About the blog

Microbiome is a new word. It was first used by Joshua Lederberg in 2001 to describe “the ecological community of commensal, synbiotic, and pathogenic microorganisms that literally share our body space...” (enthusiastic etymologists can click here). Since then, ‘microbiome’ has been used as an all encompassing term for the study of bacterial proteins (proteomics) and  genes (metagenomics) in the environment, as well as working out which species of bacteria make up the communities living in, on and around us.

Microbiome research is a completely new world for me as well. I trained as a veterinary surgeon in the UK. I spent a bit of time in a laboratory during my final year, mainly because it involved no on call shifts, weekend work or stressful situations. My project was loosely based around chicken intestinal muscous, Campylobacter and spotty liver disease. Apart from that, I always planned on working in clinics.

After graduating, I spent two years working as a vet in Colombia. I was working with the things that I liked best, infectious diseases and traumatic injuries... but I began to want something more. I started to look for PhD projects at universities. One caught my eye, studying the chicken intestinal microbiome to improve and inform the use of probiotics. I had used probiotics in practice, usually after blitzing a parvovirus puppy with antibiotics, but I had never seen any real evidence for their use in animals. I prescribed them more on a hunch than any informed clinical decision. When I thought about it this bothered me. On what basis was I using probiotics as medication? Were they doing any good? This doctoral project sounded right up my street. I applied and 6 months later I was at the university, sat at my desk, wondering where to start.

I launched myself straight into the research looking at the chicken intestinal microbiome. The more I read, the more I realised that I couldn't just read the Results and Discussion and expect to understand or interpret what was being said. I had never had any training in DNA sequencing or PCR. I was baffled by clone libraries, bemused by 454 pyrosequencing and befuddled by chimeras. It was time to take a step back and start right at the beginning. Everything you do, how you take samples, how they're stored, any and every procedure done to the sample before analysis will affect your results.

The aim of this blog is to look at these aspects of microbiome research. Perhaps not as thrilling as looking at the actual results, but equally important. A lot of the available information is very dry, and difficult to read. My aim is to read and summarise this information, presenting it in an accessible way with pictures and animations. I hope that this blog will act as a resource for people who want to truly understand the results coming out of microbiome research. Do you remember in maths classes, when your teacher would tell you that the answer isn't the most important part, but your working is essential? The same applies to scientific research.

I don't claim to yet be an expert in microbial research, but I hope this blog will track my progress and act as a forum for discussion throughout my research.