Characterization of the cecum microbiome from wild and captive rock ptarmigans indigenous to Arctic Norway

Rock ptarmigans (Lagopus muta) are gallinaceous birds inhabiting arctic and sub-arctic environments. Their diet varies by season, including plants or plant parts of high nutritional value, but also toxic plant secondary metabolites (PSMs). Little is known about the microbes driving organic matter decomposition in the cecum of ptarmigans, especially the last steps leading to methanogenesis. The cecum microbiome in wild rock ptarmigans from Arctic Norway was characterized to unveil their functional potential for PSM detoxification, methanogenesis and polysaccharides degradation. Cecal samples were collected from wild ptarmigans from Svalbard (L. m. hyperborea) and northern Norway (L. m. muta) during autumn/winter (Sept-Dec). Samples from captive Svalbard ptarmigans fed commercial pelleted feed were included to investigate the effect of diet on microbial composition and function. Abundances of methanogens and bacteria were determined by qRT-PCR, while microbial community composition and functional potential were studied using 16S rRNA gene sequencing and shotgun metagenomics. Abundances of bacteria and methanogenic Archaea were higher in wild ptarmigans compared to captive birds. The ceca of wild ptarmigans housed bacterial groups involved in PSM-degradation, and genes mediating the conversion of phenol compounds to pyruvate. Methanomassiliicoccaceae was the major archaeal family in wild ptarmigans, carrying the genes for methanogenesis from methanol. It might be related to increased methanol production from pectin degradation in wild birds due to a diet consisting of primarily fresh pectin-rich plants. Both wild and captive ptarmigans possessed a broad suite of genes for the depolymerization of hemicellulose and non-cellulosic polysaccharides (e.g. starch). In conclusion, there were no physiological and phenotypical dissimilarities in the microbiota found in the cecum of wild ptarmigans on mainland Norway and Svalbard. While substantial differences in the functional potential for PSM degradation and methanogenesis in wild and captive birds seem to be a direct consequence of their dissimilar diets.

岩雷鸟（Rock ptarmigan，学名Lagopus muta）是栖息于北极及亚北极环境的鸡形目鸟类。其食谱随季节动态变化，既包含高营养价值的植物或植物组织，也会摄入有毒的植物次生代谢物（plant secondary metabolites，以下简称PSMs）。目前学界对雷鸟盲肠内驱动有机质分解的微生物，尤其是产甲烷过程的最终步骤，仍所知寥寥。
为揭示野外岩雷鸟盲肠菌群在PSMs脱毒、产甲烷作用及多糖降解方面的功能潜力，研究人员对北极挪威地区的野生岩雷鸟盲肠微生物组进行了表征。研究于秋、冬季（9月至12月）分别从斯瓦尔巴群岛（L. m. hyperborea）与挪威北部（L. m. muta）的野生岩雷鸟体内采集盲肠样本；同时设置喂食商业颗粒饲料的圈养斯瓦尔巴岩雷鸟组，以探究饮食对微生物组成与功能的影响。
研究采用定量实时荧光定量PCR（qRT-PCR）测定产甲烷菌与细菌的丰度，并通过16S rRNA基因测序及鸟枪宏基因组学分析微生物群落组成与功能潜力。结果显示，野生岩雷鸟体内的细菌与产甲烷古菌丰度均高于圈养个体。野生岩雷鸟的盲肠内存在参与PSMs降解的细菌类群，以及介导酚类化合物转化为丙酮酸的功能基因；甲烷嗜甲醇球菌科（Methanomassiliicoccaceae）是野生岩雷鸟体内的主要古菌科，携带有利用甲醇进行产甲烷的功能基因，这可能与野生个体主要食用富含果胶的新鲜植物，使得果胶降解过程产生更多甲醇相关。无论野生还是圈养岩雷鸟，均携带大量参与半纤维素与非纤维素多糖（如淀粉）解聚的功能基因。
综上，挪威本土与斯瓦尔巴群岛的野生岩雷鸟盲肠菌群未表现出生理与表型差异；而野生与圈养岩雷鸟在PSMs降解及产甲烷功能潜力上的显著差异，似乎直接源于二者饮食结构的不同。