Minimizing caging effects in murine lung microbiome studies.
Minimizing caging effects in murine lung microbiome studies.
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最大限度地减少小鼠肺微生物组研究中的笼养效应。
DOI：
10.1152/ajplung.00144.2022
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发表时间：
2022
期刊：
影响因子：
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通讯作者：
Evans,ScottE
中科院分区：
文献类型：
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作者：
PantaleónGarcía,Jezreel;Dickson,RobertP;Evans,ScottE
致编辑：我们饶有兴趣地阅读了Abdelgawad等人的作品。(1)关于Toll样受体（TLR）在塑造肺部微生物组中的作用。我们对我们的工作（2，3）进行了澄清，并提供了我们用于解决我们与Abdelgawad等人共同关注的问题的策略的见解，即环境因素（如共住房）是小鼠肺部微生物群落研究中潜在偏倚的来源。首先，我们的吸入性Pam 2 β寡脱氧核苷酸（ODN）疗法由TLR 2/6异二聚体和TLR 9同二聚体的协同激动剂组成（4-6）。它在编辑焦点中被错误地识别为TLR 2，6和9的抑制剂，可能会影响读者对我们工作的理解。另一方面，我们热情地支持他们对笼效应作为潜在实验混杂因素的批判性评价。许多环境因素（例如，供应商，运输，合住，床上用品，饮食和同窝仔）影响不同暴露和肠道微生物群之间的关系（7，8）。类似地，笼化效应可以改变健康小鼠中感兴趣的暴露（E）和作为结果（O）的肺微生物群之间的因果关系（图1A）。基因相同小鼠的基线肺部微生物群落在先前共同饲养的小鼠中最相似，并且随着到达后环境因素的增加而最不相似，当小鼠在初始交付后共同饲养时，这些基线差异随着时间的推移而收敛（9）。类似地，当小鼠被随机共同圈养时，具有不同TLR敲除突变的小鼠的肺部微生物群落的基线差异收敛（10）。这些观察结果强调了笼化效应在肺部微生物组研究中的重要性。由先前共饲养引起的肺微生物群的间接效应改变（X 0）和由递送后共饲养引起的直接效应改变（X1）都强调需要使用随机化和分层策略来最小化笼化效应。在我们确定TLR操作不会持久改变健康肺微生物组的研究中，我们有意寻求通过在我们的实验设计中纳入分层随机共笼策略来先验地减轻笼化效应（图1 B; 2，3）。在分层随机策略中，将最初共同圈养的小鼠随机分布，与来自所有实验组的小鼠一起关笼。然后，额外的分层
TO THE EDITOR: We read with interest the work by Abdelgawad et al.(1) regarding the role of Toll-like receptors (TLRs) in shaping the pulmonary microbiome. We offer a clarification regarding our work (2, 3) that was addressed in the Editorial Focus and provide insights into strategies we have used to address the concern that we share with Abdelgawad et al. that environmental factors such as cohousing are sources of potential bias in the study of microbial communities in mouse lungs. First, our inhaled Pam2 þ oligodeoxynucleotide (ODN) therapy is composed of synergistic agonists of the TLR2/6 heterodimer and the TLR9 homodimer (4–6). It is incorrectly identified in the Editorial Focus as an inhibitor of TLRs 2, 6, and 9, potentially impacting readers’ understanding of our work. On the other hand, we enthusiastically endorse their critical appraisal of caging effects as potential experimental confounders. Many environmental factors (eg, vendor, shipment, cohousing, bedding, diet, and littermates) influence relationships between different exposures and gut microbiota (7, 8). Similarly, caging effects can alter causal relationships between an exposure of interest (E) and lung microbiota as an outcome (O) in healthy mice (Fig. 1 A). Baseline lung microbial communities of genetically identical mice are most similar among previously cohoused mice and most dissimilar as increasing numbers of environmental factors differ upon arrival, with these baseline differences converging over time when mice are cohoused after initial delivery (9). Similarly, baseline differences in lung microbial communities of mice with different TLR knockout mutations converged when mice are randomly cohoused (10).These observations underscore the importance of caging effects in lung microbiome studies. Both indirect effect modifications (X0) of the lung microbiota resulting from prior cohousing and direct effect modifications (X1) from postdelivery cohousing emphasize the need to minimize caging effects using randomization and stratification strategies. In our studies that determined that TLR manipulation did not durably alter the healthy lung microbiome, we intentionally sought to mitigate caging effects a priori by incorporating stratified random cohousing strategies in our experimental designs (Fig. 1 B; 2, 3). In stratified random strategies, originally cohoused mice are randomly distributed for caging with mice from all experimental groups. Then, additional stratified
影响因子：
8.8
作者：
Robertson, Susan J.;Lemire, Paul;Philpott, Dana J.
通讯作者：
Philpott, Dana J.
Toll 样受体：肺部微生物群的塑造者？
DOI：
10.1152/ajplung.00279.2021
发表时间：
2021
期刊：
American journal of physiology. Lung cellular and molecular physiology
影响因子：
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作者：
Abdelgawad,AhmedS;Lal,CVivek;Ambalavanan,Namasivayam;Willis,KentA
通讯作者：
Willis,KentA