Learn to analyze microbial communities and find changes associated with Human Health using Metagenomics Next Generation Sequencing Data
The study of the microbiome in their natural environment and community composition using next generation sequencing (NGS) is known as metagenomics. The microorganisms form a stable environment called a “microbiome”, which functions together, developing complex symbiotic relationships with their hosts that result in both positive and negative impacts on human, animal and plant health. In humans, microbiota in the gut, skin, mouth or even brain can play an important role in a variety of diseases, so the role of the microbiome is important to consider in the context of disease progression and drug response.
Next generation sequencing is an essential technology for microbiome studies. Using NGS, we can study the sequences of microbial genes and analyze this data to understand the microbiota composition, species richness and function. These studies have led to an excitement about potential breakthroughs in medicine, biotechnology, and agriculture. Many researchers use ribosomal RNA to study variability of microorganisms in a given sample, which reduces costs and provides accurate information on the community level. Specific regions of this gene display variability at the taxonomic level, making them useful for taxonomic composition studies. However, these approximations are now being examined. In a recent study published in Nature, a group of researchers were looking at the “Influence of 16S rRNA target region on the outcome of microbiome studies in soil and saliva samples”. Studies like this helps in understanding the role of Next Generation Sequencing for the study of the microbiome.
Metagenomics has a wide range of applications right from understanding the correlation between diseases and human health to increasing crop yield by analyzing the microbiota in a soil sample. In our upcoming OmicsLogic Metagenomics Program, we will learn about the various NGS data analysis to compare microbial composition in different conditions, learn about the sequencing of viral samples, and discuss how microbes evade the immune response of the host as well as evade treatment. The one month program will cover the important topics in Metagenomics Data analysis focusing on the use of Public repositories like Silva, GreenGenes, NCBI.
Microbiome, Cancer susceptibility and Impact on Immunotherapy.
With the advent of next-generation sequencing, we have an unprecedented ability to study tumors and host genomes as well as those of the vast array of microorganisms that exist within living organisms. Evidence now suggests that these microbes may confer susceptibility to certain cancers and may also influence response to therapeutics. A prime example of this is seen with immunotherapy, for which gut microbes have been implicated in influencing therapeutic responses in preclinical models and patient cohorts. https://www.nature.com/articles/s41591-019-0377-7
Microbiome and Neurodegenerative diseases
Alzheimer’s disease (AD) is the most frequent cause of dementia characterized by a progressive decline in cognitive function associated with the formation of amyloid beta (Aβ) plaques and neurofibrillary tangles. Alterations in the gut microbiota composition induce increased permeability of the gut barrier and immune activation leading to systemic inflammation, which in turn may impair the blood-brain barrier and promote neuroinflammation, neural injury, and ultimately neurodegeneration https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6326209/. Recent studies showed that the populations of enterotype I and enterotype III bacteria were strongly associated with dementia, independent of the traditional dementia biomarkers. These types of discoveries are made possible by analyzing microbiome high throughput sequencing data.
Gut Health, Antibiotics and Clostridium difficile Infection (CDI)
Clostridium difficile is a Gram-positive toxin- and spore-producing anaerobe and one of the members in normal gut microbiota. Catalytic activity of C. difficile toxins damages cytoskeleton and colonic epithelial barrier integrity, thereby inducing aberrant inflammatory response and cell death. It is postulated that dominant gut microbiota species confer protection to the host by employing colonization resistance mechanisms against overgrowth of C. difficile in normal microbiome. Antibiotic administration perturbs the gut microbial communities and reduces their diversity, especially secondary bile acids-synthesizing dominant microbes such as C. scindens. As a result, there is a significant reduction in microbial bioconversion of primary bile acids into antimicrobial secondary bile acids, leading to reduced inhibition of C. difficile vegetative growth, allowing C difficile outgrowth and colonization of the empty niches, leading to higher susceptibility of the host toward CDI. https://www.frontiersin.org/articles/10.3389/fmicb.2018.01835/full
Microbiome and Preterm Birth
Recent studies have examined the role of the vaginal, gastrointestinal, and oral microbiome and possible associations with PTB. Several microorganisms in normal microbiomes display low virulence unless they reach the intrauterine environment. Intraamniotic infection with these and other organisms causes an inflammatory cascade of events during which prostaglandins, metalloproteases, and proinflammatory cytokines are released, resulting in uterine contractions and remodeling of the collagen in the cervix causing it to soften. It has been proposed that the increased stability of the vaginal microbiome during pregnancy may play a protective role in the prevention of ascending vaginal infection by means of the dominance of Lactobacilli. Disturbances in Lactobacilli in the vaginal microbiome often lead to dysbiosis and bacterial vaginosis (BV), a known risk factor for preterm delivery. https://www.fertstert.org/article/S0015-0282(15)01965-2/fulltext
Our OmicsLogic Programs are designed to not only give you an understanding of how the current state of research works but also get you started on your own research journey. In the Metagenomics Program, we will be taking the examples from the following projects to understand the role of microbiome in relation to human health and diseases some like the very common skin condition – Acne.
The program will start on August 31, 2020 and you will have 1 month of access to online courses, T-Bio Info server as well as the opportunity to work on a project of your own. The program research phase will end by October 02, 2020. Register and Join today to get additional (extended) access till the start of the program.
Learn more here – https://edu.tbioinfo.com/metagenomics
Program Cost – $150 USD
To complete your registration, please follow the following steps:
- Start by creating a free account on https://edu.t-bio.info/
- Proceed to checkout** here, the code is pre-applied – https://edu.t-bio.info/membership-checkout/?level=34
Once you complete your registration, you will be automatically added to the program organization page and will receive the further details on program access, payment receipt and necessary details.
Benefits for participants:
The following are some of the long term benefits of attending a program like the Metagenomics Program:
- An in-depth understanding of analysis methods for NGS Data Analysis approaches to the study of Microbiome.
- Hands-on experience in analyzing data from public domain repositories using the T-Bio Info Platform.
- Opportunity to work on your project and get it reviewed by experts in our community and also publish it in F1000 portals for peer review. You can see some project examples from our previous programs here – https://edu.t-bio.info/project-examples/
- A team offering you support every step of the way.
For any questions, please write to us – firstname.lastname@example.org