Gut microbiome of migratory shorebirds: Current status and future perspectives

Abstract

Migratory shorebirds have many unique life history characteristics, such as long-distance travel between breeding sites, stopover sites, and wintering sites. The physiological challenges for migrant energy requirement and immunity may affect their gut microbiome community. Here, we reviewed the specific features (e.g., relatively high proportion of Corynebacterium and Fusobacterium) in the gut microbiome of 18 migratory shorebirds, and the factors (e.g., diet, migration, environment, and phylogeny) affecting the gut microbiome. We discussed possible future studies of the gut microbiome in migratory shorebirds, including the composition and function of the spatial-temporal gut microbiome, and the potential contributions made by the gut microbiome to energy requirement during migration.

Keywords: composition and function; energy requirement; migratory shorebirds; the gut microbiome.

FIGURE 1

The analysis of the published bacterial 16S ribosomal RNA gene data (using high‐throughput sequencing) of the migratory shorebirds. (a) Phylum level. (b) Genus level. Details of the published data are shown in Table 1. The trimmomatic function was used for quality control on these raw datasets (Bolger et al., 2014). Operational taxonomic units (OTU) were defined as sharing >97% sequence identity by searching clean sequences against the SILVA132 database by pick‐up‐closed‐OTU methods (Christian et al., 2013). Taxon summary was created using the OTUs table (2,000 sequences per sample) in QIIME 1.9 (Caporaso et al., 2010)

FIGURE 2

The specific features in the gut microbiome of the migratory shorebirds based on the analysis of the published bacterial 16S Ribosomal RNA gene data (using high‐throughput sequencing). (a) Corynebacterium. (b) Fusobacterium and Cetobacterium (c) Campylobacter and Helicobacter. Details of the published data are shown in Table 1

FIGURE 3

The re‐analysis on the gut microbiome community of eight migratory shorebirds (Grond et al., 2019). (a) Nonmetric multidimensional scaling (NMDS) using unweighted UniFrac distance displayed the mixed pattern in the gut microbiome among eight migratory shorebirds. (b) LEfSe (linear discriminant analysis effective size) determined the significant difference in the abundance of the gut microbial taxon among eight migratory shorebirds. AMGP, Pluvialis dominica; DUNL, Calidris alpine; LBDO, Limnodromus scolopaceus; PESA, Calidris melanotos; REPH, Phalaropus fulicarius; RNPH, Phalaropus lobatus; SESA, Calidris pusilla; WESA, Calidris mauri. The raw dataset of sediment microbiome came from Risely et al. (2017)

FIGURE 4

The PCoA analysis of the published bacterial 16S ribosomal RNA gene data of the migratory shorebirds using unweighted UniFrac distance. (a) The data source; (b) sampling time; (c) sample type; (d) study area; (e) sampling site. Details of the published data are shown in Table 1

FIGURE 5

The main migration route worldwide (The sample location data were referred to published data: Cho & Lee, 2020; Grond et al., 2020; Grond et al., 2019; Risely et al., 2018; Risely et al., 2017; Ryu et al., 2014; Santos et al., 2012. The number represents the research location: 1 = MacKenzie River Delta in Alaska and Canada; 2 = Delaware Bay, USA; 3 = Sirius Passet; North Greenland; 4 = Tagus estuary, Portugal; 5 = Broome, Western Australia; 6 = Victoria, Eastern Australia. The migration route is redrawn according to the content of the URL https://www.sovon.nl/ and https://www.wwt.org.uk/. The black dotted line indicates the East Asia–Australia migration route. The red dotted line indicates the Central Asia–India migration route. The orange dotted line indicates the migration route from West Asia to East Africa. The yellow dotted line indicates the Mediterranean–Black Sea migration route. The green dotted line indicates the migration route in the eastern Atlantic Ocean. The cyan dotted line indicates the migration route of the western Atlantic Ocean. The blue dotted line indicates the Mississippi migration route. The purple dotted line indicates the migration route in the eastern Pacific Ocean)