Gut microbiota of endangered crested ibis: Establishment, diversity, and association with reproductive output

Abstract

Gut microbiota is known to influence the host’s health; an imbalance of the gut microbial community leads to various intestinal and non-intestinal diseases. Research on gut microbes of endangered birds is vital for their conservation. However, a thorough understanding of the gut microbiome composition present in crested ibises at different ages and its correlation with crested ibis reproductive capacity has remained elusive. Here, we used 16S rRNA gene sequencing to explore the fecal microbial structure of nestlings and adult birds, and the difference in gut microbiota between healthy and sterile crested ibises. We observed that (1) bacterial microbiota, alpha and beta diversity of one-day-old nestlings significantly distinguished from other nestlings; abundance of Proteobacteria decreased, while that of Fusobacteria increased with an increase in the age of the nestlings; (2) there was no significant difference in community composition among adult crested ibises aged one, two, three, and five years; (3) the abundance of Proteobacteria and alpha diversity indices were higher in sterile crested ibises than in healthy crested ibises; thus, Proteobacteria can act as a diagnostic biomarker of reproductive dysfunction in crested ibises. This study significantly contributes to the field of ecology and conservation, as it provides a platform for assessing the reproductive capacity of endangered crested ibises, based on the gut microbiota composition. Further studies may unravel additional factors influencing crested ibises’ reproductive health, which will further help the management and control of the crested ibis population.

Establishment of Gut Microbiome During Early Life and Its Relationship With Growth in Endangered Crested Ibis (Nipponia nippon)

“…Sampling at crested ibis hatching already revealed diverse gut microbiota ( Figure 2A ), which are consistent with previous observations ( Ran et al, 2021 ). According to the results, crested ibis could acquire microbiota when inside the egg and bacterial colonization occurred before hatching.…”

“…Notably, in the present study, Fusobacteria (Cetobacterium and other unassigned genera; Figure 6) were more dominant from 27 days and enriched in diet type 2 when fresh loach was introduced to chick formula, however, Fusobacteria increased significantly in the Deqing population (another crested ibis's breeding center in China) from 9 days or earlier, as observed by Ran et al (2021). Fusobacteria colonization was potentially due to the ingestion of fresh loach, since the time of Fusobacteria colonization is consistent with the addition of fresh loach based on the results of two studies on crested ibis (addition of fresh loach began on day 5 in the Deqing population, personal communication with Ran Jian).…”

“…Gut microbiota diversity (both alpha and beta) exhibited non-linear changes ( Figure 2A ) during the sampling period, as expected. Such a pattern was not observed in other age-related studies, including in another study on crested ibis ( Ran et al, 2021 ) and other avian species, due to infrequent sampling. Our findings revealed that bacteria colonization and extinctions occurred throughout the development in crested ibis, and mainly occurred in Proteobacteria and Firmicutes phyla.…”

“…During the indoor stage, crested ibis undergo a diet change and two environmental changes ( Ding, 2004 ). Gut microbiota composition at hatching is distinguished from other life stages ( Ran et al, 2021 ), however, it is unclear whether community structure is mainly influenced by biological (such as age) or ecological variables (such as diet and environmental changes) during early life. In addition, variation in chick growth rate has been previously observed but whether it is due to gut microbiota remains to be determined.…”

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

“…The significance of identifying the gut microbial community is that it provides a scientific basis for protecting endangered animals. Previous studies have confirmed that Proteobacteria is a diagnostic biomarker of reproductive dysfunction in crested ibises due to the abundance of Proteobacteria, and alpha-diversity indices were higher in sterile crested ibises than in healthy crested ibises ( Ran et al, 2021 ). Similarly, the crested ibis chick growth rate was negatively associated with gut microbiota diversity and negatively correlated with the abundance of Dietziaceae, Halomonadaceae, Corynebacteriaceae, and Streptococci ( Zhu et al, 2021 ).…”