There is so much that can be learned from studying the gut microbiome. The community of bacteria co-habiting with their human host share a curious symbiotic relationship, one that can have a significant affect on health. This is a complex relationship where the abundance and diversity of the microbiome can affect various aspects of human physiology, metabolism, immune response, and psychology. Conversely, many factors within the human host’s control can alter the microbial community, even causing extinction events, such as dietary changes, geographical location, lifestyle, or antibiotic use. When this delicate balance is shifted, this may result in consequences for the host’s health. Therefore, it is essential to characterize the human microbiome and understand what factors alter this complex, reciprocal relationship.Read More
DNA Genotek's Microbiome Collection and Stabilization Blog
DNA Genotek Inc. is pleased to announce that the Harvard T.H. Chan School of Public Health has selected DNA Genotek’s OMNIgene® family of microbiome collection devices to provide reliable self-collection of microbial samples for The Biobank for Microbiome Research in Massachusetts (BIOM-Mass). DNA Genotek will also provide customization, fulfillment and logistics services through its GenoFIND™ services offering.Read More
Crohn’s and Colitis Awareness week was developed to raise awareness and increase understanding of these common diseases. Crohn’s disease and Ulcerative Colitis, together referred to as Inflammatory Bowel Disease, are serious illnesses that affect more than 5 million people worldwide. We would like to shed some light on these diseases, the treatments, and the interactions between the microbiome and IBD.Read More
The human microbiome is one of the hottest topics of interest in the scientific community. The microbes in and on a healthy human adult are estimated to at least equal the number of human cells, which highlights the need for the scientific and medical community to better understand the broader impact on health and susceptibility to certain diseases/conditions and chronic illnesses. In particular, the gastrointestinal microbiome has captured the attention of researchers with stool specimens offering the most accessible means of assessing the gut microbial community. However, there are few publications that focus on methods for collecting stool samples for large, population-based studies.Read More
Evolution of sequencing technology
Since the human genome was sequenced and famously published in Nature and Science in 2001(1)(2), sequencing technology has experienced significant advancement. In 2005 several high- throughput approaches, collectively referred to as Next Generation Sequencing (NGS), quickly became preferable for larger projects compared to the more traditional Sanger sequencing, a capillary electrophoresis-based method used widely for close to 40 years. NGS technology produces many very short overlapping reads simultaneously, using massively parallel sequencing technology, such that each section of DNA (or RNA) is sequenced multiple times for exceptionally high coverage. The introduction of NGS played a huge role in revolutionizing the genomics field by lowering the cost of genome sequencing and by providing results 100 times faster than the Sanger approach. In 2010, the emergence of Third-Generation Sequencing (TGS) - enabled sequencing from a single molecule of DNA, thus eliminating the need for amplification and reducing PCR-derived bias. TGS produces substantially longer reads at 10K-15K base pairs compared to 100-600 base pairs for NGS, resulting in increased quality of genome assemblies through higher consensus accuracy and more uniform sequence coverage. For perspective on the evolution of sequencing, the 13-year-long, $2.7-billion international project (Human Genome Project) that sequenced the first human genome back in 2001, today would take little more than a day and would cost around $1,500 using NGS.Read More
At the recent Digestive Disease Week (DDW) meeting in Chicago, the microbiome took center stage with over 40 sessions featuring intestinal (gut) microbiota. Over the course of the meeting, I attended numerous presentations that described associations between the gut microbiome and such clinical outcomes as response to medication, efficacy of fecal microbiome transplants and success of diet-based interventions.Read More
Due to its implication in the pathogenesis of several digestive disorders, including inflammatory bowel disease, the intestinal microbiota was a hot topic this year at Digestive Disease Week (DDW). The microbiome was featured in over 40 sessions as the target of various therapeutic approaches, including fecal microbiota transplantation (FMT), probiotics, prebiotics, and antibiotics. Here, we would like to share with you a few of the microbiome-focused takeaways from DDW.Read More
One of the most critical components of studying the microbiome is ensuring you have a profile that is representative of the microbial community present in the donor. The reality of microbiome research, and any research for that matter, is that a variety of factors can impact the quality of your sample and its microbial community and thus, the quality of your data. Assume for example, that the microbial profile resembles Diagram “A” when in the in vivo state. The goal is to minimize any potential source of variability so that your sample accurately reflects that of the in vivo state (Diagram B) rather than an “ex vivo” artefact (Diagram C). Think of it like this: you could take a “snapshot” of the microbial community at the time of collection, preserve it through the analysis and generate an accurate microbiome profile.Read More
Much research in the microbiome field involves the collection of stool samples from adult populations and looking at the diversity and composition of their microbiome profiles. But what about stool samples from other populations like children or newborn babies? What for example, can be uncovered by looking at a newborn’s first stool, known as meconium, and is there anything we can learn from this? We had the opportunity to speak with Dr. Connie Mulligan, Professor and Associate Chair from the University of Florida about her very interesting research out of the Democratic Republic of the Congo. Dr. Mulligan is the principal investigator of this research project and has been to the Congo three different times to ensure the smooth running of the project which has been expanding ever since 2012.
Dr. Mulligan’s research team is looking at the effects of maternal stress on newborn health. As Dr. Mulligan explains, eastern Congo has gone through a 20 year Civil war, a war that was characterized by sexual violence and rape, thus creating an extreme stressor for women. They are looking to see if stress actually leaves an epigenetic signature on the genome. They would then take that signature and look at other populations like U.S. populations, who are stressed but in a different way and look to see if that epigenetic signature of stress is universal. The meconium sample, which is one sample that Mulligan’s team is collecting, reflects a very unique microbiome sample because the newborn is still in utero when the sample is produced. It’s very much influenced by the mother’s microbiome but also provides insight into the microbiome of the newborn. Since meconium is a tissue that is both maternal and fetal it might provide some information on how maternal stress is passed on to the newborn and passed on in a way that is remembered decades later.
Standardization of microbiome protocols is an increasing hot topic. It was recently discussed at a National Institute for Standards and Technology workshop and is required to make large scale microbiome research efforts like the White Houses’ National Microbiome Initiative possible. The only thing that is potentially discussed as often as standardization is the “inevitable” jump from using 16S rRNA sequencing to query microbiome profiles to a whole genome sequencing (WGS) based approach. In a recent publication in Nature’s Scientific Reports entitled “A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome”, Dr. Ericka Anderson along with colleagues and collaborators from HLI and JCVI tackle both of these topics as part of the HLI program to bring standardization to their microbiome sequencing process.Read More