Summary

After talking to fellow researchers at IWA-MEWE and beyond, I have created a Slack for our research community that I hope will facilitate more communication outside of conferences. I was inspired by several other great Slacks (Anvi’o and Microbial ‘omics), and since these already exist, the drinking water microbiome Slack will not be a bioinformatics help forum. Instead, I’d love to see it used as a place where we can offer feedback on preliminary experimental designs, work toward the standardization and scientific rigor needed for our methods to be useful to the water industry, and informally discuss challenges in our field.

Join drinking-water-omics slack!

Rationale

DNA sequencing methods featured prominently throughout the International Water Association-Microbial Ecology and Water Engineering Specialty Conference (IWA-MEWE), including in drinking water. The multi-omics workshop led by Trina McMahon, Elizabeth McDaniel and others yielded useful discussions about methods and highlighted some ongoing struggles around use of multi-omics in water engineering. In light of the importance of these discussions, I’ve been thinking about ways that the microbial ecology and water engineering community can continue to communicate beyond conferences and publications. I found myself wondering what could happen if we communicated more at the beginning of and throughout our research projects, rather than solely at conferences and through publications of completed studies. To me, the beautiful thing about environmental engineering is that we aren’t working to be the “first in the field” so much as we are working to find new ways to improve treatments, quantify risks, and reach new fundamental understandings. Hence, our community is open to sharing information more than in other fields of science. However, we are often limited in funding relative to the scale of the topics we study. The combination of these factors favors and necessitates more frequent communication and broader collaboration.

I believe we need a place to make these connections throughout all phases of our research, and that this communication platform should be equally accessible to everyone in the international drinking water research community, including students, postdocs, researchers, and faculty. I propose that to accomplish this, we create an online forum using Slack.

Benefits of an online forum:

• Maximize our impact by using shared methods so that results from different studies can be compared
• Improve the quality of research in our field by receiving and providing feedback at various stages
• Extend the opportunity for discussion outside of our immediate networks, especially internationally
• Provide resources to researchers/labs that are new to sequencing-based methods (and complementary methods)

In particular, the issue of methodological standardization in drinking water microbiome research could be a unifying topic of discussion across the forum. A recent workshop (NSF, March 2018) led to a call for a drinking water microbiome consortium that would facilitate standardization of methods (Hull et al. 2019). Similarly, Zhang and Liu 2019 comment that, “…studies have strongly suggested that variation in microbiomes from different samples could be caused by biases associated with procedures in sampling, DNA extraction, sequencing, and data analysis. Action: This highlights an urgent need to call for collaborative actions to standardize analytical procedures for future data comparison among studies on drinking water microbiomes.” To date, these conversations have taken place amongst a subset of practitioners. To find real solutions will require input and discussion across the broader research community, and the opportunity for successful solutions to be shared in real-time.

But what if standardization diminishes originality and inventiveness in our investigations? I don’t think it’s likely that one method will “take over” because there won’t be one method that works for all studies. I hope that users of the forum will encourage each other to find the best method for their experimental question, rather than a one-size-fits-all approach. Having a forum can keep us on our toes to develop and share new solutions to problems that we encounter with existing methods. It can also provide a place to discuss biases we observe as we test new methods. Finally, this forum can allow a diversity of perspectives to be heard, pushing us to engage more with each other. Based on what I heard at IWA-MEWE, the following major challenges for scientific/engineering practice in drinking water microbiome research might be good broader discussion topics:

• How do we get from “who is there” to a full picture of a system? In particular, activity is very hard to assess in the drinking water environment.
• How do we obtain actionable results?
• How can we establish what is “safe” and “normal” in a drinking water treatment facility or distribution system?
• How do we communicate our work to utilities and regulators (and to the public)?

Why Slack and not a different medium?

• To allow for more technical conversations than Twitter
• To increase access to discussions that typically occur over email (e.g. asking another lab for a protocol or for tips on reproducing something they published), particularly across universities and countries
• Because ResearchGate, BioStars, and StackOverflow are too general for these purposes

Details: drinking-water-microbiome slack

Summary: A public forum for discussions about drinking water microbiome work in progress. Goals: foster collaboration, exchange methods, and work toward standardization and reproducibility.

Ground rules: Please engage in respectful conversation, cite sources in your posts (either say it’s your own unpublished work/opinion, or cite a source), and acknowledge all help received here in future publications/presentations.

Possible channels:

• Experimental design - place for peer review of designs
  • Replicates and controls vs. time/cost
• Sampling methods - discuss biomass sampling (filtration and biofilm) for DNA extraction
  • How to include controls and account for contamination
• DNA extraction from drinking water biomass - share your unpublished/unpublishable pre-experiments
  • How to include controls and account for contamination
• Sequencing - methods and technologies
• Physicochemical data - what minimum info is required?
• Test methods - find partners willing to test your methods on their samples or your samples with their methods
• Match methods - find partners in other labs who will use matching methods on similar systems for cross-comparability
• Viability - share ideas for how to address the influence of DNA/RNA from non-viable organisms in sequencing and other non-culture-based microbial methods
• Bioinformatic analyses:
  • Decontamination
  • Assembly methods
  • Statistical analyses to apply
• Major challenges for scientific/engineering practice in drinking water microbiome research

References

Hull, N. M., Ling, F., Pinto, A. J., Albertsen, M., Jang, H. G., Hong, P.-Y., et al. (2019). Drinking Water Microbiome Project: Is it Time? Trends in Microbiology, 27(8), 670–677. http://doi.org/10.1016/j.tim.2019.03.011

NSF workshop 3/2018. Advancing understanding of Microbiomes in Drinking Water Distribution Systems and Premise Plumbing Using Meta-omics Techniques.

Zhang, Y., & Liu, W.-T. (2019). The application of molecular tools to study the drinking water microbiome – Current understanding and future needs. Critical Reviews in Environmental Science and Technology, 49(13), 1188–1235. http://doi.org/10.1080/10643389.2019.1571351