Abstract
Adult giant pandas (Ailuropoda melanoleuca) express transitional characteristics in that they consume bamboos, despite their carnivore-like digestive tracts. Their genome contains no cellulolytic enzymes; therefore, understanding the development of the giant panda gut microbiome, especially in early life, is important for decoding the rules underlying gut microbial formation, inheritance and dietary transitions. With deep metagenomic sequencing, we investigated the gut microbiomes of two newborn giant panda brothers and their parents living in Macao, China, from 2016 to 2017. Both giant panda cubs exhibited progressive increases in gut microbial richness during growth, particularly from the 6th month after birth. Enterobacteriaceae dominated the gut microbial compositions in both adult giant pandas and cubs. A total of 583 co-abundance genes (CAGs) and about 79 metagenomic species (MGS) from bacteria or viruses displayed significant changes with age. Seven genera (Shewanella, Oblitimonas, Helicobacter, Haemophilus, Aeromonas, Listeria, and Fusobacterium) showed great importance with respect to gut microbial structural determination in the nursing stage of giant panda cubs. Furthermore, 10 orthologous gene functions and 44 pathways showed significant changes with age. Of the significant pathways, 16 from Escherichia, Klebsiella, Propionibacterium, Lactobacillus, and Lactococcus displayed marked differences between parents and their cubs at birth, while 29 pathways from Escherichia, Campylobacter and Lactobacillus exhibited significant increase in cubs from 6 to 9 months of age. In addition, oxidoreductases, transferases, and hydrolases dominated the significantly changed gut microbial enzymes during the growth of giant panda cubs, while few of them were involved in cellulose degradation. The findings indicated diet-stimulated gut microbiome transitions and the important role of Enterobacteriaceae in the guts of giant panda in early life.
Highlights
The giant panda, a bamboo specialist, harbors hundreds of bacterial operational taxonomic units (OTUs) in its gut as an adult, mostly from Firmicutes or Proteobacteria, and dominated by Escherichia, Shigella, and Streptococcus (Xue et al, 2015)
Increasing numbers of studies of the significant gut microbes or pathways in giant panda have been reported in recent years (Xue et al, 2015; Wu et al, 2017; Guo et al, 2018; Yang et al, 2018; Zhang et al, 2018), few focused on giant panda cubs (Xue et al, 2015; Zhang et al, 2018) or established linkages between the significant gut microbes and pathways in cubs
A consecutive and close study minimizing the factors except diet to trace gut microbiome transitions within the same giant panda cub after birth is urgently needed
Summary
The giant panda, a bamboo specialist, harbors hundreds of bacterial operational taxonomic units (OTUs) in its gut as an adult, mostly from Firmicutes or Proteobacteria, and dominated by Escherichia, Shigella, and Streptococcus (Xue et al, 2015). Despite their high fiber diet, cellulolytic species typically present in herbivore guts, e.g., members of Ruminococcaceae or. The gut microbiota compositions of adult giant pandas exhibited extensive seasonal variation (Xue et al, 2015; Wu et al, 2017). Biofilm (Hall-Stoodley et al, 2004) or surfactin (Zhou et al, 2018) secreted by internal microbes of giant panda can stabilize the gut microbial structure
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