Application of multiple culture media in characterization of microbial diversity in the crested ibis gut

Abstract:

[Background] The gut microorganisms are closely associated with host health. As a first-class protected species in China, investigating the composition and structure of the gut microbiota in crested ibises holds significant importance for the restoration of their population. [Objective] To investigate the microbial diversity (cultivable microorganisms) in the gut of crested ibis (Nipponia nippon) and explore the beneficial microbial resources. [Methods] We used eighteen subtypes of culture media belonging to three main types to isolate gut bacteria from healthy adult crested ibises. The isolated bacteria were identified and analyzed by 16S rRNA gene amplification and sequence analysis. [Results] A total of 1 245 bacterial strains were isolated and identified as 82 species belonging to 22 genera of three phyla. The dominant phylum was Proteobacteria, with the isolates accounting for 71.00% of the total isolates. Proteobacteria and Bacilli were the dominant classes, with the isolates accounting for 71.00% and 27.23%, respectively. Escherichia was the dominant genus, with the isolates accounting for 46.75% of the total isolates. Basic media constituted the first type, including nine subtypes, on which 561 bacterial strains were isolated, primarily including Escherichia, Pseudomonas, Enterococcus, and Streptomyces belonging to Actinomycetota. The media supplemented with fecal supernatant constituted the second type, including six subtypes, on which 539 bacterial strains were isolated, predominantly including Pseudomonas, Bacillus, Vagococcus, Clostridium, Exiguobacterium, and Lysinibacillus. The media supplemented with fish were the third type, including three subtypes, on which 145 bacterial strains were isolated, predominantly including Aeromonas, Citrobacter, Hafnia, and Obesumbacterium. The three main types of media exhibited different selectivity toward microorganisms at various taxonomic levels. The dominant phylum isolated by MRS and MRS selective media was Firmicutes, while that isolated by other media was Proteobacteria. Among the 96 strains of Enterococcus, 82 strains were reported to have probiotic effects, accounting for 6.59% of the total isolates. Additionally, 62 strains were identified as potential new species, accounting for 4.98% of the total isolates, and they were mainly isolated by the basic media and the media supplemented with fecal supernatant. [Conclusion] We employed multiple culture media to investigate the microbial diversity in the crested ibis gut. The findings enriched the variety of microorganisms found in the crested ibis gut, lay a solid foundation for the future exploration of gut microbial resources in the crested ibis, and accumulate a wealth of rare strain resources for the development of beneficial microorganisms.

Key words:crested ibis;gut microorganisms;16S rRNA gene;multiple medium combination;microbial diversity