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Prophage
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- August 27, 2016
- 07:44 PM
- 83 views
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
- 233 views
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
- 258 views
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 »
Schirmer, M., Ijaz, U., D'Amore, R., Hall, N., Sloan, W., & Quince, C. (2015) Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Research, 43(6). DOI: 10.1093/nar/gku1341
Schirmer, M., D’Amore, R., Ijaz, U., Hall, N., & Quince, C. (2016) Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data. BMC Bioinformatics, 17(1). DOI: 10.1186/s12859-016-0976-y
- March 6, 2016
- 09:46 PM
- 394 views
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 »
Bradley, C., Morris, D., Rankin, S., Cain, C., Misic, A., Houser, T., Mauldin, E., & Grice, E. (2016) Longitudinal evaluation of the skin microbiome and association with microenvironment and treatment in canine atopic dermatitis. Journal of Investigative Dermatology. DOI: 10.1016/j.jid.2016.01.023
- February 14, 2016
- 04:00 PM
- 486 views
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
- 285 views
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
- 390 views
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 »
Frasier TR. (2015) A note on the use of multiple linear regression in molecular ecology. Molecular ecology resources. PMID: 26650184
- December 27, 2015
- 11:19 PM
- 438 views
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 »
Lemaître JP, Duroux A, Pimpie R, Duez JM, & Milat ML. (2015) Listeria phage and phage tail induction triggered by components of bacterial growth media (phosphate, LiCl, nalidixic acid, and acriflavine). Applied and environmental microbiology, 81(6), 2117-24. PMID: 25595760
- December 6, 2015
- 10:12 PM
- 365 views
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 »
Bahr, S., Weidemann, B., Castro, A., Walsh, J., deLeon, O., Burnett, C., Pearson, N., Murry, D., Grobe, J., & Kirby, J. (2015) Risperidone-induced weight gain is mediated through shifts in the gut microbiome and suppression of energy expenditure. EBioMedicine, 2(11), 1725-1734. DOI: 10.1016/j.ebiom.2015.10.018
- October 31, 2015
- 06:22 PM
- 590 views
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 »
Hannigan, G., Meisel, J., Tyldsley, A., Zheng, Q., Hodkinson, B., SanMiguel, A., Minot, S., Bushman, F., & Grice, E. (2015) The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome. mBio, 6(5). DOI: 10.1128/mBio.01578-15
- July 19, 2015
- 03:38 PM
- 950 views
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 »
Gomaa, A., Klumpe, H., Luo, M., Selle, K., Barrangou, R., & Beisel, C. (2014) Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems. mBio, 5(1). DOI: 10.1128/mBio.00928-13
- July 12, 2015
- 11:38 PM
- 572 views
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 »
Jalali S, Kohli S, Latka C, Bhatia S, Vellarikal SK, Sivasubbu S, Scaria V, & Ramachandran S. (2015) Screening currency notes for microbial pathogens and antibiotic resistance genes using a shotgun metagenomic approach. PloS one, 10(6). PMID: 26035208
- May 17, 2015
- 11:03 PM
- 690 views
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
- 713 views
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 »
Pincus, N., Reckhow, J., Saleem, D., Jammeh, M., Datta, S., & Myles, I. (2015) Strain Specific Phage Treatment for Staphylococcus aureus Infection Is Influenced by Host Immunity and Site of Infection. PLOS ONE, 10(4). DOI: 10.1371/journal.pone.0124280
- February 28, 2015
- 04:42 PM
- 962 views
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
- 893 views
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
- January 7, 2015
- 06:28 PM
- 757 views
A Recent Review of How Today's Clinicians Are Treating Fractures
by Geoffrey Hannigan in Prophage
[WARNING: GRAPHIC CONTENT]
Open fractures are bone fractures in which the bone breaks through the skin, leaving it exposed to the external environment (see figure below for example). As you can imagine, this exposure leaves the fracture particularly vulnerable to infection and other related complications, including an inability of the bone to heal properly...... Read more »
Hannigan, G., Pulos, N., Grice, E., & Mehta, S. (2014) Current Concepts and Ongoing Research in the Prevention and Treatment of Open Fracture Infections. Advances in Wound Care, 2147483647. DOI: 10.1089/wound.2014.0531
- November 27, 2014
- 11:30 AM
- 717 views
Potential New Roles for Bacteria and B Cells in Promoting the Stomach Flu
by Geoffrey Hannigan in Prophage
We are all unfortunately familiar with the notorious stomach flu. Most of us have experienced that awful nausea, vomiting, diarrhea, and tiredness associated with catching some stomach bug. While there are many viral causes of the stomach flu (also called gastroenteritis), one of the most common is the Norovirus. The Norovirus is a common and contagious virus that is currently the leading cause of viral gastroenteritis...... Read more »
Jones, M., Watanabe, M., Zhu, S., Graves, C., Keyes, L., Grau, K., Gonzalez-Hernandez, M., Iovine, N., Wobus, C., Vinje, J.... (2014) Enteric bacteria promote human and mouse norovirus infection of B cells. Science, 346(6210), 755-759. DOI: 10.1126/science.1257147
- November 9, 2014
- 09:02 PM
- 798 views
Using Specific Bacteria to Treat Antibiotic-Induced Diarrheal Disease (C. difficile)
by Geoffrey Hannigan in Prophage
There has been a lot of talk about the microbiome and Clostridium difficile infections. This is because patient antibiotic or chemotherapeutic exposure (both of which can destroy your commensal bacterial communities) increases the risk of C. difficile infection. This observation suggests a role for commensal bacteria in mediating infection resistance. The exact commensal bacteria that mediate protection against C. difficile infection are not known, but luckily for us, scientists are working o........ Read more »
Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L, Gobourne A, No D, Liu H, Kinnebrew M, Viale A.... (2014) Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature. PMID: 25337874
- October 12, 2014
- 11:30 AM
- 813 views
Your Artificial Sweeteners, Your Bacteria, and Your Health
by Geoffrey Hannigan in Prophage
It seems like one cannot help hearing about this paper throughout the microbiome and related fields. The paper "Artificial Sweeteners Induce Glucose Intolerance by Altering the Gut Microbiota" was recently published in Nature, and it has had a lot of press...... Read more »
Suez, J., Korem, T., Zeevi, D., Zilberman-Schapira, G., Thaiss, C., Maza, O., Israeli, D., Zmora, N., Gilad, S., Weinberger, A.... (2014) Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature. DOI: 10.1038/nature13793
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