AJRCCM Islands perspective

[Katrine Whiteson]

Hi Guys,

It's not exactly July in Colorado anymore, but this Island Biogeography piece is still going strong. Paul really helped make it more punchy, Megan made a bunch of concrete suggestions for criteria that demonstrate that a sputum microbe is not just a contaminant, Heather Maughan (a scientist who is working as an editor with us: http://www.heathermaughan.ca/) did some wonders with the writing organization... I think we are close.

AJRCCM suggested a deadline of October 30th, and gave me a couple week extension. I'd like to submit next week. Please give this a final read and send comments by Monday Nov 11th.

A few small things:

1) Robby is working on Figure 1, new draft coming this week

2) the suggested length is 2500-3000 words, and we are now at 1850. So there is room for more, but as Paul and Peter remind me, we risk losing the punch in the message. 

3) There are also 37 refs, 50 are allowed, and it's possible some ref. contributions may have been lost in the many rounds of suggestions and edits. I left the refs in a format that includes author-date. I'll change it to the numbering found in AJRCCM papers later.

4) if you find anything missing or have suggestions about how to handle the author list, please let me know

thanks!

Katrine

[Jonathan Kirk Harris]

Katrine,
Excellent draft. I've made a few small suggestions, use as you like.

Kirk
________________________________________
From: cftellu...@googlegroups.com [cftellu...@googlegroups.com] On Behalf Of Katrine Whiteson [katrine...@gmail.com]
Sent: Tuesday, November 05, 2013 1:20 PM
To: cftellu...@googlegroups.com
Subject: AJRCCM Islands perspective

[mfip mfip]

Hi Katrine,

Hi Guys,

 

Very nice "DEF-version". I add some comments.

Cheers

Laurence

2013/11/5 Katrine Whiteson <katrine...@gmail.com>

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_______________________________________

Katrine Whiteson, PhD

http://www.whiteson.org/katrine/

949.241.7347 cell

[Robby Quinn]

Is this better for Fig.1? I am a microbiologist masquerading as an artist. I gave anonymous lung man his teeth as I see those as another source of inoculum with different microbes than the other regions of the upper airway.

RAQ

--
Robert Quinn, Ph.D

CFRI Postdoctoral Fellow

NLS 301, 5500 Campanile Dr, 

San Diego State University

San Diego, CA, 92182

[Jonathan Kirk Harris]

Looks good to me. I like the teeth included, and agree that's another potential source.

Kirk
________________________________________
From: cftellu...@googlegroups.com [cftellu...@googlegroups.com] On Behalf Of Robby Quinn [quinn...@gmail.com]
Sent: Wednesday, November 06, 2013 11:30 AM
To: Jonathan Kirk Harris; Ryan Hunter
Cc: Katrine Whiteson; cftellu...@googlegroups.com
Subject: Re: AJRCCM Islands perspective

Is this better for Fig.1? I am a microbiologist masquerading as an artist. I gave anonymous lung man his teeth as I see those as another source of inoculum with different microbes than the other regions of the upper airway.
RAQ

On Wed, Nov 6, 2013 at 6:42 AM, mfip mfip <mfip.d...@gmail.com<mailto:mfip.d...@gmail.com>> wrote:
Hi Katrine,
Hi Guys,

Very nice "DEF-version". I add some comments.
Cheers
Laurence

2013/11/5 Katrine Whiteson <katrine...@gmail.com<mailto:katrine...@gmail.com>>

Hi Guys,

It's not exactly July in Colorado anymore, but this Island Biogeography piece is still going strong. Paul really helped make it more punchy, Megan made a bunch of concrete suggestions for criteria that demonstrate that a sputum microbe is not just a contaminant, Heather Maughan (a scientist who is working as an editor with us: http://www.heathermaughan.ca/) did some wonders with the writing organization... I think we are close.

AJRCCM suggested a deadline of October 30th, and gave me a couple week extension. I'd like to submit next week. Please give this a final read and send comments by Monday Nov 11th.

A few small things:

1) Robby is working on Figure 1, new draft coming this week
2) the suggested length is 2500-3000 words, and we are now at 1850. So there is room for more, but as Paul and Peter remind me, we risk losing the punch in the message.
3) There are also 37 refs, 50 are allowed, and it's possible some ref. contributions may have been lost in the many rounds of suggestions and edits. I left the refs in a format that includes author-date. I'll change it to the numbering found in AJRCCM papers later.
4) if you find anything missing or have suggestions about how to handle the author list, please let me know

thanks!
Katrine


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_______________________________________
Katrine Whiteson, PhD
http://www.whiteson.org/katrine/

949.241.7347<tel:949.241.7347> cell

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Robert Quinn, Ph.D
CFRI Postdoctoral Fellow
NLS 301, 5500 Campanile Dr,
San Diego State University
San Diego, CA, 92182

[Megan Bergkessel]

I think the figure looks pretty good too.  The only change I might suggest is that the air around mr. lung man gets the same color as the mainland, and the mouth/teeth/trachea/sinuses get island colors.  It seems like the text compares the "outside of human" reservoir of microbes to the mainland, and the niches within the airway all to increasingly remote islands. 

-megan

[Megan Bergkessel]

Here are a few comments and suggestions for minor re-wording.  Of course disregard if you don't agree. I think in general that it couldn't hurt to give more background and fully flesh out transitions in a few places.  I tried to do that some, but there may be other places where it could help.  I agree with Ryan that it probably isn't necessary to show the re-analysis of the data from the Goddard paper - I think the other points made are plenty strong without it.  

-megan

[Doug's Email]

Katrine,

Ryan has been in Minnesota for just a few months!  check this out….   http://en.wikipedia.org/wiki/Minnesota_nice.

Seriously now,  I favor keeping the Goddard data in as long as it is done appropriately and with good intention.  I think the wording is gentle as it is.  I suggested alternative wording in this version that avoids the terms "extended analysis" or "reanalysis" that might make others more comfortable.  

I also think that investigators make data publicly available for a reason and that is to allow others to do exactly what we are doing to share perspectives of the same data.  I think its a healthy dialog….

Best

Doug

[Wagner, Brandie D]

Katerine,

 

My comments are attached. I think it reads well and does a good job of getting the main point across. I agree with the others that the re-analysis isn't necessary and think it may distract from the overall message because the results could be interpreted differently by different people. If you decide you want to keep it in then maybe Barb and I can work on better explaining our interpretation of the MDS plot.

 

Thanks so much for taking the lead on this, I think it is great that we could this venue to accomplish something useful for the whole group.

 

Brandie

[Megan Bergkessel]

Hi all,

I know I have missed the deadline for additional comments, but I have been thinking a lot about this and I think I made some re-arrangements and additions that help the MDS analysis contribute more strongly to our main points.  I have attached a new version that includes these changes and also responds to some of Brandie's comments, which were about sections that I had changed.  If people disagree with my changes or think they are too big this late in the game, my feelings will not be hurt :)  I just felt that I should put this out there, and we can take it or leave it.  Also, i explicitly referred to the little island biogeography graphs, so maybe they should be made a bit bigger in the figure.  Maybe they could replace the person-to-person island part of the figure, which is never really referred to in the text.  Below is a long editorial about why I thought the MDS analysis wasn't as strong as other parts of the text - I wrote it first and then figured I should just make the changes I was talking about instead of suggesting they be made by someone else.  Sorry to send this so late, but here it is...

-megan

editorial:

With respect to the re-analysis, I definitely agree that the approach in the text as it stands is perfectly respectful and civil, and I also agree that published data is really doing its job if it begins a discussion.  My main concern is that the re-analysis, and the associated text as it stands, does not really contribute to the point I think we are trying to make as strongly as many of the other parts of the paper.  I think that the authors of the paper would say that the MDS analysis confirms their point.  It's true that for some of the samples, the sputum communities are very similar to the lung communities, and for some of the samples, the sputum communities are not similar to the lung communities and are more similar to the throat communities.  They acknowledge this in the text of their paper as well.  They then point out that the sputum samples that are different than their corresponding lung communities are the ones that contain significant numbers of oral microbes, while the sputum samples that are similar to their lung communities are the ones dominated only by classical CF pathogens.  This is also precisely what the MDS shows.  In cases where both samples only have classical CF pathogens, they cluster together.  In cases where the sputum samples contain oral microbes, they cluster apart from their corresponding lung samples.  The authors never detect large numbers of oral microbes in the lung explant samples, and they detect oral microbes in sputum samples sometimes.  The MDS reflects this.  I think where we disagree with the authors is in the interpretation of these findings.  First, their result is essentially a negative one.  They fail to find oral microbes in their lung explant samples.  Their sample size is small.  This doesn't really prove anything.  Others have reported finding oral microbes in lung explant samples and as Kirk noted, trans-tracheal sampling found them in the large airway in the 80s, and I think most would agree that oral microbe colonization of lower airways is likely to be very heterogeneous if it happens. It is an overinterpretation of their data, I think, for them to claim that their failure to find large numbers of oral microbes in their small number of lung explant samples shows that all oral microbes found in sputum samples are contaminants from the upper airways.  Secondly, even if oral microbes are never found in large numbers in the lower airways, they can still have a large impact on the pathophysiology of the disease, due to interactions with the resident "classical" CF pathogens of the lower airways.  Because we don't yet understand these potential interactions, it would be a tragedy to discard or filter out the very data that could yield some insight, yet this is precisely what the authors are suggesting should be done.  They claim that because differences in 16S detection of oral microbe taxa doesn't correlate with disease state, it clearly isn't important.  This is just ludicrous, because it completely ignores the possibility that these microbes could have different activities at different times.  Just because 16S data doesn't by itself completely solve the puzzle of how different airway microbial communities interact, doesn't mean that it can't contribute a piece to the solution of that puzzle. Thirdly, their explanted lung samples themselves are a pretty extreme representation of the lung microbiota.  It may be clinically much more important to understand what is going on with parts of the lung that are still actively exchanging air with the upper airways, and that is not likely to be true of any of the lung regions they sampled.  I think it is intuitively easy to accept that the explanted regions they sampled are mostly mutually exclusive with sputum samples.  These lower airways in end stage disease are probably too clogged to ever get cleared by coughing, and sputum obviously comes from regions that are not too clogged to be cleared by coughing.  But I think it is still a completely open question which regions are more important to exacerbations and disease progression.  It seems to me that one could make a strong case that we would much rather understand the community dynamics of lung regions that are still exchanging with the upper airways, and that sputum may in fact be the best representation we have of those regions.  I think it is productive to then discuss analysis that could be done, going forward, to try to really understand where in the lungs sputum samples are coming from (has Becky published anything about her imaging techniques yet?) and to follow communities with frequent deep sequencing over time to get a better sense of the dynamics.  I think we do this in the opinion piece as it stands.  

What do other people think? 

[Jonathan Kirk Harris]

Hi all,
I like the new version. I accepted changes and cleared comments on areas that I thought were resolved (or couldn't really be resolved and should be removed from consideration). This was mainly to remove the clutter and make it easier to read. I think we're at a point where we just need to make the call on a couple sections and get this submitted.

that leaves the paragraph on page 3 where citations would be nice. However, I note that while I agree with the sentiment I'm unaware of specific citations. Thus, it maybe should just go as is.

The other sticking point is the "re-analysis" section. I'm fine with keeping this, but think we need to be careful with the wording. As stated it sounds like we're saying the initial analysis was deficient (why repeat otherwise?). When really we have the same answer, but favor the other side of the equivocal result. Laying out the specific result, 3/6 look similar but 3/6 don't is the main point we want/need to make. Maybe just using the equivalency point is adequate, and we can then say data presented using RF/MDS plots.

Thoughts?

Kirk
________________________________________
From: Megan Bergkessel [bergk...@gmail.com]
Sent: Thursday, November 14, 2013 4:49 PM
To: Wagner, Brandie D
Cc: Katrine Whiteson; Robby Quinn; Ryan Hunter; cftellu...@googlegroups.com; Jonathan Kirk Harris

Subject: Re: AJRCCM Islands perspective

Hi all,

I know I have missed the deadline for additional comments, but I have been thinking a lot about this and I think I made some re-arrangements and additions that help the MDS analysis contribute more strongly to our main points. I have attached a new version that includes these changes and also responds to some of Brandie's comments, which were about sections that I had changed. If people disagree with my changes or think they are too big this late in the game, my feelings will not be hurt :) I just felt that I should put this out there, and we can take it or leave it. Also, i explicitly referred to the little island biogeography graphs, so maybe they should be made a bit bigger in the figure. Maybe they could replace the person-to-person island part of the figure, which is never really referred to in the text. Below is a long editorial about why I thought the MDS analysis wasn't as strong as other parts of the text - I wrote it first and then figured I should just make the changes I was talking about instead of suggesting they be made by someone else. Sorry to send this so late, but here it is...

-megan

editorial:

With respect to the re-analysis, I definitely agree that the approach in the text as it stands is perfectly respectful and civil, and I also agree that published data is really doing its job if it begins a discussion. My main concern is that the re-analysis, and the associated text as it stands, does not really contribute to the point I think we are trying to make as strongly as many of the other parts of the paper. I think that the authors of the paper would say that the MDS analysis confirms their point. It's true that for some of the samples, the sputum communities are very similar to the lung communities, and for some of the samples, the sputum communities are not similar to the lung communities and are more similar to the throat communities. They acknowledge this in the text of their paper as well. They then point out that the sputum samples that are different than their corresponding lung communities are the ones that contain significant numbers of oral microbes, while the sputum samples that are similar to their lung communities are the ones dominated only by classical CF pathogens. This is also precisely what the MDS shows. In cases where both samples only have classical CF pathogens, they cluster together. In cases where the sputum samples contain oral microbes, they cluster apart from their corresponding lung samples. The authors never detect large numbers of oral microbes in the lung explant samples, and they detect oral microbes in sputum samples sometimes. The MDS reflects this. I think where we disagree with the authors is in the interpretation of these findings. First, their result is essentially a negative one. They fail to find oral microbes in their lung explant samples. Their sample size is small. This doesn't really prove anything. Others have reported finding oral microbes in lung explant samples and as Kirk noted, trans-tracheal sampling found them in the large airway in the 80s, and I think most would agree that oral microbe colonization of lower airways is likely to be very heterogeneous if it happens. It is an overinterpretation of their data, I think, for them to claim that their failure to find large numbers of oral microbes in their small number of lung explant samples shows that all oral microbes found in sputum samples are contaminants from the upper airways. Secondly, even if oral microbes are never found in large numbers in the lower airways, they can still have a large impact on the pathophysiology of the disease, due to interactions with the resident "classical" CF pathogens of the lower airways. Because we don't yet understand these potential interactions, it would be a tragedy to discard or filter out the very data that could yield some insight, yet this is precisely what the authors are suggesting should be done. They claim that because differences in 16S detection of oral microbe taxa doesn't correlate with disease state, it clearly isn't important. This is just ludicrous, because it completely ignores the possibility that these microbes could have different activities at different times. Just because 16S data doesn't by itself completely solve the puzzle of how different airway microbial communities interact, doesn't mean that it can't contribute a piece to the solution of that puzzle. Thirdly, their explanted lung samples themselves are a pretty extreme representation of the lung microbiota. It may be clinically much more important to understand what is going on with parts of the lung that are still actively exchanging air with the upper airways, and that is not likely to be true of any of the lung regions they sampled. I think it is intuitively easy to accept that the explanted regions they sampled are mostly mutually exclusive with sputum samples. These lower airways in end stage disease are probably too clogged to ever get cleared by coughing, and sputum obviously comes from regions that are not too clogged to be cleared by coughing. But I think it is still a completely open question which regions are more important to exacerbations and disease progression. It seems to me that one could make a strong case that we would much rather understand the community dynamics of lung regions that are still exchanging with the upper airways, and that sputum may in fact be the best representation we have of those regions. I think it is productive to then discuss analysis that could be done, going forward, to try to really understand where in the lungs sputum samples are coming from (has Becky published anything about her imaging techniques yet?) and to follow communities with frequent deep sequencing over time to get a better sense of the dynamics. I think we do this in the opinion piece as it stands.

What do other people think?

On Sun, Nov 10, 2013 at 11:54 AM, Wagner, Brandie D <Brandie...@ucdenver.edu<mailto:Brandie...@ucdenver.edu>> wrote:
Katerine,

My comments are attached. I think it reads well and does a good job of getting the main point across. I agree with the others that the re-analysis isn't necessary and think it may distract from the overall message because the results could be interpreted differently by different people. If you decide you want to keep it in then maybe Barb and I can work on better explaining our interpretation of the MDS plot.

Thanks so much for taking the lead on this, I think it is great that we could this venue to accomplish something useful for the whole group.

Brandie

From: cftellu...@googlegroups.com<mailto:cftellu...@googlegroups.com> [mailto:cftellu...@googlegroups.com<mailto:cftellu...@googlegroups.com>] On Behalf Of Megan Bergkessel
Sent: Saturday, November 09, 2013 2:05 AM
To: Jonathan Kirk Harris
Cc: Robby Quinn; Ryan Hunter; Katrine Whiteson; cftellu...@googlegroups.com<mailto:cftellu...@googlegroups.com>

Subject: Re: AJRCCM Islands perspective

Here are a few comments and suggestions for minor re-wording. Of course disregard if you don't agree. I think in general that it couldn't hurt to give more background and fully flesh out transitions in a few places. I tried to do that some, but there may be other places where it could help. I agree with Ryan that it probably isn't necessary to show the re-analysis of the data from the Goddard paper - I think the other points made are plenty strong without it.
-megan

On Thu, Nov 7, 2013 at 2:43 PM, Megan Bergkessel <bergk...@gmail.com<mailto:bergk...@gmail.com>> wrote:
I think the figure looks pretty good too. The only change I might suggest is that the air around mr. lung man gets the same color as the mainland, and the mouth/teeth/trachea/sinuses get island colors. It seems like the text compares the "outside of human" reservoir of microbes to the mainland, and the niches within the airway all to increasingly remote islands.
-megan

On Wed, Nov 6, 2013 at 11:57 AM, Jonathan Kirk Harris <Jonatha...@colorado.edu<mailto:Jonatha...@colorado.edu>> wrote:
Looks good to me. I like the teeth included, and agree that's another potential source.

Kirk
________________________________________

From: cftellu...@googlegroups.com<mailto:cftellu...@googlegroups.com> [cftellu...@googlegroups.com<mailto:cftellu...@googlegroups.com>] On Behalf Of Robby Quinn [quinn...@gmail.com<mailto:quinn...@gmail.com>]

Sent: Wednesday, November 06, 2013 11:30 AM
To: Jonathan Kirk Harris; Ryan Hunter

Cc: Katrine Whiteson; cftellu...@googlegroups.com<mailto:cftellu...@googlegroups.com>

Subject: Re: AJRCCM Islands perspective
Is this better for Fig.1? I am a microbiologist masquerading as an artist. I gave anonymous lung man his teeth as I see those as another source of inoculum with different microbes than the other regions of the upper airway.
RAQ

On Wed, Nov 6, 2013 at 6:42 AM, mfip mfip <mfip.d...@gmail.com<mailto:mfip.d...@gmail.com><mailto:mfip.d...@gmail.com<mailto:mfip.d...@gmail.com>>> wrote:
Hi Katrine,
Hi Guys,

Very nice "DEF-version". I add some comments.
Cheers
Laurence

2013/11/5 Katrine Whiteson <katrine...@gmail.com<mailto:katrine...@gmail.com><mailto:katrine...@gmail.com<mailto:katrine...@gmail.com>>>

Hi Guys,

It's not exactly July in Colorado anymore, but this Island Biogeography piece is still going strong. Paul really helped make it more punchy, Megan made a bunch of concrete suggestions for criteria that demonstrate that a sputum microbe is not just a contaminant, Heather Maughan (a scientist who is working as an editor with us: http://www.heathermaughan.ca/) did some wonders with the writing organization... I think we are close.

AJRCCM suggested a deadline of October 30th, and gave me a couple week extension. I'd like to submit next week. Please give this a final read and send comments by Monday Nov 11th.

A few small things:

1) Robby is working on Figure 1, new draft coming this week
2) the suggested length is 2500-3000 words, and we are now at 1850. So there is room for more, but as Paul and Peter remind me, we risk losing the punch in the message.
3) There are also 37 refs, 50 are allowed, and it's possible some ref. contributions may have been lost in the many rounds of suggestions and edits. I left the refs in a format that includes author-date. I'll change it to the numbering found in AJRCCM papers later.
4) if you find anything missing or have suggestions about how to handle the author list, please let me know

thanks!
Katrine


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_______________________________________
Katrine Whiteson, PhD
http://www.whiteson.org/katrine/

949.241.7347<tel:949.241.7347><tel:949.241.7347<tel:949.241.7347>> cell

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Robert Quinn, Ph.D
CFRI Postdoctoral Fellow
NLS 301, 5500 Campanile Dr,
San Diego State University
San Diego, CA, 92182

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[Katrine Whiteson]

Hi Guys,

Thanks for pushing this forward Kirk...

I'm working to include some suggestions from Paul Rainey to give the piece more of a narrative. I hope to send it today, I just have had manuscript/grant/job application deadlines sneaking up on me.

The re-analysis is still tricky to handle, I like the idea of pointing out that 3/6 look similar. I think even the 3 that are different still are good indicators of the main microbes in the lung too.

:)
Katrine

> To unsubscribe from this group and stop receiving emails from it, send an email to cftelluride20...@googlegroups.com.

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> <IslandsOpinionPieceNov4jkh_rch_kw_mb_bw2jkh.docx>

[Katrine Whiteson]

Hi everyone,

Thanks again Kirk. Like I said, I am working on the flow and narrative with Paul Rainey. Forest is back too, I'm hoping to run it by him tomorrow, we usually have lots of CF meetings on Fridays at SDSU. Then I'll send it around one final time and submit.

I am getting the submission going on the AJRCCM website, and it reminds me that we definitely need reviewers. You offered this at one point... how about:

Gary Huffnagle

Frederic Bushman

GB Rogers

KD Bruce

Susan Lynch

John Lipuma

other ideas??

thanks!

Katrine

_______________________________________

Katrine Whiteson, PhD

http://www.whiteson.org/katrine/

949.241.7347 cell

On Nov 19, 2013, at 8:11 AM, Jonathan Kirk Harris wrote:

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<IslandsOpinionPieceNov4jkh_rch_kw_mb_bw2jkh.docx>

[Ryan Hunter]

I would propose any of the Danish group (Soren, Helle) that study the upper airways and CF sinuses.  

Marianne Muhlebach at UNC might also take an interest.

From: cftellu...@googlegroups.com<mailto:cftellu...@googlegroups.com> [mailto:cftelluride2013@googlegroups.com<mailto:cftellu...@googlegroups.com>] On Behalf Of Megan Bergkessel
Sent: Saturday, November 09, 2013 2:05 AM
To: Jonathan Kirk Harris
Cc: Robby Quinn; Ryan Hunter; Katrine Whiteson; cftellu...@googlegroups.com<mailto:cftellu...@googlegroups.com>

Subject: Re: AJRCCM Islands perspective

Here are a few comments and suggestions for minor re-wording.  Of course disregard if you don't agree. I think in general that it couldn't hurt to give more background and fully flesh out transitions in a few places.  I tried to do that some, but there may be other places where it could help.  I agree with Ryan that it probably isn't necessary to show the re-analysis of the data from the Goddard paper - I think the other points made are plenty strong without it.
-megan

On Thu, Nov 7, 2013 at 2:43 PM, Megan Bergkessel <bergk...@gmail.com<mailto:bergk...@gmail.com>> wrote:
I think the figure looks pretty good too.  The only change I might suggest is that the air around mr. lung man gets the same color as the mainland, and the mouth/teeth/trachea/sinuses get island colors.  It seems like the text compares the "outside of human" reservoir of microbes to the mainland, and the niches within the airway all to increasingly remote islands.
-megan

On Wed, Nov 6, 2013 at 11:57 AM, Jonathan Kirk Harris <Jonatha...@colorado.edu<mailto:Jonatha...@colorado.edu>> wrote:
Looks good to me. I like the teeth included, and agree that's another potential source.

Kirk
________________________________________
From: cftellu...@googlegroups.com<mailto:cftellu...@googlegroups.com> [cftellu...@googlegroups.com<mailto:cftellu...@googlegroups.com>] On Behalf Of Robby Quinn [quinn...@gmail.com<mailto:quinn...@gmail.com>]
Sent: Wednesday, November 06, 2013 11:30 AM
To: Jonathan Kirk Harris; Ryan Hunter
Cc: Katrine Whiteson; cftellu...@googlegroups.com<mailto:cftellu...@googlegroups.com>
Subject: Re: AJRCCM Islands perspective
Is this better for Fig.1? I am a microbiologist masquerading as an artist. I gave anonymous lung man his teeth as I see those as another source of inoculum with different microbes than the other regions of the upper airway.
RAQ

On Wed, Nov 6, 2013 at 6:42 AM, mfip mfip <mfip.d...@gmail.com<mailto:mfip.d...@gmail.com><mailto:mfip.delhaes@gmail.com<mailto:mfip.d...@gmail.com>>> wrote:
Hi Katrine,
Hi Guys,

Very nice "DEF-version". I add some comments.
Cheers
Laurence

2013/11/5 Katrine Whiteson <katrine...@gmail.com<mailto:katrine...@gmail.com><mailto:katrinewhiteson@gmail.com<mailto:katrine...@gmail.com>>>

Hi Guys,

It's not exactly July in Colorado anymore, but this Island Biogeography piece is still going strong. Paul really helped make it more punchy, Megan made a bunch of concrete suggestions for criteria that demonstrate that a sputum microbe is not just a contaminant, Heather Maughan (a scientist who is working as an editor with us: http://www.heathermaughan.ca/) did some wonders with the writing organization... I think we are close.

AJRCCM suggested a deadline of October 30th, and gave me a couple week extension. I'd like to submit next week. Please give this a final read and send comments by Monday Nov 11th.

A few small things:

1) Robby is working on Figure 1, new draft coming this week
2) the suggested length is 2500-3000 words, and we are now at 1850. So there is room for more, but as Paul and Peter remind me, we risk losing the punch in the message.
3) There are also 37 refs, 50 are allowed, and it's possible some ref. contributions may have been lost in the many rounds of suggestions and edits. I left the refs in a format that includes author-date. I'll change it to the numbering found in AJRCCM papers later.
4) if you find anything missing or have suggestions about how to handle the author list, please let me know

thanks!
Katrine


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Katrine Whiteson, PhD
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