A comprehensive comparison of fecal microbiota in three ecological bird groups of raptors, waders, and waterfowl

Abstract

Gut microbiota plays a vital role in maintaining the health and immunity of wild birds. However, less is known about the comparison of fecal microbiota between different ecological groups of wild birds, particularly in the Yellow River National Wetland in Baotou, China, an important transit point for birds migrating all over the East Asia-Australian and Central Asian flyways. In this study, we characterized the fecal microbiota and potential microbial function in nine bird species of raptors, waders, and waterfowl using 16S rRNA gene amplicon sequencing to reveal the microbiota differences and interaction patterns. The results indicated that there was no significant difference in α-diversity, but a significant difference in β-diversity between the three groups of birds. The fecal bacterial microbiota was dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes in all groups of birds. Furthermore, we identified five bacterial genera that were significantly higher in raptors, five genera that were significantly higher in waders, and two genera that were more abundant in waterfowl. The bacterial co-occurrence network results revealed 15 and 26 key genera in raptors and waterfowls, respectively. The microbial network in waterfowl exhibited a stronger correlation pattern than that in raptors. PICRUSt2 predictions indicated that fecal bacterial function was significantly enriched in the antibiotic biosynthesis pathway in all three groups. Metabolic pathways related to cell motility (bacterial chemotaxis and flagellar assembly) were significantly more abundant in raptors than in waders, whereas waders were enriched in lipid metabolism (synthesis and degradation of ketone bodies and fatty acid biosynthesis). The fecal microbiota in waterfowl harbored more abundant vitamin B6 metabolism, RNA polymerase, and tyrosine and tryptophan biosynthesis. This comparative study revealed the microbial community structure, microbial co-occurrence patterns, and potential functions, providing a better understanding of the ecology and conservation of wild birds. Future studies may focus on unraveling metagenomic functions and dynamics along with the migration routine or different seasons by metagenomics or metatranscriptomics.

Falcon gut microbiota is shaped by diet and enriched in Salmonella

“…Firmicutes was the dominant phylum (73% of total reads) in the falcon gut followed by Actinobacteria and Proteobacteria (Fig 4A). These observations are consistent with previous studies that have found falcon gut microbiomes to consist of Firmicutes, Proteobacteria and Actinobacteria [17][18][19][20][22][23][24]. All but one of the studies have small sample sizes (n = 1-11, S4 Table) [18][19][20][22][23][24].…”

“…Although recent studies have revealed flight, body size, and migration patterns are associated with the gut microbiota in birds [16] the effect of evolutionary histories and diet on the bird gut microbiota remains poorly characterized. Furthermore, studies investigating gut microbiomes of uber-carnivorous raptors whose diet almost exclusively consists of animal flesh, are underrepresented, with the exception of a few studies that include a small number of raptors [16][17][18][19][20][21][22][23][24]. Birds of the genus Falco (henceforth referred to as falcons) are unique among raptors as they are genetically distinct from other flesh-eating birds of prey such as hawks, eagles and vultures, all of which belong to a single taxonomic order-Accipitriformes [25].…”

Comparative analysis of the intestinal microbiota of black−necked cranes (Grus nigricollis) in different wintering areas

“…Regarding genera, the intestinal microbiota of black-necked cranes comprised 15 dominant bacterial genera and 18 dominant fungal genera. A higher percentage of these were Lactobacillus , Megamonas , and Enterococcus , which were widely distributed in other birds and were influential in regulating intestinal health, metabolic capacity, and antimicrobial activity ( Gao et al., 2021 ; Zhao et al., 2022 ). Remarkably, we also discovered several genera that are opportunistically pathogenic, including Pseudomonas , Pantoe , Escherichia , Burkholderia , Helicobacter , Fusarium , and Rhodotorula ( Xiang et al., 2019 ; Wang et al., 2020 ; Wu et al., 2022 ).…”

“…We conducted an LEfSe analysis taking into account the different overwintering regions and found a few unique flora at the genus level, such as Enterococcus , Tausonia , and Botrytis in the LZ group; Lactobacillus , Naganishia , Mycosphaerella , Rhodotorula , Alternaria , and Sporisorium in the SN group; Clostridium, Fusarium, Debaryomyces, Cephalotrichum , and Arthrinium in the LS group; and Megamonas , Fusobacterium , Anaerobiospirillum , Campylobacter , Escherichia , Filobasidium , and Sporobolomyces in the RKZ group. Probiotics such as Enterococcus , Megamonas , Clostridium , and Lactobacillus have been proven in studies to enhance intestinal microenvironment, metabolic capacity, and antimicrobial activity ( Yang et al., 2012 ; Gao et al., 2021 ; Zhao et al., 2022 ). However, Fusarium and Rhodotorula may be harmful to cranes ( Wu et al., 2022 ).…”

“…to enhance intestinal microenvironment, metabolic capacity, and antimicrobial activity (Yang et al, 2012;Gao et al, 2021;Zhao et al, 2022). However, Fusarium and Rhodotorula may be harmful to cranes (Wu et al, 2022).…”