Jia H. Investigating Human Diseases with the Microbiome: Metagenomics Bench to Bedside.ISBN: 9780323913690
Cutting-edge neuroscience for more efficient artificial intelligence. TBD.
Jia H. Investigating Human Diseases with the Microbiome: Metagenomics Bench to Bedside.ISBN: 9780323913690
Cutting-edge neuroscience for more efficient artificial intelligence. TBD.
Donia MS, She Q, Huber JA, Jia H. (One paragraph each) Creating a unique culture. Cell. 177(6), 1369 (2019).
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
Highlighted in: Tang L. Human gut bacterial genome reference. Nat Methods. 16, 286 (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.
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).
Highlighted in: 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).
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. 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. 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. 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). doi.org/10.1016/j.cels.2016.10.004
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. 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. 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. 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. 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. 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.