Respiratory microbiota of humpback whales may be reduced in diversity and richness the longer they fast

Abstract

Humpback whales endure several months of fasting while undertaking one of the longest annual migrations of any mammal, which depletes the whales’ energy stores and likely compromises their physiological state. Airway microbiota are linked to respiratory health in mammals. To illuminate the dynamics of airway microbiota in a physiologically challenged mammal, we investigated the bacterial communities in the blow of East Australian humpback whales at two stages of their migration: at the beginning (n = 20) and several months into their migration (n = 20), using barcoded tag sequencing of the bacterial 16S rRNA gene. We show that early in the fasting the whale blow samples had a higher diversity and richness combined with a larger number of core taxa and a different bacterial composition than later in the fasting. This study provides some evidence that the rich blow microbiota at the beginning of their fasting might reflect the whales’ uncompromised physiology and that changes in the microbiota occur during the whales’ migration.

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

“…Statistical significance was evaluated with the anova.manyglm function, which uses pit-trap resampling [43], considering the sum-of-likelihood ratio statistics compared to a model excluding the factor of interest. This approach to the analysis of microbiota composition with mvabund has been previously described in detail by Vendl et al [51] (Supplementary materials S3).…”

“…We extracted the nucleic acids from blow and water samples following the manufacturer's protocol (MP Biomedicals, Santa Ana, California, USA). For amplification of the genetic regions (V1 -V3) of the samples' nucleic acids, we followed the protocol in Vendl et al [51]. We included the following samples as technical controls in the DNA amplification process: two positive PCR controls (PCR reagents plus the genomic DNA of Escherischia coli), seven negative PCR controls (PCR reagents only with sterile water instead of DNA sample) and four blank DNA extractions (reagents for DNA extraction only).…”

“…We performed an initial quality check with FastQC [52], and processed the paired-end reads with USEARCH version 10.240 [53]. We followed the protocol of Vendl et al [51] for further bioinformatic processing. As in Vendl et al [51] the reads were clustered into zeroradius operational taxonomic units (zOTUs) with 100% similarity.…”

“…We followed the protocol of Vendl et al [51] for further bioinformatic processing. As in Vendl et al [51] the reads were clustered into zeroradius operational taxonomic units (zOTUs) with 100% similarity. The use of zOTUs is therefore a similar approach to the formation of amplicon sequence variants (ASV) [54].…”

Current applications and future promise of genetic/genomic data for conservation in an Aotearoa New Zealand context

“…For example, Asian tiger mosquitoes (Aedes albopictus) introduced to Italy show lower microbiomic diversity than mosquitos from within the native range (Rosso et al, 2018). Additional processes that can impact microbiome diversity include captivity (e.g., Tasmanian devils, Sarcophilus harrisii; Cheng et al, 2015); and other species as summarised by West et al (2019)), poor physiological condition of individuals (e.g., fasting humpback whales, Megaptera novaeangliae; Vendl et al, 2020), and the presence of pathogens (Van Cise et al, 2020). Reductions in microbiome diversity are important as they are associated with negative health outcomes (Vangay et al, 2018).…”