About | Sustainable to Be(e) lab
Sustainable to Be(e)
Microbiome surveillance and application for wild bee protection
Agriculture and urbanization have resulted in limited plant diversity and habitat for pollinators. The key pollinators, bees have been threatened, nevertheless, a few of them have adapted to the city environment providing significant ecological service.
Gut microbiome has been increasingly appreciated for animal health and adaptation. Gut microbiome has been well-studied and revealed to be vital for western honeybees, but little is known about other bees, especially indigenous bees in cities. Taking advantage of high-throughput sequencing, besides the biodiversity, the gut microbiome of wild bees can be simultaneously monitored at the structure and function level. The impacts of the city environment on wild bees can be evaluated via biodiversity and microbiome analysis, which can further guide us to manage city landscapes concerning nutrition metabolism and pathogen prevalence to benefit wild bees. Potential probiotics can also be cultured and applied to help restore impaired pollinator bees essential for urban sustainability.
Collaboration with Prof. Xin Zhou, Dr. Yi Zou, Dr. Michael Orr
Honeybee host-gut bacterium symbiosis
An animal and its symbiotic microbiota form a distinct biological entity known as the “holobiont”, an intriguing system that has received considerable attentions. The evolutionary dynamic of symbiosis during ecological adaptation remains an enigma.
Honeybee core gut microbiota deliver significant benefits to the hosts, with most bacterial phylotypes and strains formed through co-diversification with the hosts.
We are interested in and have been studying the host-symbiont interaction and co-evolution, and Ph. D. students are welcome for this intriguing topic!
Collaboration with Prof. Xin Zhou, Dr. Shanlin Liu
The latest review paper for you to learn this field: The honeybee microbiota and its impact on health and disease
Gut microbiome study for wild ungulate conservation on the Tibetan Plateau
Gut microbes have been increasingly appreciated for their contribution to host adaptation.
Here we study the gut microbiome of wild ungulates on the Tibetan Plate using the feces and metagenomics, aim to understand the diet composition and how the gut bacteria help with host nutrition metabolism.
Collaboration with Dr. Lingyun Xiao
Metagenomics to learn biodiversity and gut microbiome of dragonflies in Suzhou wetlands
Collaborating with Dr. Yuqing Feng, the head of Suzhou Wetland Protection Management Station, we aim to learn comprehensive knowledge on the biodiversity and gut microbiome of dragonflies in Suzhou wetlands.
Aquatic insects are a crucial indicator of wetland quality and the status of wetland conservation. There are more than 400 lakes of various sizes and over 20,000 rivers in Suzhou. The wetland coverage rate reaches 38.35%, while 60% of wetlands are under protection by law. Natural wetlands account for 1/3 of the total area of the city, the highest in all of China. However, the biodiversity of aquatic insects are unknown. We will initiate their biodiversity survey starting with dragonflies, one of the primary and important aquatic insect lineages. DNA barcoding and metagenomics will applied to overcome the identification difficult for nymphs. At the same time, the gut metagenome analysis for dragonflies reveals not just their diet composition but also associated gut microbes.
The dynamic interplay between brain and gut microbiota in migraine
Collaboration with Prof. Minyan Wang
Wang lab have developed established migraine model using rats, and we collaboratively work on the dynamic interplay between the cortical spreading depression (CSD) and the gut microbiome.
Gut-brain axis in zebrafish with brain disorder
Prof. Alan Kaluev and I have initiated a collaborative project to study the gut-brain axis in brain disorders using the zebrafish model. We aim to learn the role of gut bacteria in brain disorder and potential pathways underlying the gut-brain crosstalk.
Unravelling seasonal dynamics of arthropod predator-prey networks by genomic approach in flower strip mediated rice agroecosystems
Predator-prey network forms the backbones of ecosystem, and detailed knowledge of predator-prey interaction can enhance understanding of the community and its supporting ecosystem service like pest control. Enhancing biological pest control effectiveness in rice production is critical for sustainable rice production. Flower strips have been implemented in rice paddy to enhance pest control. However, the seasonal dynamic of species level network of predator-prey interactions remained poorly understood. This research aims to investigate how flower strips affect the dynamic of species level arthropod predator-prey network, and how that further affect the efficiency of pest control in rice paddy by combining field experiment and biodiversity metagenomics analysis.
This collaborative project is co-supervised by Dr. Xueqing He.
Alumni
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Ya Wang |
Zhiwei Chen |
Xingyu Hu |
Mingrui Li |
Muhan Li |
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Xintong Zhou |
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Call for PhD students
PhD student recruitment for project：
以下项目招聘博士生:
1. Host-gut bacterium interaction and co-evolution using honeybee model利用蜜蜂模型研究宿主-肠道共生菌互作及共进化机制 *fees-only scholarship and TA stipend 免学费奖学金+助教工资 （1 has joined）
2. Microbiome surveillance and application for wild bee protection野生蜂肠道菌群研究及其保护应用 *fees-only scholarship and TA stipend 免学费奖学金+助教工资 (1 will join in 2025)
3. Unravelling seasonal dynamics of arthropod predator-prey networks by genomic approach in flower strip mediated rice agroecosystems. <co-supervision with Dr. Xueqing He> 水稻田配置花带对自然天敌和害虫季节动态的影响 <合作导师：何雪清博士> *fees-only scholarship and TA stipend 免学费奖学金+助教工资 (1 has joined)
4. Microbiome surveillance for conservation of wild ungulates on the Tibetan Plate <co-supervision with Dr. Lingyun Xiao> 青藏高原野生食草动物肠道菌群研究及其保护应用 <合作博导：肖凌云 博士> (1 will join in 2025)
5. The dynamic interplay between brain and gut microbiota in migraine <co-supervision with Prof. Minyan Wang > 肠道菌群与偏头痛中枢敏化互作机制 <合作博导：王旻艳 教授>
6. Gut-brain axis in zebrafish with brain disorder <co-supervision with Prof. Alan Kaluev> 斑马鱼脑紊乱模型中脑肠轴的研究 <合作博导：Alan Kaluev 教授>
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Publications
2023
Screening and Functional Analyses of Novel Cecropins from Insect Transcriptome
Guo, L., Tang, M., Luo, S. & Zhou, X., Oct 2023, In: Insects. 14, 10, 794.
Reactive oxygen species are regulated by immune deficiency and Toll pathways in determining the host specificity of honeybee gut bacteria
Guo, L., Tang, J., Tang, M., Luo, S. & Zhou, X., 15 Aug 2023, In: PNAS. 120, 33, p. e2219634120
Opportunities and challenges in Asian bee research and conservation
Michael Orr, 2023, (Accepted/In press) In: Biological Conservation. 285, 110173.
2022
Significant compositional and functional variation reveals the patterns of gut microbiota evolution among the widespread Asian honeybee populations
Su, Q.#, Tang, M.#, Hu, J., Tang, J., Zhang, X., Li, X., Niu, Q., Zhou, X., Luo, S. & Zhou, X., 2 Sept 2022, In: Frontiers in Microbiology. 13, 934459.
Community Dynamics in Structure and Function of Honey Bee Gut Bacteria in Response to Winter Dietary Shift
Li, C., Tang, M., Li, X. & Zhou, X., Sept 2022, In: mBio. 13, 5
Amplicon Sequencing of Single-Copy Protein-Coding Genes Reveals Accurate Diversity for Sequence-Discrete Microbiome Populations
Yang, C., Su, Q., Tang, M., Luo, S., Zheng, H., Zhang, X. & Zhou, X., Apr 2022, In: Microbiology Spectrum. 10, 2
Tracing the origin of honey products based on metagenomics and machine learning
Liu, S., Lang, D., Meng, G., Hu, J., Tang, M. & Zhou, X., 1 Mar 2022, In: Food Chemistry. 371, 131066.
Genomic features underlying the evolutionary transitions of Apibacter to honey bee gut symbionts
Zhang, W., Zhang, X., Su, Q., Tang, M., Zheng, H. & Zhou, X., Feb 2022, In: Insect Science. 29, 1, p. 259-275 17 p.
2020
Using full-length metabarcoding and DNA barcoding to infer community assembly for speciose taxonomic groups: a case study
Hao, M., Jin, Q., Meng, G., Yang, C., Yang, S., Shi, Z., Tang, M., Liu, S., Li, Y., Li, J., Zhang, D., Su, X., Shih, C., Sun, Y., Wilson, J. J., Zhou, X. & Zhang, A., Dec 2020, In: Evolutionary Ecology. 34, 6, p. 1063-1088 26 p.
Regional assemblages shaped by historical and contemporary factors: Evidence from a species-rich insect group
Hao, M., Jin, Q., Meng, G., Yang, C., Yang, S., Shi, Z., Tang, M., Liu, S., Li, Y., Zhang, D., Su, X., Shih, C., Sun, Y., Zhou, X. & Zhang, A. B., 1 Jul 2020, In: Molecular Ecology. 29, 13, p. 2492-2510 19 p.
The phylogeny of leaf beetles (Chrysomelidae) inferred from mitochondrial genomes
Nie, R. E., Andújar, C., Gómez-Rodríguez, C., Bai, M., Xue, H. J., Tang, M., Yang, C. T., Tang, P., Yang, X. K. & Vogler, A. P., 1 Jan 2020, In: Systematic Entomology. 45, 1, p. 188-204 17 p.
2019
Genome-skimming provides accurate quantification for pollen mixtures
Lang, D.#, Tang, M.#, Hu, J. & Zhou, X., 1 Nov 2019, In: Molecular Ecology Resources. 19, 6, p. 1433-1446 14 p.
A new perspective on landscape impact in bee populations: Considering the bee gut microbiome
Tang, M., Zou, Y., Su, Q. & Zhou, X., 2019, In: Biodiversity Science. 27, 5, p. 516-525 10 p.
First mitochondrial genomes of five hoverfly species of the genus eristalinus (Diptera: Syrphidae)
Sonet, G., De Smet, Y., Tang, M., Virgilio, M., Young, A. D., Skevington, J. H., Mengual, X., Backeljau, T., Liu, S., Zhou, X., De Meyer, M. & Jordaens, K., 2019, In: Genome. 62, 10, p. 677-687 11 p.
2018
Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples
Bista, I., Carvalho, G. R., Tang, M., Walsh, K., Zhou, X., Hajibabaei, M., Shokralla, S., Seymour, M., Bradley, D., Liu, S., Christmas, M. & Creer, S., Sept 2018, In: Molecular Ecology Resources. 18, 5, p. 1020-1034 15 p.
The genome of an underwater architect, the caddisfly Stenopsyche tienmushanensis Hwang (Insecta: Trichoptera)
Luo, S., Tang, M., Frandsen, P. B., Stewart, R. J. & Zhou, X., 2018, In: GigaScience. 7, 12, giy143.
2016
Mitochondrial capture enriches mito-DNA 100 fold, enabling PCR-free mitogenomics biodiversity analysis
Liu, S., Wang, X., Xie, L., Tan, M., Li, Z., Su, X., Zhang, H., Misof, B., Kjer, K. M., Tang, M., Niehuis, O., Jiang, H. & Zhou, X., 1 Mar 2016, In: Molecular Ecology Resources. 16, 2, p. 470-479 10 p.
2015
High-throughput monitoring of wild bee diversity and abundance via mitogenomics
Tang, M.#, Hardman, C. J.#, Ji, Y.#, Meng, G., Liu, S., Tan, M., Yang, S., Moss, E. D., Wang, J., Yang, C., Bruce, C., Nevard, T., Potts, S. G., Zhou, X. & Yu, D. W., 1 Sept 2015, In: Methods in Ecology and Evolution. 6, 9, p. 1034-1043 10 p.
2014
Multiplex sequencing of pooled mitochondrial genomes - A crucial step toward biodiversity analysis using mito-metagenomics
Tang, M., Tan, M., Meng, G., Yang, S., Su, X., Liu, S., Song, W., Li, Y., Wu, Q., Zhang, A. & Zhou, X., 16 Dec 2014, In: Nucleic Acids Research. 42, 22, e166.
Phylogenomics resolves the timing and pattern of insect evolution
Misof, B., Liu, S., Meusemann, K., Peters, R. S., Donath, A., Mayer, C., Frandsen, P. B., Ware, J., Flouri, T., Beutel, R. G., Niehuis, O., Petersen, M., Izquierdo-Carrasco, F., Wappler, T., Rust, J., Aberer, A. J., Aspöck, U., Aspöck, H., Bartel, D., Blanke, A., & ..., Tang, M., ..., Zhou, X., 7 Nov 2014, In: Science. 346, 6210, p. 763-767 5 p.
2013
SOAPBarcode: Revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons
Liu, S., Li, Y., Lu, J., Su, X., Tang, M., Zhang, R., Zhou, L., Zhou, C., Yang, Q., Ji, Y., Yu, D. W. & Zhou, X., Dec 2013, In: Methods in Ecology and Evolution. 4, 12, p. 1142-1150 9 p.
Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification
Zhou, X., Li, Y., Liu, S., Yang, Q., Su, X., Zhou, L., Tang, M., Fu, R., Li, J. & Huang, Q., 2013, In: GigaScience. 2, 1, 4.
2012
Distinctive heat-shock response of bioleaching microorganism Acidithiobacillus ferrooxidans observed using genome-wide microarray
Yin H#, Tang M#, Zhou Z, Fu X, Shen L, Liang Y, Li Q, Liu H, Liu X.*, 2012 May, In: Can J Microbiol. 58(5):628-36.