Plants in Space!

Today, Robert Ferl gave a seminar on space biology at the Princeton Environmental Geology and Geochemistry Seminar and it was so cool that I wanted to post about it here!  Robert is an expert on how plants respond to changes in gravity and has led experiments to study how Arabidopsis responds to parabolic flight campaigns (aka a vomit comet) and life on the International Space Station.  Now, it is pretty clear that zero g is probably one of the coolest “field sites” you could work at but what really got me excited was the amount of knowledge we can gain from such a small plant and the sophisticated methods that were being used.

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Searching for the 4th domain

This past weekend I participated in the first sampling for Phase II of the Microbial Dark Matter (MDM) project.  For this project we are searching for deep branching microbes with no cultured representatives that may reveal new phyla or domains of life using single cell genomics.  Prior to this study, Phase I of the MDM project identified genomes of microorganisms belonging to, what scientists proposed to be, two new super phyla and generated over 200 previously-unidentified genomes to help improve the taxonomic assignment of metagenomic reads.

With Phase II of this project, we want to continue the exploration of enigmatic members of the tree of life Continue reading

GUSTA ME: Statistics Helper

I am happy to report that, in a world of packages, a package that has been built to educate the user is finally here!  The GUide to STatistical Analysis in Microbial Ecology (GUSTA ME) is an online venue developed  by German researchers to explore different types of data analysis techniques and decide which method is appropriate for your problem at hand.  On top of that, they provide code to help you perform PCA, CCA, NMDS, ANOSIM, etc. on your data and an open forum for discussion.  Check it out!


The past few months I have been working with a microbial ecology toolkit called mothur.  So far, it is the most flexible tool I have found to calculate distance matrices from 16S alignments and, subsequently, cluster these sequences into OTUs.  Many people have asked me about how to use mothur so this post will serve as a tutorial.

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ISME Day 4

Today was the last day of ISME and a great conclusion to the conference.  Today’s theme seemed to surround microbial methods and my favorite talks were split between 2 subterranauts, Karen Lloyd and Roland Hatzenpichler.  Karen spoke in the archaea themed session about exploring single cell genomes and exploring novel enzyme function in the uncultured MCG archaea group and  Roland presented in the single cell session about a new technique to visualize newly synthesized proteins in situ.

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ISME Day 3

Today was a busy day but, at the end of the day, the one talk that stands out in my mind is Ruth Ley’s talk on the human microbiome.  Personally, I find this topic to be extremely interesting and Ruth’s presentation did not disappoint.  The talk began with an introduction to a phenomenon in human history: the introduction of agriculture.  Now, we can all imagine that during the shift from hunting and gathering to farming the human microbiome changed to adjust to the new diet.  Perhaps one of the most important changes was the introduction of starch heavy foods that were not the basis of hunter-gather diets.  One gene in particular, AMY1, codes for  Continue reading

ISME Day 2

There were some really cool sessions at ISME today.   The morning started off with a plenary talk by Lars Peter Nielsen about cable bacteria and I sampled the sessions on “Unusual strategies of microbial energy acquisition,” “Network microbial ecology,” and “Meta-ome information to microbial ecology.”  For each session I have picked a favorite talk starting with Victoria Orphan‘s talk on the archaeal-bacterial partnerships responsible for sulfate-coupled anaerobic oxidation of methane (AOM). Continue reading

ISME Day 1

This week I am at the International Society of Microbial Ecology (ISME15) Conference in Seoul, South Korea!  I want to share with you some of my favorite talks from each day.  Today, I spent most of my time in the “Microbiomes of marine ecosystems” session and made some stops at other sequencing related talks.  Perhaps my favorite talk of the day goes to… Antje Boetius!  Her talk focused on the microbial diversity of the surface of seafloor sediment and  Continue reading

Sequencing Depth and World Cup Paninis

The World Cup is underway and I am back to the blog!  I was recently inspired by the World Cup Paninis to write a post about sequencing depth.  In sequencing, the problem we are often faced with is whether or not enough sequences have been generated to be representative of a population.  Tools we often use to determine whether we have sampled enough are rarefaction curves and the Chao estimate but how many sequences would we need to generate in order to capture a 16S from every organism present in an environment? Continue reading


In my last post, I described what a De Bruijn Graph assembler is and will now go into a short tutorial of how to begin using MetaVelvet.  MetaVelvet is an extension of the popular single genome De Bruijn Graph assembler, Velvet, and is optimized to handle the varying coverage and diversity of genomes in metagenomic samples and is executed through 3 steps: velveth, velvetg, and meta-velvetg.

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