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For: Wen T, Niu G, Chen T, Shen Q, Yuan J, Liu YX. The best practice for microbiome analysis using R. Protein Cell 2023;14:713-725. [PMID: 37128855 PMCID: PMC10599642 DOI: 10.1093/procel/pwad024] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/02/2023] [Indexed: 05/03/2023]  Open
Number Cited by Other Article(s)
1
Li R, Li Z, Zhang K, Zhang C, Sun Y, Zhang J, Zheng Y, Yao Y, Qin X. The responses of root exudates and microbiome in the rhizosphere of main plant and aromatic intercrops to soil Cr stress. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2025;366:125528. [PMID: 39672367 DOI: 10.1016/j.envpol.2024.125528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Revised: 11/30/2024] [Accepted: 12/11/2024] [Indexed: 12/15/2024]
2
Su FZ, Zhu EL, Bai CX, Zhang WS, Liu M, Li B, Jia CC, Zhang P, Zhang BW, Zou R, Li QX, Yang BY, Kuang HX, Wang QH. A comparative study on the antipyretic effect and underlying mechanisms of different bile-fermented Arisaemas. JOURNAL OF ETHNOPHARMACOLOGY 2025;337:118951. [PMID: 39423945 DOI: 10.1016/j.jep.2024.118951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 10/11/2024] [Accepted: 10/14/2024] [Indexed: 10/21/2024]
3
Zhao X, Liang X, Zhu Z, Yuan Z, Yu S, Liu Y, Wang J, Mason-Jones K, Kuzyakov Y, Chen J, Ge T, Wang S. Phages Affect Soil Dissolved Organic Matter Mineralization by Shaping Bacterial Communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2025. [PMID: 39836728 DOI: 10.1021/acs.est.4c08274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2025]
4
Yang QE, Lin Z, Gan D, Li M, Liu X, Zhou S, Walsh TR. Microplastics mediates the spread of antimicrobial resistance plasmids via modulating conjugal gene expression. ENVIRONMENT INTERNATIONAL 2025;195:109261. [PMID: 39813956 DOI: 10.1016/j.envint.2025.109261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Revised: 01/06/2025] [Accepted: 01/07/2025] [Indexed: 01/18/2025]
5
Weng R, Xu Y, Gao X, Cao L, Su J, Yang H, Li H, Ding C, Pu J, Zhang M, Hao J, Xu W, Ni W, Qian K, Gu Y. Non-Invasive Diagnosis of Moyamoya Disease Using Serum Metabolic Fingerprints and Machine Learning. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2405580. [PMID: 39737836 DOI: 10.1002/advs.202405580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 11/03/2024] [Indexed: 01/01/2025]
6
Wang M, Lin M, Liu Q, Zhang Y, Luo R, Pang X. Altitudinal decline of vegetation restoration effects on soil microbial communities on high-altitude roadside slops: Environmental drivers and management implications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024;957:177424. [PMID: 39522786 DOI: 10.1016/j.scitotenv.2024.177424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2024] [Revised: 11/03/2024] [Accepted: 11/04/2024] [Indexed: 11/16/2024]
7
Xiong X, Yu C, Qiu M, Zhang Z, Hu C, Zhu S, Yang L, Peng H, Song X, Chen J, Xia B, Wang J, Qing Y, Yang C. Genomic and Gut Microbiome Evaluations of Growth and Feed Efficiency Traits in Broilers. Animals (Basel) 2024;14:3615. [PMID: 39765519 PMCID: PMC11672845 DOI: 10.3390/ani14243615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Revised: 12/10/2024] [Accepted: 12/13/2024] [Indexed: 01/11/2025]  Open
8
Ma Y, Zhu X, Ni L, Du C, Sang W, Xu C, Shi J, Li Y, Li S, Pang Y, Zhang L. Effects of artemisinin sustained-release algaecides on in-situ cyanobacterial inhibition and microbes-floating plants dominated ecosystem functions in artificial landscape lake. JOURNAL OF HAZARDOUS MATERIALS 2024;480:136182. [PMID: 39427356 DOI: 10.1016/j.jhazmat.2024.136182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 10/09/2024] [Accepted: 10/14/2024] [Indexed: 10/22/2024]
9
Mogna-Peláez P, Riezu-Boj JI, Milagro FI, Clemente-Larramendi I, Esteban Echeverría S, Herrero JI, Elorz M, Benito-Boillos A, Tobaruela-Resola AL, González-Muniesa P, Tur JA, Martínez JA, Abete I, Zulet MA. Sex-Dependent Gut Microbiota Features and Functional Signatures in Metabolic Disfunction-Associated Steatotic Liver Disease. Nutrients 2024;16:4198. [PMID: 39683591 DOI: 10.3390/nu16234198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Revised: 11/30/2024] [Accepted: 12/02/2024] [Indexed: 12/18/2024]  Open
10
Zhang T, Li H, Jiang M, Hou H, Gao Y, Li Y, Wang F, Wang J, Peng K, Liu YX. Nanopore sequencing: flourishing in its teenage years. J Genet Genomics 2024;51:1361-1374. [PMID: 39293510 DOI: 10.1016/j.jgg.2024.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 09/09/2024] [Accepted: 09/10/2024] [Indexed: 09/20/2024]
11
Kostka A, Gruszecka‐Kosowska A, Ruiz‐Rodríguez A, Aguilera M. Multi-omics approach in gut and environmental microbiota research under the One Health concept. EFSA J 2024;22:e221104. [PMID: 39712914 PMCID: PMC11659745 DOI: 10.2903/j.efsa.2024.e221104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]  Open
12
Tang G, Song Q, Dou J, Chen Z, Hu X, Li Z, Li X, Wang T, Dong S, Zhang H. Neutrophil-centric analysis of gastric cancer: prognostic modeling and molecular insights. Cell Mol Life Sci 2024;81:452. [PMID: 39540948 PMCID: PMC11564594 DOI: 10.1007/s00018-024-05484-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Revised: 10/05/2024] [Accepted: 10/18/2024] [Indexed: 11/16/2024]
13
Wu X, Yang X, Dai Y, Zhao Z, Zhu J, Guo H, Yang R. Single-cell sequencing to multi-omics: technologies and applications. Biomark Res 2024;12:110. [PMID: 39334490 PMCID: PMC11438019 DOI: 10.1186/s40364-024-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 08/17/2024] [Indexed: 09/30/2024]  Open
14
Fitzjerrells RL, Ollberding NJ, Mangalam AK. Looking at the full picture, using topic modeling to observe microbiome communities associated with disease. GUT MICROBES REPORTS 2024;1:1-11. [PMID: 39183943 PMCID: PMC11340690 DOI: 10.1080/29933935.2024.2378067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/24/2024] [Accepted: 07/01/2024] [Indexed: 08/27/2024]
15
Piłsyk S, Perlińska-Lenart U, Janik A, Skalmowska P, Znój A, Gawor J, Grzesiak J, Kruszewska JS. Native and Alien Antarctic Grasses as a Habitat for Fungi. Int J Mol Sci 2024;25:8475. [PMID: 39126044 PMCID: PMC11313430 DOI: 10.3390/ijms25158475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 07/31/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024]  Open
16
Park CE, Jo YJ, Jung DR, Park HC, Shin JH. Comparative Analysis of Gut Microbiota between Captive and Wild Long-Tailed Gorals for Ex Situ Conservation. Microorganisms 2024;12:1419. [PMID: 39065187 PMCID: PMC11278867 DOI: 10.3390/microorganisms12071419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024]  Open
17
Li C, Liu C, Li H, Liao H, Xu L, Yao M, Li X. The microgeo: an R package rapidly displays the biogeography of soil microbial community traits on maps. FEMS Microbiol Ecol 2024;100:fiae087. [PMID: 38866720 PMCID: PMC11212663 DOI: 10.1093/femsec/fiae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/26/2024] [Accepted: 06/11/2024] [Indexed: 06/14/2024]  Open
18
Huang W, Ma T, Liu X, Xu Y, Gu J, Gu Y, Yuan J, Wen T, Xue C, Shen Q. Degradation of Complex Carbon Sources in Organic Fertilizers Facilitates Nitrogen Fixation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024;72:12988-13000. [PMID: 38820247 DOI: 10.1021/acs.jafc.4c01727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
19
Yang M, Chen T, Liu Y, Huang L. Visualizing set relationships: EVenn's comprehensive approach to Venn diagrams. IMETA 2024;3:e184. [PMID: 38898979 PMCID: PMC11183158 DOI: 10.1002/imt2.184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 02/24/2024] [Accepted: 03/01/2024] [Indexed: 06/21/2024]
20
Wang T, Li P, Bai X, Tian S, Yang M, Leng D, Kui H, Zhang S, Yan X, Zheng Q, Luo P, He C, Jia Y, Wu Z, Qiu H, Li J, Wan F, Ali MA, Mao R, Liu Y, Li D. Vaginal microbiota are associated with in vitro fertilization during female infertility. IMETA 2024;3:e185. [PMID: 38898981 PMCID: PMC11183179 DOI: 10.1002/imt2.185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/02/2024] [Accepted: 03/02/2024] [Indexed: 06/21/2024]
21
Dantas CWD, Martins DT, Nogueira WG, Alegria OVC, Ramos RTJ. Tools and methodology to in silico phage discovery in freshwater environments. Front Microbiol 2024;15:1390726. [PMID: 38881659 PMCID: PMC11176557 DOI: 10.3389/fmicb.2024.1390726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/16/2024] [Indexed: 06/18/2024]  Open
22
Parente E, Ricciardi A. A Comprehensive View of Food Microbiota: Introducing FoodMicrobionet v5. Foods 2024;13:1689. [PMID: 38890917 PMCID: PMC11171936 DOI: 10.3390/foods13111689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024]  Open
23
Zhu L, Li J, Yang J, Li X, Lin D, Wang M. Fermentation broth from fruit and vegetable waste works: Reducing the risk of human bacterial pathogens in soil by inhibiting quorum sensing. ENVIRONMENT INTERNATIONAL 2024;188:108753. [PMID: 38761431 DOI: 10.1016/j.envint.2024.108753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/06/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
24
Zaparte A, Dore E, White S, Paliarin F, Gabriel C, Copenhaver K, Basavanhalli S, Garcia E, Vaddavalli R, Luo M, Taylor CM, Welsh DA, Maiya R. Standard rodent diets differentially impact alcohol consumption, preference, and gut microbiome diversity. Front Neurosci 2024;18:1383181. [PMID: 38803684 PMCID: PMC11129685 DOI: 10.3389/fnins.2024.1383181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/12/2024] [Indexed: 05/29/2024]  Open
25
Wang M, Lin M, Liu Q, Li C, Pang X. Fungal, but not bacterial, diversity and network complexity promote network stability during roadside slope restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024;922:171007. [PMID: 38401731 DOI: 10.1016/j.scitotenv.2024.171007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 02/10/2024] [Accepted: 02/13/2024] [Indexed: 02/26/2024]
26
Ranauda MA, Zuzolo D, Maisto M, Tartaglia M, Scarano P, Prigioniero A, Sciarrillo R, Guarino C. Microplastics affect soil-plant system: Implications for rhizosphere biology and fitness of sage (Salvia officinalis L.). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024;346:123656. [PMID: 38408506 DOI: 10.1016/j.envpol.2024.123656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/23/2024] [Accepted: 02/24/2024] [Indexed: 02/28/2024]
27
Yan Z, Lei Y, Zhao P, Zhang D, Shen J, Zhang G, Wei R, Liu H, Liu X, He Y, Shen S, Liu D. Natural mating ability is associated with gut microbiota composition and function in captive male giant pandas. Ecol Evol 2024;14:e11189. [PMID: 38571808 PMCID: PMC10985376 DOI: 10.1002/ece3.11189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/05/2024] [Accepted: 03/12/2024] [Indexed: 04/05/2024]  Open
28
Zhong S, Sun YQ, Huo JX, Xu WY, Yang YN, Yang JB, Wu WJ, Liu YX, Wu CM, Li YG. The gut microbiota-aromatic hydrocarbon receptor (AhR) axis mediates the anticolitic effect of polyphenol-rich extracts from Sanghuangporus. IMETA 2024;3:e180. [PMID: 38882491 PMCID: PMC11170970 DOI: 10.1002/imt2.180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 06/18/2024]
29
Gao Y, Zhang G, Jiang S, Liu Y. Wekemo Bioincloud: A user-friendly platform for meta-omics data analyses. IMETA 2024;3:e175. [PMID: 38868508 PMCID: PMC10989175 DOI: 10.1002/imt2.175] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 06/14/2024]
30
Lin D, Xu JY, Wang L, Du S, Zhu D. Long-term application of organic fertilizer prompting the dispersal of antibiotic resistance genes and their health risks in the soil plastisphere. ENVIRONMENT INTERNATIONAL 2024;183:108431. [PMID: 38217904 DOI: 10.1016/j.envint.2024.108431] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/15/2024]
31
Bu Y, Feng L, Xu D, Zhang S, Liang L, Si J, Lu Y, Liu Q, Yan G, Wang Y, Lan G, Liang J. Changes in Gut Microbiota Associated with Parity in Large White Sows. Animals (Basel) 2023;14:112. [PMID: 38200843 PMCID: PMC10778104 DOI: 10.3390/ani14010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024]  Open
32
Gao Y, Li D, Liu YX. Microbiome research outlook: past, present, and future. Protein Cell 2023;14:709-712. [PMID: 37219087 PMCID: PMC10599639 DOI: 10.1093/procel/pwad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/24/2023]  Open
33
Salas-Espejo E, Terrón-Camero LC, Ruiz JL, Molina NM, Andrés-León E. Exploring the Microbiome in Human Reproductive Tract: High-Throughput Methods for the Taxonomic Characterization of Microorganisms. Semin Reprod Med 2023;41:125-143. [PMID: 38320576 DOI: 10.1055/s-0044-1779025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
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