Category Archives: metagenomics

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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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

New branches on the tree of life

Posted on 12 Apr, 2016 by Kelle Freel

(Trees from Darwin (1837), Haeckel (1866), and Woese (1990)) We’ve come quite a long way since Darwin sketched out his tree in 1837 connecting, with branch tips representing animals and microbes currently in existence and branches and trunks their ancestors. … Continue reading →

Posted in bioinformatics, community ecology, evolution, genomics, metagenomics, microbiology, phylogenetics | Tagged , , , , | 1 Comment

The dangers of not thinking about the relics

Posted on 31 Mar, 2016 by Kelle Freel

No, I’m not talking about Saint Erik’s skull from his beheading in 1160, which (as it turns out) might just be real. A hot topic in microbiology is a different kind of relic. Amazing developments in microbial ecology in recent years … Continue reading →

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Old dogs, and 'carnivorous' pandas

Posted on 4 Jun, 2015 by Arun Sethuraman

It was a good fortnight for large mammals! Two recent studies attempt to date the emergence of modern canids, and offer insights into the gut microbiomes of giant pandas. Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and … Continue reading →

Posted in adaptation, evolution, genomics, metagenomics, microbiology, natural history, Paleogenomics, population genetics, speciation | Tagged , , , | Leave a comment

Rooting eukaryotes in the Arctic Ocean

Posted on 14 May, 2015 by Arun Sethuraman

While the general consensus has centered around the evolution of eukaryotes within the TACK superphylum of Archaea (Thaum-, Aigar-, Cren-, and Kor-archaeota), considerable controversy yet remains with (a) the rooting of the eukaryote common ancestor, and (b) ‘missing’ links in … Continue reading →

Posted in evolution, metagenomics, speciation, species delimitation | Tagged , , | Leave a comment

Socially structured gut microbiomes in wild baboons

Posted on 17 Mar, 2015 by Noah Snyder-Mackler

“You can pick your friends and you can pick your nose, but you can’t pick your friend’s nose.” Well, that old adage may still be true, but baboons certainly pick (up) their friends’ gut microbes. A new study by Jenny … Continue reading →

Posted in community ecology, genomics, metagenomics, natural history, primates | Tagged , , | 5 Comments

A current review of modern and ancient eDNA

Posted on 14 Jan, 2015 by Rob Denton

There is something romantic about environmental DNA. The ability to discover the presence of almost any species just by detecting the microscopic bread crumbs they leave behind? That is really just a deerstalker and pipette away from Sherlock-level science. But if … Continue reading →

Posted in DNA barcoding, genomics, metagenomics, Paleogenomics | Tagged , | 2 Comments

Genetics reveal the diversity of pollinators' other cargo: fungi

Posted on 28 Oct, 2014 by Jeremy Yoder

The following is a cross-posting from the Stanford CEHG Blog by Jeremy Hsu, a graduate student in Elizabeth Hadley’s lab at Stanford University. Many animals that visit flowers are known to carry microfungal communities; these fungi are important ecologically because … Continue reading →

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