesn’t cause any noticeable problems. Sometimes the antibiotic disrupts the balance of gut bacteria, and the patient gets diarrhoea. Rarely, it can disrupt the balance so much that one bacteria- Clostridium difficile ( or C. diff) can take over, as we’ve destroyed all it’s competition, and cause life-threatening illness.  We also worry that if we destroy most of the bacteria, all that will be left will be those that cannot be killed by antibiotics (‘antibiotic resistant bacteria‘).

4)      The disc marked ‘MEM’ contains Meropenem – an antibiotic often called our ‘last line’ treatment. Meropenem (and it’s ‘cousins’, the Carbapenem antibiotics), are our last, really effective antibiotic that can kill a range of bacteria without toxic side effects. This is the one we’re really worried about – if many bacteria become resistant to this (i.e.  the meropenem antibiotic becomes ineffective in killing many bacteria) we have to use older, more toxic antibiotics. You can see that already the dark blue Klebsiella is able to survive much closer to the Meropenem antibiotic disc, than the purple E.coli, which is killed. The presence of the dark blue Klebsiella bacteria surviving close to our ‘last line’ antibiotic Meropenem is meant to convey a worrying message – that we are already seeing bacteria which cannot be treated with ‘last line’ antibiotics. Modern medicine (including surgical operations and cancer treatment) depends on having effective antibiotics to protect people from infection. These are already running out.


If you click on this image you can get an awesome close-up of the large Klebsiella colonies growing big and gloopy when their competition is removed

5) The Meropenem antibiotic kills the purple E.coli and turquoise Citrobacter, effectively removing the competition for space and nutrients, so the resistant blue Klebsiella is able to grow unimpeded into big, blue, gloopy colonies instead of the small pinpricks seen elsewhere.  To me, this again reminds me of the ‘unintended consequences’ of over-using strong antibiotics. It’s a bit like spreading weed-killer over a garden – plants that are resistant to the weedkiller chemicals can survive, and rapidly take over the depleted garden.


The inspiration for this piece and the ivy/vine motif is from a run in the old-growth forests along the Beaulieu River, near Southampton, where we stopped for the night a few months ago. The forest is full of oak trees of various ages – the younger ones growing straight and tall, the older ones gnarled and stooped, and covered in moss and ivy, yet still living on, until slowly they are weakened by the burden they support, and die.  I don’t know whether it is simply that the younger ones have not lived enough time for vines to grow, or whether they have some other ability to resist this slow usurping of the balance of power. I suspect the latter plays some role, having seen ivy take over our garden fence in little over a year.  It made me think of my grandfather, and how the balance of power between his body and the bacteria it supported changed with time and age. Previously a fit and mobile chap (still going on walking holidays in the Scottish Fells at the age of 80-something) a succession of infections slowly weakened him, until antibiotics could only hold at bay the infections that recurred when they were stopped – his own immune system unable to control the bacteria now taking over.  He was like the oldest of oaks in that forest – having sheltered many of the young things over the years, finally the the moss, the lichens, the ivy, so long living in balance, had become the dominant force – and no amount of weedkiller, herbicides, or gardening efforts at that point, would bring the oak tree back to strength. My grandfather’s wish on leaving hospital for the final time was to see his garden once more, and thanks to a wonderful Occupational Therapist from the Hammersmith Hospital, he saw his final days looking out on his much-loved Mimosa tree. So I think he wouldn’t have minded awfully being likened to an old oak, though I suspect he might have asked for something a bit less craggy.


Notes on creation:

Creating this piece has been a lot of fun, and a surprising amount of work. You know the old showbiz adage of ‘never work with children and animals?’ – I sort-of feel the same way about bacteria and art- they seldom behave the way you want them to, steadfastly refuse to do what you expect, and create no end of inconveniences for you by their behaviour. There were more than a few test-runs, created with out-of-date agars….

It seems bacteria don’t seem to like following stencils – they just grow underneath them. They don’t mind being stamped, but then insist on dripping sideways and blurring the lines. They have inconvenient growth times, so you have to go into the lab at 11pm to take them out of the incubator when they’re ‘just right’. The Klebsiella, in particular, was a nightmare- it grew twice as fast as the other strains, totally crowding them out. I tried giving everything else a head start but the bacteria didn’t like being smooshed by a second-stamping and turned into a smudgy mess.  Hence in the end I had to use it in around 100/1000-fold less concentrations, so that the others could be seen – actually this turned out to be quite a nice analogy for what goes on in the gut anyway, and represents the sort of ratios I’ve seen in many of the poo samples I’ve studied.  The whole experience is rather like developing an old-school photograph- you create the image, and then have to wait for it to develop and for things to become visible…and if you got it wrong, you just have to start all-over again…

IMG_1385 IMG_1350


Earlier attempts! Trying different ways of mixing the bacteria, and creating patterns. Here also the value of a lightbox and a proper photographer are seen…



How and why this was created:

This work was created by me, Dr Nicola Fawcett –  I’m a hospital doctor currently working in the Department of Microbiology, doing a PhD with the Nuffield Department of Medicine and the University of Oxford. I work with the Modernising Medical Microbiology Group, and I’m funded by the Medical Research Council (MRC) UK, who were kind enough to give me a Clinical Research Training Fellowship.

The piece is meant to convey key themes in my research study– the Antibiotic Resistance in the Microbiome Oxford (or ARMORD) Study. You can read more about the study here: It aims to study the gut bacteria of Oxfordshire adults by studying poo samples, and see how factors like antibiotics, diet, travel and contact with hospitals affect the gut bacteria.

It owes a huge amount to Anna Dumitriu, our Research Consortium’s Award-winning Artist-in-Residence, who I’ve been lucky enough to work with, and learn from. A lot of the themes in are from themes discussed whilst working together, massaging poop into linen (her… I wimped out…). We’re hoping to collaborate on a larger project … watch this space! You can see her work at:, or instagram here.

This work has been created as part of our public engagement programme, to communicate the science we do, and why we do it at:


The bacterial garden, and representing the gut bacteria as an ecosystem is an analogy made by many scientists studying the bacterial world. I credit Jonathan Eisen‘s twitter feed, Prof. Michael Wilson of UCH, Tom Lewis and the messages of ‘Listen to your Gut’, a lot of wonderful writing by Ed Yong and of course above all -Anna Dumitriu for influencing my portrayal of the gut bacteria and the larger concept of the ‘microbiome’  – the unseen microbial community that lives on us, and around us. There’s a really nice writeup of the microbiome here:  which likens the gut microbiome to a rainforest. The combination of the beautiful but slightly threatening motif I credit to the effect that the writings of Jeff Vandermeer have had on my brain – Annihilation in particular, which I can’t recommend highly enough. It has influenced my developing relationship with bacteria from one of hostility, to complete about-turn bacteria-are-beautiful-yay-bacteria, to one where I can’t really resolve bacteria as good or bad – in fact seeing the discussion of intent as meaningless- and currently seeing them more as strange, powerful, scary-beautiful, even alien, things, that we live in an enforced, uneasy, sometimes beneficial sort-of-truce with. I worry that currently, bacteria are winning, and just making bigger guns isn’t going to make this better – we’re going to have to find a way to get the message to both sides.




The bacteria have been mixed together and diluted in water, which is then spread onto a rubber stamp, and pressed onto the jelly-like agar, which contains nutrients to allow the bacteria to grow  The stamp is then disinfected with very strong laboratory-grade disinfectant, and doesn’t leave the lab!  The antibiotic discs are added, which stick to the agar, and the antibiotics dissolve into the agar, and spread out in a ‘halo’.  The plate is then incubated in a room at 37’c (body temperature = optimum growth) overnight, and the bacteria divide rapidly, doubling about once every 20 minutes. By morning 10 bacteria can become a billion. They can either form in colonies (the round, individual dots) or the colonies can merge together. If the colonies are competing for nutrients, they only grow small. If they’ve got no competition they can grow bigger. Bacteria can create a mucus-like covering, and form really big, gloopy colonies if given space.  Klebsiella is particularly good at this.

This particular sort of agar (we call ‘chromogenic’ or ‘colour generating’) contains a mixture of dyes which dissolve in water, and can also dissolve in agar, and the watery mucus-like substance surrounding the bacterial colonies**.  The dyes are initially colourless, unless they encounter enzymes in certain types of bacteria, which convert them into colourful substances. An enzyme found in the E.coli bacterium causes one dye to turn purple. An enzyme in Citrobacter species causes another dye to turn turquoise, and an enzyme found in Klebsiella will turn a third dye dark blue.  Thus the different colonies of bacteria are dyed different colors as they grow.  These colourful agars are used by the Microbiology Department to find out which bacteria are growing in urine, and may be making someone ill. We also use them in the Research Laboratory to study the bacteria in poo samples as a way of studying the bacteria which live,( or used to live!) in people’s guts.

*note: I’ve used common names, and abbreviations, rather than sticking rigidly to standard nomenclature. Apologies to Microbiologists who I know can find this intensely irritating. I’ve aimed for a non-specialist audience, who may recognise E.coli but not Escherichia, for instance.

** The actual agar is BD™ CHROMagar™ Orientation Medium. Mainly because that’s what we already have stocks of. They normally have a printed label along the middle, which sort of got in the way, Initially I tried just lifting the agar disc into a plain dish, but this created bubbles (you can see in earlier attempts). In the end, I melted the agar down and repoured it into plain dishes.


All images on this post are by Chris Wood. If you re-use them, please do put a stamp on the image or include a link to this blog, and  attribute them to: Chris Wood, Oxford Medical Illustration and Nicola Fawcett (Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0))


28/9/15 -Edited


BBC News  – Oxford scientist makes art from the gut

ITV News  –  Bacteria turned into artwork reveal the limits of antibiotics 

BMJ News – The Garden in our Gut

Gizmodo – This is the most beautiful view of poop you’re ever going to see

Jiemian( Chinese language) –

Espanol – Esta es la más hermosa vista de Poop alguna vez va a Ver

And totally awesome write up by Kate Horowitz of Mental Floss which explains things much better than I did, especially the colony growing bit:  Elevating poop science to art 

(and correcting grammar pickup in post above!)

University of Oxford – Microbe artwork shows the limits of antibiotics


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