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 use metagenomic shotgun sequencing of individual specimens to compare the 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 find significantly diverged microbiomes amongst 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 there-off 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 observe distinct microbiomes amongst two Atlantic cod (Gadus morhua) ecotypes (NEAC and NCC) with distinct behavior and habitats. In contrast, interspecific patterns of variation are more variable. For instance, we do not observe interspecific differentiation between the microbiomes of coastal cod (NCC) and Norway pout (Trisopterus esmarkii) whose lineages have evolutionary separated 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.

宿主特异性选择或环境因素在确定野生脊椎动物肠道微生物组组成中的相对重要性仍然知之甚少。在这里，我们使用宏基因组shot弹枪对单个标本进行测序，以比较大西洋鳕鱼（Gadus morhua）的两种生态型（NEAC和NCC）的肠道微生物组群落的种内和种间变异，它们具有不同的行为和栖息地，并且具有三种Ga科占据一系列生态位的物种。有趣的是，我们发现两种大西洋鳕鱼生态型之间的微生物群落明显不同。种间变异的模式更具可变性，对于大多数物种的比较而言，群落具有明显的差异，除了沿海鳕鱼（NCC）和挪威p鱼（Trisopterus esmarkii）之间的比较，后者的群落组成没有明显差异。缺乏一致的物种特异性微生物群落表明，外部环境因素，例如温度，饮食或二者的结合构成了鳕鱼肠道群落组成的主要驱动力。

重要性与硬骨鱼相关的肠道微生物群落的组成受到多种因素的影响，从内部因素（例如宿主特定的选择）到外部因素（例如利基职业）。这些因素通常很难分开，因为利基占据的差异（例如饮食，温度或盐度）可能与不同的进化轨迹相关。在这里，我们研究了四个进化物种和不同生态位占领水平的对比。使用宏基因组shot弹枪测序，我们观察到两个大西洋鳕鱼（Gadus morhua）具有不同行为和栖息地的生态型（NEAC和NCC）。相反，种间变异模式则更具可变性。例如，我们没有观察到沿海鳕鱼（NCC）和挪威p（Trisopterus esmarkii）的微生物群之间的种间差异，后者在2000万年前已经进化分离。因此，这些生态型占地物种中微生物组变异的观察模式可以用生态位占据的差异来最简洁地解释。