Recommended Read October 2013

The Gut Microbiota

This month’s recommended read is guest edited by Richard Hansen, Clinical Lecturer in Child Health in University of Aberdeen.

  Dr Rafeeq Muhammed asked me to highlight some key articles on the microbiota that might be of interest to our membership. The gut microbiota is an exciting area in medical science at the moment and has gained coverage in the top science journals and even made the front page of the Economist recently (, so has now transcended traditional medical science into broader culture. I decided that a simple list of articles was probably of fairly limited interest to anyone, so instead decided to write a blog-type piece where I instead signpost articles and explain why I think they’re worth seeking out. On this occasion, I’ll stick to articles about the healthy gut microbiota rather than delve into disease states.
  I’ll start with some definitions to make some of the terminology clear. The word “microbiota” describes the organisms that share our body space, so can relate to the skin, lungs, gut, etc and can also relate to bacteria, fungi, viruses and parasites. “Microbiota” and “microbiome” are often used synonymously, thought it could be argued this is incorrect. “Microbiome” was initially coined to mean exactly the same thing as “microbiota”, though in science journals often refers to the genetic contribution of the organisms. Even more confusingly, “biome” in biology refers to an ecosystem so it could be argued that “gut microbiome” should relate to the entire ecological habitat of the gut. To cut my monologue of pedantry short, in the literature the two are often synonymous. Here I will use “microbiota” to refer to the organisms and “microbiome” to refer to their genetic contribution.

  The first article I will point you to is, somewhat narcissistically, one of my own, however the reason I think it’s a good starting place is that it is a review of all the different methodologies used in assessing the microbiota, with explanations of each and a glossary at the end. So, to start with, have a look at “Characterizing the microbiota in IBD” ( which is free to read after a brief registration.
  Probably the most seminal paper on the microbiota came from Paul Eckburg and colleagues, led from Stanford, published in Science back in 2005. “Diversity of the human intestinal microbial fora” ( looked at three healthy adult subjects and examined their microbiota through different colonic mucosal sites from the caecum to the rectum and compared this to faeces (see Figure 1). The finding, often forgotten in the research community, here is that colonic sites remain fairly consistent, but represent a distinct ecosystem to faeces. Studies looking at faeces are therefore a proxy at best when extrapolated back to mucosal health/disease.

  Taking into account the last point about the difference between biopsies and faeces, it is apparent that faeces is a more readily-available biological sample and therefore of greater utility in population-type studies or where colonoscopy is inappropriate. Arguably the most important single microbiota paper came from Junjie Qin and colleagues in Nature in 2010. “A human gut microbial gene catalogue established by metagenomic sequencing” ( took an unprecedented approach by using “shotgun sequencing” to examine every gene within the microbiota, presenting the first “metagenome” paper of the human gut microbiota. Thus the microbiome of 124 European individuals, including 25 IBD patients, was explored and reported for the first time. The paper went on to try and define the minimal gut genome and to look at functional aspects of the genes represented. An intriguing supplementary figure (Supplementary Figure 8) hints that IBD may involve a reduction in gene diversity when compared to healthy individuals. It has to be stated once more however that this was based on faecal sampling and so perhaps doesn’t represent the mucosal state.

  A paper that received a lot of press attention at the time was Manimozhiyan Arumugam and colleagues’ “Enterotypes of the human gut microbiome” ( which again used a metagenomic approach in faecal samples (as in Qin et al), but this time looked for microbial patterns of similarity between individuals. This paper famously suggested that the enormous complexity of the gut microbiota could be succinctly distilled into three distinct “enterotypes”. This finding suggested a stratified microbial colonisation rather than colonisation on a continuous spectrum. The three enterotypes each centred around a single main contributing organism and were Bacteroides-predominant, Prevotella-predominant and Ruminococcus-predominant. Gary Wu and colleagues then extended our understanding of these enterotypes by examining them against host diet in “Linking long-term dietary patterns with gut microbial enterotypes” ( It appears that those who have a diet rich in protein and animal fat are most likely to have a Bacteroides-predominant enterotypes whilst Prevotella-predominant individuals were more likely to have a diet rich in carbohydrate. The third enterotype (Ruminococcus-predominant) did not feature strongly in this study and was largely integrated into the Bacteroides-predominant group. There was a suggestion in the study that enterotypes might be driven by diet, rather than vice versa, as a dietary intervention study reported in the same paper did alter the observed microbiota though this quickly reverted on cessation of the intervention.

  A recent paper by Omry Koren and colleagues titled “A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets” ( has suggested that the enterotype theory may not hold true and that bacterial colonisation may be on a spectrum without stratification as such. It seem the jury’s still out on enterotypes! The issue of dietary impact on the gut microbiota was also addressed in a lovely study from Carlotta De Filippo and colleagues, led by Paolo Lionetti’s group from Florence, which looked at children from a rural village in Burkina Faso (Africa) against urban children from Florence (Italy). The study, “Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa” ( found that the microbiota of the Burkina Faso children, who ate a diet rich in fibre, carbohydrate and non-animal protein was hugely dominated by bacteria from the Bacteroidetes phylum with a corresponding reduction in the phylum Firmicutes. The Italian children on the other hand were Firmicutes-predominant and had a significant enrichment of the bacterial family Enterobacteriaceae (including Shigella and Escherichia) and, perhaps unsurprisingly, ate a predominantly Western diet high in animal protein, sugar, starch and fat and low in fibre. Although not an original paper, a recent commentary on the impact of diet on the microbiota was written by Georgina Hold with the conclusion that they are what we eat in “Western lifestyle: a ‘master’ manipulator of the intestinal microbiota?” (

  Finally, and bringing the story up-to-date, Catherine Lozupone and colleagues have recently published an important paper, “Meta-analyses of studies of the human microbiota” ( based on a combined analysis of data from 12 published microbiota studies, originally analysed on a similar computer platform. Importantly, they identified that “noise” from the methodology chosen in each study might obscure small but important findings, but that bigger findings, such as the changes in the microbiota with age, or changes based on body site, are still seen across different studies. They suggest an integrated approach in the future with the use of a shared methodology to facilitate such meta-analyses. This paper suggests that, as happened recently in IBD genetics, large meta-analyses of smaller studies of the gut microbiota might reveal increasing detail as the sample size increases, but first we have to standardise methodology across studies.’’

  I hope that you would enjoy reading this special edition of recommended read and please follow the links as suggested by Richard. Richard is the BSPGHAN’s twitter voice; hence please do not hesitate to start active discussion on this topic in Twitter. I am taking this opportunity to thank Richard on behalf of education committee for this brilliant contribution.

As usual please send your feedback to Carla.
Yours sincerely,

Chair of Education committee
October 2013