Issue cover
Research Article | 18 May 2026

Comparative characterization of oral and cloacal microbiomes in captive adult and juvenile coconut lorikeets (Trichoglossus haematodus) using full-length 16S rRNA sequencing

Rini Rachmatika1, Siti Nuramaliati Prijono1, Ki Ageng Sarwono1, Suhendra Pakpahan1, Andri Permata Sari1, Sinta Maharani1, Sugiyono Saputra2, Ainissya Fitri1, Roni Ridwan1, Wahju Widodo3, R Taufiq Purna Nugraha1, Windri Handayani4, and Luthfiralda Sjahfirdi4 Show more
VETERINARY WORLD | Article No. 22 | pg no. 2117-2132 | Vol. 19, Issue 5 | DOI: 10.14202/vetworld.2026.2117-2132
Citations: —
View PDF

Cite this Article

  • APA
  • MLA
  • Chicago
  • Vancouver
  • Harvard

                            
                        


                    


                


            


            


            
        

              


                  

                      
ABSTRACT

                      
Background and Aim: The coconut lorikeet (Trichoglossus haematodus) is a nectarivorous parrot species of conservation concern in Indonesia, where captive breeding programs are increasingly implemented to reduce pressure on wild populations. Dietary modifications in captivity may influence host-associated microbiota, which play a critical role in health, nutrition, and adaptation. This study aimed to characterize and compare the oral and cloacal microbiomes of adult and juvenile T. haematodus using full-length 16S rRNA sequencing to elucidate age- and site-specific microbial patterns. 
Materials and Methods: Six clinically healthy captive T. haematodus (three adults and three juveniles) were maintained under standardized environmental and dietary conditions. Oral and cloacal swabs were collected, yielding twelve samples, which were subsequently pooled into four groups: adult oral (AO), adult cloaca (AC), juvenile oral (JO), and juvenile cloaca (JC). DNA was extracted and subjected to full-length 16S rRNA sequencing using Oxford Nanopore Technology. Bioinformatic analyses included taxonomic classification, alpha diversity (Observed operational taxonomic unit (OTU), abundance-based coverage estimator (ACE), Simpson, Fisher)), and beta diversity (Venn diagram and principal coordinates analysis). 
Results: A total of 1859 bacterial species were identified across all groups. Microbial composition differed markedly by age and anatomical site. Cloacal samples in both adults and juveniles were dominated by Rosenbergiella, with higher abundance in adults (~42%) than juveniles (~24%). Oral microbiota showed greater diversity, with Alcaligenes predominating in adults and Psittacicella in juveniles. Alpha diversity indices indicated higher richness in juvenile cloacal and AO samples, whereas adult cloacal samples exhibited lower diversity. Beta diversity analysis demonstrated clear separation among groups, indicating distinct microbial community structures influenced by both age and sampling site. Core microbiota shared across groups were limited, with substantial unique operational taxonomic units in each category. 
Conclusion: This study provides the first comprehensive characterization of oral and cloacal microbiomes in captive T. haematodus. Microbial diversity and composition are strongly influenced by age and anatomical location, with cloacal microbiota showing greater stability and oral microbiota reflecting dietary and developmental differences. The dominance of nectar-associated bacteria such as Rosenbergiella highlights the ecological linkage between host diet and microbiome. These findings offer valuable insights for optimizing captive nutrition, improving health monitoring, and supporting conservation strategies for nectarivorous parrots. 
                      
Keywords: age-related variation, avian microbiome, captive breeding, cloacal microbiota, coconut lorikeet, microbial diversity, nectarivore, oral microbiota.