Detailed duel between phage(s) and host

May 15, 2015
It's not every day we get to see an arms race in action. Every gory detail is laid out by Paez-Espino et al in the March/April issue of mBio*. The authors use deep DNA sequencing to track CRISPR acquisition in the bacterium Streptococcus thermophilus when challenged with Streptococcus phage 2972 (a phage featured in Life in Our Phage World). 

As S. thermophilus evolved in the presence of 2972, its CRISPR loci acquired new spacers employed to recognize future invasions of 2972 phage DNA, thereby foiling future attacks by that phage. At least 160,000 spacer acquisitions were observed in the three experiments that each lasted 250 days. The bacteria didn't waste any time, but they did make mistakes. On average 0.02% of spacer acquisitions did not match phage DNA, they matched host DNA. A costly mistake, as that hapless host would recognize its own DNA as foreign and chop it up. Instant death. 

The phage had its own strategy for escaping the host's recognition of its DNA: mutation. The phage's mutation rate was on the order of ~10^-6 per nucleotide per host generation, roughly 1000-fold higher than the mutation rate in the host. These mutations were clustered in the genomic regions that matched spacers acquired in the host, enabling the phage to briefly get one step ahead of the host. But once again, the host would counter with another spacer acquisition, and boom, no more invading phage. 

At this point it looked like the host might win. In one experiment the phage was undetectable by day 35. In the other two experiments, the phage survived longer, over 200 days. Extended survival may have been possible with a little help from a phage friend, Streptococcus phage 2766. Although this phage was not intentionally included in the experiment, it "migrated" into the cultures and offered genomic fragments to 2972, saving its life and promoting escape from the host's CRISPR recognition system. 

Phages, too, get by with a little help from their phriends. 

*disclaimer: I take full responsibility for any conclusions in this post that are over the top.
 

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...
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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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