Comparative analysis of gut DNA viromes in wild and captive Himalayan vultures

Abstract

IntroductionHimalayan vultures (Gyps hinalayensis) are widely distributed on the Qinghai-Tibetan Plateau and play a crucial role in maintaining the ecological balance by feeding on decayed corpses of wild and domestic animals. Large-scale culture and metagenomics studies have broadened our understanding of viral diversity in animals’ gastrointestinal tracts. However, despite the importance of gut viral communities in regulating bacterial diversity and performing symbiotic functions, no gut viral study has been conducted on Himalayan vultures. Furthermore, the impact of captivity on the gut virome of these vultures remains unknown.MethodsIn this study, metagenomic sequencing methods targeting DNA of virus-like particles enriched from feces were used to characterize the gut DNA viromes of wild and captive Himalayan vultures.ResultsIn total, 22,938 unique viral operational taxonomic units (vOTUs) were identified and assigned to 140 viral genera in 41 viral families. These families included viruses associated with bacteria, animals, plants, insects, and archaea. Phage communities, including Siphoviridae, Microviridae, Myoviridae, Inoviridae, and Herelleviridae, dominated the gut virome of Himalayan vultures. Wild vultures exhibited higher viral richness and diversity compared with those in captivity. The functional capacity of the gut virome was characterized by identifying 93 KEGG pathways, which were significantly enriched in metabolism and genetic information processing. Abundant auxiliary metabolic genes, such as carbohydrate-active enzyme, and antibiotic resistance genes, were also found in the vultures’ gut virome.DiscussionOur findings reveal the complex and diverse viral community present in the gut virome of Himalayan vultures, which varies between wild, and captive states. The DNA virome dataset establishes a baseline for the vultures’ gut virome and will serve as a reference for future virus isolation and cultivation. Understanding the impact of captivity on the gut virome contributes to our knowledge of vultures’ response to captivity and aids in optimizing their rehabilitation and implementing protective measures.

The Potential of Co-Evolution and Interactions of Gut Bacteria–Phages in Bamboo-Eating Pandas: Insights from Dietary Preference-Based Metagenomic Analysis

“…Furthermore, the living environment is also a crucial factor influencing the host gut phage community [59,122]. Limited previous research evidence in species such as vulture (Gyps hinalayensis) [123], Tasmanian devil (Sarcophilus harrisii) [124], and giant panda (Ailuropoda melanoleuca) [59] have indicated that controlled captive environments (e.g., dietary changes, microbial transmission, and human interference) can alter the composition and diversity of the host gut phage community. We speculate that the unique captive environment of giant pandas [4,16,52,61,104,125,126], characterized by factors such as a high-starch and -milkfat diet, increased antibiotic usage, and frequent human contact, may contribute in part to the pivotal role of phages in shaping the coexistence pattern of the gut bacterial and phage communities in captive giant pandas.…”