Catching a world within
24 Sep 2015 by Evoluted New Media
The human microbiome holds immense potential when it comes to drug development and disease insight. But can sampling methods catch up with analysis methods when it comes to the study of the microbiome?
The human microbiome holds immense potential when it comes to drug development and disease insight. But can sampling methods catch up with analysis methods when it comes to the study of the microbiome?
Although a relatively recent focus area for the research community, microbiome analysis is rapidly becoming one of the most exciting. In correlation with increased commercial interest from large companies such as Johnson & Johnson and Pfizer, there has been a rise in the development of new technologies created to improve research into the microbiome.
The human microbiome is a complex population of over 100 trillion microorganisms that live in our gut, mouth, skin and elsewhere in our bodies. The largest proportion of these bacteria reside in the gastrointestinal (GI) tract making up the gut microbiome. These microbiota have a profound impact on human health and disease; dysbiosis of the gut microbiome has been associated with multiple inflammatory and metabolic conditions including Crohn’s disease, inflammatory bowel diseases (IBD), colorectal cancer and obesity.
Currently, worldwide research is being conducted to ‘map’ the human microbiome with the aim of better understanding the relationship between the microbiome and human health. Advances in DNA sequencing technologies have created a new field of research, called metagenomics. Insight into the microbiota of healthy subjects allows comparisons with that of compromised subjects. In the case of IBD, such an approach has uncovered significant differences in overall diversity as well as in specific bacteria. However, despite these improvements in the science, many of the techniques for collecting samples remain primitive, which is impacting the ability for research to meet its potential.
The most commonly used sampling methods are stool collection, rectal swab and mucosal biopsy. The sampling method, storage and processing of samples can impact on the microbiota profile, each sample method has its own limitations.
Stool samples are convenient for patients and low cost, however they do not fully replicate mucosa-associated bacteria. In addition, stool samples are usually taken by the patient at home rather than immediately in the clinic. There are issues with compliance, as some patients do not like handling stool samples. There is also a risk of contamination during collection, delay in freezing the sample, variations in home freezer temperatures, and thawing during transport to the laboratory. Compelling evidence suggests that these factors may introduce sample variation large enough to compromise microbial diagnostics. A biopsy of the intestinal mucosa produces a standardised sample containing mucosally-adherent bacteria, however the bowel preparation required pre-biopsy may affect the microbiota profile. This sampling method is also invasive, expensive, time-consuming, and produces a very small samples that is difficult to process. Rectal swabs can be taken immediately in the clinic and stored in a standardised way, but the amount of material collected is unreliable and considerably smaller than with other methods.
A prerequisite for using microbiota analysis as a clinical tool is efficient and consistent sampling and sample preservation. An important factor in this regard is the influence of sample handling and the effect of intestinal preparation by bowel cleansing on composition of microbiota in stool and the mucosal layer of the colon. An ideal sample type for use in routine diagnostics should be easy to obtain in a standardised fashion and reflect the microbiota in situ.
There are solutions available for standardised sample collection that offer clinicians a simple, and effective tool for sampling the rectal mucosa without the need for prior fasting or bowel preparation. On such is OriCol – developed by Origin Sciences Sampling. The device incorporates a nitrile membrane, which after insertion into the rectum via a standard proctoscope, is inflated to make contact with the rectal mucosa. The membrane is then deflated and retracted into the device prior to removal from the patient. Upon retraction the material sampled from the rectal mucosa is retained on the inverted membrane. The device can either be stored frozen or a suitable buffer added to preserve the material for subsequent analysis. An alternative option is Micropharma’s ingestible medical device which can sample the mucosa at pre-determined locations throughout the GI tract, including the small intestine.
Despite these new techniques there is still a significant shortage of products available for sampling the microbiome effectively. There is a clear need to develop improved sampling methods that collect mucosal samples to adequately characterise the complex microbiota of the colon and to develop a standardised collection method and DNA extraction technique. Without new techniques or approaches, the potential of the microbiome in developing new drugs and treatments may never be fulfilled.
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