EMeyer Posted January 28, 2019 Share Posted January 28, 2019 (edited) Hi everyone, Researchers analyze the microbial communities of animals or aquariums using DNA sequencing. If you, as a hobbyist, had access to a service that could measure the microbiome in your tank: what question would you be most curious in asking, with this test? We have some serious reef keeping expertise on this forum and I'm curious to hear your perspective on applications for a test like this. Thanks for any insights you can share. -Eli Edited January 28, 2019 by EMeyer 1 Quote Link to comment Share on other sites More sharing options...
TheClark Posted January 29, 2019 Share Posted January 29, 2019 Interesting! I would want to establish a baseline on known successful tanks I have personally seen. The best of the best. So that there was something to compare the results to. Because the thing is, I have no idea what I would do with the results otherwise without something to compare against. 4 Quote Link to comment Share on other sites More sharing options...
Manny Tavan Posted January 29, 2019 Share Posted January 29, 2019 (edited) I want to know how much of my own dna is now part of the reef Edited January 29, 2019 by Manny Tavan 1 2 Quote Link to comment Share on other sites More sharing options...
SuncrestReef Posted January 29, 2019 Share Posted January 29, 2019 1 hour ago, Manny Tavan said: I want to know how much of my own dna is now part of the reef Or how much of the reef DNA is now part of me? 😬 1 Quote Link to comment Share on other sites More sharing options...
EMeyer Posted January 29, 2019 Author Share Posted January 29, 2019 2 hours ago, TheClark said: Interesting! I would want to establish a baseline on known successful tanks I have personally seen. The best of the best. So that there was something to compare the results to. Because the thing is, I have no idea what I would do with the results otherwise without something to compare against. Absolutely. I think both hobbyist reef tanks and coral aquaculture tanks will be interesting comparisons. Thanks, thats exactly the kind of question I'm looking for. 1 Quote Link to comment Share on other sites More sharing options...
albertareef Posted January 29, 2019 Share Posted January 29, 2019 24 minutes ago, EMeyer said: Absolutely. I think both hobbyist reef tanks and coral aquaculture tanks will be interesting comparisons. Thanks, thats exactly the kind of question I'm looking for. Indeed it would be interesting to see if one could identify a profile that was indicative of “successful” tanks. 1 Quote Link to comment Share on other sites More sharing options...
milesmiles902 Posted January 29, 2019 Share Posted January 29, 2019 3 hours ago, EMeyer said: Hi everyone, Researchers analyze the microbial communities of animals or aquariums using DNA sequencing. If you, as a hobbyist, had access to a service that could measure the microbiome in your tank: what question would you be most curious in asking, with this test? We have some serious reef keeping expertise on this forum and I'm curious to hear your perspective on applications for a test like this. Thanks for any insights you can share. -Eli What shouldn't we have in our aquarium. Quote Link to comment Share on other sites More sharing options...
milesmiles902 Posted January 29, 2019 Share Posted January 29, 2019 Also, isn't there flaws with this? Don't they have to assemble the DNA fragments from a single colony using PCR? Won't the most competitive plated species out compete the others? Quote Link to comment Share on other sites More sharing options...
milesmiles902 Posted January 29, 2019 Share Posted January 29, 2019 Quote Link to comment Share on other sites More sharing options...
EMeyer Posted January 29, 2019 Author Share Posted January 29, 2019 9 hours ago, milesmiles902 said: Also, isn't there flaws with this? Don't they have to assemble the DNA fragments from a single colony using PCR? Won't the most competitive plated species out compete the others? Good question. Nope, modern methods for studying microbial diversity don't rely on plating or culturing at all. We directly extract DNA from the sample, amplify the genetic markers with PCR, and sequence the resulting DNA millions of reads at a time. The results are not perfectly quantitative for comparing between different bugs, but very good for comparing frequency of a partciular bug between samples. And theyre not affected by culturability. 2 Quote Link to comment Share on other sites More sharing options...
milesmiles902 Posted January 30, 2019 Share Posted January 30, 2019 Evaluating Methods for Studying Microbial Biodiversity As mentioned above, nearly all of the publications addressing the evaluation of methods for studying microbial biodiversity (theme Methods) focused on evaluating laboratory methods for characterizing microorganisms or their DNA. Nevertheless, we could distinguish between methods that were evaluated based on environmental samples and those that were evaluated based on strains from collections. For the former, we noted whether multiple independent samples were employed in the study, and for the latter, we noted whether an independent collection of strains was used to validate the method (Fig. 2). Among the 94 publications analyzed under this theme, 85% were based on environmental samples (aliquots of water or soil, for example) and the remainder were based on strains from collections to evaluate methods of characterization. For the studies employing environmental samples, about 75% exploited multiple samples as the basis for evaluating the method. In the other 25% of studies, the evaluation of the method was based on only a single environmental sample. None of the studies employing strains from laboratories or national collections validated their conclusion with results from a second independent collection of strains. In some cases, independent collections have been combined to determine the genetic diversity within a given species. Tamplin et al. (259) used two laboratory collections (53 environmental and 78 clinical isolates) to determine the genetic variability within Vibrio vulnificus. https://mmbr.asm.org/content/66/4/592 Quote Link to comment Share on other sites More sharing options...
milesmiles902 Posted January 30, 2019 Share Posted January 30, 2019 On 1/28/2019 at 4:32 PM, TheClark said: Interesting! I would want to establish a baseline on known successful tanks I have personally seen. The best of the best. So that there was something to compare the results to. Because the thing is, I have no idea what I would do with the results otherwise without something to compare against. As stated in the article, having a backed database of all strains is critical to evaluating the quality of a micro-biome. Quote Link to comment Share on other sites More sharing options...
TheClark Posted January 30, 2019 Share Posted January 30, 2019 This thread is getting deep! Glad you can hang Miles, I will just observe Quote Link to comment Share on other sites More sharing options...
EMeyer Posted January 30, 2019 Author Share Posted January 30, 2019 <1% of marine microbes can be cultured. Focusing on culturable species only is incredibly limiting, which is why modern research has stopped focusing on them and now uses DNA sequencing to study all the bugs instead. Obviously there is huge value in working with the culturable strains, for functional studies, but the huge and growing field of microbiomics now uses DNA sequencing for most work. Here are some of my questions: Does adding bacteria in a bottle actually change the microbiome of your tank? Does starting with live rock lead to a more diverse microbiome? How do commonly used aquarium supplements affect the microbiome? Could probiotics (bacterial food) be used to deliberately increase microbial diversity? Instead of asking whether my new tank is cycled in an indirect way, by measuring nutrient levels with terribly inaccurate hobbyist kits, can we use direct measurements of the microbiome? And I share the interest in the question already brought up -- how does my tank's microbiome compare to that of a wildly successful SPS reef tank? What else would people be curious to ask using this technology, if it were to suddenly one day become available for the aquarium hobby? 3 Quote Link to comment Share on other sites More sharing options...
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