Chronic Wound Mycobiome

A new paper has just come out in mBio, and it represents an exploration of the fungi associated with chronic foot wounds in diabetic patients. This paper represents the last project for which I did benchwork before becoming all 'computational' all the time! I designed the approach for using MiSeq to sequence fungal ITS1 (which included designing and testing new primers specific for the platform) and executed the benchwork along with the first round of computational analyses. I appreciate Michael Loesche and Lindsay Kalan picking it up and performing a lot of necessary work to properly finish it off after I moved on from my position in the Grice Lab at the University of Pennsylvania.

The major finding was that certain aspects of the 'mycobiome' (i.e., the full set of fungi present) are associated with delayed healing, indicating that fungal profiling could become an important aspect of chronic wound care as medicine moves forward. Have a look at the link at the bottom of this post!

Pathogens are associated with poor outcomes. Mean proportion of pathogens (y axis) by end of study reason (x axis). Error bars indicate standard errors of the means.

- Brendan

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Reference:

Kalan, L., M. A. Loesche, B. P. Hodkinson, K. P. Heilmann, G. Ruthel, S. E. Gardner, and E. A. Grice. 2016. Redefining the chronic wound microbiome: fungal communities are prevalent, dynamic, and associated with delayed healing. mBio 7(5): e01058-16.
Download publication (PDF file)

Cancer and HIV

We are at a point in time when the field of cancer research is becoming dominated by immunoncology - the study of how cancer interacts with the immune system.  One interesting aspect of this is that certain viral infections and certain cancer types might be most effectively treated using some of the same cellular and molecular machinery.  This CNN article addresses this in the context of HIV + acute myeloid leukemia and specifically mentions the generation and maintenance of CD8 T-cells as one way of combating both viral infections and specific types of cancer:
http://www.cnn.com/2016/07/15/health/cancer-research-hiv-cure/

- Brendan

Why Design Matters

Recently an article resulting from some of my research at the University of Pennsylvania was published.  It highlights how methods, approach, and experimental design can heavily influence the conclusions of studies on microbial communities.  Specifically, it shows that the most common primers used for microbiome studies (amplifying the 16S-V4 region) do a poor job of amplifying DNA from certain crucial microbes in the skin microbiome (such as Propionibacterium), biasing results and giving an overall inaccurate picture of skin microbial diversity.  A related observation was that the species of Staphylococcus could not be reliably identified using the V4 region, as shown here:

Relative abundance of Staphylococcus sequences able to be classified at the species level. (Top) Staphylococcus species in the Whole Metagenomic Sequence dataset were classified using MetaPhlAn. (Middle and Bottom) 16S-V1-V3 and 16S-V4 species level classifications were determined by pplacer. Pie charts depict the percentage of sequences classified as Staphylococcus at the genus level that were further classified at the species level.

To read a lengthier summary of the article, check out my friend and co-author Geof Hannigan's blog post!

- Brendan

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Reference

Meisel, J., G. D. Hannigan, A. Tyldsley, A. J. SanMiguel, B. P. Hodkinson, Q. Zheng, and E. A. Grice. 2016. Skin microbiome surveys are strongly influenced by experimental design. Journal of Investigative Dermatology DOI: 10.1016/j.jid.2016.01.016.
Download manuscript (PDF file)

Citations

A quick look at Google Scholar the other day showed me that there have been over 2300 citations to my papers. The other citation metrics were interesting, too, like the h-index (currently 24, meaning that 24 of my papers have been cited 24 times or more) and the i10 index (currently 39, meaning that I have had 39 papers cited 10 times or more). These numbers only take into account the peer-reviewed publications, but I do have quite a number of additional non-peer-reviewed works. If I count up the peer-reviewed papers plus my other types of publications (abstracts, book reviews, annotated bibliographies, etc.), I now have well over 100 publications!

As an aside, one metric having to do with publication that is commonly used is the 'impact factor.' Although this number is meant to evaluate journals as a whole, it is often used by institutions to evaluate researchers, using the journals in which they publish as a proxy for their overall impact as scientists. This is, of course, highly controversial. One aspect that makes it even more problematic is that metrics like impact factor can be highly dependent on the database used for compiling the raw citation data. My wife published a paper a few years back in which this issue was explored quantitatively (Gray & Hodkinson 2008). In a set of 50 journals, many rankings were seen to differ by numbers that ran up into the double digits depending on the database used, calling into question the accuracy of any given journal's impact factor.

- Brendan

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Reference

Gray, E, and S. Z. Hodkinson. 2008. Comparison of Journal Citation Reports and Scopus Impact Factors for Ecology and Environmental Sciences Journals. Issues in Science and Technology Librarianship DOI:10.5062/F4FF3Q9G.
View publication (website)

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Note: Citation values updated May 29, 2018

Skin Virome

The human skin is covered in many microbes, and until recently, the viral component has remained poorly understood. A recent paper presents the research into the human skin virome that I worked on while in the Dermatology Department at the University of Pennsylvania.

A cross-section of the skin (showing viruses and other microbes).

Thanks to Geof Hannigan for conceptualizing and taking the lead on this project. You can read his description of it and an overview of the results here:
http://prophage.blogspot.com/2015/10/new-study-looking-at-viruses-colonizing.html

There is also a good article for the general public here that describes the work:

http://arstechnica.com/science/2015/11/vast-uncharted-viral-world-discovered-on-human-skin/

- Brendan

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Reference

Hannigan, G. D., J. S. Meisel, A. S. Tyldsley, Q. Zheng, B. P. Hodkinson, A. J. SanMiguel, S. Minot, F. D. Bushman, and E. A. Grice. 2015. The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome. mBio 6(5): e01578-15.
Download publication (PDF file)

patPRO: Visualizing Longitudinal Microbiome Data

Recently some of my collaborators from the University of Pennsylvania and I released a new R package on CRAN (Comprehensive R Archive Network). It is called 'patPRO' (short for 'Patient Profiler'), and provides a number of functions to facilitate the visualization of longitudinal microbiome data. Although we developed it for examining changes in human microbiomes over time, it could just as easily be used for changes in microbial populations in water supplies, agricultural soils, or livestock, just to name a few possibilities.

This is an example of a plot that can be made, simultaneously showing changes in multiple dimensions of the microbiome:



Here is the official page for the package, with links to the reference manual and source code:
http://cran.us.r-project.org/web/packages/patPRO/index.html

This link provides a version of the reference manual in a series of webpages:
http://rpackages.ianhowson.com/cran/patPRO/

- Brendan

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Reference

Hannigan, G. D., M. A. Loesche, B. P. Hodkinson, S. Mehta, and E. A. Grice. 2015. patPRO: Visualizing Temporal Microbiome Data. R package version 1.0.0. http://cran.r-project.org/web/packages/patPRO/index.html
Download package (website)

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Note: One implementation of R gave me an error indicating that 'stringi' was needed when I tried to install 'patPRO.' After installing 'stringi,' I ran across no further issues with patPRO.

Insights into Parmeliaceae

The results of a large-scale collaborative Parmeliaceae systematics project, in which I participated, were recently published in New Phytologist. To read the article, check out the link at the bottom of this post; I have pasted the abstract below.

• We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi.
• We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs).
• The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene.
• Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene–Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes.

- Brendan

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Reference

Divakar, P. K., A. Crespo, M. Wedin, S. D. Leavitt, L. Myllys, B. McCune, T. Randlane, J. W. Bjerke, Y. Ohmura, I. Schmitt, C. G. Boluda, D. Alors, B. Roca-Valiente, R. Del-Prado, Constantino Ruibal, K. Buaruang, J. Núñez-Zapata, G. Amo de Paz, V. J. Rico, M. C. Molina, J. A. Elix, T. L. Esslinger, I. K. K. Tronstad, H. Lindgren, D. Ertz, C. Gueidan, L. Saag, T. Tõrra, G. Singh, F. Dal Grande, S. Parnmen, A. Beck, M. N. Benatti, D. Blanchon, M. Candan, P. Clerc, T. Goward, M. Grube, B. P. Hodkinson, J.-S. Hur, G. Kantvilas, P. M. Kirika, J. Lendemer, J.-E. Mattsson, M. I. Messuti, J. Miadlikowska, M. Nelsen, J. I. Ohlson, S. Pérez-Ortega, A. Saag, H. J. M. Sipman, M. Sohrabi, A. Thell, G. Thor, C. Truong, R. Yahr, D. K. Upreti, D. L. Hawksworth, P. Cubas, and H. T. Lumbsch. 2015. Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi. New Phytologist DOI: 10.1111/nph.13553.
Download publication (PDF file)

New Job

I have officially started a new job at Janssen Research & Development, a member of the Johnson & Johnson family of companies! I am working within Oncology Translational Research as a Post-Doctoral Fellow in Computational Biology. With Janssen, I look forward to many opportunities to do groundbreaking research and really make an impact in people's lives!

- Brendan

PICS-Ord on Mac

In a previous post, I wrote about how to get the program PICS-Ord to run easily on a PC. Other operating systems presented some special problems associated with getting the different dependencies to find one another. I recently found Homebrew, which solves a lot of the problems typically found with Mac computers, and I put together some instructions for running PICS-Ord on the current Mac OS.

Running PICS-Ord on Mac OS X (10.9 or 10.10):

(1) Download and install R from here:
https://cran.r-project.org/bin/macosx/R-3.2.2.pkg
Open the file and follow the instructions.

(2) Install CMake and Boost using Homebrew; use the following three commands in the terminal to first install Homebrew and then the two Ngila dependencies:
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew install cmake
brew install boost --with-python

(3) Install Ngila by using the following commands in the terminal (if you already have wget, you can ignore the first line):
brew install wget
wget http://scit.us/projects/files/ngila/Releases/ngila-release.tar.gz
tar zxvf ngila-release.tar.gz
cd ngila-1.3-release/
cmake . && make
make install
cd ..

(4) Download PICS-Ord from here:
http://scit.us/projects/files/ngila/picsord.zip
Open the zip file to create the picsord directory.

(5) Run PICS-Ord by moving the FASTA files into the picsord directory, navigating to the picsord directory in the terminal, and running the following:
Rscript picsord.R region_1.fas > region_1.phy
Rscript picsord.R region_2.fas > region_2.phy
Rscript picsord.R region_3.fas > region_3.phy
Rscript picsord.R region_4.fas > region_4.phy

- Brendan

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Reference

Lücking, R., B. P. Hodkinson, A. Stamatakis, and R. A. Cartwright. 2011. PICS-Ord: Unlimited Coding of Ambiguous Regions by Pairwise Identity and Cost Scores Ordination. BMC Bioinformatics 12: 10.
Download publication (PDF file)
Download R-based program (zipped program package)
View program wiki (website)

Shared Microbiota of Humans and Their Pets

I recently co-authored a paper from a study in which we examined the microbiota of humans and their pets.  The full text can be seen here:

http://www.microbiomejournal.com/content/3/1/2/

Abstract -

Background: Staphylococcus aureus and other coagulase-positive staphylococci (CPS) colonize skin and mucous membrane sites and can cause skin and soft tissue infections (SSTIs) in humans and animals. Factors modulating methicillin-resistant S. aureus (MRSA) colonization and infection in humans remain unclear, including the role of the greater microbial community and environmental factors such as contact with companion animals. In the context of a parent study evaluating the households of outpatients with community MRSA SSTI, the objectives of this study were 1) to characterize the microbiota that colonizes typical coagulase-positive Staphylococcus spp. carriage sites in humans and their companion pets, 2) to analyze associations between Staphylococcus infection and carriage and the composition and diversity of microbial communities, and 3) to analyze factors that influence sharing of microbiota between pets and humans.

Results:We enrolled 25 households containing 56 pets and 30 humans. Sampling locations were matched to anatomical sites cultured by the parent study for MRSA and other CPS. Bacterial microbiota were characterized by sequencing of 16S ribosomal RNA genes. Household membership was strongly associated with microbial communities, in both humans and pets. Pets were colonized with a greater relative abundance of Proteobacteria, whereas people were colonized with greater relative abundances of Firmicutes and Actinobacteria. We did not detect differences in microbiota associated with MRSA SSTI, or carriage of MRSA, S. aureus or CPS. Humans in households without pets were more similar to each other than humans in pet-owning households, suggesting that companion animals may play a role in microbial transfer. We examined changes in microbiota over a 3-month time period and found that pet staphylococcal carriage sites were more stable than human carriage sites.

Conclusions: We characterized and identified patterns of microbiota sharing and stability between humans and companion animals. While we did not detect associations with MRSA SSTI, or carriage of MRSA, S. aureus or CPS in this small sample size, larger studies are warranted to fully explore how microbial communities may be associated with and contribute to MRSA and/or CPS colonization, infection, and recurrence.

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Reference

Misic, A. M., M. F. Davis, A. S. Tyldsley, B. P. Hodkinson, P. Tolomeo, B. Hu, I. Nachamkin, E. Lautenbach, D. O. Morris, and E. A. Grice. 2015. The shared microbiota of humans and companion animals as evaluated from Staphylococcus carriage sites. Microbiome 3: 2.
Download publication (PDF file)

Next-Gen Sequencing: A Review

I recently wrote up a review with Dr. Elizabeth Grice of next-generation sequencing technologies. We specifically focused on their applications for microbiome research. While it was published it in a wound care journal, the techniques outlined are broadly applicable to any system with a diversity of microbes. Please have a look at the manuscript below!

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Reference

Hodkinson, B. P., and E. A. Grice. 2015. Next-generation sequencing: a review of technologies and tools for wound microbiome research. Advances in Wound Care 4(1): 50-58.
Download manuscript (PDF file)

Mole Day

This year I am teaching several sections of High School Chemistry, and this past week we had celebrations for Mole Day!  Here's a rundown of some of the snacks and activities.

Moles May Attend:
Make A Mole - For extra credit students can make stuffed animal moles from a pattern (just Google it). It's great to have some homemade moles in attendance at the party!

Food:
Guacamole - Trader Joe's has a guacamole dip called "Avocado's Number" that actually has a picture of Amadeo Avogadro on it, which is a great prop. I also decided to make fresh guacamole for the students, which provided everyone with a bit of a show.
Molasses cookies - OK, so the only real connection here is that 'mol' is in the word, but who doesn't like cookies?!

Sing-Along:
Rock Me Amadeo - The song 'Rock Me Amadeus' by Falco has an awesome video that highlights the time-period in Europe when Amadeo Avogadro was alive (which overlaps with the time period when Wolfgang Amadeus Mozart was alive, which is the reason that the video is set in this time period). Students can sing 'Amadeo' instead of 'Amadeus' on the chorus and you've got a catchy theme song for Mole Day!

Game Show:
More Than, Less Than, or Equal to a Mole - You can take objects that are basically made of one type of compound and ask students if they are more than a mole, less than a mole, or equal to a mole. Students can be split into two teams, and pairs (with one from each team) can stand on either side of a bell and compete to ring in first. If the first to answer is incorrect, the other person gets a chance to guess. I have to give credit to Mrs. Swieson (also of Delaware County Christian School) for coming up with this one!

Most of all, we just partied and had a great time hanging out as a class!

Electronic Publication of Taxa

Hodkinson, B. P., and J. C. Lendemer. 2014. A clarification of effective electronic publication. Taxon 63(4): 911-913.
Download publication (PDF file)

Lecanoromycetes

Please check out the newest publication that we've put together on the phylogeny and taxonomy of the fungal class Lecanoromycetes (the main group of lichen-forming fungi). This publication is more all-encompassing than any before it, including analyses of molecular sequence data from 1307 different fungi!

Miadlikowska, J., F. Kauff, F. Högnabba, J. C. Oliver, K. Molnár, E. Fraker, E. Gaya, J. Hafellner, V. Hofstetter, C. Gueidan, M. A. G. Otálora, B. Hodkinson, M. Kukwa, R. Lücking, C. Björk, H. J. M. Sipman, A. R. Burgaz, A. Thell, A. Passo, L. Myllys, T. Goward, S. Fernández-Brime, G. Hestmark, J. Lendemer, H. T. Lumbsch, M. Schmull, C. L. Schoch, E. Sérusiaux, D. R. Maddison, A. E. Arnold, S. Stenroos, and F. Lutzoni. 2014. A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families. Molecular Phylogenetics and Evolution 79: 132-168.
Download publication (PDF file)
Download supplementary file 1 (PDF file)
Download supplementary file 2 (PDF file)
Download supplementary file 3 (PDF file)
Download supplementary file 4 (PDF file)
Download supplementary file 5 (docx file)
Download supplementary file 6 (PDF file)
Download supplementary file 7 (docx file)

Spider Bite

[WARNING: Graphic Content]

Over the past month, my wife has been dealing with an ulcer on her shoulder that was most likely caused by a spider bite (I'm guessing that some type of Sac Spider is to blame). At first, it raised up like a volcano with a base diameter of about 2-3 cm and a height of about 1-2 cm. Then after a couple of days, the center became necrotic (see "June 15" below). She had the part that was entirely necrotic taken out by a doctor, leaving a bit of a hole in the center ("June 17"). She then treated it daily with honey and kept it covered for the next few weeks. During this time, there was a period of a few days where the whole area started to become red and inflamed ("July 1"), so she got on an antifungal (Fluconazole) and two antibiotics (Keflex & Minocycline), which quickly cleared up that particular issue. It is now healing up nicely ("July 4") and we hope it will finish up without any additional complications!

Timeline (all treatments follow doctors' recommendations):
June 12 - noticed painful swelling
June 15 - Keflex treatment begun (for potential general infection)
June 16 - Keflex treatment terminated, Bactrim treatment begun (for potential MRSA infection)
June 17 - necrotic center removed/biopsied, treatment with honey begun
June 19 - Bactrim treatment terminated (no signs of infection from lab tests)
July 1 - Keflex, Minocycline and Fluconozole treatment begun (swelling and redness seen around the area)

- Brendan

Sticta sylvatica

I recently had a paper published that talks about the status of the rare species Sticta sylvatica in my part of the world (Hodkinson et al. 2014). The article was actually featured on the cover! Here's the abstract:

"The presence of the foliose cyanolichen Sticta sylvatica in eastern North America has been called into question due to the absence of high-quality, verifiable material and the common misuse of its name. Recently, specimens collected in the Great Smoky Mountains have been verified as having the typical S. sylvatica morphology. Although molecular data remain inconclusive regarding the entity’s genetic distinctiveness from the phenotypically dissimilar S. limbata, we argue that the decline in the abundance of this morphological entity worldwide along with the need for further genetic study make continued conservation efforts imperative."

Sticta sylvatica in the field.

- Brendan

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Reference

Hodkinson, B. P., J. C. Lendemer, T. McDonald, and R. C. Harris. 2014. The status of Sticta sylvatica, an ‘exceedingly rare’ lichen species, in eastern North America. Evansia 31(1): 17-24.
Download publication (PDF file)
Download journal issue cover (PDF file)

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[This work was supported by the National Science Foundation under awards EF-1115086 and DEB-1145511.]

Molecular Ecology

A few years back, I began working on a collaborative project led by Greg Bonito to examine fungal and bacterial communities associated with plant roots.  We used next-generation sequencing on the 454 GS-FLX platform for profiling using four different loci (one bacterial and three fungal).  The fungal ITS and LSU primers were identical to those used in my recent Mycosphere paper (Hodkinson & Lendemer 2013), and the 16S primers are the ones I designed for my Environmental Microbiology paper from a couple of years back (Hodkinson et al. 2012).  The paper is finally out in Molecular Ecology; check it out!

- Brendan

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References

Bonito, G., H. Reynolds, M. S. Robeson, J. Nelson, B. P. Hodkinson, G. Tuskan, C. W. Schadt, and R. Vilgalys. 2014. Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants. Molecular Ecology 23(13): 3356-3370.
Download publication (PDF file)

Hodkinson, B. P., and J. C. Lendemer. 2013. Next-generation sequencing reveals sterile crustose lichen phylogeny. Mycosphere 4(6): 1028-1039.
Download publication (PDF file)
Download data and sequence-processing scripts (ZIP archive)
Download Ascomycota LSU alignment and analysis files (ZIP archive)
Download Arthoniales LSU alignment and analysis files (ZIP archive)

Hodkinson, B. P., N. R. Gottel, C. W. Schadt, and F. Lutzoni. 2012. Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome. Environmental Microbiology 14(1): 147-161.
Download publication (PDF file)
View publication (publisher's website)Download supplementary phylogeny (PDF file)
Download data and analysis file archive (ZIP file)

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[Support for my work on this project was provided in part by the National Science Foundation under awards EF-0832858, DEB-1011504, and DEB-1145511.]

Lichens As Food

Here's an article about how lichens are a trendy new food item!
http://www.independent.co.uk/life-style/food-and-drink/features/lichen-is-the-surprise-new-ingredient-on-finedining-menus-thanks-to-our-love-of-scandinavian-and-indian-cuisines-9268419.html

Dynamic Periodic Table

Here's a really cool dynamic periodic table that nicely lays out all sorts of information about the various elements (with all sorts of tabs and sliders):

http://www.ptable.com/

I wish there had been something like this when I was in high school and college!

- Brendan

Open Fracture Microbiome

I recently co-authored a paper with a team of dermatologists (those who study skin) and orthopaedists (those who study bone) in which we present the results of microbiome analyses on open fracture wounds. These are the types of wounds where bones actually break through the surface of the skin. We found that the wound-associated microbial communities change over time, becoming significantly more similar to the adjacent skin communities as healing progresses. There are also a number of bacterial groups and aspects of the microbiome that tend to be associated different clinical factors. Please have a look at the publication at the links below!

- Brendan

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Reference

Hannigan, G. D., B. P. Hodkinson, K. McGinnis, A. S. Tyldsley, J. B. Anari, A. D. Horan, E. A. Grice, and S. Mehta. 2014. Culture-independent pilot study of microbiota colonizing open fractures and association with severity, mechanism, location, and complication from presentation to early outpatient follow-up. Journal of Orthopaedic Research 32(4): 597-605.
Download publication (PDF file)
Download supplemental methods (PDF file)
Download sample metadata (QIIME mapping file)
Download OTU table (bzip2-compressed BIOM file)
Download OTU representative sequences (bzip2-compressed FASTA file)

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[This work was funded in part by NIAMS/NIH R00 AR060873.]