Metagenomics: what it means and its applications

Metagenomics is composed of two terms: meta - transcendent (beyond or above the normal range) and genomics - the study of genes, their structure, function, and expression of a single organism. It simply means the analysis of the genome of multiple organisms at once.

Metagenomics refers to the study of collective genomes from a mixed community of microorganisms directly recovered from their natural environment. Numerous distinct microbes thrive throughout the biosphere under different conditions. Besides surroundings, each living entity harbors a colossal array of microbes both inside and outside. Microbial diversity is vast and exhibits distinctive roles ranging from synthesizing antibiotics to energy production and detoxifying ingested compounds to protecting pathogens. Most of them are not studied yet because of their nature and difficulty to culture by traditional methods.

In such cases, metagenomics helps us to study individual organisms and their role in the community at once by analyzing their DNA directly from an environmental sample without obtaining a pure culture. Moreover, it is a modern approach in observing microbial communities on a broader scale addressing the fundamental question of microbial diversity, evolution, and ecology.

 

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Gut microbiota and its importance

Gut microbiota is a melange of microorganisms inhabiting the gastrointestinal tract of humans and other animals, including insects. The gut microbiota and its host have a mutualistic relationship. Every individual has their own set of microorganisms and performs a wide range of functions, including food digestion, immune support, enzymatic reactions, energy production, and communication with the central nervous system.

American Gut Project is the world’s largest crowdfunded and crowdsourced scientific research project, which aimed to better understand the human microbiome - which types of bacteria live where, how many of each, and how they are influenced by diet, lifestyle, and disease. The American Gut Project was co-founded in November 2012 by Rob Knight, Ph.D., Jeff Leach, Ph.D., and Jack Gilbert, Ph.D. Anyone can participate in this project by signing up on the American gut website and registering themselves. Participants make a monetary contribution, submit personal microbiome samples, and receive information about their microbiome.  As of mid-2017, the project included microbial sequence data from 15,096 samples provided by 11,336 people, representing primarily the United States, United Kingdom, and Australia, along with 42 other countries or territories.

Relevant Publications:

1. Health and disease markers correlate with gut microbiome composition across thousands of people

2. American Gut: an Open Platform for Citizen Science Microbiome Research

gary and chris

 
Upcoming Sci-Omics sessions

In the month of January, Sci-Omics has organized two guest lectures by experts in the field of metagenomics. 

Session 1 - Dr. Gareth Trubl, Staff Scientist, Lawrence Livermore National Laboratory.

Dr. Trubl earned his B.S. in Environmental Science with an emphasis on microbiology at The University of Arizona and worked for the USDA for two years researching how to use fungi as a biocontrol on crops instead of pesticides. He then did an M.S. in Environmental Science and Health at the University of Nevada Reno and the Desert Research Institute where he researched active bacteria inhabiting the subzero temperature Lake Vida brine in Antarctica.

He finished his studies by earning a Ph.D. in microbiology at The Ohio State University where he characterized viruses in soils underlain with permafrost and their roles in ecosystem carbon processing. Gary did his postdoc at Lawrence Livermore National Laboratory (LLNL) in 2018, where he used stable isotope probing combined with metagenomics/ viromics to track microbial and viral activity and substrate utilization in various soils. Gary is currently a staff scientist at LLNL where he continues to use meta-omics combined with other techniques (e.g., isotope probing) to characterize viruses, microbes, and virus-microbe dynamics.

 

Google Scholar: https://scholar.google.com/citations?user=1vlixDwAAAAJ&hl=en&oi=ao

Title of his talk - "Unraveling the hidden potential of active microbial and viral communities"

Date - 7th of January 2022

Time - 2 PM CST || 8 PM GMT

 

Session 2 - Dr. Christopher M. Taylor, Associate Professor, Department of Microbiology, Immunology & Parasitology, Louisiana State University Health Sciences Center New Orleans

Dr. Taylor joined LSUHSC-NO in December 2012 as an Associate Professor in the Department of Microbiology, Immunology, and Parasitology. He is a founding member of the Microbial Genomics Resource Group and has built an informatics laboratory at the School of Medicine focused on microbial community sequencing, analysis, and visualization. He was appointed in July 2016 as the Director of the Bioinformatics, Biostatistics, and Computational Biology Core of the Louisiana Biomedical Research Network (LBRN) and was awarded Tenure from LSUHSC-NO in 2017.

Dr. Taylor co-organizes an annual conference on bioinformatics and computational biology for the LBRN and his research laboratory maintains several terabytes of sequence data and designs innovative software systems for visualization and analysis of high-throughput sequencing experiments. He also serves as the contact PI for a recently awarded NSF grant that was utilized to acquire and establish a high-performance computing cluster called Tigerfish for computational biology and bioinformatics research at LSUHSC-NO. Dr. Taylor's research interests currently focus on dynamic changes in the vaginal microbiota associated with various STIs including BV, Chlamydia, and HIV. 

PubMed: https://www.ncbi.nlm.nih.gov/sites/myncbi/christopher.taylor.1/bibliography/43101263/public/?sort=date&direction=descending

Title of his talk - "Metagenomics and microbial communities"

Date - 21st of January 2022

Time - 3 PM CST || 9 PM GMT

 


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Are you interested in learning more about metagenomics?

Get started with the OmicsLogic Metagenomics training program. An asynchronous mentor-guided project-based course designed by the experts at Pine Biotech. Also, get a unique hands-on learning experience with the help of the t-bio.info server.

Register today at https://learn.omicslogic.com/programs/metagenomics

 

This blog was written in association with Ms. Sabita Tamang