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This is how technology cores can help with studying the gut microbiome

In our bodies there are ten bacteria per human cell. This microbial richness plays a key role in our health and in the development of certain diseases. It was, however, a little understood role until the publication of research by Jeffrey I. Gordon, Director of the Center for Genome Sciences and Systems Biology at the University of Washington, who discovered the complex relationship between gut microbiota and nutrition and health, in addition to its impact on problems such as obesity.

“The impact of the microbiome on health has been known for some time,” explains Dr Malú Calle from the Department of Systems Biology at the University of Vic. She is referring to the microorganisms that are part of the organism, 90% of which are bacteria and which many are now calling the “last organ”. 


Geralt (Pixabay)


In recent years, research has determined the role of the microbiome in digestion and the immune system and has also pointed out its possible association with disorders such as autism or human immunodeficiency virus (HIV) infection. Initiatives such as Stick Out Your Tongue, sponsored by the Centre for Genomic Regulation, the Centre for Research in Environmental Epidemiology and La Caixa Foundation, study patient samples to analyse oral microbiome and check its variability and relationship with the phenotypic and environmental characteristics of the participants. Research into the microbiome was also discussed at The Human Microbiome, Present Status and Future Prospects meeting hosted by B-Debate, an initiative by Biocat and La Caixa Foundation. But how can technology cores help such microbiome studies? What role does gut microbiota, almost certainly the most evaluated, play in our health? Do the results of these studies come from using technology cores?

Microbiome big data

“Genome sequencing enables us to quantify the diversity, composition and quantity of the microorganisms in each patient,” says Calle, something which will help with conducting more thorough research. Here technological advances have led to key quantitative measurements, especially in relation to gut microbiota. The scientist from the University of Vic believes that in the future we will be able to gain greater insight into the role of pulmonary microbiota in the development of respiratory illnesses and into the study of skin bacteria and saliva, as is being done in the Stick Out Your Tongue project. As Calle notes, these latter samples could also be related to an increased risk of pancreatic cancer so they could be used as a biomarker.

“First we need to characterise the composition and characteristics of the microbiome in healthy people, so we can then determine the variability and establish patterns in patients,” she argues. These studies will enable us to identify markers to determine the risk of disease and even predict the evolution of a specific disorder. The information generated is microbiome big data, which is based on genome sequencing of microorganisms. “That means we can establish not only bacterial abundance, but also the abundance of genes with a specific function,” says Calle, the scientific leader of the B-Debate on the microbiome. “There are microorganisms of certain species involved in metabolic aspects, while others are related to immunological parameters or diet.”


John Goode (Flickr)


What challenges do technology cores now face in this type of research? In Calle’s view, the future of microbiome research will address two different stages. Firstly “we need to develop bioinformatics tools that enable us to avoid the fundamental mistake presented by data generated by genomic sequencing.” The second stage will consist of building multivariate statistical analysis which also helps us evaluate the networks formed by these microorganisms, and thus unravel their role in our body.

Chaysavanh Manichanh, a researcher at the Vall d’Hebron Research Institute (VHIR), points to a third challenge for technology cores: annotation in databases. “We are only at the beginning of the application of genomic sequencing and bioinformatics in microbiome analysis,” she says. We now know that there are ten million functions, many of them unknown, which may be relevant for understanding the role of the microbiome in health. 

Manichanh, who was part of the MetaHIT project responsible for characterising and identifying the genetic variability of microbial communities in the digestive system, has recently published a study in which she described the importance of microbiota in irritable bowel syndrome. Her findings, published in Nature Scientific Reports, show that patients with this disorder have lower microbial diversity. Her analysis of 113 people with irritable bowel syndrome and 66 healthy people, together with a study of 273 faecal samples, indicated that “the different phenotypes have a different flora, so the microbiota of each patient should also be considered when proposing treatment,” Manichanh told Biocores




As happened with previous work on the microbiome, the VHIR study demonstrates the potential of this research in prevention, diagnosis and the therapeutic approach to a wide range of diseases. This potential will be enhanced with the help of technology cores, which will enable more detailed and meticulous analysis in quantifying and assessing the role of these microorganisms in our health.