Gut microbiota enhance energy accumulation of black-necked crane to cope with impending migration.

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.

Li W ，Zhao J ，Tian H ，Shen Y ，Wang Y ，Shao M ，Xiong T ，Yao Y ，Zhang L ，Chen X ，Xiao H ，Xiong Y ，Yang S ，Tan C ，Xu H ... -  《-》

Structural changes in the gut microbiota community of the black-necked crane (Grus nigricollis) in the wintering period.

During overwintering of black-necked cranes (Grus nigricollis), the composition and function of the gut microbiota changes are of considerable interest for understanding its environmental adaption mechanism. In this study, we characterized the structure of the gut microbiota from the black-necked crane in the Dashanbao wintering area, and compared the early-winter (November) microbiota to the late-winter (March of the next year) microbiota. The results showed that the gut microbiota diversity of black-necked crane in the early-overwintering stage was higher than that in the late-overwintering stage, but it did not reach a significant level. Gut microbiota taxonomic composition analysis showed that relative abundance of Bacteroidota increased significantly, and showed decreased Firmicutes to Bacteroidota ratio at the phylum level, meanwhile, the abundance of Lactobacillus decreased significantly at the genus level. Explain gut microbiota between the early- and late-wintering showed some differences in microbiota richness but maintained a relatively conservative microbiota structure. PICRUSt2 method was used to predict and analyze the KEGG functional abundance of 16S rDNA sequences of bacteria, it was found that the changes in gut microbiota composition increased the abundance of bacteria associated with amino acid biosynthesis and acid metabolism in the late stage of overwintering. This work provides basic data for black-necked crane gut microbiota study, which might further contribute to their protection.

Zhao J ，Wang Y ，Zhang M ，Yao Y ，Tian H ，Sang Z ，Wang L ，Xu H ... -  《-》

Characterization of the gut microbiome of black-necked cranes (Grus nigricollis) in six wintering areas in China.

Wang W ，Wang F ，Li L ，Wang A ，Sharshov K ，Druzyaka A ，Lancuo Z ，Wang S ，Shi Y ... -  《-》

Gut fungi of black-necked cranes (Grus nigricollis) respond to dietary changes during wintering.

Migratory birds exhibit heterogeneity in foraging strategies during wintering to cope with environmental and migratory pressures, and gut bacteria respond to changes in host diet. However, less is known about the dynamics of diet and gut fungi during the wintering period in black-necked cranes (Grus nigricollis). In this work, we performed amplicon sequencing of the trnL-P6 loop and ITS1 regions to characterize the dietary composition and gut fungal composition of black-necked cranes during wintering. Results indicated that during the wintering period, the plant-based diet of black-necked cranes mainly consisted of families Poaceae, Solanaceae, and Polygonaceae. Among them, the abundance of Solanaceae, Polygonaceae, Fabaceae, and Caryophyllaceae was significantly higher in the late wintering period, which also led to a more even consumption of various food types by black-necked cranes during this period. The diversity of gut fungal communities and the abundance of core fungi were more conserved during the wintering period, primarily dominated by Ascomycota and Basidiomycota. LEfSe analysis (P < 0.05, LDA > 2) found that Pyxidiophora, Pseudopeziza, Sporormiella, Geotrichum, and Papiliotrema were significantly enriched in early winter, Ramularia and Dendryphion were significantly enriched in mid-winter, Barnettozyma was significantly abundant in late winter, and Pleuroascus was significantly abundant in late winter. Finally, mantel test revealed a significant correlation between winter diet and gut fungal. This study revealed the dynamic changes in the food composition and gut fungal community of black-necked cranes during wintering in Dashanbao. In the late wintering period, their response to environmental and migratory pressures was to broaden their diet, increase the intake of non-preferred foods, and promote a more balanced consumption ratio of various foods. Balanced food composition played an important role in stabilizing the structure of the gut fungal community. While gut fungal effectively enhanced the host's food utilization rate, they may also faced potential risks of introducing pathogenic fungi. Additionally, we recongnized the limitations of fecal testing in studying the composition of animal gut fungal, as it cannot effectively distinguished between fungal taxa from food or soil inadvertently ingested and intestines. Future research on functions such as cultivation and metagenomics may further elucidate the role of fungi in the gut ecosystem.

Li W ，Cheng L ，He X ，He G ，Liu Y ，Sang Z ，Wang Y ，Shao M ，Xiong T ，Xu H ，Zhao J ... -  《BMC MICROBIOLOGY》

Host genetic background rather than diet-induced gut microbiota shifts of sympatric black-necked crane, common crane and bar-headed goose.

Gut microbiota of wild birds are affected by many factors, and host genetic background and diet are considered to be two important factors affecting their structure and function. In order to clarify how these two factors influence the gut microbiota, this study selected the sympatric and closely related and similar-sized Black-necked Crane (Grus nigricollis) and Common Crane (Grus grus), as well as the distantly related and significantly different-sized Bar-headed Goose (Anser indicus). The fecal samples identified using sanger sequencing as the above three bird species were subjected to high-throughput sequencing of rbcL gene and 16S rRNA gene to identify the feeding types phytophagous food and gut microbiota. The results showed significant differences in food diversity between black-necked cranes and Common Cranes, but no significant differences in gut microbiota, Potatoes accounted for approximately 50% of their diets. Bar-headed Geese mainly feed on medicinal plants such as Angelica sinensis, Alternanthera philoxeroides, and Ranunculus repens. Black-necked cranes and Common Cranes, which have a high-starch diet, have a similar degree of enrichment in metabolism and synthesis functions, which is significantly different from Bar-headed Geese with a high-fiber diet. The differences in metabolic pathways among the three bird species are driven by food. The feeding of medicinal plants promotes the health of Bar-headed Geese, indicating that food influences the functional pathways of gut microbiota. Spearman analysis showed that there were few gut microbiota related to food, but almost all metabolic pathways were related to food. The host genetic background is the dominant factor determining the composition of the microbiota. Monitoring the changes in gut microbiota and feeding types of wild birds through bird feces is of great reference value for the conservation of other endangered species.

Wang Y ，Long Z ，Zhang Y ，Li X ，Zhang X ，Su H ... -  《-》