Catching phages in the act

April 30, 2015
Phages are everywhere but almost none of them can be easily studied. We can scoop up their DNA (and sometimes RNA), sequence it, and try to put the pieces of their biology together. But often we cannot figure out which bacteria they would infect unless we bring them into the lab, coddle their host into culture, and then experimentally mix the two. Now it is becoming feasible to isolate single bacterial cells to see which phage is lurking within, according to a new publication by Labonte et al

Start by using a cell sorting machine to isolate single bacterial cells from an environmental sample of interest (in this case, surface ocean waters). Along with each cell comes any phage bound to it surface, or already inside the cell. Those phages already inside may be lysogenic, i.e., have inserted their genome into the host chromosome, or they may be lytic and producing thousands of progeny virions. 

Next, sequence all of the DNA from each cell isolated. Here we can tell whether there is phage DNA present, and its copy number relative to the host DNA tells us whether that phage is lytic (higher DNA copy number than host) or lysogenic or bound to the cell surface (same DNA copy number as host). 

Sounds pretty simple, right? Not really of course. These researchers have taken great pains to be remarkably thorough, for example, by testing whether a phage could be sorted with a cell by 'hiding' in the cell's shadow, rather than actually having bound to or infected that cell. They also had to perform a number of experiments and analyses to determine how abundant phage DNA is compared to host bacterial DNA. This is not an easy task with the best-studied organism, and it becomes even more challenging when dealing with newly discovered phages, as the databases used for comparison would have little or nothing related. 

What was learned? 33% of cells were associated with a phage. So, 1/3 cells isolated from nature were actively infected (or being infected by) a phage. 15/20 of the phages were isolated in bacteria for which no other phages have been identified. Only 1 of the 20 phages appeared to be temperate, whereas 4 were likely in late lytic phase. The life cycle stages for 14 phages were unclear. And the last phage? Its genome sequence suggested it was similar to a virus that infects a microbial eukaryote, suggesting that the association between this virus and its "host" may have been simply a matter of non-specific binding to the cell surface. That must happen all the time in the marine milieu. 

Where will this take us? Perhaps within a few years we can regularly isolate millions of bacterial cells and see who is attached to or infecting them. Statistical associations can tell us about how loyal phages are to particular hosts, and whether they change their attitude depending on the host (e.g., more likely to lysogenize host A and lyse host B). Just a scratch on the phage-host surface, but a badly needed scratch. 
 

Life in Our Phage World published!

January 18, 2015
Have you ever wondered about the tiny viruses that are everywhere, on everything, in every organism? What do they look like? Where do they live? Who are they related to? What information is in their genomes? What do they do all day long? 

These questions are answered in Life in Our Phage World, a book I recently co-authored with Forest Rohwer, Merry Youle, Nao Hisakawa, and a brilliant group of phage researchers. Full of short action stories, and beautifully illustrated by Leah Pantea and Ben ...
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Intriguing impurities

May 23, 2013

Many microbiologists begin their workday by opening up the incubator shaker and taking out a culture flask; they then swirl it around to examine the progression of cell growth. They can examine the turbidity of the broth to tell if cells are reproducing as planned. Opening up the lid and sniffing the culture will tell seasoned microbiologists if they’re growing what they think they’re growing, because many bacterial species produce signature aromas. But w...


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Picoplankton post

March 29, 2013
My first contribution to the Small Things Considered blog: 
 

A Day in the Life: Eavesdropping on Marine Picoplankton


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Mite-y resistance

January 16, 2013
When faced with a challenge, animals have the ability to physically move away. Plants are not so lucky. Their interactions with the soil prevent them from up-rooting and finding a better place. But this does not mean that plants don't fight back. Indeed, plants produce an astonishing diversity of chemicals to ward off invaders, such as the ubiquitous arthropod pests. Many of these naturally produced chemicals are analogous to manufactured pesticides, in that they provide a strong selective pr...
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RNA for the bees

December 31, 2012
Becoming a beekeeper can be overwhelming at times. One of the most difficult things for me is figuring out how and when to treat the hives to prevent pathogens and parasites from becoming too numerous. We have attended an Integrated Pest Management course but only walked away with a list of offenders and their chemical treatments, which we had already learned through online research. Why not just treat for all, as often as possible? I'd rather not dump these chemicals (several of which are an...
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Reveling in Ronin

December 21, 2012
The Ronin Institute is a group of scholars that are trying something different.  Recognizing that one need not work at a university to contribute to knowledge, scholars of the Ronin Institute will be conducting research independently, as they find time in between life's activities (e.g., kids, hobbies, other jobs).  This is a timely endeavor as many more PhDs are being obtained than faculty positions are available.  And for many of us, university jobs are becoming less attractive as hours inc...
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Probiotic puzzle

December 4, 2012
Probiotics are live bacteria, formulas of single or multiple species, provided to help establish a healthy gastrointestinal tract.  Probiotics are a hot topic these days, and a potent marketing tool. Despite their popularity, we often don't know if they really work to relieve intestinal problems.  And for those probiotics that do work, we almost never know their mechanism(s) of action.   

Olier and colleagues have taken us a step closer to understanding the mechanism of probiotic action.  They...

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Bacterial relocation II

November 26, 2012
Continuing on the subject of bacteriotherapy, there was a fascinating paper out last month in PLoS Pathogens by Lawley et al. As I said in the last post, C. difficile infection of the gut is bad news, and one of the best cures is fecal transplantation.  Lawley et al. describe experiments in a mouse model that closely approximates the situation in humans.  They showed that the epidemic strain of C. difficile 027/BI is much more of a terror than other strains, as the bug was highly contagious a...
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Bacterial relocation

November 4, 2012
Warning: Here comes the icky diarrhea blog.  Because I primarily write about microbiota, this was only a matter of time as the literature is replete with gut microbiota studies.  This abundance is due to lots of money being poured into figuring out the role of the gut microbiota; they are likely to influence a plethora of diseases through their role in immune system development, and fecal samples are easy to obtain!

Fecal samples are also relatively easy to transplant.  This may sound gross be...
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