Abstract
Animals have stable dominant gut microbiomes under similar diets. Similar diets can also lead to similar gut microbial communities within host species levels. Giant pandas (Ailuropoda melanoleuca) and red pandas (Ailurus fulgens) have had long-term and stable bamboo diets, and seem well adapted to this highly fibrous diet. When compared to the gut microbiomes of Père David's deer (Elaphurus davidianus), humans, cheetah (Acinonyx jubatus), black-backed jackal (Canis-mesomelas), and black bear (Ursus thibetanus), giant panda gut microbiomes have high variation in the abundance of Pseudomonadaceae and Clostridiaceae, and are somewhat unstable. This high instability and dissimilarity may reflect an unstable gut environment, perturbation or selective pressure because of their carnivorous gastrointestinal system. A short digestive tract, brief digestion time and fast intestinal peristalsis may result in higher oxygen concentrations that select for the growth of aerobes and facultative anaerobes in giant pandas. Potential selection of high proportion of Pseudomonadaceae in giant panda (GP-HP) and red panda gut microbiomes may arise because of their postulated ability to degrade secondary compounds (e.g., cyanide compounds and aromatic compounds). However, high proportion of Clostridiaceae (GP-HF) may focus on cellulose and hemicellulose digestion. Thus, GP-HP and GP-HF groups have high dissimilarity on the functional level. These findings show that long-term similarities in diet do not always lead to similar or stable gut microbial system within the same host species and that other factors can drive the selection of gut taxa.
Highlights
Typical microbial colonies found on or in the body are normally benign or beneficial (Kau et al, 2011)
After comparing giant panda and read panda metagenomes to 30 Milu (Elaphurus davidianus) gut community metagenomes produced here, in addition to 39 other mammalian gut community metagenomes (Muegge et al, 2011), we found that gut community functions of GP-HP and red panda were enriched in xenobiotic biodegradation and metabolism, amino acid metabolism, metabolism of cofactors and vitamins, and lipid metabolisms and GP-HF were enriched in carbohydrate metabolism
Especially giant panda, showed high variation and instability compared with the gut microbiomes of deer, humans, black bear, cheetah and black-backed jackal
Summary
Typical microbial colonies found on or in the body are normally benign or beneficial (Kau et al, 2011). The mammal gut microbiota protects against enteropathogens, extracts nutrients and energy from diets, and contributes to normal immune function (Sonnenburg et al, 2005; Ley et al, 2008; Fukuda et al, 2011; Pope et al, 2011; Olszak et al, 2012; Yatsunenko et al, 2012). The coevolution has been invoked to describe the formation of the host-gut microbe relationship (Amato, 2013). This coevolution within the same host is relatively clear: similar diet leads to
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