Metagenomic Analysis of Bacteria, Fungi, Bacteriophages, and Helminths in the Gut of Giant Pandas

Abstract

To obtain full details of gut microbiota, including bacteria, fungi, bacteriophages, and helminths, in giant pandas (GPs), we created a comprehensive microbial genome database and used metagenomic sequences to align against the database. We delineated a detailed and different gut microbiota structures of GPs. A total of 680 species of bacteria, 198 fungi, 185 bacteriophages, and 45 helminths were found. Compared with 16S rRNA sequencing, the dominant bacterium phyla not only included Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria but also Cyanobacteria and other eight phyla. Aside from Ascomycota, Basidiomycota, and Glomeromycota, Mucoromycota, and Microsporidia were the dominant fungi phyla. The bacteriophages were predominantly dsDNA Myoviridae, Siphoviridae, Podoviridae, ssDNA Inoviridae, and Microviridae. For helminths, phylum Nematoda was the dominant. In addition to previously described parasites, another 44 species of helminths were found in GPs. Also, differences in abundance of microbiota were found between the captive, semiwild, and wild GPs. A total of 1,739 genes encoding cellulase, β-glucosidase, and cellulose β-1,4-cellobiosidase were responsible for the metabolism of cellulose, and 128,707 putative glycoside hydrolase genes were found in bacteria/fungi. Taken together, the results indicated not only bacteria but also fungi, bacteriophages, and helminths were diverse in gut of giant pandas, which provided basis for the further identification of role of gut microbiota. Besides, metagenomics revealed that the bacteria/fungi in gut of GPs harbor the ability of cellulose and hemicellulose degradation.

Succession of Gut Microbial Structure in Twin Giant Pandas During the Dietary Change Stage and Its Role in Polysaccharide Metabolism

“…These are the key enzymes in the metabolic pathway of cellulose degradation and correspond to CAZy members GH1, GH3, GH5, GH8, and GH9 [The carbohydrate-active enzyme (CAZy), 2020]. Although we detected no cellobiosidase (EC3.2.1.91) genes in the twin panda cubs (Yang et al, 2018), genes encoding cellobiose phosphorylase (GH94) increased in the gut microbial genome. Therefore, the capacity of the giant panda to degrade the cellulose in bamboo is potentially active, attributed to the enzyme gene groups of its gut microbes.…”

“…Among them, Bacteroides, a phylum that is a major source of polysaccharide-metabolizing bacterial taxa (McNulty et al, 2013;Zhu et al, 2018), but is scarce in the intestine of panda. Previous studies have shown that many members of Bacteroides could effectively degrade lignocellulose in the herbivore intestine not in the carnivore intestine (Yang et al, 2018). They may also be more adaptable to consume dietary fiber, such as grain, rather than the complex lignocellulose found in bamboo (McNulty et al, 2013).…”

Raw milk and fecal microbiota of commercial Alpine dairy cows varies with herd, fat content and diet

“…This result is in line with previously published studies of bovine raw milk [ 2 , 4 , 11 , 48 ] and fecal samples [ 16 , 18 , 21 , 24 ] in experimental herds or much smaller numbers of dairy cows. Furthermore, these three phyla are the most abundant in a variety of different mammalian species, such as human and non-human primates, laboratory mice [ 49 – 53 ], as well as wild herbivores (giant panda [ 54 ]; sika deer [ 55 ]; forest musk deer [ 56 ]). In addition, the low relative abundance of Proteobacteria found in the fecal samples of this study (2.5%) compared to Firmicutes and Bacterioides (89.6%), may reflect the health status of the cows.…”

Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome

“…Indeed, Mammalia were more likely to have higher bacterial relative to fungal diversity than Aves in our study organisms (mean difference in probability 22.9% [1.6 -45.7%). Variation among species in this model explained 19.5% [7.3 -31.2%] of the variation in relative microbial richness. Using a bivariate model with both fungal and bacterial diversity as response variables to examine patterns of absolute microbial richness across host taxonomy, only Mammalia exhibited bacterial diversity that was consistently higher than fungal diversity when controlling for variation among species (mean difference in index 5.16; [3.33 -6.96]; Fig.…”

“…The roles of animal-associated mycobiomes are currently not well understood; however, a small but growing body of research has identified the potential importance of resident fungal microbiota, termed the 'mycobiome', for host animal health. This may include diverse functions such as fat, carbon and nitrogen metabolism 17,18 , degradation of cellulose and other carbohydrates 19 , pathogen resistance 20 , initiating immune pathways and regulating inflammatory responses 9,21 , and even host dispersal 22 . Host phylogeny has repeatedly been shown to be an important predictor of bacterial microbiome structure in multiple vertebrate clades, a phenomenon known as 'phylosymbiosis' [23][24][25][26][27] .…”