metagenomics and culturomics, for a systematic and actionable understanding of the microbiome in health and disease
Dr. Huijue Jia received her B.S. in biological sciences at Fudan University in 2005, and PhD in biochemistry at Case Western Reserve University in 2011 from the laboratory of Dr. Eckhard Jankowsky. After being a postdoc in Dr. Yi Zhang’s lab then at UNC Chapel Hill, Dr. Jia worked as a scientific editor at Nature Communications in London. Dr. Jia has been studying the microbiome since joining BGI-Shenzhen in 2013, and is faculty of Fudan University and IPM since 2022.
We push boundaries in metagenomics and culturomics, for a systematic and actionable understanding of the microbiome in health and disease, which would eventually change the landscape of complex diseases in general.
Editorial board of Gigabyte magazine (2019 -);
Intestinal microecology branch of Biophysics Society (2021 -), standing member of medical microbiology branch of Guangdong precision Medicine Association (2020 -);
Member of the medical microecology Professional Committee of Shenzhen Medical Association (2021 -);
Member of the academic committee of the Key Laboratory of rapid drug detection technology of Guangdong Institute for drug control and the State Drug Administration (2019 -);
Part time associate professor, State Key Laboratory of Chinese medicine quality, University of science and technology of Macau (2015-2019);
Executive director of the Chinese medicine immunization Committee of the World Federation of traditional Chinese medicine (2015 -)
1. In 2020, Kerui Wei'an, a highly cited scholar;
2. In 2020, GPB (genomics, proteomics and bioinformatics), the "top ten advances in China's bioinformatics" and the "top ten applications in China's bioinformatics" in 2019
3. In 2015, Shenzhen Municipal Human and social resources department awarded the overseas high-level talents "peacock plan" class B talents;
4. In 2012, Medical Excellence Award (one in each department), Case Western Reserve University School of Medicine
5. In 2012, LLS fellow (postdoctoral scholarship, 12 people in the United States that year), Leukemia & Lymphoma Society
Books:
Jia H. Investigating Human Diseases with the Microbiome: Metagenomics Bench to Bedside. ISBN: 9780323913690 (link: https://www.elsevier.com/books/investigating-human-diseases-with-the-microbiome/jia/978-0-323-91369-0)
Chinese version by Tsinghua University Press. ISBN: .
Neuroscience for Artificial Intelligence. ISBN: TBD.
Commentary:
Donia MS, She Q, Huber JA, Jia H. (One paragraph each) Creating a unique culture. Cell. 177(6), 1369 (2019).
Research articles:
Reference gene catalogs and genome catalogs for the microbiome at various body sites:
1. Zhu J, Tian L, Chen P, Han M, Song L, Tong X, Sun X, Yang F, Lin Z, Liu X, Liu C, Wang X, Lin Y, Cai K, Hou Y, Xu X, Yang H, Wang J, Kristiansen K, Xiao L, Zhang T, Jia H*, Jie Z*. Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa. Genomics Proteomics Bioinformatics. 2021, S1672-0229(21)00176-5. Link-doi.org/10.1016/j.gpb.2021.05.001
2. Zou Y#, Xue W#, Luo G#, Deng Z#, Qin P#, Guo R, Sun H, Xia Y, Liang S, Dai Y, Wan D, Jiang R, Su L, Feng Q, Jie Z, Guo T, Xia Z, Liu C, Yu J, Lin Y, Tang S, Huo G, Xu X, Hou Y, Liu X, Wang J, Yang H, Kristiansen K, Li J*, Jia H*, Xiao L*. 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses. Nat Biotechnol. 37, 179-185 (2019). Link-doi.org/10.1038/s41587-018-0008-8
Tang L. Human gut bacterial genome reference. Nat Methods. 16, 286 (2019).
(2019).
Wolke T. Beyond the census of human gut dwellers. Nat Rev Microbiol. 17, 401 (2019).
3. Li F#, Chen C#, Wei W#, Wang Z, Dai J, Hao L, Song L, Zhang X, Zeng L, Du H, Tang H, Liu N, Yang H, Wang J, Madsen L, Brix S, Kristiansen K, Xu X, Li J, Wu R*, Jia H*. The metagenome of the female upper reproductive tract. GigaScience. 7(10), giy107 (2018).
4. Li X, Liang S, Xia Z, Qu J, Liu H, Liu C, Yang H, Wang J, Madsen L, Hou Y, Li J, Jia H, Kristiansen K, Xiao L. Establishment of a Macaca fascicularis gut microbiome gene catalog and comparison with the human, pig, and mouse gut microbiomes. Gigascience. 2018, 7(9):giy100.
5. Pan H#, Guo R#, Zhu J#, Wang Q, Ju Y, Xie Y, Zheng Y, Wang Z, Li T, Liu Z, Lu L, Li F, Tong B, Xiao L, Xu X, Li R, Yuan Z, Yang H, Wang J, Kristiansen K, Jia H*, Liu L*. A gene catalogue of the Sprague-Dawley rat gut metagenome GigaScience. 7(5), giy055 (2018).
6. Xiao L*, Feng Q*, Liang S*, Sonne SB, Xia Z, Qiu X, Li L, Long H, Zhang J, Zhang D, Liu C, Fang Z, Chou J, Glanville J, Hao Q, Kotowska D, Colding C, Licht TR, Wu D, Yu J, Sung JJ, Liang Q, Li J, Jia H, Lan Z, Tremaroli V, Bäckhed F, Doré J, Le Chatelier E, Ehrlich SD, Lin JC, Arumugam M, Wang J, Madsen L, Kristiansen K. A catalog of the mouse gut metagenome. Nat Biotechnol. 33, 1103-1108 (2015).
7. Bäckhed F*‡, Roswall J, Peng Y, Feng Q, Jia H, Kovatcheva-Datchary P, Li Y, Xie H, Khan MT, Zhang J, Li J, Xiao L, Al-Aama J, Zhang D, Li Y, Kotowska D, Colding C, Tremaroli V, Bergman S, Madsen L, Kristiansen K, Dahlgren J‡, Wang J‡. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe. 17, 690-703 (2015).
8. Li J#, Jia H#, Cai X#, Zhong H#, Feng Q#, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS, Manichanh C, Chen B, Zhang W, Levenez F, Wang J, Xu X, Xiao L, Liang S, Zhang D, Zhang Z, Chen W, Zhao H, Al-Aama JU, Edris S, Yang H, Wang J, Hansen T, Nielsen HB, Brunak S, Kristiansen K, Guarner F, Pedersen O, Doré J, Ehrlich SD, MetaHIT consortium, Bork P*, Wang J*, An integrated reference gene catalog of the human gut microbiome. Nat Biotechnol., 2014, 32(8): 834-841.
Microbiome and diseases:
1. Wang Q#, Sun Q#, Li X#, Wang Z#, Zheng H, Ju Y, Guo R, Peng S*, Jia H*. Linking gut microbiome to bone mineral density: a shotgun metagenomic dataset from 361 elderly women. Gigabyte, 2021, 1. https://doi.org/10.46471/gigabyte.12.
2. Chen C#, Hao L#, Wei W#, Li F#, Song L, Zhang X, Dai J, Jie Z, Li J, Song X, Wang Z, Zhang Z, Zeng L, Du H, Tang H, Zhang T, Yang H, Wang J, Brix S, Kristiansen K, Xu X, Wu R*, Jia H*. The female urinary microbiota in relation to the reproductive tract microbiota. Gigabyte, 2020, 1. https://doi.org/10.46471/gigabyte.9.
3. Zhu F#, Ju Y#, Wang W#, Wang Q#, Guo R#, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, Jie Z, Zhao B, Xiao L, Yang L, Zhang T, Feng J, Guo L, He X, Chen Y, Chen C, Gao C, Xu X, Yang H, Wang J, Dang Y, Madsen L, Brix S, Kristiansen K*, Jia H*, Ma X*. Metagenome-wide association of gut microbiome features for schizophrenia. Nature Commun, 2020, 11(1): 1612.
4. Zhu F#, Guo R#, Wang W#, Ju Y#, Wang Q#, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, Jie Z, Zhao B, Xiao L, Yang L, Zhang T, Liu B, Guo L, He X, Chen Y, Chen C, Gao C, Xu X, Yang H, Wang J, Dang Y, Madsen L, Brix S, Kristiansen K*, Jia H*, Ma X*. Transplantation of microbiota from drug-free patients with schizophrenia causes schizophrenia-like abnormal behaviors and dysregulated kynurenine metabolism in mice. Mol Psychiatry. 25, 2905-2918 (2019).
5. Moll JM, Myers PN, Zhang C, Eriksen C, Wolf J, Appelberg KS, Lindberg G, Bahl MI, Zhao H, Pan-Hammarström Q, Cai K, Jia H, Borte S, Nielsen HB, Kristiansen K, Brix S, Hammarström L. Gut Microbiota Perturbation in IgA Deficiency Is Influenced by IgA-Autoantibody Status. Gastroenterology. 2021 Jun;160(7):2423-2434.e5.
6. Zhou C, Zhao H, Xiao XY, Chen BD, Guo RJ, Wang Q, Chen H, Zhao LD, Zhang CC, Jiao YH, Ju YM, Yang HX, Fei YY, Wang L, Shen M, Li H, Wang XH, Lu X, Yang B, Liu JJ, Li J, Peng LY, Zheng WJ, Zhang CY, Zhou JX, Wu QJ, Yang YJ, Su JM, Shi Q, Wu D, Zhang W, Zhang FC, Jia HJ, Liu DP, Jie ZY, Zhang X. Metagenomic profiling of the pro-inflammatory gut microbiota in ankylosing spondylitis. J Autoimmun. 2020 Feb;107:102360.
7. Zhong H, Ren H, Lu Y, Fang C, Hou G, Yang Z, Chen B, Yang F, Zhao Y, Shi Z, Zhou B, Wu J, Zou H, Zi J, Chen J, Bao X, Hu Y, Gao Y, Zhang J, Xu X, Hou Y, Yang H, Wang J, Liu S, Jia H, Madsen L, Brix S, Kristiansen K, Liu F, Li J. Distinct gut metagenomics and metaproteomics signatures in prediabetics and treatment-naïve type 2 diabetics. EBioMedicine. 2019, 47:373-383.
8. Wang Q, Li F, Liang B, Liang Y, Chen S, Mo X, Ju Y, Zhao H, Jia H, Spector TD, Xie H, Guo R. A metagenome-wide association study of gut microbiota in asthma in UK adults. BMC Microbiol. 2018 Sep 12;18(1):114.
9. Wang Q, Yang F, Jia H. Mining the microbiome for drug targets. Methods Enzymol. 2018;610:59-72.
10. Chen C#, Song X#, Zhong H#, Wei W#, Dai J#, Lan Z#, Li F, Yu X, Feng Q, Wang Z, Xie H, Chen X, Zeng C, Wen B, Zeng L, Du H, Tang H, Xu C, Xia Y, Xia H, Yang H, Wang J, Wang J, Madsen L, Brix S, Kristiansen K, Xu X, Li J*, Wu R*, Jia H*. The Microbiota Continuum along the Female Reproductive Tract and Its Relation to Uterine-related Diseases. Nat Commun. 8, 875 (2017).
11. Jie Z#, Xia H#, Zhong S#, Feng Q#, Li S, Liang S, Zhong H, Liu Z, Gao Y, Zhao H, Zhang D, Su Z, Fang Z, Lan Z, Li J, Xiao L, Li J, Li R, Li X, Li F, Ren H, Huang Y, Peng Y, Li G, Wen B, Dong B, Chen J, Geng Q, Zhang Z, Yang H, Wang J, Wang J, Zhang X, Madsen L, Ning G, Xu X, Liu X, Hou Y, Jia H*, He K*, Kristiansen K*. The gut microbiome in atherosclerotic cardiovascular disease. Nat Communs. 8, 845 (2017).
Barrington WT & Lusis AJ. Association between the gut microbiome and atherosclerosis. Nat Rev Cardiol. 14, 699–700 (2017).
12. Wang J#,*, Jia H#,*. Metagenome-wide association studies: fine-mining the microbiome. Nat Rev Microbiol. 14, 508-522 (2016).
13. Zhang X#,*, Zhang D#, Jia H#, Feng Q#, Wang D#, Liang D#, Wu X, Li J, Tang L, Li Y, Lan Z, Chen B, Li Y, Zhong H, Xie H, Jie Z, Chen W, Tang S, Xu X, Wang X, Cai X, Liu S, Xia Y, Li J, Qiao X, Al-Aama JY, Chen H, Wang L, Wu Q, Zhang F, Zheng W, Li Y, Zhang M, Luo G, Xue W, Xiao L, Li J, Chen W, Xu X, Yin Y, Yang H, Wang J, Kristiansen K, Liu L, Li T, Huang Q, Li Y*, Wang J*. The oral and gut microbiome are perturbed in rheumatoid arthritis and partly normalized following treatment. Nat Med. 21, 895-905 (2015).
Highlighted in:
Phillips R. Rheumatoid arthritis: Microbiome reflects status of RA and response to therapy. Nat Rev Rheumatol. 2015;11:502.
Roger GB. Germs and joints: the contribution of the human microbiome to rheumatoid arthritis. Nat Med. 2015;21:839-41.
Tong Y. Metagenome-wide Association Studies Potentiate Precision Medicine for Rheumatoid Arthritis. Genomics Proteomics Bioinformatics. 2015;13:208-9.
Jakubovics NS. A new association for the oral metagenome. Oral Dis. 2016;22:77-80.
14. Yu J*, Feng Q*, Wong SH*, Zhang D*, Liang QY*, Qin Y, Tang L, Stenvang J, Li Y, Li Y, Chen N, Wu WK, Al-Aama J, Nielsen HJ, Yau TO, Lan Z, Jia H, Li J, Xiao L, Lam TY, Ng SC, Cheng AS, Wong VW, Chan FK, Xu X, Yang H, Wang J, Brünner N, Kristiansen K, Arumugam M‡, Sung JJ‡, Wang J‡. Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer. Gut. doi: 10.1136/gutjnl-2015-309800.
15. Feng Q#, Liang S#, Jia H#, Stadlmayr A#, Tang L#, Lan Z, Zhang D, Xia H, Xu X, Jie Z, Su L, Li X, Li X, Li J, Xiao L, Huber-Schönauer U, Niederseer D, Xu X, Al-Aama J, Yang H, Wang J, Kristiansen K, Arumugam M, Tilg H*, Datz C*, Wang J*. Gut microbiome development along the colorectal adenoma-carcinoma sequence. Nat Commun. 6, 6528 (2015).
Genetic determinants of the microbiome and Mendelian randomization:
1. Liu X#, Tong X#, Zhu J, Tian L, Jie Z, Zou Y, Lin X, Liang H, Li W, Ju Y, Qin Y, Zou L, Lu H, Xu X, Yang H, Wang J, Zong Y, Liu W, Hou Y, Zhu S, Jin X, Jia H*, Zhang T*. Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome. Cell Discovery, 2021, 7, 117. Link-doi.org/10.1038/s41421-021-00356-0
2. Liu X#, Tong X#, Zou Y, Lin X, Zhao H, Tian L, Jie Z, Wang Q, Zhang Z, Lu H, Xiao L, Qiu X, Zi J, Wang R, Xu X, Yang H, Wang J, Zong Y, Liu W, Hou Y, Zhu S, Jia H*, Zhang T*. Mendelian randomization analyses support causal relationships between blood metabolites and gut microbiome, Nature Genetics, 2022, 54(1): 52-61. Link-doi.org/10.1038/s41588-021-00968-y
3. Liu X, Tang S, Zhong H, Tong X, Jie Z, Ding Q, Wang D, Guo R, Xiao L, Xu X, Yang H, Wang J, Zong Y, Liu W, Liu X, Zhang Y, Brix S, Kristiansen K, Hou Y*, Jia H*; Zhang T*. A genome-wide association study for gut metagenome in Chinese adults illuminates complex diseases, Cell Discovery, 2021, 7, 9. Link-doi.org/10.1038/s41421-020-00239-w
4. Xie H#, Guo R#, Zhong H#, Feng Q#, Lan Z, Qin B, Ward KJ, Jackson M, Xia Y, Chen X, Chen B, Xia H, Xu C, Li F, Xu X, Al-Aama JY, Yang H, Wang J, Kristiansen K, Wang J, Steves CJ, Bell JT, Li J*, Spector TD*, Jia H*. Shotgun metagenomics of 250 adult twins reveals genetic and environmental impacts on the gut microbiome. Cell Systems. 3, 572-584.e3 (2016). Link-doi.org/10.1016/j.cels.2016.10.004
Microbiome-based disease detection and intervention:
1. Jie Z#,*, Liang S#, Ding Q#, Li F, Tang S, Sun X, Lin Y, Chen P, Cai K, Zhou H, Lu H, Wang X, Zhang T, Xiao L, Yang H, Wang J, Hou Y, Kristiansen K, Jia H*, Xu X. Disease trends in a young Chinese cohort according to fecal metagenome and plasma metabolites. Med Microecol 2021. Link-doi.org/10.1016/j.medmic.2021.100037
2. Jie Z#,*, Liang S#, Ding Q#, Li F, Sun X, Lin Y, Chen P, Cai K, Wang X, Zhang T, Xiao L, Yang H, Wang J, Hou Y, Kristiansen K, Jia H*, Xu X*. Dairy consumption and physical fitness tests associated with fecal microbiome in a Chinese cohort. Med Microecol 2021. Link-doi.org/10.1016/j.medmic.2021.100038
3. Jie Z#,*, Liang S#, Ding Q#, Li F, Tang S, Wang D, Lin Y, Chen P, Cai K, Qiu X, Li Q, Liao Y, Zhou D, Lian H, Zuo Y, Chen X, Rao W, Ren Y, Wang Y, Zi J, Wang R, Zhou H, Lu H, Wang X, Zhao W, Zhao T, Xiao L, Zong Y, Liu W, Yang H, Wang J, Hou Y, Liu X, Kristiansen K, Zhong H, Jia H*, Xu X*. A transomic cohort as a reference point for promoting a healthy gut microbiome. Med Microecol 2021. Link-doi.org/10.1016/j.medmic.2021.100039
4. Chen C#, Hao L#, Zhang Z#, Tian L, Song L, Zhang X, Jie Z, Tong X, Xiao L, Zhang T, Jin X, Xu X, Yang H, Wang J, Kristiansen K, Jia H*. Vaginal-cervical microbiome dynamics after oral probiotics. Journal of Genetics and Genomics, https://doi.org/10.1101/2020.06.16.155929
5. Jie Z#, Chen C#,*, Hao L, Li F, Song L, Zhang X, Zhu J, Tian L, Tong X, Cai K, Zhang Z, Ju Y, Yu X, Li Y, Zhou H, Lu H, Qiu X, Li Q, Liao Y, Zhou D, Lian H, Zuo Y, Chen X, Rao W, Ren Y, Wang Y, Zi J, Wang R, Liu N, Wu J, Zhang W, Liu X, Zong Y, Liu W, Xiao L, Hou Y, Xu X, Yang H, Wang J, Kristiansen K, Jia H*. Life History Recorded in the Vagino-cervical Microbiome Along with Multi-omics. Genomics Proteomics Bioinformatics. 2021, S1672-0229(21)00099-1. Link-doi.org/10.1016/j.gpb.2021.01.005
6. Jie Z, Yu X, Liu Y, Sun L, Chen P, Ding Q, Gao Y, Zhang X, Yu M, Liu Y, Zhang Y, Kristiansen K, Jia H, Brix S, Cai K. The baseline gut microbiota directs dieting-induced weight loss trajectories. Gastroenterology. 2021, 160(6):2029-2042.e16.
7. Zou M#, Jie Z#, Cui B#, Wang H, Feng Q, Zou Y, Zhang X, Yang H, Wang J, Zhang F*, Jia H*. Fecal microbiota transplantation results in bacterial strain displacement in patients with inflammatory bowel diseases. FEBS Open Bio. 2020,10(1):41-55.
8. Pan H#, Guo R#, Ju Y#, Wang Q#, Zhu J, Xie Y, Zheng Y, Li T, Liu Z, Lu L, Li F, Tong B, Xiao L, Xu X, Leung EL, Li R, Yang H, Wang J, Zhou H, Jia H*, Liu L*. A single bacterium restores the microbiome dysbiosis to protect bones from destruction in a rat model of rheumatoid arthritis. Microbiome. 2019, 7(1):107. Link-doi.org/10.1186/s40168-019-0719-1
9. Han M#,*, Hao L#, Lin Y, Li F, Wang J, Yang H, Xiao L, Kristiansen K, Jia H*, Li J*. A novel affordable reagent for room temperature storage and transport of fecal samples for metagenomic analyses. Microbiome. 2018, 6(1):43.
Earlier work unrelated to the microbiome:
1. Putnam AA*, Gao Z*, Liu F, Jia H, Yang Q, Jankowsky E. Division of labor in an oligomer of the DEAD-box RNA helicase Ded1p. Mol Cell. 59, 541-552 (2015).
2. Nabel CS, Jia H, Ye Y, Shen L, Goldschmidt HL, Stivers JT, Zhang Y‡, Kohli RM‡. AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation. Nat Chem Biol. 8, 751-8 (2012).
3. Jia H, Wang X, Anderson JT, Jankowsky E*, RNA unwinding by the Trf4/Air2/Mtr4 polyadenylation (TRAMP) complex, Proc Natl Acad Sci U S A, 2012, 109(19), 7292-7297.
4. Jia H, Wang X, Liu F, Guenther UP, Srinivasan S, Anderson JT, Jankowsky E*, The RNA helicase Mtr4p modulates polyadenylation in the TRAMP complex, Cell, 2011, 145(6), 890-901.
5. Del Campo M*, Mohr S*, Jiang Y, Jia H, Jankowsky E, Lambowitz AM. Unwinding by local strand separation is critical for the function of DEAD-box proteins as RNA chaperones. J Mol Biol. 389, 674-93 (2009).
6. Mohr G*, Del Campo M*, Mohr S*, Yang Q, Jia H, Jankowsky E, Lambowitz AM. Function of the C-terminal domain of the DEAD-box protein Mss116p analyzed in vivo and in vitro. J Mol Biol. 375, 1344-64 (2008).
7. Wang X, Jia H, Jankowsky E, Anderson JT. Degradation of hypomodified tRNA(iMet) in vivo involves RNA-dependent ATPase activity of the DExH helicase Mtr4p. RNA. 14, 107-16 (2008).
8. Qi M, Yu W, Liu S, Jia H, Tang L, Shen M, Yan X, Saiyin H, Lang Q, Wan B, Zhao S, Yu L. Septin1, a new interaction partner for human serine/threonine kinase aurora-B. Biochem Biophys Res Commun. 336, 994-1000 (2005).
