I had similar concerns as offline colleague #2 noted here with regard to the projected outcomes of the project:
in response to "This study will help in the development of strategies to manage the development of antimicrobial and antibiotic resistance in an intensive housing environment." How? Unless you were comparing differing strategies- cleaning methods, disinfectant use, housing type etc within the same environment. This study will help understand the presence or absence and quantitative information of whatever you are looking for but not sure how much further you can go with this project.
I really want us to be clear about exactly what are the positive outcomes (or potential outcomes) of the project and what are not. In addition to the comments above I'll make my own. The proposal says:
By identifying what bacteria and fungi occur here, we can begin to understand sources for these communities (such as animal host, soil, air, water)
I can see that this research will help us understand what microbes are found in an animal shelter versus what microbes are not. But, how does it allow you to tell if the source is animal host, soil, air, or water? Furthermore, why is this useful to know?
and identify potential effects that different environmental factors may have on microbial persistence in these building reservoirs (such as use of disinfectants, proximity to windows, moisture, sunlight). These findings can help to inform practices within animal shelters such as the use of ventilation and disinfectants to protect animal health.
Will there really be a meaningful differentiation between samples in the amount of disinfectants that were used? Wouldn't each kennel basically have the same profile as far as disinfectants, moisture, light, etc? And even if they didn't — do the microbes not move around, from one kennel to another?
If we were really going to help inform animal shelters on the use of ventilation and disinfectants I'd think we'd have to to characterize the microbial communities across multiple shelters that had varying practices. Either that or setup controlled experiments within one shelter. Right?
This also implies that certain microbial communities are "bad" and certain communities are "good". I just want to confirm that there could in fact be a set of results where we could definitively recommend to shelters that they change their practices to X. If that outcome is not possible I don't think it can be claimed that we are helping inform practices within animal shelters.
Thanks for reading the proposal and taking the time to comment on it.
I provided the two offline reviewers' comments in the spirit of openness. Typically I will have several people read a proposal before it is submitted as I did here. In this case, I have provided the initial first draft of the proposal, so there are some simple things that should be corrected. In fact, I have already started to revise the proposal based on these comments. But I'm not sure how to revise it online without changing the original document. It seems like it would be useful to have different versions of the proposal to see how it changes in response to these discussions. Or maybe I am missing how to do this? Also I wasn't sure if I should change it while some of you are reading the current version. So for now I have let the first draft online as it is.
When I wrote the somewhat careless statement that "This study will help in the development of strategies to manage the development of antimicrobial and antibiotic resistance in an intensive housing environment," this is what I was thinking about. If we find evidence for resistance genes that are associated with disinfectants that are commonly used in the animal shelter environment (and also genes for antibiotic resistance), this background information will be very informative in guiding future studies to develop specific strategies to manage the development of such resistance in bacterial communities that reside on surfaces in animal shelters. I have some specific ideas for this but they are a bit beyond the scope of this project. In any case, I have already revised this statement (and the similar one later in the proposal) offline but await further input before I upload a revised version of the proposal. In addition, it is clarifying for me to see how different people respond to it.
We can use bacterial source tracking to identify potential sources for some of the surface communities based on the many available reference collections for soil, air, water, human and animal associated communities. I did not propose collecting additional samples for that purpose here due to the limited level of funding for this project. But we can use publicly available data to begin to address potential sources.
Why do we want to identify the biogeography of bacteria in buildings? This is something that is not always clear to people who are not ecologists. Microbial ecologists believe that we need to understand what is there and how diversity varies across these environments before we can understand how such communities might change in response to environmental variation or potential interventions, such as a new approach to ventilation or disinfection. In addition to who is there, the traits exhibited by these communities can be of interest, i.e., resistance genes.
This study is not designed to compare different disinfection strategies in the different kennels. Instead it is designed to characterize the communities found living on surfaces in the dog housing area. It is designed to capture the range of variation in the dog kennels, which do differ in amount of light, humidity and proximity to windows and exits. I would also like to use data loggers to measure the amount of variation in temperature and humidity in the kennels.
This pilot study is not funded at a level to allow for comparisons of multiple shelters with different strategies. It would take something like $25,000 to do such a study (without including salaries). The project proposed here will already cost about twice as much as the current budget so I will probably drop the fungal characterization, depending on the feedback that we get from the community here.
I didn't mean to imply anything about good or bad microbial communities. What I am thinking about here is managing for the evolution and spread of antibiotic and disinfectant resistance genes in bacterial communities found on surfaces in animal shelters. First we have to start by characterizing who is there and whether they have the traits of interest.
Thanks for the constructive feedback. I will modify the proposal accordingly.
Jesse Spaulding: ThinkLab now tracks a version history for proposals. If you have a new version of the proposal I suggest you update ThinkLab with it. There will be a page you can link us to that will highlight the differences between the new version and the old version.
Jesse Spaulding: Just FYI - You no longer need to use @username to invite people to a discussion. If they are following the project they will be notified of any new comments via a daily or biweekly 'new activity' email. The @username feature can be used if you'd like to insure that the user is notified of your comment immediately. Note that users following a discussion thread will typically be notified of new comments in that thread straight away anyway.
I have already started to revise the proposal based on these comments. But I'm not sure how to revise it online without changing the original document. It seems like it would be useful to have different versions of the proposal to see how it changes in response to these discussions.
Thanks. Yes I agree having multiple versions would be useful. We will work on adding it before public launch. For now you'll just have to use whatever strategy you think is best given the limitations of the system.
With regard to the rest of the comments. I've probably reached my limit in being able to make any useful response without understanding the science.
I would just say that if any of the outcomes you are talking about refer to future studies that could be based on yours then we should probably describe them as such. We don't want people thinking they are direct outcomes from your study if they are not.