Saturday, January 28, 2017

A Model for Phage Communication and the Implications for the Human Microbiome

The research group prepared
two types of media to test phage
infection efficacy.
Well we took a bit of a break these past couple of weeks, but we are back for the new year! Welcome to the Prophage blog 2017! The year has actually been off to a good start, with a lot of interesting papers being published this January. This week I want to kick things off by covering a very cool 2017 study by Erez et al that described an new and interesting mechanism by which bacteriophages communicate using their bacterial hosts. This really is a well written and elegant study that I highly suggest you read. In this post, I want us to cover the highlights of the study, and then discuss what this will mean for future research endeavors.

The research group led by Erez et al began their work by testing the hypothesis that "bacteria secrete communication molecules to alert other bacteria of phage infection", but what they ended up finding was arguably much more interesting. They began their series of experiments by simply growing bacteria in liquid media with and without bacteriophages (see the figure to the right). They let the mixture sit long enough for the phages to infect their bacterial hosts for a couple of replication cycles (3 hours), and then removed all of the bacteria and phages from the liquid by filtration. At this point, if there was a signaling molecule released during the infection, it would still be in the media even though the phages and bacteria were removed. Additionally, if there was a signaling molecule released during the phage infection period, repeating an infection in that same media would result in altered growth patterns (for example, less bacteria killed when the molecule is present). As it turns out, this is exactly what they observed.

Sunday, December 11, 2016

How to Write a Manuscript Submission Cover Letter

The communication of our research findings is a foundational pillar to our careers as scientists. One of the most common ways we scientists share information is by publishing papers in peer-reviewed journals. This primary method of information dissemination allows us to share our research findings both to our colleagues as well as the public at large. When preparing a manuscript for submission to a journal for peer review and subsequent publication, a lot of work goes into preparing a variety of documents. One of the important documents is a cover letter to the editor. This letter represents a significant hurdle for new and young researchers because it is often unclear what a cover letter should actually look like, and what information should be included. In this week's post I want to go over what a good cover letter could look like and how you can write your own. I say this is what it could look like because there is certainly a lot of room for interpretation and personal style, and there are many correct ways to do it. Here I am just going to cover one potential way to tackle the problem.

Sunday, November 13, 2016

Summary of the 2016 International Human Microbiome Congress

Kicking off the IHMC meeting for 2016.
This week I had the privilege of attending the 2016 International Human Microbiome Congress which was hosted in Houston, Texas in the United States. The goal of this recurring meeting is to get the worldwide human microbiome community together to discuss recent progress, current challenges, and future directions. In this post I want to give a summary of the meeting for anyone who could not attend.

Sunday, October 23, 2016

Global Online Office Hours

Global online office hours will be held monthly
through Google Chat.
Interest in the microbiome has continued to skyrocket. It seems like there is a new microbiome commercialization strategy everyday, and more and more scientists are looking to incorporate the microbiome into their research programs. It is certainly an exciting time for the microbiome. Unfortunately the increased demand has been met with a somewhat insufficient supply of information and resources. Of course there are some excellent resources out there, but a lot of people don't have access to a "microbiome researcher" to answer their questions. Sometimes this means newcomers to the field make some crucial mistakes because they are forced to "go it alone". In an effort to generate even more unique resources for all of the microbiome folks out there, I decided to hold Global Online Office Hours.

Sunday, October 2, 2016

A New Look At Irritable Bowel Disease and Viruses: The Core Human "Phageome"

An illustration of the core protein clusters (PCs; groups
of similar genes) found in the photic and aphotic zones
of the ocean. This new study applies a similar approach
using phage genomes instead of genes. Source
Ongoing research has continued to implicate the microbiome in a variety of human diseases. We often hear about this in the context of bacterial communities. Certain bacterial communities appear to be associated with health, and disrupting these communities seems to be associated with disease. To better understand these bacterial communities, we sometimes group the shared members together as the "core bacterial community" that is associated with health or disease. In some ways these core bacteria are considered important to the system because they are found in every instance of health or disease. But what about the core phages (bacterial viruses) of these communities? A few weeks ago Manrique et al published a study that began addressing this question.

Sunday, September 18, 2016

How to Detect Circular Virus Genomes from Metagenomes


Many virus genomes are circular, like the olympic rings.
When analyzing virus metagenomic data, we often find it helpful to identify contigs that represent complete circular genomes [1,2]. In addition to offering biological information, this is used as a quality control technique to evaluate whether the sequencing efforts were robust enough to allow for complete genome assembly. This approach has the advantage of reference independence because it does not require aligning reads to a reference genome to evaluate sequence completion.

Saturday, August 27, 2016

Improving Human Virome Studies: Updates to Virus Classification

The proposed phage proteomic tree by Rohwer and Edwards.
Taxonomy is an important aspect of microbiome research. Whether we are studying communities of bacteria, viruses, or other microbes, there are benefits to labeling microbes. Taxonomic names immediately give us information about their relationships to each other, such as similar bacteria being grouped into the same genus. Taxonomic identities also provide some information about an organism's functionality and/or clinical pathology. For example, by mentioning that a bacteria is a member of the genus Staphylococcus, you might think that it is a round, gram-positive bacterium that might inhabit the skin and is otherwise related to other members of that genus (including genomic relationships). In the end, the practice does what it aims to do, which is classify organisms in an informative way.