Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Aug 10;9:1830.
doi: 10.3389/fmicb.2018.01830. eCollection 2018.

Comparative Analyses of the Digestive Tract Microbiota of New Guinean Passerine Birds

Affiliations
Free PMC article

Comparative Analyses of the Digestive Tract Microbiota of New Guinean Passerine Birds

Kasun H Bodawatta et al. Front Microbiol. .
Free PMC article

Abstract

The digestive tract microbiota (DTM) plays a plethora of functions that enable hosts to exploit novel niches. However, our understanding of the DTM of birds, particularly passerines, and the turnover of microbial communities along the digestive tract are limited. To better understand how passerine DTMs are assembled, and how the composition changes along the digestive tract, we investigated the DTM of seven different compartments along the digestive tract of nine New Guinean passerine bird species using Illumina MiSeq sequencing of the V4 region of the 16S rRNA. Overall, passerine DTMs were dominated by the phyla Firmicutes and Proteobacteria. We found bird species-specific DTM assemblages and the DTM of different compartments from the same species tended to cluster together. We also found a notable relationship between gut community similarity and feeding guilds (insectivores vs. omnivores). The dominant bacterial genera tended to differ between insectivores and omnivores, with insectivores mainly having lactic acid bacteria that may contribute to the breakdown of carbohydrates. Omnivorous DTMs were more diverse than insectivores and dominated by the bacterial phyla Proteobacteria and Tenericutes. These bacteria may contribute to nitrogen metabolism, and the diverse omnivorous DTMs may allow for more flexibility with varying food availability as these species have wider feeding niches. In well-sampled omnivorous species, the dominant bacterial genera changed along the digestive tracts, which was less prominent for insectivores. In conclusion, the DTMs of New Guinean passerines seem to be species specific and, at least in part, be shaped by bird diet. The sampling of DTM along the digestive tract improved capturing of a more complete set of members, with implications for our understanding of the interactions between symbiont and gut compartment functions.

Keywords: MiSeq amplicon sequencing; insectivores; microbiome; nutrition; omnivores; symbiosis.

Figures

Figure 1
Figure 1
(A) A map of the sampling localities in Papua New Guinea: the Wanang conservation area, the Mount Wilhelm transect in Madang province, and Wasaunon on the Huon Peninsula in the Morobe province. (B) The digestive tract of Melipotes fumigatus indicating six compartments dissected from the alcohol specimen. The regurgitated samples were used to analyse the crop (not shown) microbiota.
Figure 2
Figure 2
Principal component analysis (PCA) of DTM communities in different digestive tract compartments (shapes) in nine New Guinean passerine species (colors). The main dietary guilds of the bird species are indicated in front of their names in the figure key. The scree plot represents the variation in the data captured by the first 10 principal components. Arrows indicate the OTUs that mainly drive the microbial community separation: OTU 01 (unclassified Carnobacteriaceae genus, Firmicutes) and OTU 04 (Lactobacillus, Firmicutes), OTU 08 (unclassified Mycoplasmataceae genus, Tenericutes), and OTU 10 (Helicobacter, Proteobacteria).
Figure 3
Figure 3
Dendrogram based on Bray-Curtis dissimilarity of DTMs between different compartments (different shapes) of the digestive tract of nine New Guinean passerine species (different colors). Gray scale shading of clades represents the feeding guilds of the bird species.
Figure 4
Figure 4
Average ± SE Inverse Simpson's diversity index of DTM in different digestive tract compartments. The infraorders of the species and the dietary guilds indicated above the figure. Numbers of replicates are given in parentheses.
Figure 5
Figure 5
The proportion of major bacterial phyla present in the DTMs of different digestive tract compartments. The dendrogram represents the phylogenetic relationship between the bird species and the tips of the dendrogram represent the feeding guild of each species: black: insectivores, solid gray: omnivores (fruits and insects), and dashed gray: omnivores (nectar and insects). Red line indicates the separation of the bird infraorders. Photo credits: Andrew Hart Reeve.
Figure 6
Figure 6
Relative abundance of the twenty most abundant bacterial genera in digestive tract compartments of insectivorous bird species. Bacterial genera belonging to the same phylum are represented by similar shades of colors.
Figure 7
Figure 7
Relative abundance of the twenty most abundant bacterial genera in different digestive tract compartments of omnivorous bird species. Bacterial genera belonging to the same phylum are represented by similar shades of colors.

Similar articles

See all similar articles

Cited by 5 articles

References

    1. Benskin C. M. H., Wilson K., Jones K., Hartley I. R. (2009). Bacterial pathogens in wild birds: a review of the frequency and effects of infection. Biol. Rev. 84, 349–373. 10.1111/j.1469-185X.2008.00076.x - DOI - PubMed
    1. Cafaro M. J., Poulsen M., Little A. E. F., Price S. L., Gerardo N. M., Wong B., et al. . (2011). Specificity in the symbiotic association between fungus-growing ants and protective Pseudonocardia bacteria. Proc. Biol. Sci. 278, 1814–1822. 10.1098/rspb - DOI - PMC - PubMed
    1. Ceja-Navarro J. A., Vega F. A., Karaoz U., Hao Z., Jenkins S., Lim H. C., et al. . (2015). Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee. Nat. Commun. 6:7618. 10.1038/ncomms8618 - DOI - PMC - PubMed
    1. Dewar M. L., Arnold J. P. Y., Dann P., Trathan P., Groscolas R., Smith S. (2013). Interspecific variations in the gastrointestinal microbiota in penguins. Microbiologyopen 2, 195–204. 10.1002/mbo3.66 - DOI - PMC - PubMed
    1. Dickinson E. C., Christidis L., editors. (eds). (2014). The Howard and Moore Complete Checklist of the Birds of the World, Vol. 2: Passerines, 4th Edn Eastbourne: Aves Press.

LinkOut - more resources

Feedback