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Metagenomics: Illuminating the Microbial World

First, there was the genome. Then there was the proteome, and the microbiome. Today, one of the most promising emerging “omics” fields is metagenomics—the study of the genes that exist in whole microbial communities found in samples such as soil, water, and stool. It’s a tool that has the potential to unlock novel solutions in fields ranging from environmental cleanup to combating antibiotic resistance. For example, one recent study in China used metagenomic analysis of urban sewage to identify 381 different genes for antibiotic resistance that are extensively shared across the country—suggesting that monitoring sewage systems for antibiotic-resistance genes could boost antibiotic stewardship…

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 Why Metagenomics?

Microbes run the world. It’s that simple. Although we can’t usually see them, microbes are essential for every part of human life—indeed all life on Earth. Every process in the biosphere is touched by the seemingly endless capacity of microbes to transform the world around them. The chemical cycles that convert the key elements of life—carbon, nitrogen, oxygen, and sulfur—into biologically accessible forms are largely directed by and dependent on microbes.

Articles of Interest

The Disease Detective

Joe DeRisi invented a way to find pathogens that scientists didn’t even know to look for. Can it help prevent the next pandemic? The practice that DeRisi helped pioneer to skirt this problem is known as metagenomic sequencing. Unlike ordinary genomic sequencing, which tries to spell out the purified DNA of a single, known organism, metagenomic sequencing can be applied to a messy sample of just about anything — blood, mud, seawater, snot — which will often contain dozens or hundreds of different organisms, all unknown, and each with its own DNA.

Big Data and Bacteria: Mapping the New York Subway’s DNA

Across the country, researchers are combining microbiology, genomics and population genetics on a massive scale to identify the micro-organisms in the buildings and confined spaces of entire cities.

COVID-19 and what else? Researchers use metagenomics to find out

“It’s a whole-genome test. It lets you sequence every single piece of DNA and RNA in the sample. That generates a ton of information, and you should be able to find every pathogen in that,” said Dr. Sam Minot, a Fred Hutch computational biologist who is contributing to the project his expertise in wrangling massive amounts of data.

Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses

Metagenomics is a powerful approach for the detection of unknown and novel pathogens. Workflows based on Illumina short-read sequencing are becoming established in diagnostic laboratories. However, high sequencing depth requirements, long turnaround times, and limited sensitivity hinder broader adoption

Genome-resolved metagenomics: a game changer for microbiome medicine

Recent substantial evidence implicating commensal bacteria in human diseases has given rise to a new domain in biomedical research: microbiome medicine. This emerging field aims to understand and leverage the human microbiota and derivative molecules for disease prevention and treatment.

Inside the Hidden Kingdom of Viruses in Your Gut

Human innards are teeming with viruses that infect bacteria. Here’s what scientists are learning about them.

Metagenomics and artificial intelligence in the context of human health

This review provides insight into the human microbiota and its exploration and expansion through MG studies. The review elucidates the significance of MGs in studying the changing microbiota during disease conditions besides highlighting the role of AI in computational analysis of MG data.

Metagenomics and Human Health: More Than Just a Gut Feeling?

Today, metagenomics is a powerful approach that can capture entire microbial communities: it uses molecular biology to retrieve genomes directly from natural samples, bypassing the need for pure cultures. The collective genomes of all the microorganisms in a particular environment is called the microbiome.

Metagenomics and Personalized Medicine

The tools to detect and quantify the entire non-host metagenome at a reasonable cost will undoubtedly develop rapidly as metagenomic sequencing technologies and computational approaches to phylogeny and microbe detection are developed and applied. Similarly, sequencing the entire host genome is becoming more cost efficient and practical. This wealth of data will set the stage for metagenetics, but meaningful and robust analyses of the complex interactions within the metagenome will require new computational tools and new conceptualizations of gene-gene and gene-microbe interactions.

Metagenomics: Facts and Artifacts, and Computational Challenges

Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. By enabling an analysis of populations including many (so-far) unculturable and often unknown microbes, metagenomics is revolutionizing the field of microbiology, and has excited researchers in many disciplines that could benefit from the study of environmental microbes, including those in ecology, environmental sciences, and biomedicine.

Microbiomes and Metagenomics

Center for Conservation Genomics scientists use two broad strategies to find and understand the biology of microorganisms: culture-dependent and culture-independent methods. The culture-dependent method is when bacteria or microorganism is grown in a petri dish to study its biology. However, many microorganisms cannot be grown in a petri dish, so CCG scientists use culture-independent methods to find them.

Piecing Together the Next Pandemic

“Metagenomics can show what we don’t know we don’t know,” Dr. Manning said, paraphrasing a popular quote from former U.S. Secretary of Defense Donald H. Rumsfeld.

Rapid DNA analysis helps diagnose mystery diseases

This test is called “metagenomic” because DNA from all potential pathogens – bacteria, viruses, fungi and parasites – as well as the patient are simultaneously sequenced. We diagnose likely causes of infection by searching for tell-tale traces of DNA from the causative pathogen.

The modern, molecular hunt for the world’s biodiversity

The starting point for metagenomic research can be anything, including feces, in the case of the human microbiome, or a sample of ocean sediment, in case of Lokiarcheota. Ultimately these genetic profiles are known to us only as an electronic string of 1’s and 0’s in computer memory and described to us by mathematical algorithms. Such molecular and computer technologies are also how modern detectives “use DNA” to catch murderers.

The role of metagenomics in understanding the human microbiome in health and disease

In the future, this kind of approach (i.e., metagenomics) would identify biomarkers of well-being that correspond to a general and more balanced microbiota. In addition, metagenomics can also provide us with a better understanding of the relationship between us and our microbiome and the role of this interaction with health.