Functional convergence of Yunnan snub-nosed monkey and bamboo-eating panda gut microbiomes revealing the driving by dietary flexibility on mammal gut microbiome

Xia, Wancai; Liu, Guoqi; Wang, Dali; Chen, Hua; Zhu, Lifeng; Li, Dayong

doi:10.1016/j.csbj.2022.01.011

Cited by 19 publications

(29 citation statements)

References 86 publications

(105 reference statements)

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“…For example, all three types of samples harbored similar dominant families ( Pseudomonadaceae ), but the proportions of the Proteobacteria and Firmicutes phyla differed. In wild snub-nosed monkeys, the relative abundance of Bacteroidetes , Proteobacteria, and Firmicutes indicated they were the top three dominant bacteria [ 19 ], which is consistent with the present study. The significantly enriched abundance of Proteobacteria genera (e.g., Pseudomonas , Comamonas , and Acinetobacter ) might be a response to bamboo shoot intake in the diet of monkeys.…”

Section: Discussionsupporting

confidence: 91%

“…The dietary structure and the complex community of gut microbiota (i.e., its diversity) could influence the changes in SCFA quantity and proportion [ 35 ]. In the present study, higher levels of propionic acid in monkeys’ feces than in otters’ feces reflect a higher carbohydrate intake and are related to a higher abundance of Proteobacteria [ 19 ]. The gut microbiota of otters differed from that of monkeys and thus contributed to higher levels of acetic and isovaleric acids and total SCFAs, which may be related to the higher abundance of Firmicutes .…”

Section: Discussionmentioning

confidence: 99%

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Characterizing the Gut Microbiota of Eurasian Otter (Lutra lutra chinensis) and Snub-Nosed Monkey (Rhinopithecus roxellana) to Enhance Conservation Practices in the Foping National Nature Reserve of China

Zhu

Xie

et al. 2022

Animals

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Understanding the interaction between the microbial composition in the habitat and the gut of wildlife will contribute to conservation efforts since changes in the gut microbiome have been proven to influence the healthy and nutritional status of the host. This study analyzed the relationship between soil microbes and the microbial diversity and structure of the distal gut of the terrestrial golden snub-nosed monkey and Eurasian otter in the Foping National Nature Reserve (FNNR). A total of 15 otter fecal samples and 18 monkey fecal samples were collected from which 5 and 6 samples, respectively, were randomly selected for microbiome analysis. The remaining samples were used for fecal short-chain fatty acids (SCFAs) analysis. Soil samples from the otter and monkey habitats at each sampling point (eight in total) were also collected for microbiome analysis. The microbial phyla with the greatest relative abundance in soil or animal samples were Proteobacteria (41.2, 32.7, and 73.3% for soil, otters, and monkeys, respectively), Firmicutes (0.4% soil, 30.1% otters, and 14.4% monkeys), Bacteroidota (5.6% soil, 17.0% otters, and 8.3% monkeys), and Acidobacteriota (24.6% soil, 1.7% otters, and 0.1% monkeys). The estimation of alpha diversity indices revealed that the feature, Chao1, and Shannon indices of the soil microbiome were the greatest (p < 0.01) among the three groups, followed by those of the otter microbiome and those of the monkey microbiome (p < 0.01). Beta diversity analyses confirmed differences in the microbiota of the three types of samples. The determination of SCFA concentration in feces revealed that total volatile fatty acids, acetic acid, and isovaleric acid were greater (p < 0.05) in otters than in monkeys, while propionic acid followed the opposite pattern (p < 0.05). Correlation analysis of the microbiome and SCFA contents showed that propionic acid was positively correlated with significantly different bacterial groups, while acetic and butyric acid and total volatile acids were negatively correlated. This study confirmed that the fecal microbes of Eurasian otters and golden snub-nosed monkeys in the reserve are related to the soil microbial communities of their habitats, but they have different bacterial community structures and compositions, and there are different SCFA metabolic patterns in the gut of the two animals. The present study will help to improve wildlife protection in the FNNR.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Characterizing the Gut Microbiota of Eurasian Otter (Lutra lutra chinensis) and Snub-Nosed Monkey (Rhinopithecus roxellana) to Enhance Conservation Practices in the Foping National Nature Reserve of China

Zhu

Xie

et al. 2022

Animals

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“…Captive giant pandas and OC harbor a high proportion of Enterobacteriaceae (Figure 1c ), most probably due to their living environments (Huang et al, 2021 ; Zhu, Wu, et al, 2011 , 2018 ). HE and YSNM harbor a high proportion of Prevotellaceae (Figure 1c ), which might be related to the high proportion of carbohydrates in their diet (Xia et al, 2022 ; Zhu, Wu, et al, 2018 ).…”

Section: Resultsmentioning

confidence: 99%

“…(a) All six kingdoms; (b) archaeal families; (c) bacterial families; (d) fungal families; (e) protist and nematode families (combined); (f) virus families. The 123 metagenomes used in these analyses belonged to 52 giant pandas (9 from the Qinling Mountains [GPQIN, wild] (Wu et al, 2017 ), 7 from the Qionglai Mountains [GPQIO, wild] (Guo et al, 2019 ), 19 from the Xiaoxiangling Mountains [GPXXL, wild] (Yao et al, 2021 ; Zhu, Wu, et al, 2018 ), 7 from the Chengdu Breeding Center [GPCD, captive] (Zhang et al, 2018 ), and 10 from the Yaan research base of the Wolong Research Center [GPYA, captive]) (Guo et al, 2019 ); 6 red pandas from the Xiaoxiangling Mountains (RP, wild) (Zhu, Wu, et al, 2018 ); 19 meat‐eating carnivorans (CA) (Zhu, Yang, et al, 2018 ); 10 omnivorous carnivorans (OC) (Guo et al, 2018 ; Zhu, Wu, et al, 2018 ); 12 herbivores (HE) (Zhu, Wu, et al, 2018 ); and 24 Yunnan snub‐nosed monkeys (YSNM, wild) (Xia et al, 2022 ).…”

Section: Resultsmentioning

confidence: 99%

“…To begin, we chose 123 gut metagenomes from 42 mammalian species (including carnivores, omnivores, and herbivores); most of these metagenomes (approximately 104) came from our laboratory; therefore, they were obtained using the same sequencing platform to decrease the sequencing bias (Appendix S1 ). The details on the origin of the 123 metagenomes are as follows: 52 from giant pandas (9 from the Qinling Mountains [GPQIN, wild] (Wu et al, 2017 ), 7 from the Qionglai Mountains [GPQIO, wild] (Guo et al, 2019 ), 19 from the Xiaoxiangling Mountains [GPXXL, wild] (Yao et al, 2021 ; Zhu, Yang, et al, 2018 ), 7 from the Chengdu Breeding Center [GPCD, captive] (Zhang et al, 2018 ), 10 from the Yaan Research Base of the Wolong Research Center [GPYA, captive]) (Guo et al, 2019 ), 6 from red pandas from the Xiaoxiangling Mountains (RP, wild; Zhu, Yang, et al, 2018 ), 19 from meat‐eating carnivorans (CA) (Zhu, Wu, et al, 2018 ), 10 from omnivorous carnivorans (OC) (Guo et al, 2018 ; Zhu, Wu, et al, 2018 ), 12 from herbivores (HE) (Zhu, Wu, et al, 2018 ), and 24 from Yunnan snub‐nosed monkeys (YSNM, wild) (Xia et al, 2022 ). We investigated the gut microorganism composition regarding the previously mentioned kingdoms and compared their beta diversities.…”

Section: Introductionmentioning

confidence: 99%

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Beyond bacteria: Reconstructing microorganism connections and deciphering the predicted mutualisms in mammalian gut metagenomes

Dai

Ding

Cui

et al. 2023

Ecology and Evolution

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Numerous gut microbial studies have focused on bacteria. However, archaea, viruses, fungi, protists, and nematodes are also regular residents of the gut ecosystem. Little is known about the composition and potential interactions among these six kingdoms in the same samples. Here, we unraveled the complex connection among them using approximately 123 gut metagenomes from 42 mammalian species (including carnivores, omnivores, and herbivores). We observed high variation in bacterial and fungal families and relatively low variation in archaea, viruses, protists, and nematodes. We found that some fungi in the mammalian intestine might come from environmental sources (e.g., soil and dietary plants), and some might be native to the intestine (e.g., the occurrence of Neocallimastigomycetes). The Methanobacteriaceae and Plasmodiidae families (archaea and protozoa, respectively) were predominant in these metagenomes, whereas Onchocercidae and Trichuridae were the two most common nematodes, and Siphoviridae and Myoviridae the two most common virus families in these mammalian gut metagenomes. Interestingly, most of the pairwise co-occurrence patterns were significantly positive among these six kingdoms, and significantly negative networks mainly occurred between fungi and prokaryotes (both bacteria and archaea). Our study revealed some inconvenient characteristics in the mammalian gut microorganism ecosystem: (1) the community formed by members of the analyzed kingdoms reflects the life history of the host and the potential threat posed by pathogenic protists and nematodes in mammals; and (2) the networks suggest the existence of predicted mutualism among members of these six kingdoms and of the predicted competition, mainly among fungi and other kingdoms.

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Analysis of winter diet in Guizhou golden monkey (Rhinopithecus brelichi) using DNA metabarcoding data

Zhang,

Zhong,

Ran

et al. 2024

Ecology and Evolution

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The Guizhou golden monkey (Rhinopithecus brelichi) is a critically endangered wildlife species, and understanding its diet composition may be useful for assessing its feeding strategies. DNA metabarcoding was used to determine the dietary diversity of R. brelichi. DNA was extracted from 31 faecal samples and amplified chloroplast rbcL and mitochondrial COI DNA was sequenced using the Illumina NovaSeq platform. A comparative analysis of the sequences revealed that the five most abundant plant genera were Magnolia, Morinda, Viburnum, Tetradium and Eurya. In winter, R. brelichi mostly consumed shrubs, herbs and shrubs/trees according to the habit of plant genera with higher abundances comparatively. The five most abundant families in animal diet were Psychodidae, Trichinellidae, Staphylinidae, Scarabaeidae and Trichoceridae. This study is the first to show the composition of the winter animal diets of R. brelichi based on DNA metabarcoding. These results provide an important basis for understanding the diet of wild R. brelichi, which inhabits only the Fanjingshan National Nature Reserve, China.

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Functional convergence of Yunnan snub-nosed monkey and bamboo-eating panda gut microbiomes revealing the driving by dietary flexibility on mammal gut microbiome

Abstract: Graphical abstract

Cited by 19 publications

References 86 publications

Characterizing the Gut Microbiota of Eurasian Otter (Lutra lutra chinensis) and Snub-Nosed Monkey (Rhinopithecus roxellana) to Enhance Conservation Practices in the Foping National Nature Reserve of China

Characterizing the Gut Microbiota of Eurasian Otter (Lutra lutra chinensis) and Snub-Nosed Monkey (Rhinopithecus roxellana) to Enhance Conservation Practices in the Foping National Nature Reserve of China

Beyond bacteria: Reconstructing microorganism connections and deciphering the predicted mutualisms in mammalian gut metagenomes

Analysis of winter diet in Guizhou golden monkey (Rhinopithecus brelichi) using DNA metabarcoding data

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