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Category Archives: metagenomics
Loki and behold: one microbial culture that brings us one leap closer to understanding the origins of eukaryotic cells
What were you doing 10 years ago? Can you remember? Were you, perhaps, trying to sort out the origins of eukaryotic life? A pre-print (yet to be peer-reviewed) was released earlier this month by Imachi et al., describing a 12 … Continue reading →
Posted in ecology, evolution, genomics, metagenomics, microbiology
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Tagged cultivation, hydrothermal vents, Lokiarchaeota
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Snapshots of Biodiversity: eDNA as a methodology for species detection
Nicole Conner wrote this post as a project for Stacy Krueger-Hadfield’s Conservation Genetics course at the University of Alabama at Birmingham. She is a Master’s student in Dr. Thane Wibbels’ lab where she is developing new protocol to detect diamondback terrapins off … Continue reading →
Posted in bioinformatics, blogging, citizen science, community, conservation, DNA barcoding, ecology, evolution, fieldwork, metagenomics, natural history
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Tagged Blogging, conservation genetics, Science Communication, turtles, UAB
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Luck be a Korarchaeota tonight
Some tiny microbes are making a pretty big splash, and not just in the hot springs they call home in Yellowstone National Park. Recently, there was an interesting article published in Nature Microbiology about some amazing archaea, which are generally … Continue reading →
Posted in community ecology, ecology, evolution, genomics, metagenomics, microbiology, Uncategorized
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Tagged archaea, hot springs, korarchaeota, yellowstone national park
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For flexible eDNA analysis, just capture whatever you want
Environmental DNA sampling for multi-taxa species detection (i.e., the inference of species presence from genetic material in the environment) has been a hot topic lately. Some of the most exciting recent work has used high-throughput sequence (HTS) to simultaneously screen … Continue reading →
Posted in community ecology, DNA barcoding, metagenomics, methods
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Tagged environmental dna, sequence capture
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Metabarcoding for every body, every habitat, every time
The immediate reason why I wanted to write about Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles is its usefulness for the scientific community and the effort of the authors to make their study reproducible. … Continue reading →
Posted in bioinformatics, community, community ecology, DNA barcoding, fieldwork, metagenomics, next generation sequencing, phylogenetics, R
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Tagged biodiversity, bioinformatics, ecology, metabarcoding, methods, microbiome, phylogenetics
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What is DAS? A new tool to recover genomes from metagenomes
There are a lot of data out there, and if you haven’t already noticed the ‘omics train has steadily stayed its path through the fruitful (but challenging) world of metagenomics. Metagenomics offers the chance to unravel complex microbial communities without … Continue reading →
Signal Boosting a Comprehensive Review of eDNA and Metabarcoding Studies
Everything is meta these days – metabarcoding, metagenomics, and now meta blog posts that are reviews of reviews. Much like every ecologist at least dabbles in the molecular world, so most of those predisposed to molecular ecology and population genetics … Continue reading →
Posted in bioinformatics, community ecology, DNA barcoding, metagenomics, methods, microbiology, next generation sequencing, population genetics
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Tagged barcode tags, barcoding, bioinformatics, eukaryotes, Illumina, metagenomics, methods, microbial communities, microbial community analysis, microbiome, NGS
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Major new microbial groups expand diversity and alter our understanding of the tree of life
I still believe in revolutions. And sometimes they just happen, almost unnoticed. One such revolution happened on a boring 11th of April 2016 when Laura Hug et al. published their new tree of life in the journal of Nature Microbiology. … Continue reading →
Posted in bioinformatics, community ecology, evolution, genomics, metagenomics, microbiology, next generation sequencing, phylogenetics
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Tagged assembly, bioinformatics, Evolution, genome, genomics, metagenomics, NGS, phylogenetics
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Exploring the genomic diversity of tubeworm endosymbionts
Tubeworms are cool. (To be read only in your best (eleventh) Doctor Who voice). Although, depending on how close they are to a hydrothermal vent, they might be more on the hot side….Regardless, if you’re on the fence about how … Continue reading →
Posted in bioinformatics, Coevolution, community ecology, evolution, genomics, metagenomics, microbiology
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Tagged endosymbionts, Escarpia, tubeworms
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Retrieving a million sequences and avoiding primer bias, a new method that might have it all
We have come a long way since the early days when sequencing was a breakthrough method initially used to identify uncultured microbes from the environment. It is now been almost three decades, in fact, since the first microbial 16S rRNA … Continue reading →
Posted in bioinformatics, evolution, metagenomics, methods, microbiology, next generation sequencing
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Tagged 16S rRNA, classification, taxonomy
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