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The Science of Shit

by Eric Boa

'Gentle' toilets in a restaurant in Ethiopia

What we excrete has interested public health experts for many years, particularly in monitoring the spread of infectious diseases. There is, rather surprisingly, no accepted term for studying – what shall we call it? – poo, one of many coy terms used to avoid saying shit. But let’s move on. There’s a lot of poo to talk about.

Infectious diseases are caused by an impressive array of microbes, tiny creatures that are invisible to the naked eye. Their role in human diseases was suspected for many years but only really began to be elucidated with the arrival of microscopes and high-power lenses. Bacteria could be seen for the first time, though their role as pathogens, causers of disease, would require much more study. Viruses cannot be seen by light microscopy and their role as pathogens took even longer to figure out.

In the mid 19th century, a London doctor, John Snow, made a series of meticulous observations concerning cholera outbreaks. He showed a clear association of cholera cases with pumps used by people to get their drinking water. Cases were highest where the waterworks company relied on sources of water that were contaminated by sewage. Cases decreased markedly in the vicinity of pumps supplied by freshwater sources. When a pump supplying contaminated water was disabled, cholera cases declined.

Snow’s evidence was compelling but also circumstantial. He never actually saw bacteria in the water. Shortly after he published his results, Italian physician Filippo Pacini observed masses of bacteria with a distinctive comma shape in the gut of people who had died from cholera. More compelling observations but still no direct proof that these bacteria were the cause of cholera. This mattered because those who believed in the germ theory faced a formidable alternative explanation for the origin and spread of human diseases.

The prevailing theory pointed the finger at a noxious miasma floating in the air, one that arose from rotting tissues. It was a vague and unproven explanation, lacking detail and supporting evidence, yet one that appeared to satisfy many. Fortunately, those of a more rational and, as we would say today, evidence-based inclination, were sceptical of the miasma theory. Doctors such as Snow and Pacini were amongst the first to gather evidence. Robert Koch, a German doctor and bacteriologist, continued to study infectious diseases and showed beyond reasonable doubt that bacteria were the cause of anthrax and tuberculosis.

Koch was another careful observer, with one crucial advantage: he was able to manipulate bacteria. His assistant, Julius Petri, he of Petri dish fame, had developed a method for growing bacteria in pure culture. Circular glass dishes are filled with agar, a jelly-like substance, obtained from seaweed, that can be sterilised. Koch realised the importance of using pure cultures in eliminating other possible causes, including other bacteria. Did he look at poo? I’m not sure. His most important contribution to the study of diseases was to devise a series of criteria, known as Koch’s postulates, to establish causality. A microbe must be regularly found in diseased individuals, isolated in pure culture, reintroduced to a healthy host, where the symptoms of the disease are reproduced, then re-isolated.

There’s a long history of doctors doing experiments on themselves, but I’m not sure many would consider injecting themselves with Vibrio cholerae, the cholera bacterium. Or indeed any of the other nasty pathogens that infect us. There are ways round this dilemma. Use substitute hosts; mice and guinea pigs respond well (by which I mean badly) to Ebola virus. Inoculate human cell cultures. Modern molecular methods provide further evidence of how pathogens attack their host.

Medical research dominates the life sciences so it’s worth pointing out that animals and plants also get diseases. Plants are routinely inoculated with microbes to confirm pathogenicity. Indeed the first conclusive proof of the germ theory was when Anton de Bary, a German biologist, satisfied Koch’s postulates for the fungus-like organism (Phytophthora infestans) that causes late blight of potatoes. This pioneering work, and that of many other scientists who’ve artificially infected other plants with microbes, should have removed any doubt that highly specialised bacteria, fungi and viruses cause disease.

Uncertainty, however, can never entirely be eliminated. Scientists attempt to reduce it to an acceptable degree, where alternative explanations for the cause of a disease, for example, are vanishingly improbable. There are plenty of people who play on uncertainty. Thabo Mbeki, a past South African President, was sceptical about the cause of Aids, as were many others, at least in the beginning. It’s frustrating for scientists to have to explain that they can’t 100% “prove” a theory, and that “beyond reasonable doubt” is an acceptable judgement, whether it’s for medical treatments, criminal convictions or linking political decisions to economic outcomes.

I began this article after reading about recent efforts to analyse waste products in tracking not only disease, notably Covid 19, but other human activities. It’s made me think much more deeply about causality and how science works. Bertolt Brecht put it concisely in his play about Galileo: “The aim of science is not to open the door to infinite wisdom, but to set a limit to infinite error”.

One of the major discoveries in the early frenzy to investigate Covid-19, was that virus particles are shed in poo by about half those infected. Within nine months of this Dutch finding, all sewage-treatment plants in the Netherlands were being regularly sampled. The same method has been used historically to monitor polio, typhoid and dengue fever. Surveillance is a tedious and expensive business. Sampling sewage allows scientists to track pathogens in a systematic manner. It’s more difficult in rural areas in much of the world, where cesspits and communal latrines are used, but not impossible.

Village latrine, North Kivu, Democratic Rep. of the Congo. Sampling point for monitoring disease spread.

It was difficult at first to convince officials that poking into poo was worthwhile. Attitudes changed when results showed that sampling of sewage was quicker, by up to four weeks, in identifying outbreaks, compared to analysing nasal swabs. The study of sewage can yield other secrets about human behaviour, such as patterns of food consumption, the use of cocaine, alcohol and pharmaceuticals. One US initiative proposed mapping opioid exposure via sewage samples to encourage harm reduction efforts by local pharmacies in North Carolina.

All this talk of poo and science reminded me of Gillian McKeith, the woman dubbed “the awful poo lady” by Ben Goldacre in his Bad Science column in The Guardian. She was never one to hide her celebrity under a toilet seat, and despite massive debunking of her flaky scientific reasoning, and cancellation of TV shows, she’s still around. Understanding the scientific method is not difficult – gather evidence, eliminate uncertainty. Yet it’s also a painstaking procedure, and progress can be slow. The study of poo is telling us a lot about how to react quicker and smarter to public health challenges. Yet there are also many people eager for quick and pat solutions to chronic ailments. Whether such advice is based on sound scientific research is another matter. There is, after all, only a minor change in word order from the Science of Shit to Shit Science.



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