Highly abundant core taxa in the blow within and across captive bottlenose dolphins provide evidence for a temporally stable airway microbiota

Abstract

Background The analysis of blow microbiota has been proposed as a biomarker for respiratory health analysis in cetaceans. Yet, we lack crucial knowledge on the long-term stability of the blow microbiota and its potential changes during disease. Research in humans and mice have provided evidence that respiratory disease is accompanied by a shift in microbial communities of the airways. We investigate here the stability of the community composition of the blow microbiota for 13 captive bottlenose dolphins over eight months including both sick and healthy individuals. We used barcoded tag sequencing of the bacterial 16S rRNA gene. Four of the dolphins experienced distinct medical conditions and received systemic antimicrobial treatment during the study. Results We showed that each dolphin harboured a unique community of zero-radius operational taxonomic units (zOTUs) that was present throughout the entire sampling period (‘intra-core’). Although for most dolphins there was significant variation over time, overall the intra-core accounted for an average of 73% of relative abundance of the blow microbiota. In addition, the dolphins shared between 8 and 66 zOTUs on any of the sampling occasions (‘inter-core’), accounting for a relative abundance between 17 and 41% of any dolphin’s airway microbiota. The majority of the intra-core and all of the inter-core zOTUs in this study are commonly found in captive and free-ranging dolphins and have previously been reported from several different body sites. While we did not find a clear effect of microbial treatment on blow microbiota, age and sex of the dolphins did have such an effect. Conclusions The airways of dolphins were colonized by an individual intra-core ‘signature’ that varied in abundance relative to more temporary bacteria. We speculate that the intra-core bacteria interact with the immune response of the respiratory tract and support its function. This study provides the first evidence of individual-specific airway microbiota in cetaceans that is stable over eight months.

The effects of human care on the blowhole and gut microbiotas of two cohabiting dolphin species based on a year-round surveillance

“…If non-invasive blow sampling can aid in the respiratory health monitoring of cetaceans has been one of the major concerns for conservation biologists. In agreement with previous observations (Nelson et al, 2019;Vendl et al, 2021), our findings supported that blow sampling of captive dolphins can be used for their health monitoring in conservation practices. Firstly, the dolphin blow displayed more highly diverse bacterial communities compared to the feces and pool water samples, even if the potentially contaminated reads originating from the pool water were removed (Figure S1).…”

“…To eliminate potential contamination originating from the water samples, we identified contaminated OTUs using the R package {decontam} following the same parameters outlined in the study by Vendl et al, 2021. In total, we discarded 339 OTUs from the dolphin microbiota which likely originated from the pool water (Figure S2). We then removed seven blowhole samples and two fecal samples from the dataset, as the number of reads was extremely low (< 6,000) (Table S2).…”

“…Suzuki et al (2021) found that Indo-Pacific bottlenose dolphins (T. aduncus) under human care and wild environments harbored habitat-specific microbial groups and that several pathogenic bacterial genera were only detected in the dolphins under human care, which highlighted the importance of monitoring pathogenic bacteria in cetaceans under human care. Another study provided evidence that the blowhole microbiota of common bottlenose dolphins was individual-specific and stable over eight months (Vendl et al, 2021). Regardless of the potential importance of human care for the health of captive cetaceans, the seasonal stability, and the degree to which human care humanizes the microbiota of different cetacean taxa have not been explored.…”

Targeting the Pulmonary Microbiota to Fight against Respiratory Diseases

“…Initial microbial colonization in the respiratory tract is mainly impacted by delivery mode, antibiotic usage, dietary structure, environment exposure, and pathogenic infections ( Figure 1 ) [ 24 , 25 , 26 , 27 ]. In early life, caesarean delivery patterns, increasing use of antibiotics, changes in food composition, and the contacting environmental microorganisms can all directly and indirectly impact the diversity and abundance of the lung microbiome [ 28 , 29 , 30 ].…”

The Epidermal Microbiome Within An Aggregation of Leopard Sharks (Triakis Semifasciata) Has Taxonomic Flexibility With Gene Functional Stability Across Three Time-Points

“…While the respiratory microbiome of bottlenose dolphin species (Tursiops truncatus and Tursiops aduncus) maintained taxonomic stability over two months, but individual dolphins had significantly different microbiome taxonomic structures (Lima et al 2012). In an analysis of 8 months, captive dolphins had an individual signature of their lung microbiome and shared between 17 -41 % of the microbiome with other individuals (Vendl et al 2021). In contrast, 77.6 % of the microbes in the epidermal microbiome of thresher sharks (A. vulpinus) were shared across individual sharks (Doane et al 2017), however, this study was only conducted at one timepoint.…”