Author Archives: Kelle Freel

When your programming may be inadequate to the task: new options for metagenome analysis

Posted on 9 Sep, 2016 by Kelle Freel

There’s a lot of data in the form of metagenomes out there, and picking apart those mountains of data to uncover meaningful results is difficult. Recently, we received a suggestion from a reader to discuss a recent program (CLARK-S) developed … Continue reading →

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Respect the old but seek out the new: Direct 16S rRNA-seq from bacterial communities

Posted on 2 Sep, 2016 by Kelle Freel

I think it’s fair to say that it’s an ongoing struggle to figure out what the heck microbes are doing in their natural environments, and who those microbes are. Clearly, there is no silver bullet that gives us all the … Continue reading →

Posted in community ecology, microbiology, RNAseq | Tagged , , , | 1 Comment

Of microbes and men: Testing the neutral theory with the human microbiome

Posted on 22 Aug, 2016 by Kelle Freel

There is no doubt that one of the hottest current topics in microbiology revolves around the human microbiome. There have been a suite of recent studies we’ve highlighted, on organisms ranging from bees and mice, to humans. A quick google scholar search identifies … Continue reading →

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Understanding the pieces of all those meeces: characterizing mice gut microbiota

Posted on 12 Aug, 2016 by Kelle Freel

In an age where a tremendous amount of data is generated, this week has seen some moves towards providing open access to extensive data sets. These attempts have been in the realm of chemistry as well as microbiology, where in a … Continue reading →

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Understanding diverse microbial communities: An interview with A. Murat Eren (Meren)

Posted on 2 Aug, 2016 by Kelle Freel

It’s clear that microbes play a crucial role in practically every aspect of ecosystems globally. From the deepest, most remote and unexplored regions of the ocean, to the human oral cavity, there are diverse microbial assemblages driving Earth’s biogeochemical cycles. … Continue reading →

Posted in bioinformatics, community ecology, metagenomics, methods | Tagged , , , | 3 Comments

Are you my mother? Exploring the possible microbial ecology of LUCA

Posted on 28 Jul, 2016 by Kelle Freel

One persistent question has always been: where did it all begin? What was the origin of the complex life that we have today? What happened billions of years ago that resulted in beautiful giant manta rays, magnificent Sequoias, and even … Continue reading →

Posted in evolution, microbiology | Tagged | 5 Comments

Who’s really riding the subway with you? Characterization of the microbial communities on Boston transport

Posted on 29 Jun, 2016 by Kelle Freel

(Figure modified from Hsu et al., 2016, Boston transport map and wikicommons image of Boston) Understanding the microbes around us is an important challenge to take on. There have been articles covering changes in microbial communities among rural and more … Continue reading →

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Microbes are going to infinity and beyond! Monitoring community changes on a simulated space station

Posted on 8 Jun, 2016 by Kelle Freel

As we’ve discussed previously here, understanding microbes in the natural and built environment around us, has implications related to human health and disease. It has turned out to be pretty tricky to clarify what is going on with our most … Continue reading →

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Data, data everywhere and another tool to use: Taxonomer, a web-tool for metagenomics data analysis

Posted on 26 May, 2016 by Kelle Freel

Because sequencing. With all the affordable genome and metagenome sequencing available, we’ve reached an unprecedented point at which we can profile microbial communities more accurately than ever before. For this reason, it’s essential to develop efficient methods for data analysis. … Continue reading →

Posted in bioinformatics, community ecology, genomics, metagenomics, methods, microbiology, software | Tagged , , , | 1 Comment

What's all the buzz about? Bees got microbiomes too!

Posted on 11 May, 2016 by Kelle Freel

So I know we are all blabbing about the human microbiome, who isn’t fascinated by the impressive roles tiny microbes have in our lives!? Trying to unravel what exactly our microbial communities do for us, and how they relate to … Continue reading →

Posted in Coevolution, community ecology, evolution, genomics, metagenomics, microbiology | Tagged , , | 2 Comments