Category Archives: metagenomics

Diving deep: Exploring microbial communities under the seafloor

Posted on 7 Dec, 2017 by Kelle Freel

As we all sat staring at three large monitors in the front of the room, the remotely operated vehicle (ROV) Jason hung on to a borehole observatory with one hydraulic arm as the other arm plugged our sampling equipment into … Continue reading →

Posted in bioinformatics, community ecology, fieldwork, genomics, metagenomics, microbiology, transcriptomics | Tagged , , , | Leave a comment

Genomes are coming: Sequence libraries from the honey bee reflect associated microbial diversity

Posted on 20 Jul, 2017 by Kelle Freel

One of the coolest of reasons that cheap sequencing is nifty, in my opinion, is that it has allowed researchers to study individual eukaryotic organisms, and their associated microbes (their microbiome). Let’s be real, we are in the midst of … Continue reading →

Posted in Coevolution, community ecology, evolution, genomics, metagenomics, microbiology, next generation sequencing | Tagged , , | Leave a comment

A sponge and its symbionts, using genomics to unravel complex relationships

Posted on 30 Mar, 2017 by Kelle Freel

The ocean is full of interesting organisms and even more fascinating (as well as difficult to tease apart) are the interactions among them. From deep sea giant tube worms, to the adorable bobtail squid, symbioses have a central role, and … Continue reading →

Posted in Coevolution, community ecology, genomics, metagenomics, microbiology | Tagged , , | 1 Comment

The importance of culturing the uncultured, delving into the microbial consortia in the human gut

Posted on 15 Nov, 2016 by Kelle Freel

The molecular side of ecology has grown by leaps and bounds in recent decades. The review we covered not too long ago, did a nice job of summarizing many key aspects highlighting the importance of this relatively new molecular view … Continue reading →

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

There are more microbes than meet the eye: exploring the genomic diversity in an aquifer

Posted on 8 Nov, 2016 by Kelle Freel

First: it’s Tuesday, November 8th, 2016 – before you even think about putting your feet up and reading this post, I hope you’ve managed to wrangle yourself one of those highly prized “I voted” stickers. Now, on to more microbial … Continue reading →

Posted in bioinformatics, community ecology, metagenomics, microbiology, next generation sequencing | Tagged , , | 1 Comment

Making ecology “count”: a review of the why and how of molecular ecology  

Posted on 25 Oct, 2016 by Kelle Freel

It’s likely that everyone has been asked by either a friend or family member “What do you do?” Which, depending on what level of detail you shoot for, might be relatively straight forward. The follow-up question, however, can be a … Continue reading →

Posted in bioinformatics, community, community ecology, metagenomics | Tagged , , , | 1 Comment

It's not the size that counts: teeny tiny SAR11 bacteria play a big role in our oceans

Posted on 11 Oct, 2016 by Kelle Freel

Microbes account for a huge chunk of the diversity on this planet, are essential in all sorts of biogeochemical processes, and we are still figuring out how everything is related. Teeny tiny bacterial cells are abundant both on land as … Continue reading →

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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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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 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