Fwd: idea for a PULMONARY AND CRITICAL CARE PERSPECTIVE

[Katrine Whiteson]

Hi Everyone,

Good news from AJRCCM! We are invited to submit a perspective. No word from PLOS Biology yet, so we may be faced with too many choices :).

I am attaching the latest drafts with comments incorporated from some of you. I'm still hoping to get all your comments by Wednesday October 2nd.

Also, to be included as an author, in addition to providing comments please email me the following info - then I know for sure you are happy to have your name behind this...

thanks!

Katrine

Author info

Name as you would like it to appear:

email:

Department:

Institution:

Street Address:

City:

Zip:

[Jonathan Kirk Harris]

Kathrine,
That's excellent news. I've added comments and edits to the attached version. Author info:

Name as you would like it to appear: J. Kirk Harris
email: jonatha...@ucdenver.edu
Department: Pediatrics
Institution: University of Colorado Denver
Street Address: 13123 E. 16th Ave, Box B395
City: Aurora, CO
Zip: 80045

________________________________________
From: cftellu...@googlegroups.com [cftellu...@googlegroups.com] On Behalf Of Katrine Whiteson [katrine...@gmail.com]
Sent: Saturday, September 28, 2013 5:14 PM
To: cftellu...@googlegroups.com
Cc: Laurence.Delhaes Delhaes; Forest Rohwer
Subject: Fwd: idea for a PULMONARY AND CRITICAL CARE PERSPECTIVE

[Megan Bergkessel]

Hi all,

Apologies for being a little late to the party here - I think the piece is really great, and I am so glad that you have taken the lead in putting it together, Katrine!  I added a bunch of small edits that I hope improve readability a little bit for an audience that might not think about these topics as much.  I think everything I added was already more or less implied, but I thought it might be a little clearer with these things more spelled out.  I also added a couple transitional sentences to help smooth the connections between paragraphs.  Feel free to disregard any of it if you think it doesn't help. 

-megan

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[fe...@rohan.sdsu.edu]

Hi Katrine,

Here are some minor "readability" edits for the perspective.
Unfortunately, I have an older version of msword and some of the spacing
got munched in the conversion. I didn't bother to try to correct it,
assuming you'd just take the edits you want and apply them to your
latest copy. I used the last version from Kirk as my base (as the file
name implies).

I have some concern that the points that are most important to you are
not clearly enough stated and emphasized. I know you want to avoid
stomping on toes, but the important points need to stand out.
Unfortunately, at this point, there is not a smooth flow and readability
to the paper, and some of the important points may be lost in the
struggle to read and understand what's there. This is often a
difficulty with so many authors...so I'm glad you're the one that's
pulling it all together rather than me! :)

I asked Carol to read the paper and then asked her what she thought the
intent was. Her response was that the CF lung should be viewed as a
microbial community that may be influenced by other proximally located
microbial communities. She didn't feel there was much of a case
presented for sputum being uncontaminated or minimally contaminated, or
how that contamination might be dealt with.

So, is the intent just to present the perspective that the CF lung
microbial community may be influenced by other microbial communities in
or around the body? Or is it to also make a case for sputum as a viable
method for sampling that community? If it's the later, then we need to
try to make that clearer to the reader.

As I started this email, I noticed that Megan had sent her edits after I
last checked my email. I perused her version and noticed that a few of
her edits were the same as mine, and that she added some more
transitional and background verbiage that may help. I'll have to read
her version (or your next version?) later to see what I think...I've
been looking at this too much to have any perspective right now...and I
want to go for a run at the beach!

Ben

> Begin forwarded message:
>
>> From: John C Kerpan <j-ke...@northwestern.edu>
>> Subject: RE: idea for a PULMONARY AND CRITICAL CARE PERSPECTIVE
>> Date: September 27, 2013 1:17:36 PM PDT
>> To: "katrine...@gmail.com" <katrine...@gmail.com>
>> Cc: Jacob I Sznajder <j-szn...@northwestern.edu>
>>
>> Dear Dr. Whiteson,
>>
>> Thank you for your e-mail and interest in submitting to the AJRCCM. The
>> Editors have discussed your proposal/outline and agree that this topic
>> is timely and interesting. Therefore, on behalf of Dr. Sznajder and the
>> Editors of the AJRCCM, we would like to invite you to contribute a
>> Pulmonary Perspective on the topic of �The upper respiratory tract as a
>> microbial source for pulmonary infections: Parallels from Island
>> Biogeography,� or similar title. As you may know, Pulmonary Perspectives
>> focus on the more scientific aspects of a given subject. They resemble
>> State-of-the-Art review articles in their scientific focus, but they are
>> narrower in scope and shorter in length. They provide a forum for
>> authors to give their personal perspective on a given topic.
>>
>> Your Pulmonary Perspective should be in the area of 2,500-3,000 words;
>> in addition, up to 50 references can be included. An unstructured
>> abstract of no more than 250 words should be included. We would like to
>> recive this submission by October 30, 2013.
>>
>> If you agree, when you have completed your Pulmonary Perspective, please
>> upload it via the Scholar One system, which you can access
>> herehttp://mc.manuscriptcentral.com/ajrccm
>>
>> Please choose "PP" from the Manuscript Type drop-down menu, and mention
>> that this was invited by Dr. Sznajder in your cover letter.
>>
>> Please let us know if you have any questions.
>>
>> Sincerely,
>>
>> John
>>
>> John C. Kerpan
>> Editorial Assistant, AJRCCM
>> j-ke...@northwestern.edu
>>
>>
>> From: Katrine Whiteson [mailto:katrine...@gmail.com]
>> Sent: Wednesday, September 25, 2013 3:38 PM
>> To: Jacob I Sznajder
>> Subject: idea for a PULMONARY AND CRITICAL CARE PERSPECTIVE
>>
>> Dear Dr. Sznajder,
>>
>> After a recent gathering of microbiologists, ecologists, mathematicians
>> and physicians to discuss CF viral and microbial communities in
>> Telluride, Colorado, we decided to write a perspective about the
>> connection between oral cavity and airways microbiota (participant list
>> attached). In our discussion we felt there is a gap between biologists
>> and some CF physicians, where ecological and evolution theory is
>> relevant and could reframe the interpretation of recent studies
>> comparing communities from lung explant samples, sputum samples and
>> oropharyngeal swabs. Many clinical labs evaluating CF sputum samples
>> disregard microbes of oral etiology as contamination, without clinical
>> relevance. We view this oral "contamination" as "inoculation", where a
>> continuously mixed set of communities colonizes various points in the
>> respiratory tract, with colonization constraints based on distance and
>> survival.
>>
>> The description I read on the AJRCCM website of a pulmonary and critical
>> care perspective made me think this could be a great forum to discuss
>> these ideas. We could prepare a draft with all authors approval by
>> October 15, 2013. An outline is provided below.
>>
>> Please let me know what you think!
>>
>> thank you,
>> Katrine
>>
>> _______________________________________
>> Katrine Whiteson, PhD
>> http://www.whiteson.org/katrine/
>> Rohwer lab: http://phuckitphage.org/
>> 949.241.7347 cell
>>
>> Title: The upper respiratory tract as a microbial source for pulmonary
>> infections: Parallels from Island Biogeography
>>
>>
>>
>> Outline
>>
>> 1. Colonization depends on both distance and survival rate in the new
>> territory - principles of Island Biogeography become relevant for
>> considering lung colonization by environmental and oral microbes. A
>> figure illustrating the parallels in these ideas will be drawn.
>>
>>
>>
>> 1a. Adaptation of species to a new environment creates an important link
>> between ecology and evolution witnessed on islands in an archipelago
>> just as well as niches on the human body. Comparison of oral and lung
>> habitats in health disease.
>>
>> 1b. Parallels between island biogeography and evidence from the human
>> microbiome project of selection and adaptation on different human
>> habitats: consistent common
>>
>> features define different human body habitats.
>>
>> 1c. David Relman, a pioneer in the application of macroecology to human
>> oral microbes, says �No man is an island� but the teeth are an
>> archipelago� in reference to
>>
>> unique communities on each tooth
>>
>> 2. Sources of microbes in the CF lung include a) environmental microbes
>> from the home, food, air and soil, b) host-associated microbes from
>> other mammals such as family members and pets, and c) microbes from
>> other habitats in the same person, which may have originated from (a) or
>> (b).
>>
>> 2a. Colonization success influenced by ability to survive, not just
>> ability to reach a particular habitat. While healthy lungs have the
>> coordinated action of cilia beating at ~12
>>
>> Hz, forcing microbes out, the epithelia lining CF airways lack
>> functioning cilia as they are trapped in abnormally dense mucus.
>>
>> 2b. Airway microbes are in contact with the oral cavity in the same way
>> that oral microbes can be aspirated and come into contact with the
>> airway; this continuum leads to
>>
>> constant mixing of the communities under circumstances with increased
>> mucus often brought on by inflammation.
>>
>> 2c. For some conditions, such as pneumonia, the role of oral microbes is
>> accepted in airway infection etiology. Potential link with original work
>> 150 years ago by Joseph
>>
>> Lister to make surgery sterile, and avoid infection with commensal skin
>> organisms.
>>
>> 3. A discussion of throat, sputum and deep lung transplant samples from
>> Goddard 2012 (1), and potential re-analysis using multivariate
>> statistics to explore relationship between the samples.
>>
>> 3a. Additional evidence from recent culture-independent studies of
>> sputum, where microbes traditionally considered "oral" are found to
>> dominate sputum samples,
>>
>> suggesting they are substantial members of the airway community in
>> sometimes large volumes of sputum
>>
>> 3b. Adaptation and long-term antibiotic treatment significantly shapes
>> the community over time; many groups have found severe patients with
>> communities dominated by
>>
>> one organism in their sputum and lung samples just before needing a
>> transplant.
>>
>> 4. Conclusions
>>
>> 4a. Some infections with clinical relevance are polymicrobial in nature,
>> including pneumonia, respiratory exacerbations in CF & COPD, gum
>> disease, and otitis media.
>>
>> Exposure and survival rates of microbes influence microbial community
>> composition and interactions
>>
>> 4b. Sputum samples are relatively safe and accessible, and exhibit
>> similar microbial composition between lower and upper airways
>>
>>
>>
>> (1) Goddard, A. F., Staudinger, B. J., Dowd, S. E., Joshi-Datar, A.,
>> Wolcott, R. D., Aitken, M. L., Fligner, C. L., and Singh, P. K. (2012)
>> Direct sampling of cystic fibrosis lungs indicates that DNA-based
>> analyses of upper-airway specimens can misrepresent lung microbiota.
>> Proc. Natl. Acad. Sci. U.S.A. 109, 13769�13774.
>> PULMONARY AND CRITICAL CARE PERSPECTIVES
>>
>> Pulmonary and Critical Care Perspectives focus on the more scientific
>> aspects of a given subject. They resemble concise State-of-the-Art
>> review articles in that they focus on the most recent and relevant
>> scientific data supported by the best experimental evidence, but they
>> are narrower in scope and shorter in length. The authors are allowed and
>> encouraged to provide a more narrowly focused perspective in the subject
>> area than would be appropriate for a State-of-the-Art review. The target
>> length is approximately 3,000 words and two figures; in addition, up to
>> 50 references can be included. An unstructured abstract of no more than
>> 250 words should be provided. Invited Perspectives will undergo
>> expedited peer review.
>>
>> While many Perspectives will be by invitation, unsolicited proposals for
>> Perspective articles are welcome. Potential authors should submit an
>> outline describing the contents of the proposed article to the Editor,
>> Jacob I. Sznajder, MD (j-szn...@northwestern.edu) BEFORE starting to
>> write a Pulmonary or Critical Care Perspective. Additionally, authors
>> should compose a paragraph stating the importance of the proposed topic
>> and recent developments and/or novel aspects that will be addressed by
>> the Perspective. Authors should list previously published articles on
>> the same topic, and explain how the new manuscript comments on or adds
>> to these works. Authors should state the date they expect to submit the
>> completed manuscript.
>>
>> All submitted manuscripts undergo peer-review, and even commissioned
>> manuscripts may be declined for publication.

>>
>>
>>
>>
>>
>
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> <html><head><base href="x-msg://853/"></head><body style="word-wrap:
> break-word; -webkit-nbsp-mode: space; -webkit-line-break:
> after-white-space; "><div></div><div><br></div><div><br>
> <div><br><div>Begin forwarded message:</div><br
> class="Apple-interchange-newline"><blockquote type="cite"><div
> style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px;
> margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium;
> color:rgba(0, 0, 0, 1.0);"><b>From: </b></span><span
> style="font-family:'Helvetica'; font-size:medium;">John C Kerpan &lt;<a
> href="mailto:j-ke...@northwestern.edu">j-ke...@northwestern.edu</a>&gt;<br></span></div><div
> style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px;
> margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium;
> color:rgba(0, 0, 0, 1.0);"><b>Subject: </b></span><span
> style="font-family:'Helvetica'; font-size:medium;"><b>RE: idea for a
> PULMONARY AND CRITICAL CARE PERSPECTIVE</b><br></span></div><div
> style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px;
> margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium;
> color:rgba(0, 0, 0, 1.0);"><b>Date: </b></span><span
> style="font-family:'Helvetica'; font-size:medium;">September 27, 2013
> 1:17:36 PM PDT<br></span></div><div style="margin-top: 0px; margin-right:
> 0px; margin-bottom: 0px; margin-left: 0px;"><span
> style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0,
> 1.0);"><b>To: </b></span><span style="font-family:'Helvetica';
> font-size:medium;">"<a
> href="mailto:katrine...@gmail.com">katrine...@gmail.com</a>"
> &lt;<a
> href="mailto:katrine...@gmail.com">katrine...@gmail.com</a>&gt;<br></span></div><div
> style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px;
> margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium;
> color:rgba(0, 0, 0, 1.0);"><b>Cc: </b></span><span
> style="font-family:'Helvetica'; font-size:medium;">Jacob I Sznajder &lt;<a
> href="mailto:j-szn...@northwestern.edu">j-szn...@northwestern.edu</a>&gt;<br></span></div><br><div
> lang="EN-US" link="blue" vlink="purple"><div class="WordSection1"
> style="page: WordSection1; "><div style="margin-right: 0in; margin-left:
> 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top:
> 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family:
> Calibri, sans-serif; ">Dear Dr. Whiteson,</span><o:p></o:p></div><div
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;
> "><span style="font-size: 11pt; font-family: Calibri, sans-serif;
> ">&nbsp;</span><o:p></o:p></div><div style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt;
> font-family: Calibri, sans-serif; ">Thank you for your e-mail and interest
> in submitting to the AJRCCM. The Editors have discussed your
> proposal/outline and agree that this topic is timely and interesting.
> Therefore, on behalf of Dr. Sznajder and the Editors of the AJRCCM, we
> would like to invite you to contribute a Pulmonary Perspective on the
> topic of �The upper respiratory tract as a microbial source for pulmonary
> infections: Parallels from Island Biogeography,� or similar title. As you
> may know, Pulmonary Perspectives focus on the more scientific aspects of a
> given subject. They resemble State-of-the-Art review articles in their
> scientific focus, but they are narrower in scope and shorter in length.
> They provide a forum for authors to give their personal perspective on a
> given topic.</span><o:p></o:p></div><div style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt;
> font-family: Calibri, sans-serif; ">&nbsp;</span><o:p></o:p></div><div
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;
> "><span style="font-size: 11pt; font-family: Calibri, sans-serif; ">Your
> Pulmonary Perspective should be in the area of 2,500-3,000 words; in
> addition, up to 50 references can be included. An unstructured abstract of
> no more than 250 words should be included. We would like to recive this
> submission by<span class="Apple-converted-space">&nbsp;</span><b>October
> 30, 2013.</b></span><o:p></o:p></div><div style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt;
> font-family: Calibri, sans-serif; ">&nbsp;</span><o:p></o:p></div><div
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;
> "><span style="font-size: 11pt; font-family: Calibri, sans-serif; ">If you
> agree, when you have completed your Pulmonary Perspective, please upload
> it via the Scholar One system, which you can access here<a
> href="http://mc.manuscriptcentral.com/ajrccm" style="color: blue;
> text-decoration: underline;
> ">http://mc.manuscriptcentral.com/ajrccm</a><br><br>Please choose "PP"
> from the Manuscript Type drop-down menu, and mention that this was invited
> by Dr. Sznajder in your cover letter.<br><br>Please let us know if you
> have any questions.</span><o:p></o:p></div><div style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt;
> font-family: Calibri, sans-serif; ">&nbsp;</span><o:p></o:p></div><div
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;
> "><span style="font-size: 11pt; font-family: Calibri, sans-serif;
> ">Sincerely,<o:p></o:p></span></div><div style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt;
> font-family: Calibri, sans-serif; "><o:p>&nbsp;</o:p></span></div><div
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;
> "><span style="font-size: 11pt; font-family: Calibri, sans-serif;
> ">John<o:p></o:p></span></div><div style="margin-right: 0in; margin-left:
> 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top:
> 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family:
> Calibri, sans-serif; color: rgb(31, 73, 125);
> "><o:p>&nbsp;</o:p></span></div><div style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> margin-top: 0in; margin-bottom: 0.0001pt; "><b><span style="font-size:
> 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">John C.
> Kerpan<o:p></o:p></span></b></div><div style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt;
> font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Editorial
> Assistant, AJRCCM<o:p></o:p></span></div><div style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt;
> font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><a
> href="mailto:j-ke...@northwestern.edu" style="color: blue;
> text-decoration: underline;
> ">j-ke...@northwestern.edu</a><o:p></o:p></span></div><div
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;
> "><o:p>&nbsp;</o:p></div><div style="margin-right: 0in; margin-left: 0in;
> font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in;
> margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family:
> Calibri, sans-serif; color: rgb(31, 73, 125);
> "><o:p>&nbsp;</o:p></span></div><blockquote style="margin-top: 5pt;
> margin-bottom: 5pt; "><div><div><div style="border-right-style: none;
> border-bottom-style: none; border-left-style: none; border-width: initial;
> border-color: initial; border-top-style: solid; border-top-color: rgb(181,
> 196, 223); border-top-width: 1pt; padding-top: 3pt; padding-right: 0in;
> padding-bottom: 0in; padding-left: 0in; "><div style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> margin-top: 0in; margin-bottom: 0.0001pt; "><b><span style="font-size:
> 10pt; font-family: Tahoma, sans-serif; ">From:</span></b><span
> style="font-size: 10pt; font-family: Tahoma, sans-serif; "><span
> class="Apple-converted-space">&nbsp;</span>Katrine Whiteson [<a
> href="mailto:katrine...@gmail.com" style="color: blue;
> text-decoration: underline; ">mailto:katrine...@gmail.com</a>]<span
> class="Apple-converted-space">&nbsp;</span><br><b>Sent:</b><span
> class="Apple-converted-space">&nbsp;</span>Wednesday, September 25, 2013
> 3:38 PM<br><b>To:</b><span
> class="Apple-converted-space">&nbsp;</span>Jacob I
> Sznajder<br><b>Subject:</b><span
> class="Apple-converted-space">&nbsp;</span>idea for a PULMONARY AND
> CRITICAL CARE PERSPECTIVE</span><o:p></o:p></div></div></div><div
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;
> ">&nbsp;<o:p></o:p></div><div><div style="margin-right: 0in; margin-left:
> 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top:
> 0in; margin-bottom: 0.0001pt; ">Dear Dr.
> Sznajder,<o:p></o:p></div><div><div style="margin-right: 0in; margin-left:
> 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top:
> 0in; margin-bottom: 0.0001pt; ">&nbsp;<o:p></o:p></div></div><div><div
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;
> ">After a recent gathering of microbiologists, ecologists, mathematicians
> and physicians to discuss CF viral and microbial communities in Telluride,
> Colorado, we decided to write a perspective about the connection between
> oral cavity and airways microbiota (participant list attached).&nbsp;In
> our discussion we felt there is a gap between biologists and some CF
> physicians, where ecological and evolution theory is relevant and could
> reframe the interpretation of recent studies comparing communities from
> lung explant samples, sputum samples and oropharyngeal swabs. Many
> clinical labs evaluating CF sputum samples disregard microbes of oral
> etiology as contamination, without clinical relevance. We view this oral
> "contamination" as "inoculation", where a continuously mixed set of
> communities colonizes various points in the respiratory tract, with
> colonization constraints based on distance and
> survival.<o:p></o:p></div></div><div><div style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> margin-top: 0in; margin-bottom: 0.0001pt;
> ">&nbsp;<o:p></o:p></div></div><div><div style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> margin-top: 0in; margin-bottom: 0.0001pt; ">The description I read on the
> AJRCCM website of a pulmonary and critical care perspective made me think
> this could be a great forum to discuss these ideas.&nbsp;We could prepare
> a draft with all authors approval by October 15, 2013. An outline is
> provided below.<o:p></o:p></div></div><div><div style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> margin-top: 0in; margin-bottom: 0.0001pt;
> ">&nbsp;<o:p></o:p></div></div><div><div style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> margin-top: 0in; margin-bottom: 0.0001pt; ">Please let me know what you
> think!<o:p></o:p></div></div><div><div style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> margin-top: 0in; margin-bottom: 0.0001pt;
> ">&nbsp;<o:p></o:p></div></div><div><div style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> margin-top: 0in; margin-bottom: 0.0001pt; ">thank
> you,<o:p></o:p></div></div><div><div style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> margin-top: 0in; margin-bottom: 0.0001pt;
> ">Katrine<o:p></o:p></div></div><div><div style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> margin-top: 0in; margin-bottom: 0.0001pt;
> ">&nbsp;<o:p></o:p></div></div><div><div><div style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> margin-top: 0in; margin-bottom: 0.0001pt;
> ">_______________________________________<o:p></o:p></div></div><div><div
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;
> ">Katrine Whiteson, PhD<o:p></o:p></div></div><div><div
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><a
> href="http://www.whiteson.org/katrine/" style="color: blue;
> text-decoration: underline;
> ">http://www.whiteson.org/katrine/</a><o:p></o:p></div></div></div><div><div
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;
> ">Rohwer lab:&nbsp;<a href="http://phuckitphage.org/" style="color: blue;
> text-decoration: underline;
> ">http://phuckitphage.org/</a><o:p></o:p></div></div><div><div
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;
> ">949.241.7347 cell<o:p></o:p></div></div><div><div style="margin-right:
> 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman',
> serif; margin-top: 0in; margin-bottom: 0.0001pt;
> ">&nbsp;<o:p></o:p></div></div><div><p class="xmsonormal"
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; ">Title:&nbsp;<b>The upper respiratory tract as
> a microbial source for pulmonary infections: Parallels from Island
> Biogeography</b><o:p></o:p></p><p class="xmsonormal" style="margin-right:
> 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman',
> serif; margin-bottom: 12pt; ">&nbsp;<o:p></o:p></p><p class="xmsonormal"
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; margin-bottom: 12pt; "><b><u><span
> style="font-family: Helvetica, sans-serif;
> ">Outline</span></u></b><o:p></o:p></p><p class="xmsonormal"
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; margin-bottom: 12pt; "><span style="font-family:
> Helvetica, sans-serif; ">1. Colonization depends on both distance and
> survival rate in the new territory - principles of Island Biogeography
> become relevant for considering lung colonization by environmental and
> oral microbes. A figure illustrating the parallels in these ideas will be
> drawn.</span><o:p></o:p></p><p class="xmsonormal" style="margin-right:
> 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman',
> serif; margin-bottom: 12pt; "><span style="font-family: Helvetica,
> sans-serif; ">&nbsp;</span><o:p></o:p></p><p class="xmsonormal"
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; margin-bottom: 12pt; ">1a. Adaptation of species
> to a new environment creates an important link between ecology and
> evolution witnessed on islands in an archipelago just as well as niches on
> the human body. Comparison of oral and lung habitats in health
> disease.<o:p></o:p></p><p class="xmsonormal" style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> "><span style="font-family: Helvetica, sans-serif; ">1b. Parallels between
> island biogeography and evidence from the human microbiome project of
> selection and adaptation on different human habitats: consistent
> common</span><o:p></o:p></p><p class="xmsonormal" style="margin-right:
> 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman',
> serif; "><span style="font-family: Helvetica, sans-serif; ">features
> define different human body habitats. &nbsp;</span><o:p></o:p></p><p
> class="xmsonormal" style="margin-right: 0in; margin-left: 0in; font-size:
> 12pt; font-family: 'Times New Roman', serif; "><span style="font-family:
> Helvetica, sans-serif; ">1c.&nbsp;David Relman, a pioneer in the
> application of macroecology to human oral microbes, says �No man is an
> island� but the teeth are an archipelago� in reference
> to</span><o:p></o:p></p><p class="xmsonormal" style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> "><span style="font-family: Helvetica, sans-serif; ">unique communities on
> each tooth</span><o:p></o:p></p><p class="xmsonormal" style="margin-right:
> 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman',
> serif; margin-bottom: 12pt; "><span style="font-family: Helvetica,
> sans-serif; ">2. Sources of microbes in the CF lung include a)
> environmental microbes from the home, food, air and soil, b)
> host-associated microbes from other mammals such as family members and
> pets, and c) microbes from other habitats in the same person, which may
> have originated from (a) or (b).&nbsp;</span><o:p></o:p></p><p
> class="xmsonormal" style="margin-right: 0in; margin-left: 0in; font-size:
> 12pt; font-family: 'Times New Roman', serif; "><span style="font-family:
> Helvetica, sans-serif; ">2a. Colonization success influenced by ability to
> survive, not just ability to reach a particular habitat.&nbsp;While
> healthy lungs have the coordinated action of cilia beating at
> ~12</span><o:p></o:p></p><p class="xmsonormal" style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> "><span style="font-family: Helvetica, sans-serif; ">Hz, forcing microbes
> out, the epithelia lining CF airways lack functioning cilia as they are
> trapped in abnormally dense mucus.</span>&nbsp;<o:p></o:p></p><p
> class="xmsonormal" style="margin-right: 0in; margin-left: 0in; font-size:
> 12pt; font-family: 'Times New Roman', serif; "><span style="font-family:
> Helvetica, sans-serif; ">2b. Airway microbes are in contact with the oral
> cavity in the same way that oral microbes can be aspirated and come into
> contact with the airway; this continuum leads to</span><o:p></o:p></p><p
> class="xmsonormal" style="margin-right: 0in; margin-left: 0in; font-size:
> 12pt; font-family: 'Times New Roman', serif; "><span style="font-family:
> Helvetica, sans-serif; ">constant mixing of the communities under
> circumstances with increased mucus often brought on by
> inflammation.</span><o:p></o:p></p><p class="xmsonormal"
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; "><span style="font-family: Helvetica,
> sans-serif; ">2c. For some conditions, such as pneumonia, the role of oral
> microbes is accepted in airway infection etiology. Potential link with
> original work 150 years ago by Joseph</span><o:p></o:p></p><p
> class="xmsonormal" style="margin-right: 0in; margin-left: 0in; font-size:
> 12pt; font-family: 'Times New Roman', serif; "><span style="font-family:
> Helvetica, sans-serif; ">Lister to make surgery sterile, and avoid
> infection with commensal skin organisms.</span><o:p></o:p></p><p
> class="xmsonormal" style="margin-right: 0in; margin-left: 0in; font-size:
> 12pt; font-family: 'Times New Roman', serif; margin-bottom: 12pt; "><span
> style="font-family: Helvetica, sans-serif; ">3. A discussion of throat,
> sputum and deep lung transplant samples from Goddard 2012 (1), and
> potential re-analysis&nbsp;using multivariate statistics to explore
> relationship between the samples.</span><o:p></o:p></p><p
> class="xmsonormal" style="margin-right: 0in; margin-left: 0in; font-size:
> 12pt; font-family: 'Times New Roman', serif; "><span style="font-family:
> Helvetica, sans-serif; ">3a. Additional evidence from recent
> culture-independent studies of sputum, where microbes traditionally
> considered "oral" are found to dominate sputum
> samples,</span><o:p></o:p></p><p class="xmsonormal" style="margin-right:
> 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman',
> serif; "><span style="font-family: Helvetica, sans-serif; ">suggesting
> they are substantial members of the airway community in sometimes large
> volumes of sputum</span><o:p></o:p></p><p class="xmsonormal"
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; "><span style="font-family: Helvetica,
> sans-serif; ">3b. Adaptation and long-term antibiotic treatment
> significantly shapes the community over time; many groups have found
> severe patients with communities dominated by</span><o:p></o:p></p><p
> class="xmsonormal" style="margin-right: 0in; margin-left: 0in; font-size:
> 12pt; font-family: 'Times New Roman', serif; "><span style="font-family:
> Helvetica, sans-serif; ">one organism in their sputum and lung samples
> just before needing a transplant.&nbsp;</span><o:p></o:p></p><p
> class="xmsonormal" style="margin-right: 0in; margin-left: 0in; font-size:
> 12pt; font-family: 'Times New Roman', serif; margin-bottom: 12pt; "><span
> style="font-family: Helvetica, sans-serif; ">4.
> Conclusions</span><o:p></o:p></p><p class="xmsonormal"
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; "><span style="font-family: Helvetica,
> sans-serif; ">4a. Some infections with clinical relevance are
> polymicrobial in nature, including pneumonia, respiratory exacerbations in
> CF &amp; COPD, gum disease, and otitis media.</span><o:p></o:p></p><p
> class="xmsonormal" style="margin-right: 0in; margin-left: 0in; font-size:
> 12pt; font-family: 'Times New Roman', serif; "><span style="font-family:
> Helvetica, sans-serif; ">Exposure and survival rates of microbes influence
> microbial community composition and interactions</span><o:p></o:p></p><p
> class="xmsonormal" style="margin-right: 0in; margin-left: 0in; font-size:
> 12pt; font-family: 'Times New Roman', serif; "><span style="font-family:
> Helvetica, sans-serif; ">4b. Sputum samples are relatively safe and
> accessible, and exhibit similar microbial composition between lower and
> upper airways&nbsp;</span><o:p></o:p></p></div><div><div
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;
> ">&nbsp;<o:p></o:p></div></div><div><div style="margin-right: 0in;
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif;
> margin-top: 0in; margin-bottom: 0.0001pt;
> ">&nbsp;<o:p></o:p></div></div><div><div><div><div style="margin-right:
> 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman',
> serif; margin-top: 0in; margin-bottom: 0.0001pt; ">(1) Goddard, A. F.,
> Staudinger, B. J., Dowd, S. E., Joshi-Datar, A., Wolcott, R. D., Aitken,
> M. L., Fligner, C. L., and Singh, P. K. (2012) Direct sampling of cystic
> fibrosis lungs indicates that DNA-based analyses of upper-airway specimens
> can misrepresent lung microbiota.<span
> class="Apple-converted-space">&nbsp;</span><i>Proc. Natl. Acad. Sci.
> U.S.A.</i><span class="Apple-converted-space">&nbsp;</span><i>109</i>,
> 13769�13774.<o:p></o:p></div></div></div></div><div><p
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; "><b>PULMONARY AND CRITICAL CARE
> PERSPECTIVES</b><o:p></o:p></p><p style="margin-right: 0in; margin-left:
> 0in; font-size: 12pt; font-family: 'Times New Roman', serif; ">Pulmonary
> and Critical Care Perspectives focus on the more scientific aspects of a
> given subject. They resemble concise State-of-the-Art review articles in
> that they focus on the most recent and relevant scientific data supported
> by the best experimental evidence, but they are narrower in scope and
> shorter in length. The authors are allowed and encouraged to provide a
> more narrowly focused perspective in the subject area than would be
> appropriate for a State-of-the-Art<span
> class="Apple-converted-space">&nbsp;</span><i>review. The target length is
> approximately 3,000 words and two figures; in addition, up to 50
> references can be included. An unstructured abstract of no more than 250
> words should be provided. Invited Perspectives will undergo expedited peer
> review.<span class="Apple-converted-space">&nbsp;</span><br><br></i>While
> many Perspectives will be by invitation, unsolicited proposals for
> Perspective articles are welcome.&nbsp;Potential authors should submit an
> outline describing the contents of the proposed article to the Editor,
> Jacob I. Sznajder, MD (<a href="mailto:j-szn...@northwestern.edu"
> style="color: blue; text-decoration: underline;
> ">j-szn...@northwestern.edu</a>)&nbsp;BEFORE starting to write a
> Pulmonary or Critical Care Perspective. Additionally, authors should
> compose a paragraph stating the importance of the proposed topic and
> recent developments and/or novel aspects that will be addressed by the
> Perspective. Authors should list previously published articles on the same
> topic, and explain how the new manuscript comments on or adds to these
> works.&nbsp;Authors should state the date they expect to submit the
> completed manuscript.<span
> class="Apple-converted-space">&nbsp;</span><br><br>All submitted
> manuscripts undergo peer-review, and even commissioned manuscripts may be
> declined for
> publication.<o:p></o:p></p></div></div><div><div><div><div><div
> style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
> 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;
> ">&nbsp;<o:p></o:p></div></div><p class="MsoNormal" style="margin-right:
> 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman',
> serif; margin-top: 0in; margin-bottom: 12pt;
> ">&nbsp;<o:p></o:p></p></div><div style="margin-right: 0in; margin-left:
> 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top:
> 0in; margin-bottom: 0.0001pt;
> ">&nbsp;<o:p></o:p></div></div></div></div></blockquote></div></div></blockquote></div><br></div></body></html>

[Peter Salamon]

Ben makes a good point. And the unacknowledged fact is that sputum gets mixed with saliva on the way out. This has no analog in the archipelago. I think you need a head-on paragraph that acknowledges this and starts with the topic sentence: 

How good a reflection of lung microbiomes are sputum samples? 

You dance around the topic for the second half of the paper, and say much of relevance to this question but avoid hitting it head on. Yes, a polymicrobial community has lots of good things going for it. Nonetheless it is not a lung sample. Explicitly stating the question and summarizing your conclusions about it would make a nice concluding paragraph. It sort of is your concluding paragraph but a little too subtle for Ben and me.

Peter 

<IslandBiogeographyofCF Lungs_Telluride28Septjkh2Octbf.doc>

Professor Peter Salamon

Dept. of Math & Stats

San Diego State University

San Diego, CA 92182-7720

(619) 594-7204

sal...@sdsu.edu

http://www-rohan.sdsu.edu/~psalamon/

[Jonathan Kirk Harris]

Katrine,
Working on other stuff this weekend and I was reminded of some early CF work using transtracheal aspirates. This is essentially a needle through the neck into the trachea (not very popular these days). The interesting thing is they see the same organisms by culture that we see by molecular tools (and interesting differences in concurrent sputum). That included Bacteroides melaninogenicus (Prevotella melaningenica), Veillonella parvula and several types of streptococci (alpha and gamma hemolytic, species not specified in abstract). These are clearly not "oral" contaminants since the sample did not go through the oral cavity, and I'd suggest this is a good example of the island biogeography model.

Here's the citation: Brook I & Fink R (1983) Transtracheal aspiration in pulmonary infection in children with cystic fibrosis. Eur J Respir Dis 64(1):51-57.

Kirk
________________________________________
From: cftellu...@googlegroups.com [cftellu...@googlegroups.com] On Behalf Of Peter Salamon [peter...@gmail.com]
Sent: Sunday, October 06, 2013 11:42 PM
To: Katrine Whiteson; Ben Felts
Cc: cftellu...@googlegroups.com; Laurence.Delhaes Delhaes; Forest Rohwer
Subject: Re: idea for a PULMONARY AND CRITICAL CARE PERSPECTIVE

Ben makes a good point. And the unacknowledged fact is that sputum gets mixed with saliva on the way out. This has no analog in the archipelago. I think you need a head-on paragraph that acknowledges this and starts with the topic sentence:

How good a reflection of lung microbiomes are sputum samples?

You dance around the topic for the second half of the paper, and say much of relevance to this question but avoid hitting it head on. Yes, a polymicrobial community has lots of good things going for it. Nonetheless it is not a lung sample. Explicitly stating the question and summarizing your conclusions about it would make a nice concluding paragraph. It sort of is your concluding paragraph but a little too subtle for Ben and me.

Peter

j-ke...@northwestern.edu<mailto:j-ke...@northwestern.edu>

Jacob I. Sznajder, MD (j-szn...@northwestern.edu<mailto:j-szn...@northwestern.edu>) BEFORE starting to

write a Pulmonary or Critical Care Perspective. Additionally, authors
should compose a paragraph stating the importance of the proposed topic
and recent developments and/or novel aspects that will be addressed by
the Perspective. Authors should list previously published articles on
the same topic, and explain how the new manuscript comments on or adds
to these works. Authors should state the date they expect to submit the
completed manuscript.

All submitted manuscripts undergo peer-review, and even commissioned
manuscripts may be declined for publication.






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<html><head><base href="x-msg://853/"></head><body style="word-wrap:
break-word; -webkit-nbsp-mode: space; -webkit-line-break:
after-white-space; "><div></div><div><br></div><div><br>
<div><br><div>Begin forwarded message:</div><br
class="Apple-interchange-newline"><blockquote type="cite"><div
style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px;
margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium;
color:rgba(0, 0, 0, 1.0);"><b>From: </b></span><span
style="font-family:'Helvetica'; font-size:medium;">John C Kerpan &lt;<a

href="mailto:j-ke...@northwestern.edu">j-ke...@northwestern.edu<mailto:j-ke...@northwestern.edu></a>&gt;<br></span></div><div

style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px;
margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium;
color:rgba(0, 0, 0, 1.0);"><b>Subject: </b></span><span
style="font-family:'Helvetica'; font-size:medium;"><b>RE: idea for a
PULMONARY AND CRITICAL CARE PERSPECTIVE</b><br></span></div><div
style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px;
margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium;
color:rgba(0, 0, 0, 1.0);"><b>Date: </b></span><span
style="font-family:'Helvetica'; font-size:medium;">September 27, 2013
1:17:36 PM PDT<br></span></div><div style="margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px;"><span
style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0,
1.0);"><b>To: </b></span><span style="font-family:'Helvetica';
font-size:medium;">"<a

href="mailto:katrine...@gmail.com">katrine...@gmail.com<mailto:katrine...@gmail.com></a>"
&lt;<a
href="mailto:katrine...@gmail.com">katrine...@gmail.com<mailto:katrine...@gmail.com></a>&gt;<br></span></div><div

style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px;
margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium;
color:rgba(0, 0, 0, 1.0);"><b>Cc: </b></span><span
style="font-family:'Helvetica'; font-size:medium;">Jacob I Sznajder &lt;<a

href="mailto:j-szn...@northwestern.edu">j-szn...@northwestern.edu<mailto:j-szn...@northwestern.edu></a>&gt;<br></span></div><br><div

">j-ke...@northwestern.edu<mailto:j-ke...@northwestern.edu></a><o:p></o:p></span></div><div

">j-szn...@northwestern.edu<mailto:j-szn...@northwestern.edu></a>)&nbsp;BEFORE starting to write a

Pulmonary or Critical Care Perspective. Additionally, authors should
compose a paragraph stating the importance of the proposed topic and
recent developments and/or novel aspects that will be addressed by the
Perspective. Authors should list previously published articles on the same
topic, and explain how the new manuscript comments on or adds to these
works.&nbsp;Authors should state the date they expect to submit the
completed manuscript.<span
class="Apple-converted-space">&nbsp;</span><br><br>All submitted
manuscripts undergo peer-review, and even commissioned manuscripts may be
declined for
publication.<o:p></o:p></p></div></div><div><div><div><div><div
style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family:
'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;
">&nbsp;<o:p></o:p></div></div><p class="MsoNormal" style="margin-right:
0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman',
serif; margin-top: 0in; margin-bottom: 12pt;
">&nbsp;<o:p></o:p></p></div><div style="margin-right: 0in; margin-left:
0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top:
0in; margin-bottom: 0.0001pt;
">&nbsp;<o:p></o:p></div></div></div></div></blockquote></div></div></blockquote></div><br></div></body></html>

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<IslandBiogeographyofCF Lungs_Telluride28Septjkh2Octbf.doc>

Professor Peter Salamon
Dept. of Math & Stats
San Diego State University
San Diego, CA 92182-7720

(619) 594-7204

sal...@sdsu.edu<mailto:sal...@sdsu.edu>
http://www-rohan.sdsu.edu/~psalamon/