Metagenomic characterization of microbial communities associated with alphaherpesvirinae detection in magnificent frigatebirds from French Guiana

Abstract

Introduction A population of Magnificent Frigatebirds (Fregata magnificens, Suliformes) inhabiting French Guiana has been under investigation since 2005 due to high chick mortality rates associated with nodular proliferative skin lesions, characterized by featherless areas on the body. An initial study conducted in 2009 reported the presence of an alphaherpesvirus detected in a crust from a single individual in the same frigatebird population. However, the cause of the outbreaks and the associated high mortality in the frigatebird population remained undetermined. Methods Almost 15 years later, in 2024, we collected beak swabs, cloacal swabs, and blood samples from 14 animals. Six animals were clinically healthy, while eight showed clinical signs including skin crusts, hyperkeratosis on the eyes, corneal thickening, and signs of distress. To investigate the potential causes of those signs, we screened the samples for herpesviruses. To characterize bacterial and viral communities and investigate potential co-infections, we selected four beak swabs for metagenomic analysis: two from herpesvirus-positive individuals and two from herpesvirus-negative controls (one healthy and one with clinical signs), and sequenced them using metagenomic Next Generation Sequencing (NGS). Results and discussion Two individuals tested positive for herpesviruses in beak swabs, one healthy and one with clinical signs. Analysis of the bacterial community revealed that the most abundant phyla were Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Fusobacteria, which typically inhabit the gut microbiota. All reported bacterial phyla were detected in every sequenced sample. At the viral level, among non-bacteriophage viruses, Orthoherpesviridae showed the highest abundance in PCR-positive animals, followed by Adenoviridae- and Hepadnaviridae-related sequences. Sequence analysis of the DNA-directed DNA polymerase (DdDp) region of Orthoherpesviridae identified two sequences: one with 98.1% nucleotide identity to sequences reported in the same geographic area in 2005, and the other with 72.1% identity to a vulture herpesvirus from India. The bacterial and viral populations detected were largely similar between animals with and without clinical signs. Due to the limited sample size, it was not possible to determine whether the detected microorganisms were associated with the observed clinical signs.