Wild gut microbiomes reveal individuals, species, and location as drivers of variation in two critically endangered Hawaiian honeycreepers

Abstract

Background The gut microbiome of animals is an important component that has strong influence on the health, fitness, and behavior of its host. Most research in the microbiome field has focused on human populations and commercially important species. However, researchers are now considering the link between endangered species conservation and the microbiome. In Hawaiʻi, several threats (e.g., avian malaria and habitat loss) have caused widespread population declines of Hawaiian honeycreepers (subfamily: Carduelinae). These threats can have a significant effect on the avian gut microbiome and may even lead to disruption of microbial function. However, the gut microbiome of honeycreeper in the wild has yet to be explored. Methods We collected 13 and 42 fecal samples, respectively, from two critically endangered honeycreeper species, the ʻakikiki (Oreomystis bairdi) and the ʻakekeʻe (Loxops caeruleirostris). The 16S rRNA gene was sequenced and processed though a MOTHUR-based bioinformatics pipeline. Bacterial ASVs were identified using the DADA2 program and bacterial community analyses, including alpha and beta diversity measures, were conducted using R packages Phyloseq and vegan. Results A total of 8,958 bacterial ASVs were identified from the fecal samples. Intraspecific differences in the gut microbiome among individual birds explained most of the variation present in the dataset, however differences between species did exist. Both species had distinct microbiomes with minimal overlap in beta diversity. ‘Akikiki had a more diverse microbiome compared to ‘akekeʻe. Additionally, small but stastically significant differences in beta diversity also exist between sampling location and sexes in ʻakikiki. Conclusion ʻAkikiki and ʻakekeʻe are currently the focus of captive breeding efforts and plans to translocate the two species to other islands are underway. This baseline knowledge will help inform management decisions for these honeycreeper species in their native habitats, on other islands, and in captivity.

High resolution lidar data shed light on inter‐island translocation of endangered bird species in the Hawaiian Islands

“…Another factor to consider for translocation is the fact that 'akikiki and 'akeke'e raised in captivity have been reared in a sterile environment different from that of the wild. More research into gut microbiota, foraging ability, and predator avoidance of captively bred individuals could help determine the viability of translocation (Berry et al, 2019; Costantini et al, 2021). Additional understanding of 'akikiki and 'akeke'e biotic habitat constraints and needs, such as introduced predators and food availability, through direct measurement or modeling is necessary before selection of sites within recommended areas produced by this study (Terhune et al, 2010).…”

“…Therefore, the narrower distribution centered around steeper slopes of east Maui compared to Kaua'i values does favor 'akeke'e general‐use habitat over 'akikiki. However, given a recent molecular diet analysis of 'akikiki and 'akeke'e, 'akikiki may be more able to forage in a novel habitat given their more generalist diet (Costantini et al, 2021).…”

Effect of Methionine Hydroxy Analog on Hu Sheep Digestibility, Rumen Fermentation, and Rumen Microbial Community In Vitro

“…Chao1, ACE, Shannon, Simpson, Good’s coverage, and Pielou’s evenness indices were calculated using QIIME ( , accessed on 18 November 2022) [ 29 ] (version 1.9.1). Multivariate statistical techniques, principal coordinates analysis (PCoA) of (un)weighted UniFrac, Jaccard, and Bray–Curtis distances were generated using the R project Vegan package [ 30 ] (version 2.5.3) and plotted in the R project ggplot2 package (version 2.2.1). KEGG pathway analysis of OTUs/ASV was performed using Tax4Fun [ 31 ] (version 1.0) or PICRUSt [ 32 ] (version 2.1.4).…”

The Mangrove Microbiome of the Malay Peninsula

“…As climate change progresses and coastal habitats are further degraded by land use changes, eutrophication, and other anthropogenic activities, many of these coastal ecosystems are predicted to become net sources of carbon instead of sinks as microbial communities change in response and sequestered carbon becomes available for microbial cycling [17,[19][20][21][22][23][24]. Consequently, mangroves and other coastal habitats, along with their associated blue carbon stocks, are unlikely to fulfil their claimed potential as nature based climate solutions, and many of their benefits are likely overstated [15,[25][26][27][28] The importance of the microbiome in maintaining and promoting host health has been recognised in many organisms in both terrestrial and marine environments [29][30][31][32][33], and the role of the microbiome in promoting plant growth and resilience in terrestrial plants is well established [34,35]. However, the ecological importance of the coastal microbiome is not yet well-understood, although several studies have shown that fungal and bacterial diversity are key to habitat restoration in marine environments [5,8].…”

“…The importance of the microbiome in maintaining and promoting host health has been recognised in many organisms in both terrestrial and marine environments [29–33], and the role of the microbiome in promoting plant growth and resilience in terrestrial plants is well established [34, 35]. However, the ecological importance of the coastal microbiome is not yet well-understood, although several studies have shown that fungal and bacterial diversity are key to habitat restoration in marine environments [5, 8].…”