Tom started in high spirits and many of his fellow students were jealous of his unlimited junk food budget. As he put it:

I felt good for three days, then slowly went downhill, I became more lethargic, and by a week my friends thought I had gone a strange grey colour. The last few days were a real struggle. I felt really unwell, but definitely had no addictive withdrawal symptoms and when I finally finished, I rushed (uncharacteristically) to the shops to get some salad and fruit.

While it was clear the intensive diet had made him feel temporarily unwell, we had to wait a few months for the results to arrive back. The results came from Cornell University in the US and the crowdfunded British Gut Project, which allows people to get their microbiome tested with the results shared on the web for anyone to analyze. They all told the same story: Tom’s community of gut microbes (called a microbiome) had been devastated.

Tom’s gut had seen massive shifts in his common microbe groups for reasons that are still unclear. Firmicutes were replaced with Bacteroidetes as the dominant type, while friendly bifidobacteria that suppress inflammation halved. However the clearest marker of an unhealthy gut is losing species diversity and after just a few days Tom had lost an estimated 1,400 species – nearly 40% of his total. The changes persisted and even two weeks after the diet his microbes had not recovered. Loss of diversity is a universal signal of ill health in the guts of obese and diabetic people and triggers a range of immunity problems in lab mice.