Resources on Antibiotic Resistance and the Microbiome

Below are 2 excellent resource (curtsey of QIAGEN) that give a great background on antibiotic resistance in hospital infections and using metagenomic techniques to study the microbiome.  We do not claim ownership of the slides or any product, techniques, or studies used and are not attempting to promote them.  They all belong to QIAGEN and associated researchers.  We simply recognize the value of the introductory information and wish to share the slides for educational purposes.

The slide decks can be found online below:

Know Your Lingo 2.0: Landmark Microbiome and Metagenomic Projects

We’ve already gone over some of the basic terminology involved with microbiome studies (here) but some other key phrases frequently come up when discussing microbiome studies.  These phrases usually reference several landmark studies that deal with the microbiome.  Here we will review some of the most important landmark studies that will likely be discussed or encountered in microbiome research.

Human Microbiome Project– The full name of this project is “The NIH Human Microbiome Project” but in casual conversation the “NIH” portion is sometimes left off.  This was one of the first major efforts to study the human microbiome that utilized Next Generation high-throughput sequencing and involved many prominent microbiome researchers, such as Rob Knight.  The health implications of such a project are astounding and provide us with a much more comprehensive understanding of the microbes that live inside us.  If you happen to be in the Raleigh, NC area the Museum of Natural Sciences has a phenomenal and engaging exhibit that highlights research done for the NIH Human Microbiome Project.  It’s called “The Secret World Inside You”, go see it!

Sargasso Sea– The Sargasso Sea is a region of the North Atlantic Ocean and contains the island of Bermuda.  But why would this body of water be referenced by microbial ecologists?  Well, it was actually part of Global Ocean Sampling Survey (GOS) conducted by J. Craig Venter, think sequencing the human genome, and his colleagues.  They initially suspected low microbial diversity but after performing shotgun sequencing, they discovered a vast array of microbes present.  Perhaps the most surprising result was the huge amount of viral DNA present in the Sargasso Sea when compared to the other areas sampled.  The GOS radically shifted how we think of oceanic diversity.

Earth Microbiome Project– This ambitious project was started by Rob Knight and Jack Gilbert as a way to map the microbiomes of different environments all over the world.  Being able to transpose that information onto a global map would be insanely cool and relevant with global warming and environmental policy changing around the world all the time.  Mapping the microbiomes around the world is a huge undertaking and as a result requires massive global collaborations and that’s not even the hardest part.  With a plethora or researchers comes a plethora of techniques, which can be advantageous but can also result in incomparable results.  In order to combat this, the Earth Microbiome Project requires that a standard set of protocols be followed in order to submit your information to them.  Everyone uses the same kits, primers, and file types to ensure that the samples are processed in the same way.  Standardization of protocols and global collaboration make this project groundbreaking.

Wildlife of Our Homes– How do you get people involved and interested in science?  One way is to put them right in the thick of the experiment.  The Wildlife of our Homes does just that with its citizen science approach, which means the public and not just scientists are involved.  Headed up by Robb Dunn (NCSU- Go Wolfpack!), the project had people take swabs from designated areas around their homes and send them research labs for processing.  After providing relevant information about the number of family members, where they had pets, location, and other details, the results for different homes could be seen for different states, rooms, and much more.  By not only engaging the public but using the home as a model, Robb Dunn shows the public that microbes are everywhere and science is amazing.

American Gut– No you did not read that wrong.  The American Gut project is another citizen science project aimed to characterize, you guessed it, the American gut.  And army of researchers, including Rob Knight, Jeff Leach, Jack Gilbert, and Robb Dunn, collaborate on the support the project.  The American Gut project celebrates the diversity of Americans.  People from different ethnicities, locations, and backgrounds are encouraged to submit samples for analysis.  In a time when America can seem extremely divided, especially over science, implementing a project that celebrates our differences and emphasizes our commonalities is rare and greatly appreciated.  A British and Asia version of the project have also been slated.

Consortium For Sequencing The Food Supply Chain – This was created by IBM and MARS in 2015 to sequence to microbiome of the food supply chain.  They will be sequencing the core or “normal” microbiome of foods, processing plants, and even home counters.  The project looks at the bacterial, viral, and fungal DNA, which will provide a full picture of the microbial ecology of that food or surface.  Since this is a fairly new program there is still a lot of questions about how the project will work but with big names like BIO-RAD attaching themselves to it, it’s definitely one to watch.

If you want to learn more about any of these projects click on the project name and it will navigate you to their website.  Happy hunting and stay curious!

Know Your Lingo: How to Read Microbiome and Metagenomic Articles

With the advent of metagenomic studies, scientists need to understand the terminology used in them.  Much like metagenomics itself, the vocabulary used contains words from multiple disciplines such as ecology, bioinformatics, and microbiology. However, these terms may have slightly different meaning and nuances when used in metagenomics studies.  To help clear up the usage of some of these terms and provide a little back ground on them, I have complied a guide that breaks down the meaning and associated nuances for some of the most frequently used terms in metagenomics studies.

Microbiome- All the microbial (bacterial, fungal, viral, eukaryote, or a combination of any of these) DNA in an environment, community, or ecosystem.  This data is usually obtained by use of high throughput sequencing.  This term functions as a microbial census of “who is there?”  Results can be obtained through 16S, 18S, and ITS markers (which will be defined more fully later.)  Because microbiomes are composed of DNA found through sequencing, just because an organisms’ DNA is part of the microbiome doesn’t mean that organism is alive within the community.

Microbiota- All the microbes (bacterial, fungal, viral, eukaryote, or a combination of any of these) in an environment, community, or ecosystem.  This is subtly different from the microbiome because it describes all of the organisms present, not just the DNA found.  These microbes are the ones alive and functioning in a particular environment, community, or ecosystem and can also encompass all microbes, bacteria, fungi, virus, or some eukaryotes.

Metagenomics- The genetic analysis of microorganisms in conjunction with relevant data.  These studies extract total DNA from a sample and collect information about that sample that can be useful in analysis.  These studies often revolve around “who is there” and/or “what are they doing”.  By characterizing a microbial community and learning how that microbial community functions, or shifts can provide insight into microbial based intervention and a greater understanding of microbial ecology.

WGS- This is an acronym that stands for “Whole Genome Shotgun Sequencing”, sometime this is just referred to as “Shotgun”.  WGS is method of determining the entire sequence of a genome (for example a bacterial genome) by the use of sequencing fragments of the genome and piecing them back together.  The genome is broken into small segments which are then sequenced and put back together with a reference genome or de novo (done without a reference) by utilizing to overlapping portions of the segment.  The FDA is employing this kind of methodology in GenomeTrackr to aid in outbreak tracking and identification.

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CALS Stewards of the Future: Collaboration and Microbiomes

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Microbiomes are the future.  Versions of this statement have been uttered time and again by some of the most influential minds in science.  The CALS Stewards of the future seminar at NCSU echoed this call in late October with an entire day focused on studying the microbiome, the implications these studies have on the future of science, and how collaboration is needed to succeed.  The talks ranged from basic to applied studies and emphasized how this technology could be applied to agricultural fields. Continue reading