PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation

Study information

Reviewed Marked as Reviewed by Svetlana up on 2024-3-15

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

37805557

DOI Digital object identifier for electronic documents.

https://doi.org/10.1186/s40168-023-01657-0

URI

Authors

Huang G, Shi W, Wang L, Qu Q, Zuo Z, Wang J, Zhao F, Wei F

Journal

Microbiome

Year

2023

Keywords:

Adaptive evolution, Conservation, Diversity, Giant panda, Gut microbiome, Wild mammal

BACKGROUND: The gut microbiota play important roles in host adaptation and evolution, but are understudied in natural population of wild mammals. To address host adaptive evolution and improve conservation efforts of threatened mammals from a metagenomic perspective, we established a high-quality gut microbiome catalog of the giant panda (pandaGUT) to resolve the microbiome diversity, functional, and resistome landscapes using approximately 7 Tbp of long- and short-read sequencing data from 439 stool samples. RESULTS: The pandaGUT catalog comprises 820 metagenome-assembled genomes, including 40 complete closed genomes, and 64.5% of which belong to species that have not been previously reported, greatly expanding the coverage of most prokaryotic lineages. The catalog contains 2.37 million unique genes, with 74.8% possessing complete open read frames, facilitating future mining of microbial functional potential. We identified three microbial enterotypes across wild and captive panda populations characterized by Clostridium, Pseudomonas, and Escherichia, respectively. We found that wild pandas exhibited host genetic-specific microbial structures and functions, suggesting host-gut microbiota phylosymbiosis, while the captive cohorts encoded more multi-drug resistance genes. CONCLUSIONS: Our study provides largely untapped resources for biochemical and biotechnological applications as well as potential intervention avenues via the rational manipulation of microbial diversity and reducing antibiotic usage for future conservation management of wildlife. Video Abstract.

Experiment 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-3-15

Curated date: 2024/03/15

Curator: Svetlana up

Revision editor(s): Svetlana up

Subjects

Location of subjects: China

Host species Species from which microbiome was sampled. Contact us to have more species added.: Ailuropoda melanoleuca

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Diet Dietary,Diets,Diet,diet

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Pandas in shoot-eating season

Group 1 name Corresponds to the case (exposed) group for case-control studies: Pandas in leaf-eating season

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Pandas in leaf-eating season from the Qinling cohort of wild pandas

Group 0 sample size Number of subjects in the control (unexposed) group: 24

Group 1 sample size Number of subjects in the case (exposed) group: 33

Lab analysis

Sequencing type: WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: Mann-Whitney (Wilcoxon)

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Signature 1

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Curated date: 2024/03/15

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Revision editor(s): Svetlana up, Omojokunoluwatomisin

Source: Figure 3A

Description: A very challenging figure to interpret: Significantly differentially abundant taxa between diet seasons. Increased abundance in pandas leaf-eating season.

Abundance in Group 1: increased abundance in Pandas in leaf-eating season

NCBI	Quality Control	Links
Clostridium sp.
Peptoclostridium spp.Peptoclostridium spp.

Revision editor(s): Svetlana up, Omojokunoluwatomisin

Experiment 2

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Curated date: 2024/04/20

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: MIN wild pandas

Group 1 name Corresponds to the case (exposed) group for case-control studies: QXL wild pandas

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Only 1864 wild giant pandas are extant and are distributed in six mountain ranges including the Qinling (QIN), Minshan (MIN), Qionglai (QIO), Daxiangling (DXL), Xiaoxiangling (XXL), and Liangshan (LSH) mountains that can be classified into three genetic populations including the QIN, MIN, and QIO-DXL-XXL-LSH (QXL) populations