Antibiotic Resistance Trifecta: Interactions of Antibiotics, Microbes, and the Gut Microbiome

There are many concerns about how the gut microbiota is impacted by antibiotics.  Since the widespread use, and sometimes over use of antibiotics began around 80 years ago, bacterial antibiotics has increase worldwide.  This makes bacterial infections harder to treat and increases the risk of severe side effects.  If was only this year in January that a woman died from a bacterial infection contracted after surgery that was resistant to 23 different antibiotics.

It’s clear that bacterial antibiotic resistance has risen alarmingly.  What is less clear is how those antibiotics effect the gut microflora.  Studies recently performed have shown that a dysbiosis, an “unbalanced” or abnormal state of the microbiome, in the gut can cause unchecked microbial growth of low abundance organisms known as opportunistic pathogens.  These opportunists are usually kept in check by other dominant microbes but when those microbes decrease in number, the opportunists can grow unchecked and cause devastating health issues.

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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


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

IAFP Reflection: Metagenomics and Microbiomes

Feedback buzzes through the cramped room lined with fabric walls.  The sounds of not-quite quiet shuffling are interspersed with scratch of clearing throats, the rustle of turning program pages, and the hum of lowered chattering voices.  Despite the subdued noise- the room is anything but dead.  Excitement crackles along the edges of every whisper and movement because the microbiome and metagenomics session is about to start.  Welcome to IAFP 2016.

For those who can come, the IAFP annual meeting is a wildly exciting dive into the new, innovative, and well-loved world of food safety.  The relatively small conference allows one-on-one interaction with dedicated companies, passionate researchers, and students from all over.  The sessions are intensive, the reunions joyful, and the mixers lively.  IAFP is conference like no other.

Microbiomes have been around for a while now but it’s only recently that they have been applied to a wide array of areas, including food.  MARS and IBM are launching a food microbiome project that aims to characterize the microbiomes of different food products.  The FDA implemented GenomeTrakr, which uses whole genome shotgun sequencing (WGS) to aid in outbreak investigations (think whole genome PulseNet).  And companies are starting to use microbiomes and metagenomics internally. Considering all of this, it’s no wonder that IAFP placed a marked emphasis on microbiomes, metagenomics, and their role in food safety.  For a self-proclaimed metagenomics and microbiome enthusiast (I have occasionally signed off on emails with “Metagenomic Meg”), this created the session list of my dreams.


Notably, a session on how to apply microbiome data and studies to food safety was a highlight for me.  The panel on stage answered questions on how this newly accessible technology can be applied to food companies and outbreak investigations.  Now that there are so many resources for microbiome studies of the 16S, functional, and WGS varieties, performing these types of studies and analyzing the data obtained is easier than ever.  Many of analysis tools are open access and can generate graphs and figures easily.  These characteristics make applying this technology possible at both large and small scale operations.  There were lots of questions about how to standardize the process of sampling, experimentation, and analysis so results can be compared more easily.  Another issue that came up was how to interpret the data.  This type of sequencing can be exquisitely sensitive.  However, that leads to detection of microbes at lower levels.  For an academic, this is thrilling.  For a company, slightly ambiguous.  What happens if they get a Salmonella hit?  Do they have to shut down everything or is there a level where it is of no concern?  How can they make these calls when the science isn’t there to back it up?  Is a good idea to implement this? I had never looked at microbiomes in this way but I could see why it was a concern.

Another panel that stood out and highlighted the emerging role of microbiomes in the food world was the Delmarva panel.  The Delmarva peninsula is located off of Maryland and contains Delaware and Virginia.  A high intensity agriculture and tourism area, the Delmarva fences in the Chesapeake Bay and is a vacation spot for many (including this former Marylander) in the midatlantic area.  Historically, tomatoes grown in the Delmarva area have been associated with Salmonella Bareilly outbreaks with a much greater frequency than those grown on the west coast.  The presenters laid out a case study of the work that has gone into determining the reservoir of S. Bareilly in the Delmarva, how it acts in tomatoes, why it is seen so frequently in the Delmarva, and what can be done to mitigate outbreaks.  A fascinating story unfolded that found S. Bareilly in several sources (notable stream sediment and water) and determined that it acts like a plant pathogen in tomatoes.  Virulence behaviors occurred upon internalization to S. Bareilly such as pulling in the flagella to better hide from the plant by not presenting as many antigens.  One of the most fascinating studies performed was the metagenomic analysis of the soil from Delmarva farms and California farms.  The soil houses extremely different microbial ecosystems.  Soils on the west coast contained more competitors for Salmonella spp. while the Delmarva soil contained much less.  But the experiment did not end there.  The FDA took it a step further and is now performing studies with strains of bacteria similar to those found in the west coast soil that could be inoculated into Delmarva soil and act as competitive inhibitors for S. Bareilly.  This story amazes me.  Microbiome studies and metagenomics were being used to solve a historical and far-reaching food safety problem.


But how could they do all of this?  It turns out they had industry partners who were also concerned about the consistent outbreaks and wanted to help stop them.  Even now, extension and outreach in the Delmarva area continues to help farmers produce safe tomatoes.  That’s the real point of IAFP- to create meaningful connections to help solve food safety problems.  By working together and implementing innovative technology and creative thinkers we are able to solve food safety problems of enormous magnitude.  IAFP houses one of the best areas to make these connections and solve these problems.  Which is why people go back every year and why I will go back.

Microbiomes and Campylobacter : How They Fit Together and Why They’re Important

While not many people have heard of Campylobacter, as described in our last post, almost everyone has heard of microbiomes.  The term has become familiar to both scientists and the general public through the Human Microbiome Project and Earth Microbiome Project.  The idea of having a healthy population of “good bacteria” in one’s stomach or home to provide protection from pathogenic or spoilage bacteria has become accepted and is even embraced in today’s world.  To see this attitude in action all one has to do is look the products popping up in stores, like a bacterial scrub in lieu of soap or probiotics.  Combine all of that with the soaring number of publication dealing with microbiomes and this topic is definitely here to stay.

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Figure 1: Phase Contrast Image of the cecal content of a conventionally raised 5 week-old turkey. Campylobacter is circled in red.

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