Abstract
BackgroundComprehensive studies of wild bird microbiomes are often limited by difficulties of sample acquisition. However, widely used non-invasive cloacal swab methods and under-explored museum specimens preserved in alcohol provide promising avenues to increase our understanding of wild bird microbiomes, provided that they accurately portray natural microbial community compositions. To investigate this assertion, we used 16S rRNA amplicon sequencing of Great tit (Parus major) gut microbiomes to compare 1) microbial communities obtained from dissected digestive tract regions and cloacal swabs, and 2) microbial communities obtained from freshly dissected gut regions and from samples preserved in alcohol for 2 weeks or 2 months, respectively.ResultsWe found no significant differences in alpha diversities in communities of different gut regions and cloacal swabs (except in OTU richness between the dissected cloacal region and the cloacal swabs), or between fresh and alcohol preserved samples. However, we did find significant differences in beta diversity and community composition of cloacal swab samples compared to different gut regions. Despite these community-level differences, swab samples qualitatively captured the majority of the bacterial diversity throughout the gut better than any single compartment. Bacterial community compositions of alcohol-preserved specimens did not differ significantly from freshly dissected samples, although some low-abundant taxa were lost in the alcohol preserved specimens.ConclusionsOur findings suggest that cloacal swabs, similar to non-invasive fecal sampling, qualitatively depict the gut microbiota composition without having to collect birds to extract the full digestive tract. The satisfactory depiction of gut microbial communities in alcohol preserved samples opens up for the possibility of using an enormous resource readily available through museum collections to characterize bird gut microbiomes. The use of extensive museum specimen collections of birds for microbial gut analyses would allow for investigations of temporal patterns of wild bird gut microbiomes, including the potential effects of climate change and anthropogenic impacts. Overall, the utilization of cloacal swabs and museum alcohol specimens can positively impact bird gut microbiome research to help increase our understanding of the role and evolution of wild bird hosts and gut microbial communities.
Highlights
Comprehensive studies of wild bird microbiomes are often limited by difficulties of sample acquisition
Microbial community composition differences between freshly dissected gut regions and cloacal swabs Using amplicon sequencing of the 16S rRNA gene, we acquired 1,055,295 sequences from freshly dissected gut regions and cloacal swabs, which classified into 2189 operational taxonomic units (OTUs) at the 97% similarity level (Additional file 1: Table S1)
84.1% of the total number of OTUs belonged to the phylum Firmicutes, while Proteobacteria accounted for 7.5%, Bacteroidetes 3.8% and Actinobacteria 2.3%
Summary
Comprehensive studies of wild bird microbiomes are often limited by difficulties of sample acquisition. Widely used non-invasive cloacal swab methods and under-explored museum specimens preserved in alcohol provide promising avenues to increase our understanding of wild bird microbiomes, provided that they accurately portray natural microbial community compositions. The small number of studies that have investigated the validity of non-invasive sampling methods to characterize bird gut microbiomes have shown that non-invasive methods only represent gut microbiome compositions qualitatively [2, 32, 33] This implies that we must be cautious in our conclusions about full gut community structure when utilizing non-invasive approaches, but at the same time emphasizes that noninvasive methods can identify symbiont lineages present within guts. If -acquirable cloacal swabs adequately portray wild bird gut microbiomes, this could facilitate more studies and increase our understanding of wild bird-gut microbial symbioses [9, 34,35,36]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
