Full title: Gut microbiome monitoring in the critically ill

Aim: explore new technology to analyse gut bacteria in ICU patients to provide information with the intention of understanding and improving patient management in the future.

Background: long-stay patients on the adult intensive care unit (ICU) are among the sickest and most vulnerable in the hospital. In healthy people the gut especially the colon is home to a rich and largely stable collection of bacteria known as the microbiome. These bacteria are often considered ‘good bacteria’ as they perform many functions including the digestion of nutrients. However, in the long-stay ICU patient, a disruption in bacterial variation in the digestive tract from the mouth to the anus may occur. Indeed, it is possible for some of the ‘good bacteria’ to disappear leaving only a single or just a few bacterial species present. Studies so far have used a method of detecting bacteria in faecal samples which provides insufficient information on the numbers and types of bacteria present and their potential antibiotic resistance. Fortunately, following a pioneering study using direct analysis of bacterial DNA in faecal samples (a process known as metagenomics), we have an exciting new opportunity to carry out research into gut bacteria in ICU patients.