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首页> 外文期刊>Applied Microbiology >Metagenomic Shotgun Analyses Reveal Complex Patterns of Intra- and Interspecific Variation in the Intestinal Microbiomes of Codfishes
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Metagenomic Shotgun Analyses Reveal Complex Patterns of Intra- and Interspecific Variation in the Intestinal Microbiomes of Codfishes

机译：Metagenomic Shotgun分析揭示了分类症肠道微生物体内的复杂和间隙变异的复杂模式

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The relative importance of host-specific selection or environmental factors in determining the composition of the intestinal microbiome in wild vertebrates remains poorly understood. Here, we used metagenomic shotgun sequencing of individual specimens to compare the levels of intra- and interspecific variation of intestinal microbiome communities in two ecotypes (NEAC and NCC) of Atlantic cod ( Gadus morhua ) that have distinct behavior and habitats and three Gadidae species that occupy a range of ecological niches. Interestingly, we found significantly diverged microbiomes among the two Atlantic cod ecotypes. Interspecific patterns of variation are more variable, with significantly diverged communities for most species’ comparisons, apart from the comparison between coastal cod (NCC) and Norway pout ( Trisopterus esmarkii ), whose community compositions are not significantly diverged. The absence of consistent species-specific microbiomes suggests that external environmental factors, such as temperature, diet, or a combination thereof, comprise major drivers of the intestinal community composition of codfishes.IMPORTANCE The composition of the intestinal microbial community associated with teleost fish is influenced by a diversity of factors, ranging from internal factors (such as host-specific selection) to external factors (such as niche occupation). These factors are often difficult to separate, as differences in niche occupation (e.g., diet, temperature, or salinity) may correlate with distinct evolutionary trajectories. Here, we investigate four gadoid species with contrasting levels of evolutionary separation and niche occupation. Using metagenomic shotgun sequencing, we observed distinct microbiomes among two Atlantic cod ( Gadus morhua ) ecotypes (NEAC and NCC) with distinct behavior and habitats. In contrast, interspecific patterns of variation were more variable. For instance, we did not observe interspecific differentiation between the microbiomes of coastal cod (NCC) and Norway pout ( Trisopterus esmarkii ), whose lineages underwent evolutionary separation over 20 million years ago. The observed pattern of microbiome variation in these gadoid species is therefore most parsimoniously explained by differences in niche occupation.
机译：宿主特异性选择或环境因素在确定野生脊椎动物中肠道微生物组的组成的相对重要性仍然明白。在这里，我们使用单个样本的偏心菌霰弹枪测序来比较大西洋鳕鱼（GADUS MORHUA）中肠道微生物组群中的肠道微生物组群的肠道内和间隙水平，具有不同的行为和栖息地以及三种肉豆蔻种类占据一系列生态利基。有趣的是，我们发现两个大西洋COD生态型中的微生物显着分化。除了沿海鳕鱼（NCC）和挪威POUT（Trisopterus esMarkii）的比较之外，大多数物种的比较，各种各样的群体的变异模式都是更具变量的，对于大多数物种的比较，除了沿海鳕鱼（NCC）和挪威POUT（Trisopterus esMarkii）的比较，其社区组成没有显着分歧。没有一致的物种特异性微生物酶表明，外部环境因素，例如温度，饮食或其组合，包括肠群体组成的分数群体的主要驱动因素。分析与远程鱼类相关的肠道微生物群落的组成受影响通过多样性的因素，从内部因素（例如宿主特定的选择）到外部因素（如利基占领）。这些因素往往难以分离，因为利基占用（例如，饮食，温度或盐度）的差异可以与不同的进化轨迹相关。在这里，我们研究了四个毒素种类，具有对比的进化分离和利基占用水平。采用偏蛋白霰弹枪测序，我们观察了两种大西洋鳕鱼（GADUS MORHUA）生态型（NEAC和NCC）的不同的微生物，具有明显的行为和栖息地。相反，变异的间隙模式更具变量。例如，我们没有观察到沿海鳕鱼（NCC）和挪威噘嘴（Trisopterus esMarkii）的微生物体之间的差异分化，其血统在2000多万年前进行了进化分离。因此，观察到这些毒素物种中的微生物组变化的模式是最纵传地解释的利基占用的差异。

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