Category Archives: community ecology

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

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

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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  

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

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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

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

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

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

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

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

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

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)

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

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

(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

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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