Metagenomes and Metagenome-Assembled Genomes from Tidal Lagoons at a New York City Waterfront Park
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Abstract
We report the sequencing and analysis of 15 shotgun metagenomes, including the reconstruction of 129 high-quality metagenome-assembled genomes, from tidal lagoons and bay water at Bush Terminal Piers Park in Brooklyn, NY sampled from July to September 2024.. Our metagenomic database for this site provides an important baseline for ongoing studies of the microbial communities of public parks and waterfront areas. In particular, we provide rich functional and taxonomic annotations that enable the use of these metagenomes and metagenome-assembled genomes for a wide variety of downstream applications.
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Our reconstructed MAGs had diverse taxonomic affiliations and functional content. Notably, 16 of our MAGs could not be classified at the genus level to anything in the GTDB v220 taxonomy.
Did you try BLASTing any of the contigs, or searching against assemblies in MGNify? You might try using sourmash as well to see if there are any other metagenomes that have similar species to try and get a hint as to what these are or where they occur. Including a reference that does something simialr!
https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1328083/full
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We obtained 1016 total bins, 129 of which were determined to be high quality with less than 5% contamination and being over 90% complete with the total number of contigs ranging from 8-692 and the average contig length ranging from 4,785-372,700bp (S1 Table; [22]). Another 366 were determined to be of medium quality (<10% contamination,>50% completeness). All bins have annotations, including trait data, but we restrict our discussion of results to our high-quality bins. Our high-quality bins span 10 phyla and at least 45 genera. A total of 16 high-quality bins could not be confidently assigned to a known genus and our lone bin from the Chlamydiota could not be assigned to a known family, potentially representing novel diversity at these taxonomic levels.
What fraction of your reads assembled? What fraction map back to bins?
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prokka
It might be worth looking into Bakta in the future for annotation
https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000685
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paired-end sequencing
How long? What was the average insert size?
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during low tide, when the site forms distinct inner and outer lagoons disconnected from the bay, with the oyster reef located in the inner lagoon
Do you have a hypothesis about how much the microbial communities might change based on sampling time? Is low time a particularly important distinguishing factor?
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metagenomic database
Is this a public website or downloadable data asset? (I assume that this will be answered later in the pub but it would be helpful to know upfront how other users can interact with this cool dataset!)
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