The Microbiome and Our Health - New Application Using the Echo Acoustic Liquid Handler for Metagenomic Studies

Written by Labcyte on April 20, 2018

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As we dive into understanding of the microbiome, scientists are discovering important metabolic pathways of bacteria are intertwined with the biochemical processes of the human body. Our health and organ systems are tied to the type and number of bacteria in our gut. We need to decipher how the different microbes interact with each other and with us.

Within any ecological system, a delicate balance is required for proper functioning of the community. Communities of microbial organisms are tremendously complex. Introduction of a new species can cause a huge change in activity, core pathways, waste buildup, and probability of infection. The use of antibiotics to treat infections may completely eradicate all bugs, creating a germ-free ecosystem. However, there is no guarantee that microbial species will return to baseline levels following antibiotic treatment..

Recent studies have suggested that gut microbiota affect several disease states. We now know that the microbiome influences the immune response to cancer treatment. The impact of antibiotics can decrease cancer survival. Scientists have also studied the gut microbiota of patients with Crohn’s disease and found that probiotic treatment has alleviated their symptoms. Other scientists found that blood pressure in mice fed a high-salt diet could be reduced with probiotic treatment. Analyses related to these disease states suggest that the gut microbiome has a significant impact on the symptoms.

A complex microbial ecosystem may form a symbiotic relationship with its host. In a recent article published in the American Society for Microbiology, investigators took a deeper look at the influence of gut microbiota on the innate immune system. Current assumptions support the belief that proinflammatory pathways are triggered by pathogenic bacteria; leading to inflammation and illness. However, it seems that one type of bacteria in our guts, Bacteroides dorei, produces a special type of lipopolysaccharide that has an immunoinhibitory effect. Eliminating B. dorei from the body actually causes greater inflammation, but despite the positives, there can also be too much of a good thing. For example, children with very high levels of B. dorei have a higher susceptibility to allergies and autoimmune diseases.

Lipopolysaccharides (LPS) are components of the outer membranes of some bacteria and are released when the bacteria die. LPS are a potent signal that the body is under attack. The LPS will trigger fever, inflammation and shock.

If bacteria in our guts produce lipopolysaccharides (LPS), and lipopolysaccharides make us ill, why is it that we don’t get sick?

After comparing metagenomic data from healthy adults, they found that the lipopolysaccharides in our gut are actually released from a consortium of intestinal bacteria from the order Bacteroidales; not just a single species. An important proinflammatory pathway is actively suppressed by bacterially released LPS. Therefore, this aids the survival of the entire bacterial community within the host organism.

This is the first report describing a phylum-wide microbiome-intrinsic mechanism actively damping immune activation in the healthy gut. Most importantly, this redefines how we view the immune system response to the host-microbiota relationship. The gut microbiome must be reassessed to accurately determine the impact of commensal microbes on health and disease.

To answer this question in regard to gut microbiota, scientists pooled samples to examine community diversity. They used the Echo Liquid Handler to pool samples, then sequenced and analyzed the metagenomic samples. A common method for assessing diversity and phylogenetic classification is 16S rRNA amplicon sequencing. It is frequently used for quick diagnosis of pooled samples and for obtaining metagenomic information. At Labcyte, we’ve created a new application for expediting this process by miniaturizing reaction volumes needed for 16S amplicon sequencing.

Using the Echo Liquid Handler, we were able to reduce reaction volumes and input sample 5-fold while maintaining sufficient read depth to accurately capture the community. The miniaturized process produced plenty of amplicon library for downstream sequencing. Reducing the sample input DNA requirement did not influence the results or analyses. This new application for metagenomics and microbiome analysis saves valuable input DNA and costly reagents. For more information on how this technique can help your research, please visit

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