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.
Highlights
In this study we investigate multiple digestive tract compartments of nine New Guinean passerine bird species belonging to two feeding guilds; Colluricincla megarhyncha, Ifrita kowaldi, Rhipidura atra, Crateroscelis robusta, Sericornis nouhuysi, Melipotes fumigatus, Melanocharis nigra, Melanocharis versteri, Toxorhamphus poliopterus, and assess the appropriateness of investigating single compartments of the digestive tract to capture the full digestive tract microbiota (DTM) diversity
The stomach and the beginning of the small intestine were typically dominated by 2–3 bacterial genera mainly belonging to Firmicutes (Figures 5, 6), while bacterial communities in the crop and the lower digestive tract were inhabited by more genera and phyla, such as Firmicutes, Proteobacteria, and Verrucomicrobia
Guinean passerine bird species and found that Firmicutes and Proteobacteria dominate the DTMs, which is consistent with previous studies of the passerine gut microbiota (Hird et al, 2014, 2015; Lewis et al, 2016; Kropáčková et al, 2017; García-Amado et al, 2018; Teyssier et al, 2018)
Summary
Animal bodies are sophisticated centers of symbiotic interactions (Ley et al, 2008; Huttenhower and The human microbiome project consortium, 2012; Macke et al, 2017) that have allowed for adaptations enabling hosts to exploit new niches (Russell et al, 2009; Godoy-Vitorino et al, 2012; Dietrich et al, 2014; Macke et al, 2017). This assumption is supported by a few studies that have compared different digestive tract compartments and found differences in microbial community compositions (Videvall et al, 2017; Zhang et al, 2017; Drovetski et al, 2018; García-Amado et al., 2018) These studies demonstrated that the DTMs of cloacal or fecal samples may qualitatively represent the microbiota of other sections of the digestive tract but not quantitatively (Videvall et al, 2017; Zhang et al, 2017). More comparative studies on the DTM of digestive tract compartments of wild birds may improve our understanding of what determines the composition of microbial communities in natural conditions and identify the bacterial symbionts that play important roles along the digestive tract. Diagnostic PCR was conducted at the University of Copenhagen to confirm the
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