亚洲象粪便病毒宏基因组学研究：病毒群落组成及保护意义

doi:10.11707/j.1001-7488.LYKX20250074

Abstract

Abstract:

Objective: This study aims to investigate the fecal virus metagenome of captive and wild Asian elephants in Yunnan, so as to provide a theoretical foundation for the conservation of this endangered species. Method: Fresh fecal samples from captive breastfed young elephants, captive adult elephants, and wild adult elephants were collected. The metagenomic sequencing and virus metagenomics analysis methods were used to comprehensively understand the landscape structure of the Asian elephant fecal DNA virus community. Result: The results revealed that Myoviridae emerged as the most prevalent virus family in the fecal matter of calves, whereas Siphoviridae dominated in the adult elephants. Wild adults exhibited clearly higher Podoviridae abundance than captive adults. At the species level, Synechococcus phage S-CRM01 and Erwinia phage Ea35-70 were dominant in calves, whereas uncultured Mediterranean phage uvMED was most prevalent in adults. Wild adults showed notably higher abundance of EBPR podovirus 3 than captive adults. Furthermore, this study uncovered the presence of herpesvirus in the fecal samples of the calves, having the possible association of this virus family with EEHV. Conclusion: There are significant differences in the composition of fecal viral communities between captive and wild elephants, as well as between calves and adults. This work sheds light on the possible risk of EEHV infection among Asian elephant populations in Yunnan, and suggests the need for proactive conservation strategies and continued surveillance efforts.

Key words: Asian elephant, fecal virus composition, viral metagenome, herpesvirus

CLC Number:

Chengbo Zhang,Junmin Chen,Nanyu Han,Bo Xu,Yiren Gao,Zixian Chen,Jiawen Wang,Qingzhong Shen,Bin Wang,Mingwei Bao,Zunxi Huang. Study on the Fecal Virus Metagenome of Asian Elephant: Viral Community Composition and Conservation Implications[J]. Scientia Silvae Sinicae, 2026, 62(2): 154-159.

Figures/Tables 3

References 0

	国家林业和草原局等. 《国家重点保护野生动物名录》(2021年2月1日修订). 野生动物学报, 2021, 42 (2): 605- 640. doi: 10.3969/j.issn.1672-7789.2022.01.010
	National Forestry and Grassland Administration, et al. List of wildlife under state key protection (revised on February 1, 2021). Chinese Journal of Wildlife, 2021, 42 (2): 605- 640. doi: 10.3969/j.issn.1672-7789.2022.01.010
	姜志诚, 李正玲, 保明伟, 等. 中国亚洲象取食植物种类统计与分析. 兽类学报, 2019, 39 (5): 514- 530. doi: 10.16829/j.slxb.150237
	Jiang Z C, Li Z L, Bao M W, et al. The statistics and analysis of foraging plants species eaten by Asian elephant (Elephas maximus) in China. Acta Theriologica Sinica, 2019, 39 (5): 514- 530. doi: 10.16829/j.slxb.150237
	沈青春, 仉　伟, 刘　青, 等. 宏基因组技术诊断亲内皮疱疹病毒感染致濒危亚洲象死亡病例. 畜牧兽医学报, 2024, 55 (6): 2569- 2577. doi: 10.11843/j.issn.0366-6964.2024.06.028
	Shen Q C, Zhang W, Liu Q, et al. Diagnosis of death cases of an endangered Asian elephants caused by endothelial herpesvirus infection with metagenomic technology. Acta Veterinaria et Zootechnica Sinica, 2024, 55 (6): 2569- 2577. doi: 10.11843/j.issn.0366-6964.2024.06.028
	吴得卿, 魏建华, 樊　辉. 南滚河流域土地利用变化对亚洲象生境的影响. 生态学报, 2021, 41 (16): 6476- 6485. doi: 10.5846/stxb202010112587
	Wu D Q, Wei J H, Fan H. Impacts of land use changes on the habitat of Asian elephants in the Nangun River basin. Acta Ecologica Sinica, 2021, 41 (16): 6476- 6485. doi: 10.5846/stxb202010112587
	张呈波, 黄遵锡. 2023. 亚洲象肠道微生物研究. 北京: 中国林业出版社.
	Zhang C B, Huang Z X. 2023. Studies on intestinal microbes of Asian elephant. Beijing: China Forestry Publishing House. ［in Chinese］
	周　贝, 林　焱, 朱伟云. 猪肠道大肠杆菌噬菌体对产肠毒素大肠杆菌的抑菌作用. 畜牧兽医学报, 2020, 51 (7): 1748- 1755. doi: 10.11843/j.issn.0366-6964.2020.07.027
	Zhou B, Lin Y, Zhu W Y. Study on the bacteriostatic effect of porcine coliphages on enterotoxigenic Escherichia coli. Acta Veterinaria et Zootechnica Sinica, 2020, 51 (7): 1748- 1755. doi: 10.11843/j.issn.0366-6964.2020.07.027
	Bao H D, Zhou Y, Shahin K, et al. The complete genome of lytic Salmonella phage vB_SenM-PA13076 and therapeutic potency in the treatment of lethal Salmonella Enteritidis infections in mice. Microbiological Research, 2020, 237, 126471. doi: 10.1016/j.micres.2020.126471
	Barr J J, Auro R, Furlan M, et al. Bacteriophage adhering to mucus provide a non–host-derived immunity. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110 (26): 10771- 10776.
	Buchfink B, Xie C, Huson D H. Fast and sensitive protein alignment using DIAMOND. Nature Methods, 2015, 12 (1): 59- 60. doi: 10.1038/nmeth.3176
	Camarillo-Guerrero L F, Almeida A, Rangel-Pineros G, et al. 2021. Massive expansion of human gut bacteriophage diversity. Cell, 184(4): 1098–1109.
	Campos-Arceiz A, Blake S. Megagardeners of the forest–the role of elephants in seed dispersal. Acta Oecologica, 2011, 37 (6): 542- 553. doi: 10.1016/j.actao.2011.01.014
	Chen L X, Banfield J F. COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes. Nature Microbiology, 2024, 9 (3): 737- 750. doi: 10.1038/s41564-023-01598-2
	Common S M, Yun Y, Silva-Fletcher A, et al. Developing a non-invasive method of detecting elephant endotheliotropic herpesvirus infections using faecal samples. Veterinary Record, 2022, 190 (2): e833. doi: 10.1002/vetr.833
	Fu L M, Niu B F, Zhu Z W, et al. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics, 2012, 28 (23): 3150- 3152. doi: 10.1093/bioinformatics/bts565
	Gao S M, Fei H L, Li Q, et al. Eco-evolutionary dynamics of gut phageome in wild gibbons (Hoolock tianxing) with seasonal diet variations. Nature Communications, 2024, 15, 1254. doi: 10.1038/s41467-024-45663-8
	Gayder S, Parcey M, Castle A J, et al. Host range of bacteriophages against a world-wide collection of Erwinia amylovora determined using a quantitative PCR assay. Viruses, 2019, 11 (10): 910. doi: 10.3390/v11100910
	Gregory A C, Zayed A A, Conceição-Neto N, et al. 2019. Marine DNA viral macro- and microdiversity from pole to pole. Cell, 177(5): 1109–1123.
	Hernández-Santos N, Klein B S. Through the scope darkly: the gut mycobiome comes into focus. Cell Host & Microbe, 2017, 22 (6): 728- 729.
	Kozloff L M, Chapman V, DeLong S. Defective packing of an unusual DNA in a virulent Erwinia phage, Erh 1. Progress in Clinical and Biological Research, 1981, 64, 253- 269.
	Lavigne R, Darius P, Summer E J, et al. Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiology, 2009, 9 (1): 224. doi: 10.1186/1471-2180-9-224
	Li D H, Liu C M, Luo R B, et al. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics, 2015, 31 (10): 1674- 1676. doi: 10.1093/bioinformatics/btv033
	Li R Q, Li Y R, Kristiansen K, et al. SOAP: short oligonucleotide alignment program. Bioinformatics, 2008, 24 (5): 713- 714. doi: 10.1093/bioinformatics/btn025
	Li X, Chen J M, Zhang C B, et al. Fecal metagenomics study reveals that a low-fiber diet drives the migration of wild Asian elephants in Xishuangbanna, China. Animals (Basel), 2023, 13 (20): 3193.
	Minakshi P, Ghosh M, Kumar R, et al. An insight into nanomedicinal approaches to combat viral zoonoses. Current Topics in Medicinal Chemistry, 2020, 20 (11): 915- 962. doi: 10.2174/1568026620666200325114400
	Ning S Y, Lu X, Zhao M, et al. Virome in fecal samples from wild giant pandas (Ailuropoda melanoleuca). Frontiers in Veterinary Science, 2021, 8, 767494. doi: 10.3389/fvets.2021.767494
	Noguchi H, Park J, Takagi T. MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Research, 2006, 34 (19): 5623- 5630. doi: 10.1093/nar/gkl723
	Ossent P, Guscetti F, Metzler A E, et al. Acute and fatal herpesvirus infection in a young Asian elephant (Elephas maximus). Veterinary Pathology, 1990, 27 (2): 131- 133. doi: 10.1177/030098589002700212
	Richman L K, Montali R J, Cambre R C, et al. Clinical and pathological findings of a newly recognized disease of elephants caused by endotheliotropic herpesviruses. Journal of Wildlife Diseases, 2000, 36 (1): 1- 12. doi: 10.7589/0090-3558-36.1.1
	Son J S, Lee S J, Jun S Y, et al. Antibacterial and biofilm removal activity of a Podoviridae Staphylococcus aureus bacteriophage SAP-2 and a derived recombinant cell-wall-degrading enzyme. Applied Microbiology and Biotechnology, 2010, 86 (5): 1439- 1449. doi: 10.1007/s00253-009-2386-9
	Stupak A, Kwiatek M, Gęca T, et al. A virome and proteomic analysis of placental microbiota in pregnancies with and without fetal growth restriction. Cells, 2024, 13 (21): 1753. doi: 10.3390/cells13211753
	Sun Y, K Chen Y, Díaz-Sacco J J, et al. Assessing population structure and body condition to inform conservation strategies for a small isolated Asian elephant (Elephas maximus) population in southwest China. PLoS One, 2021, 16 (3): e0248210. doi: 10.1371/journal.pone.0248210
	Veesler D, Cambillau C. A common evolutionary origin for tailed-bacteriophage functional modules and bacterial machineries. Microbiology and Molecular Biology Reviews, 2011, 75 (3): 423- 433. doi: 10.1128/MMBR.00014-11
	Wiedner E B, Peddie J, Peddie L R, et al. Strangulating intestinal obstructions in four captive elephants (Elephas maximus and Loxodonta africana). Journal of Zoo and Wildlife Medicine, 2012, 43 (1): 125- 130. doi: 10.1638/2011-0088.1
	Wilkie G S, Davison A J, Kerr K, et al. First fatality associated with elephant endotheliotropic herpesvirus 5 in an Asian elephant: pathological findings and complete viral genome sequence. Scientific Reports, 2014, 4 (1): 6299. doi: 10.1038/srep06299
	Yan M, Pratama A A, Somasundaram S, et al. Interrogating the viral dark matter of the rumen ecosystem with a global virome database. Nature Communications, 2023, 14 (1): 5254. doi: 10.1038/s41467-023-41075-2
	Zhang C B, Chen J M, Wu Q, et al. The gut microbiota of young Asian elephants with different milk-containing diets. Animals, 2023a, 13 (5): 916. doi: 10.3390/ani13050916
	Zhang C B, Lian Z H, Xu B, et al. 2023b. Gut microbiome variation along a lifestyle gradient reveals threats faced by Asian elephants. Genomics, Proteomics & Bioinformatics, 21(1): 150–163.
	Zhang C B, Xu B, Huang Z X, et al. Metagenomic analysis of the fecal microbiomes of wild Asian elephants reveals microflora and enzymes that mainly digest hemicellulose. Journal of Microbiology and Biotechnology, 2019, 29 (8): 1255- 1265. doi: 10.4014/jmb.1904.04033

[1]	Fei Chen,Jiejing Zhang,Jishan Wang,Weixiong Luo,Yongjing Tang,hui Fan. Prediction of Potential Habitat of Global Wild Asian Elephants under Climate Change [J]. Scientia Silvae Sinicae, 2025, 61(12): 124-134.
[2]	Yuxuan Hu,Junfeng Chen,Yi Xie. Measures for Governing Human-Elephant Conflicts Based on Choice Experiment of Farmers in Xishuangbanna [J]. Scientia Silvae Sinicae, 2023, 59(10): 162-170.

Study on the Fecal Virus Metagenome of Asian Elephant: Viral Community Composition and Conservation Implications

RichHTML

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

Figures/Tables 3

References 0

Related Articles 2

Recommended Articles

Metrics

Comments