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Cellular and Organismic Networks

16S2Genome: Genomic traits for 16S rDNA microbiota studies

Posted on April 2, 2014February 2, 2018

Molecular sequencing techniques help to understand microbial biodiversity with regard to species richness, assembly structure and function. In this context, available methods are barcoding, metabarcoding, genomics and metagenomics. The first two are restricted to taxonomic assignments, whilst genomics only refers to functional capabilities of a single organism. Metagenomics by contrast yields information about organismal and functional diversity of a community. However currently it is very demanding regarding labour and costs and thus not applicable to most laboratories. Here, we show in a proof-of-concept that computational approaches are able to retain functional information about microbial communities assessed through 16S rDNA (meta)barcoding by referring to reference genomes. We developed an automatic pipeline to show that such integration may infer preliminary or supplementary genomic content of a community.

Reference: Keller A, Horn H, Förster F, Schultz J. (2014) Computational integration of genomic traits into 16S rDNA microbiota sequencing studies. Gene. 549:1 186–191

Github: https://github.com/molbiodiv/16S2Genome

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CiyaTheFox
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alinecmar Aline C. Martins @alinecmar ·
2 Sep

Happy to share our paper on stingless bees foraging behavior on the Cerrado biodiversity hotspot!
Read and spread! 🐝🌼
With Carol Proença Fernanda Carvalho @TNCVasconcelos @ajcaguiar @CiyaTheFox
And other amazing students and colleagues

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biorxivpreprint bioRxiv @biorxivpreprint ·
23 Jun

Opportunistic bacteria of grapevine crown galls are equipped with the genomic repertoire for opine utilization https://biorxiv.org/cgi/content/short/2023.06.20.545721v1 #bioRxiv

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ciyathefox Alexander Keller @ciyathefox ·
15 Jun

Semi-automated curation and manual addition of sequences to build reliable and extensive reference databases for ITS2 vascular plant DNA (meta-)barcoding

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alinecmar Aline C. Martins @alinecmar ·
8 Jun

New preprint

Contrasting patterns of foraging behavior in Neotropical stingless bees using pollen and honey metabarcoding

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geobiodiversity Senckenberg Research @geobiodiversity ·
30 May

#Invasive alien species not only colonize foreign regions, but they can also carry #invasive #microbiomes on their skin and in their gut. This may pose an undiscovered threat to native ecosystems, according to a recent study. 👉http://sgn.one/m8z
#SenckenbergScience

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