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Essays, thoughts, notes, and ideas about current bacteria and bacteriophage related research.

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  • April 8, 2017
  • 09:53 AM

Publication Alert: High Nucleotide Resolution Study of the Skin Virome

by Geoffrey Hannigan in Prophage

A few weeks ago some colleagues and myself published a new manuscript looking at the diversity of the human skin virome. In our previous previous work, we evaluated the diversity of viruses on the skin. Other groups have looked at virus diversity at other body sites including the gut, lungs...... Read more »

  • January 28, 2017
  • 07:52 PM

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

by Geoffrey Hannigan in Prophage

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...... Read more »

Erez, Z., Steinberger-Levy, I., Shamir, M., Doron, S., Stokar-Avihail, A., Peleg, Y., Melamed, S., Leavitt, A., Savidor, A., Albeck, S.... (2017) Communication between viruses guides lysis–lysogeny decisions. Nature, 541(7638), 488-493. DOI: 10.1038/nature21049  

  • October 2, 2016
  • 06:39 PM

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

by Geoffrey Hannigan in Prophage

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...... Read more »

Manrique P, Bolduc B, Walk ST, van der Oost J, de Vos WM, & Young MJ. (2016) Healthy human gut phageome. Proceedings of the National Academy of Sciences of the United States of America, 113(37), 10400-5. PMID: 27573828  

  • September 18, 2016
  • 03:59 PM

How to Detect Circular Virus Genomes from Metagenomes

by Geoffrey Hannigan in Prophage

When analyzing virus metagenomic data, we often find it helpful to identify...... Read more »

Minot, S., Sinha, R., Chen, J., Li, H., Keilbaugh, S., Wu, G., Lewis, J., & Bushman, F. (2011) The human gut virome: Inter-individual variation and dynamic response to diet. Genome Research, 21(10), 1616-1625. DOI: 10.1101/gr.122705.111  

Manrique, P., Bolduc, B., Walk, S., van der Oost, J., de Vos, W., & Young, M. (2016) Healthy human gut phageome. Proceedings of the National Academy of Sciences, 113(37), 10400-10405. DOI: 10.1073/pnas.1601060113  

  • August 27, 2016
  • 07:44 PM

Improving Human Virome Studies: Updates to Virus Classification

by Geoffrey Hannigan in Prophage

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...... Read more »

Krupovic, M., Dutilh, B., Adriaenssens, E., Wittmann, J., Vogensen, F., Sullivan, M., Rumnieks, J., Prangishvili, D., Lavigne, R., Kropinski, A.... (2016) Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee. Archives of Virology, 161(4), 1095-1099. DOI: 10.1007/s00705-015-2728-0  

Thompson, C., Amaral, G., Campeão, M., Edwards, R., Polz, M., Dutilh, B., Ussery, D., Sawabe, T., Swings, J., & Thompson, F. (2014) Microbial taxonomy in the post-genomic era: Rebuilding from scratch?. Archives of Microbiology, 197(3), 359-370. DOI: 10.1007/s00203-014-1071-2  

  • May 22, 2016
  • 08:17 PM

Piggybacking Instead of Killing: New Insights Into Virus Community Dynamics

by Geoffrey Hannigan in Prophage

The human microbiome is an important component of human health and disease. It is an ecosystem of microbes that exists in and on humans, and can affect disease states through disturbances in composition, diversity, metabolism, etc. Understanding the human microbiome will not only allow us to better understand human health, but it will also allow us to treat medical conditions in new and effective ways (e.g. Fecal Microbiota Transplants).... Read more »

Knowles B, Silveira CB, Bailey BA, Barott K, Cantu VA, Cobián-Güemes AG, Coutinho FH, Dinsdale EA, Felts B, Furby KA.... (2016) Lytic to temperate switching of viral communities. Nature, 531(7595), 466-70. PMID: 26982729  

  • April 3, 2016
  • 09:20 PM

The Illumina Error Profile for Metagenomic Sequencing

by Geoffrey Hannigan in Prophage

Microbiology, and especially microbial ecology, has become increasingly dependent on advanced DNA and RNA sequencing technologies. This is most evident with the increasing popularity of the human microbiome and its various impacts on human health...... Read more »

  • March 6, 2016
  • 09:46 PM

Helping Both Humans and Dogs: A Recent Study of Canine Atopic Dermatitis

by Geoffrey Hannigan in Prophage

Atopic dermatitis (AD), which is also referred to as Eczema, is a very common dermatological disease, especially in children. It is estimated that AD affects 10% of children. The disease presents as dry, scaly, itchy skin. Atopic dermatitis can be especially problematic when the victim (often a child)...... Read more »

  • February 14, 2016
  • 04:00 PM

Methods Matter: Getting Started with the Skin Microbiome

by Geoffrey Hannigan in Prophage

The field of microbiome research has been hugely popular in the past few years. It has forced us to rethink our approaches to various medical practices, and has captured the imaginations of both amateur and professional scientists...... Read more »

Meisel JS, Hannigan GD, Tyldsley AS, SanMiguel AJ, Hodkinson BP, Zheng Q, & Grice EA. (2016) Skin microbiome surveys are strongly influenced by experimental design. The Journal of investigative dermatology. PMID: 26829039  

  • January 24, 2016
  • 08:46 PM

Recent Study Reveals Role for Bacterial Viruses in Microbiome Evolution

by Geoffrey Hannigan in Prophage

Microbial communities are fierce battlegrounds between bacteria and other microbes competing for limited resources. One method some bacteria use to kill their competitors is the production of bacteriocins...... Read more »

Nedialkova LP, Sidstedt M, Koeppel MB, Spriewald S, Ring D, Gerlach RG, Bossi L, & Stecher B. (2015) Temperate phages promote colicin-dependent fitness of Salmonella enterica serovar Typhimurium. Environmental microbiology. PMID: 26439675  

  • January 17, 2016
  • 10:11 PM

A Primer on Linear Regression and its Associated Misconceptions

by Geoffrey Hannigan in Prophage

I wanted to start the year off with post about math. I know, I know, math is an intimidating way to start the year, but don't run off yet! I swear that this will be painless and we will even learn something new! We are going to keep things simple and focus on an elegant paper that presents some misconceptions about a complicated topic. This topic is multiple linear regression...... Read more »

  • December 27, 2015
  • 11:19 PM

Understanding How Silent Phages Can Prevent Detection of Potentially Deadly Food Contaminants

by Geoffrey Hannigan in Prophage

Contamination of food with bacteria is a huge issue that can sometimes cause life-threatening illness. The bacterial culprits can include E. coli, as well as Listeria monocytogenes. L. monocytogenes is a potent bacteria that can very effectively infect its human host. ..... Read more »

  • December 6, 2015
  • 10:12 PM

Recent Study Sheds New Light on the Roles of Viruses in Weight Gain

by Geoffrey Hannigan in Prophage

We know that drugs cause side effects, and sometimes these side effects include weight gain. This is the case for Risperidone, an antipsychotic drug used to control a variety of illnesses including autism and schizophrenia. As with other cases of weight gain (obesity being the poster child), the gut microbiome has been implicated as a major player. Understanding the role for microbes in weight gain...... Read more »

  • October 31, 2015
  • 06:22 PM

New Study Looking at the Viruses Colonizing Your Skin

by Geoffrey Hannigan in Prophage

Your skin is covered in microbes, including bacteria, fungi, and even viruses (see the illustration to the right)! We know viruses can directly impact your health by infecting your cells and causing diseases such as cutaneous warts and serious skin cancers like...... Read more »

  • July 19, 2015
  • 03:38 PM

Advances in Antibiotic Alternatives for Better Health: Promising Research for "Weeding" Bacterial Communities

by Geoffrey Hannigan in Prophage

The discovery and production of antibiotics, which was certainly one of the most significant medical breakthroughs of the twentieth century, has not been without its shortcomings. One shortcoming that has gained recent attention is...... Read more »

  • July 12, 2015
  • 11:38 PM

The Hidden Microbial World On Your Cash And What It Means For Your Health

by Geoffrey Hannigan in Prophage

We have all thought and talked about how dirty money is. Those notes are transferred all over the world, touched by thousands of people, and find themselves in every sort of hygienic situation. But how dirty is money really? What kinds of microbes (bacteria, viruses, etc) are sitting on your cash, and can they make you sick? To provide us with some insight ...... Read more »

  • May 17, 2015
  • 11:03 PM

A Look Into The Viruses That Control Your Stomach Bacterial Infections (Including Probiotics)

by Geoffrey Hannigan in Prophage

Biofilms continue to be hugely significant problems when treating bacterial infections. Biofilms are groups of bacteria that stick together and to a surface while surrounding themselves in a thick extracellular matrix. You can think of this as the collective bacteria sticking to a surface like a slimy ball of goo. These are very serious infections because...... Read more »

Rossmann, F., Racek, T., Wobser, D., Puchalka, J., Rabener, E., Reiger, M., Hendrickx, A., Diederich, A., Jung, K., Klein, C.... (2015) Phage-mediated Dispersal of Biofilm and Distribution of Bacterial Virulence Genes Is Induced by Quorum Sensing. PLOS Pathogens, 11(2). DOI: 10.1371/journal.ppat.1004653  

  • May 3, 2015
  • 11:08 PM

Recent Advances: Phage Therapy for Antibiotic Resistant Staph Infections

by Geoffrey Hannigan in Prophage

Most of us have experienced, know someone who experienced, or have at least heard of Staph infections. As their name implies, these infections are caused by Staph (short for the bacterial genus Staphylococcus), occur on the skin, are often acquired in hospitals...... Read more »

  • February 28, 2015
  • 04:42 PM

Coding Responsibly Part II: Keeping a Notebook

by Geoffrey Hannigan in Prophage

In my last post I started writing about the next step a coding student can take after learning the basics. This next step is of course learning not just to code, but to code responsibly. Last time I talked about using version control to keep track of code changes as you work through a project. For this next post, I want to take the conversation further by discussing...... Read more »

Perkel, J. (2011) Coding your way out of a problem. Nature Methods, 8(7), 541-543. DOI: 10.1038/nmeth.1631  

  • January 25, 2015
  • 09:19 PM

Coding Responsibly Part I: Version Control

by Geoffrey Hannigan in Prophage

As a result of the growing number of resources allowing everyone to learn how to code, as well as numerous other awesome educational efforts, programming is steadily growing in popularity and accessibility...... Read more »

Perkel, J. (2011) Coding your way out of a problem. Nature Methods, 8(7), 541-543. DOI: 10.1038/nmeth.1631  

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