College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China.
College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China.
Appl Microbiol Biotechnol. 2023 Jul;107(14):4635-4646. doi: 10.1007/s00253-023-12598-x. Epub 2023 May 30.
Less is known about the role of gut microbiota in overwintering environmental adaptation in migratory birds. Here, we performed metagenomic sequencing on fresh fecal samples (n = 24) collected during 4 periods of overwintering (Dec: early; Jan: middle I; Feb: middle II; Mar: late) to characterize gut microbial taxonomic and functional characteristics of black-necked crane (Grus nigricollis). The results demonstrated no significant change in microbial diversity among overwintering periods. Analysis of compositions of microbiomes with bias correction (ANCOM-BC) determined 15 Proteobacteria species enriched in late overwintering period. Based on previous reports, these species are associated with degradation of chitin, cellulose, and lipids. Meanwhile, fatty acid degradation and betalain biosynthesis pathways are enriched in late overwintering period. Furthermore, metagenomic binning obtained 91 high-quality bins (completeness >70% and contamination <10%), 5 of which enriched in late overwintering period. Carnobacterium maltaromaticum, unknown Enterobacteriaceae, and Yersinia frederiksenii have genes for chitin and cellulose degradation, acetate, and glutamate production. Unknown Enterobacteriaceae and Y. frederiksenii hold genes for synthesis of 10 essential amino acids required by birds, and the latter has genes for γ-aminobutyrate production. C. maltaromaticum has genes for pyridoxal synthesis. These results implied the gut microbiota is adapted to the host diet and may help black-necked cranes in pre-migratory energy accumulation by degrading the complex polysaccharide in their diet, supplying essential amino acids and vitamin pyridoxal, and producing acetate, glutamate, and γ-aminobutyrate that could stimulate host feeding. Additionally, enriched Proteobacteria also encoded more carbohydrate-active enzymes (CAZymes) and antibiotic resistance genes (ARGs) in late overwintering period. KEY POINTS: • Differences in gut microbiota function during overwintering period of black-necked cranes depend mainly on changes in core microbiota abundance • Gut microbiota of black-necked crane adapted to the diet during overwintering period • Gut microbiota could help black-necked cranes to accumulate more energy in the late overwintering period.
关于肠道微生物群在候鸟的越冬环境适应中的作用知之甚少。在这里，我们对 4 个越冬期（12 月：早期；1 月：中期 I；2 月：中期 II；3 月：晚期）采集的新鲜粪便样本（n=24）进行了宏基因组测序，以描述黑颈鹤（Grus nigricollis）肠道微生物的分类和功能特征。结果表明，在越冬期间，微生物多样性没有显著变化。通过偏倚校正（ANCOM-BC）分析微生物组组成，确定了 15 种在后期越冬期富集的变形菌。根据之前的报道，这些物种与几丁质、纤维素和脂质的降解有关。同时，晚期越冬期富含脂肪酸降解和甜菜红素生物合成途径。此外，宏基因组 binning 获得了 91 个高质量的 bin（完整性>70%，污染<10%），其中 5 个在晚期越冬期富集。乳杆菌属（Carnobacterium maltaromaticum）、未知肠杆菌科（Enterobacteriaceae）和弗雷德里克森氏菌（Yersinia frederiksenii）具有几丁质和纤维素降解、乙酸和谷氨酸产生的基因。未知肠杆菌科和弗雷德里克森氏菌持有鸟类所需的 10 种必需氨基酸合成的基因，后者具有γ-氨基丁酸产生的基因。乳杆菌属（Carnobacterium maltaromaticum）具有吡哆醛合成的基因。这些结果表明，肠道微生物群适应宿主的饮食，并通过降解其饮食中的复杂多糖、提供必需氨基酸和维生素吡哆醛以及产生乙酸、谷氨酸和γ-氨基丁酸来刺激宿主进食，从而帮助黑颈鹤在迁徙前积累能量。此外，富集的变形菌在后期越冬期还编码了更多的碳水化合物活性酶（CAZymes）和抗生素抗性基因（ARGs）。关键点：• 黑颈鹤越冬期肠道微生物功能的差异主要取决于核心微生物群丰度的变化• 黑颈鹤越冬期肠道微生物群适应饮食• 肠道微生物群可以帮助黑颈鹤在后期越冬期积累更多能量。
