Mihai Pop on changing gut microbiota in childhood diarrhoea

Posted by Biome on 30th June 2014 - 0 Comments


Diarrhoea is the second leading cause of childhood mortality worldwide in those under five, according to the World Health Organization. Whilst prevention through safe drinking water and sufficient sanitation remains the best way to decrease diarrheal disease, improving treatment is nonetheless vital. Understanding the microbiota of the gut can provide insights into the contribution of pathogens – whether causative, protective or exacerbating – that can feed into dietary or microbiological interventions for the treatment of diarrhoea. In a Genome Biology study, Mihai Pop from the University of Maryland, USA, and colleagues use high-throughput sequencing to analyse stool specimens of over 900 children with moderate to severe diarrhoea from the Gambia, Kenya, Mali and Bangladesh, uncovering novel correlations with both potentially pathogenic and protective bacteria. Here Pop discusses the importance of this work in tackling the public health burden of diarrhoea, what more is needed, and future research directions.

 

How does the public health burden of diarrhoeal diseases compare, for instance, to malaria?

According to the World Health Organization, there are about four times as many cases of diarrhoeal illness than malaria in African countries. Worldwide, diarrhoeal illness represents the most common cause of disease, and contributes to roughly twice as many deaths as malaria.

 

The contribution of the human microbiota to human disease is only just beginning to be understood; how has your recent study in Genome Biology aided research in this field?

Our study made several contributions. First, we were able to show that metagenomic methods are able to uncover new potential causative agents even in diseases as well studied as diarrhoea. Second, we have started to uncover the potential role of interactions between microorganisms within the community in preventing disease. For example, in our data Prevotella organisms appear to be associated with absence of diarrhoea and are negatively correlated with diarrhoeal-causing bacteria.

 

Were you surprised by the associations you found between diarrhoeal disease and intestinal microbial diversity?

The association between microbial diversity and diarrhoea was already well established. If anything, we were surprised by the relatively small impact of diarrhoeal disease on the observed microbial diversity. This result is in part due to the tremendous inter-personal variability of the human gut microbiome, a feature that complicates the interpretation of data derived from cross-sectional studies such as ours, requiring much higher sample sizes in order to detect significant associations. Prospective longitudinal studies will, thus, be necessary to better understand the role of the host microbiota in disease.

 

How significant has the availability of high-throughput technologies been in identifying and understanding pathogen diversity, and its contribution to disease?

High-throughput sequencing technologies have been absolutely critical to our study. When we initiated our project we were expecting to sequence less than 100 reads/sample using the traditional Sanger method. The emergence of new sequencing technologies allowed us to increase this amount by over an order of magnitude, and the much deeper sampling of the community was critical to our ability to detect new associations through robust statistical methods.

 

How important is understanding human population diversity for addressing major public health problems, such as intestinal pathogens?

Most of the studies done so far on host-associated microbiota have focused primarily on Western populations and have, thus, only sampled a small fraction of the microbial diversity living on and within the human body. The bacterial causes and contributing factors for many diseases are likely to differ across countries and socio-economic strata. As a result, conclusions drawn from Western populations cannot be easily generalised to other populations. This is particularly true for diarrhoeal disease that has a substantially higher impact within the developing world.

Recent studies, including ours, have started to paint a more complete picture of host-associated microbial communities that will ultimately enable us to better understand the interaction between the host microbiome and health or disease. The impact of such studies goes beyond the immediate needs of public health efforts in developing countries – a better understanding of the global microbial diversity may help us predict and protect against emerging pathogens, many of which originate in developing countries but have a worldwide impact on public health.

 

Is global awareness of diseases that largely affect the developing world increasing in light of research funding from large organisations like the Bill and Melinda Gates Foundation?

The work of the Bill and Melinda Gates Foundation (that funded our study), as well as that of other funding agencies, is definitely resulting in an increased focus on diseases that primarily affect the developing world. I do not have a good way to evaluate the global awareness of such diseases, but funding priorities definitely affect the directions in which scientists take their research. My personal guess is that funding is less of an incentive than a enabling factor in this research. That is, many scientists are already very interested in tackling these diseases but are not able to do so without appropriate funding.

 

What is next for your research?

Specific to the current study, we are trying to confirm the findings made through association statistics. Statistical associations are not a conclusive proof that specific bacteria contribute to diarrhoeal disease, and further in-depth analyses (both laboratory-based and computational) are needed to evaluate the hypotheses generated by our study.

On a broader scale, my lab is actively developing new approaches for metagenomic assembly, approaches necessary for conducting the deeper analysis of the putative pathogens found by our study. These tools will enhance and extend our metagenomic assembler metAMOS. We are also focusing on optimising the metAMOS pipelines, and testing and validating our code base.

 

More about the author(s)

Mihai Pop, Associate Professor, University of Maryland, USA.

Mihai Pop, Associate Professor, University of Maryland, USA.

Mihai Pop is an Associate Professor in the Department of Computer Science at the University of Maryland, USA. He received his PhD from Johns Hopkins University, USA, after which he joined the Institute for Genomic Research, USA, where he worked in bioinformatics before moving to the University of Maryland. His research interests focus on the development of computational algorithms for analysing biological data generated through high-throughput experimental techniques, with a particular interest in metagenomics. Pop is also an active member of the Human Microbiome Project.

Research

Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition

Pop M, Walker AW, Paulson J, Lindsay B, Antonio M, Hossain MA, Oundo J, Tamboura B et al.
Genome Biology 2014, 15:R76

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