Analysis of microbial diversity in the feces of Arborophila rufipectus

Abstract

IntroductionIntestinal microbiota composition plays a crucial role in modulating the health of the host. This evaluation indicator is very sensitive and profoundly impacts the protection of endangered species. Currently, information on the gut microbiota of wild birds remains scarce. Therefore, this study aimed to describe the gut microbial community structure and potentially, the pathogen composition of wild Arborophila rufipectus.MethodsTo guarantee comprehensive data analysis, we collected fecal samples from wild A. rufipectus and Lophura nycthemera in their habitats for two quarters. The 16S rRNA gene was then sequenced using high-throughput sequencing technology to examine the intestinal core microbiota, microbial diversity, and potential pathogens with the aim of determining if the composition of the intestinal microflora varies seasonally.Results and DiscussionThe gut microbiota of A. rufipectus and L. nycthemera primarily comprised four phyla: Proteobacteria (45.98%), Firmicutes (35.65%), Bacteroidetes (11.77%), and Actinobacteria (3.48%), which accounted for 96.88% of the total microbial composition in all samples. At the genus level, core microorganisms were found, including Shigella (10.38%), Clostridium (6.16%), Pseudomonas (3.03%), and Rickettsiella (1.99%). In these genera, certain microbial species have been shown to be pathogenic. This study provides important indicators for analyzing the health status of A. rufipectus and formulating protective measures.

Analysis of fungal diversity in the gut feces of wild takin (Budorcas taxicolor)

“…Zopfiella ( Fujimoto et al, 2004 ) and Podospora ( Ying et al, 2021 ) cause immune suppression. However, the isolation of potentially pathogenic fungi from feces does not provide definitive evidence of a host’s health status ( Ma et al, 2022 ). Moreover, although the distribution of these pathogens in the wild B. taxicolor is unknown, they might represent a source of zoonotic infections.…”

“…On the other hand, capturing this animal for further investigation and confirmation has proven impossible for our research team. Nevertheless, this point of view can be put forward for the scientific protection of B. taxicolor ( Ma et al, 2022 ).…”

“…On the other hand, capturing this animal for further investigation and confirmation has proven impossible for our research team. Nevertheless, this point of view can be put forward for the scientific protection of B. taxicolor (Ma et al, 2022). For different taxonomic levels, the top 30 abundant species are applied to identify different groups of species to be used as biomarkers; sqrtIVt value is the square root of the indicator value, used to compare the correlation between microorganisms and treatment groups.…”

Table2.XLSX

“…The resulting effective CCS sequences were used for further analysis (Edgar, 2013). Based on the species annotation information of 16S rDNA sequences in the Silva database (https:// www.arb-silva.de/), the operational taxonomic units (OTUs) were classified into various taxonomic levels, including phylum, class, order, family, and genus (Ma et al, 2022). Alpha diversity was assessed using Chao, ACE, Simpson, and Shannon indices.…”

Table4.CSV

“…The resulting effective CCS sequences were used for further analysis (Edgar, 2013). Based on the species annotation information of 16S rDNA sequences in the Silva database (https:// www.arb-silva.de/), the operational taxonomic units (OTUs) were classified into various taxonomic levels, including phylum, class, order, family, and genus (Ma et al, 2022). Alpha diversity was assessed using Chao, ACE, Simpson, and Shannon indices.…”