Tag Archives: next generation sequencing

American Gut

American Gut

Most of us have heard at some point or another that we have entire ecosystems of microbes living in our gut. Mostly of these microbes are happy symbionts that help us digest our food, but some can occasionally becoming pathogenic and cause health problems. Have you ever wondered what your gut microbial community looks like? Now you can find out! The Earth Microbiome Project (http://www.earthmicrobiome.org/), founded several years ago with the ambitious goal of “sequencing the microbiome of planet earth”, (or, in other words, characterizing basically all of the genetic diversity that exists on our planet), has begun a smaller, more targeted project with the aim of characterizing the gut communities of human populations.

Some of the key science questions driving this project : to what extent do gut microbial communities vary among people? At what scales can we discern patterns in microbial community composition? Are similar microbial communities found among people from similar geographic regions, with shared genetic history, or with a shared diet? And, perhaps more interestingly to most of us, to what extent does the composition of our gut community impact our own health? Once we have enough data to start answering some of these basic questions, perhaps we can even start making predictions about what sorts of lifestyles will lead to what sorts of gut flora, and how these communities, in turn, will impact our overall health.

It costs just $100 to join and get your microbiome sequenced. And the information could change your life!

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The tree of life becomes clearer with Next-Generation sequencing

Since the dawn of molecular genetics, scientists have been developing new ways to reconstruct evolutionary relationships among organisms. While historically, taxonomy was a field that relied on comparative anatomy of living organisms, or even more challenging, comparative anatomy of fossils, the comparison of genetic code allows for precise measurements of relatedness among different species. However, sequencing an entire genome was, until quite recently, prohibitively expensive for everything except well-characterized model organisms, and therefore not a viable way to measure the evolutionary relatedness of, say, two rare species of fish.

Next-generation sequencing techniques are rapidly opening new doors in the field of genomics- making it faster, more efficient, and significantly cheaper to sequence entire genomes. Scientists are finally beginning to examine the geneti code of non-model, and even very rare organisms to determine their “evolutionary place” in the tree of life. For example, micrognathozoa is a small, wormlike invertebrate with complex jaw architecture. It was entirely unknown to science until 1994, when the first specimins were discovered on an island off the west coast of Greenland. From anatomical characteristics alone, micrognathozoa was impossible to place into any existing phylum, suggesting that it diverged from other modern relatives very deep in evolutionary history. Researchers at Brown University have recently collected samples of micronathozoa and are now sequencing its bulk DNA. They are hoping to identify specific genes that will allow them to properly place the bug in a phylogenetic tree.

In addition to simply classifying organisms based on relatedness, Next-Generation sequencing is allowing scientists to study evolutionary dynamics and discern how changes in gene expression patterns lead to the divergence of species. A particularly exciting new technique, known as RNA-seq, can be used to gauge genetic activity by measuring cDNA copy number. cDNA, or complementary DNA, is produced when genes are activated. The amount of cDNA in a sample therefore reflects the relative “usage” of that gene. This technology could provide answers to questions as fundamental as how flight or swimming evolved ona  genetic level- was the activity of certain genes upregulated or downregulated?

 

 

Reference: Elizabeth Pennisi, “Tracing the Tree of Life”. Science 331: 1005-1006.