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. 2014 Jun 1;189(11):1309-15.
doi: 10.1164/rccm.201312-2129PP.

The upper respiratory tract as a microbial source for pulmonary infections in cystic fibrosis. Parallels from island biogeography

Katrine L Whiteson  1 , Barbara Bailey, Megan Bergkessel, Douglas Conrad, Laurence Delhaes, Ben Felts, J Kirk Harris, Ryan Hunter, Yan Wei Lim, Heather Maughan, Robert Quinn, Peter Salamon, James Sullivan, Brandie D Wagner, Paul B Rainey
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The upper respiratory tract as a microbial source for pulmonary infections in cystic fibrosis. Parallels from island biogeography (V体育平台登录)

Katrine L Whiteson et al. Am J Respir Crit Care Med. .

Abstract

A continuously mixed series of microbial communities inhabits various points of the respiratory tract, with community composition determined by distance from colonization sources, colonization rates, and extinction rates. Ecology and evolution theory developed in the context of biogeography is relevant to clinical microbiology and could reframe the interpretation of recent studies comparing communities from lung explant samples, sputum samples, and oropharyngeal swabs. We propose an island biogeography model of the microbial communities inhabiting different niches in human airways VSports手机版. Island biogeography as applied to communities separated by time and space is a useful parallel for exploring microbial colonization of healthy and diseased lungs, with the potential to inform our understanding of microbial community dynamics and the relevance of microbes detected in different sample types. In this perspective, we focus on the intermixed microbial communities inhabiting different regions of the airways of patients with cystic fibrosis. .

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"V体育官网" Figures

Figure 1.
Figure 1.
Parallels between island biogeography and polymicrobial lung colonization. (Left) In island biogeography theory, the mainland is the greatest source of species diversity, with individual island species composition depending on the distance from the mainland. (Middle) Human airway microbial colonization is likely to display a similar dependence on the distance from the mainland (largely the oral cavity, shown in yellow, which is the richest and most diverse source of microbes with proximity to the lung). (Right) Other people, along with the air, water, and other environments, are also important sources of microbes, which can immigrate to the islands in the human airways and influence the polymicrobial community.
Figure 2.
Figure 2.
Classic island biogeography. The richness of species depends on the colonization rate (left y-axis) and the extinction rate (right y-axis). Migration through the trachea offers colonization opportunity to microbes from multiple sources, and impaired mucociliary clearance decreases the extinction rate. Gray circle 1 represents a small distant island (i.e., the lung) with few species, whereas gray circle 2 identifies the mainland or a large proximal island with high species diversity, such as the oral cavity. Diversity is composed of both the number of species and their distribution, or evenness, and can be indicated by different measures of species richness and frequency. The number of species, or species richness, is an indicator of diversity. The term diversity is used throughout this perspective as informed by the species richness, which can be predicted in the island biogeography model. Adapted by permission from Reference .
Figure 3.
Figure 3.
Multidimensional scaling of an unsupervised Random Forest comparing the relative abundance of taxa derived from 16S sequencing of lung explant samples (red) with sputum samples (blue) and oropharyngeal swabs (green) from six patients with cystic fibrosis (CF) (15). Shared community composition leads to clustering of sputum and lung samples in most cases, whereas some sputum and throat samples cluster together. Data from Reference ; analysis conducted in R with the package Random Forest (72).
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