Bamboo Specialists from Two Mammalian Orders (Primates, Carnivora) Share a High Number of Low-Abundance Gut Microbes
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Bamboo specialization is one of the most extreme examples of convergent herbivory, yet it is unclear how this specific high-fiber diet might selectively shape the composition of the gut microbiome compared to host phylogeny. To address these questions, we used deep sequencing to investigate the nature and comparative impact of phylogenetic and dietary selection for specific gut microbial membership in three bamboo specialists—the bamboo lemur (Hapalemur griseus, Primates: Lemuridae), giant panda (Ailuropoda melanoleuca, Carnivora: Ursidae), and red panda (Ailurus fulgens, Carnivora: Musteloideadae), as well as two phylogenetic controls—the ringtail lemur (Lemur catta) and the Asian black bear (Ursus thibetanus). We detected significantly higher Shannon diversity in the bamboo lemur (10.029) compared to both the giant panda (8.256; p = 0.0001936) and the red panda (6.484; p = 0.0000029). We also detected significantly enriched bacterial taxa that distinguished each species. Our results complement previous work in finding that phylogeny predominantly governs high-level microbiome community structure. However, we also find that 48 low-abundance OTUs are shared among bamboo specialists, compared to only 8 OTUs shared by the bamboo lemur and its sister species, the ringtail lemur (Lemur catta, a generalist). Our results suggest that deep sequencing is necessary to detect low-abundance bacterial OTUs, which may be specifically adapted to a high-fiber diet. These findings provide a more comprehensive framework for understanding the evolution and ecology of the microbiome as well as the host.
KeywordsGut microbiome Convergent evolution Feeding strategy Bamboo specialist Host-microbiome relationship
The authors would like to thank the staff at the Duke Lemur Center, the National Zoological Park, and Ion Torrent for their help and support. We are also especially grateful to Dr. Robert Fleischer and Dr. Scott Langdon for providing lab space and equipment for DNA extraction and sequencing.
Conceived of and designed the experiments: EAM ADY
Collected samples: EAM MM
Analyzed and interpreted the data: EAM AR
Contributed reagents/materials/analysis tools: EAM AR ADY
Wrote the manuscript: EAM MM AR ADY
This research was funded in by the National Science Foundation (grant no. 1455848) and the Wainwright fund.
Compliance with Ethical Standards
Conflict of Interest
The authors declare that they have no conflict of interest.
Research Involving Animals
All applicable international, national, and/or institutional guidelines for the care and use of animals were followed. All procedures were reviewed and approved by Duke University IACUC under protocol number A203-11-08.
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