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10. Standardization in global environmental antibiotic resistance genes (ARGs) surveillance.

Author

Mao, Xuemei, Yin, Xiaole, Yang, Yu, Che, You, Xu, Xiaoqing, Deng, Yu, Li, Liguan, and Zhang, Tong

Subjects
*DRUG resistance in bacteria, *DRUG resistance in microorganisms, *REFERENCE sources, *RISK assessment, *RISK exposure
Abstract

Antimicrobial resistance (AMR) poses an increasing threat to global health. To deliberate the distribution and transmission of environmental resistance in a wide geographic and longitudinal scope, standardization of the analytical methods is desperately required for the extensive implementation of large-scale environmental antibiotic resistance gene (ARGs) surveillance. In this review, a standardized surveillance method using metagenomic analysis, coupled with proper quantification tools and environmental reference materials as technical benchmarks, was established to facilitate the generation of comparable and informative resistome datasets. As global and long-term ARGs surveillance has recently been performed in various environmental compartments, increasing efforts are also needed for assessing the health risks of ARGs. The development of risk assessment schemes that incorporate factors including transfer potential, host species, viability, and absolute quantification is essential to the regulatory guidelines for high-risk priority ARGs. This review provides guidance to ARGs surveillance regarding the level and the risk of ARG exposure, especially to identify and address critical hotspots. [ABSTRACT FROM AUTHOR]

Published
2024
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13. UvSMEK1, a Suppressor of MEK Null, Regulates Pathogenicity, Conidiation and Conidial Germination in Rice False Smut Fungus Ustilaginoidea virens

Author

Yu Junjie, Yu Mina, Song Tianqiao, Cao Huijuan, Yong Mingli, Pan Xiayan, Qi Zhongqiang, Du Yan, Zhang Rongsheng, Yin Xiaole, Liang Dong, and Liu Yongfeng

Subjects
suppressor, MEK null, Ustilaginoidea virens, pathogenicity, conidial germination, conidiation, Plant culture, SB1-1110
Abstract

Rice false smut, which is caused by Ustilaginoidea virens, is an emerging disease of rice spikelets in rice-growing areas worldwide. However, the infection mechanism of U. virens on rice spikelets is still unclear. Here, we characterized a suppressor of mitogen-activated protein kinase kinase or ERK kinase (MEK) null (UvSMEK1) in U. virens that is conserved among filamentous fungi. Compared with wild type U. virens strain P-1, UvSMEK1 deletion mutants were defective in pathogenicity and conidial germination. In addition, conidiation of UvSMEK1 deletion mutants was significantly reduced on yeast extract tryptone (YT) plates, but increased in YT broth compared with the wild type. Compared with UvSMEK1 expression level during the vegetative mycelia and conidiation stages, UvSMEK1 dramatically increased during infection of rice florets. Surprisingly, the UvSMEK1 deletion mutants exhibited higher tolerance to H2O2 and NaCl. In summary, presented evidence suggested that UvSMEK1 positively regulated pathogenicity, conidial germination and conidiation in YT broth, and negatively regulated conidiation on YT medium and tolerance to oxidative and osmotic stresses. The results enhance our understanding of the regulatory mechanism of pathogenicity of U. virens, and present a potential molecular target for blocking rice infection by U. virens.

Published
2021
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19. Demonstrating the Beneficial Effect of Low Protein Diet in Primary Sclerosing Cholangitis through a Randomized Clinical Trial and Multi-omics Data Analysis

Author

Yin, Xiaole, primary, Sasson, Gila, additional, Sun, Zheng, additional, Ke, Shanlin, additional, Babazadeh, Demsina, additional, Mahmood, Shaikh Danish, additional, Andrews, Macie, additional, Hurwitz, Shelley, additional, Chikowore, Tinashe, additional, Paul, Maia, additional, Javier, Nadine, additional, Dave, Malav, additional, Austin, Alexandra, additional, Gray, Linda, additional, Steinberg, Francene, additional, Souza, Elaine, additional, Bowlus, Christopher, additional, Liu, Yang-Yu, additional, and Korzenik, Joshua, additional

Published
2024
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20. The N-terminus of an Ustilaginoidea virens Ser-Thr-rich glycosylphosphatidylinositol-anchored protein elicits plant immunity as a MAMP

Author

Song, Tianqiao, Zhang, You, Zhang, Qi, Zhang, Xiong, Shen, Danyu, Yu, Junjie, Yu, Mina, Pan, Xiayan, Cao, Huijuan, Yong, Mingli, Qi, Zhongqiang, Du, Yan, Zhang, Rongsheng, Yin, Xiaole, Qiao, Junqing, Liu, Youzhou, Liu, Wende, Sun, Wenxian, Zhang, Zhengguang, Wang, Yuanchao, Dou, Daolong, Ma, Zhenchuan, and Liu, Yongfeng

Published
2021
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28. Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples

Author

Yin, Xiaole, Chen, Xi, Jiang, Xiao-Tao, Yang, Ying, Li, Bing, Shum, Marcus Ho-Hin, Lam, Tommy T Y, Leung, Gabriel M, Rose, Joan, Sanchez-Cid, Concepcion, Vogel, Timothy M, Walsh, Fiona, Berendonk, Thomas U, Midega, Janet, Uchea, Chibuzor, Frigon, Dominic, Wright, Gerard D, Bezuidenhout, Carlos, Picão, Renata C, Ahammad, Shaikh Z, Nielsen, Per Halkjær, Hugenholtz, Philip, Ashbolt, Nicholas J, Corno, Gianluca, Fatta-Kassinos, Despo, Bürgmann, Helmut, Schmitt, Heike, Cha, Chang-Jun, Pruden, Amy, Smalla, Kornelia, Cytryn, Eddie, Zhang, Yu, Yang, Min, Zhu, Yong-Guan, Dechesne, Arnaud, Smets, Barth F, Graham, David W, Gillings, Michael R, Gaze, William H, Manaia, Célia M, van Loosdrecht, Mark C M, Alvarez, Pedro J J, Blaser, Martin J, Tiedje, James M, Topp, Edward, and Zhang, Tong

Subjects
standardization, metagenomics, one-health, long-read sequencing, ARG copy per cell
Published
2023

30. Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples

Author

Yin, Xiaole (author), Chen, Xi (author), Jiang, Xiao Tao (author), Yang, Ying (author), Li, Bing (author), Shum, Marcus Ho Hin (author), Schmitt, H. (author), Cha, Chang Jun (author), van Loosdrecht, Mark C.M. (author), Yin, Xiaole (author), Chen, Xi (author), Jiang, Xiao Tao (author), Yang, Ying (author), Li, Bing (author), Shum, Marcus Ho Hin (author), Schmitt, H. (author), Cha, Chang Jun (author), and van Loosdrecht, Mark C.M. (author)

Abstract

Surveillance of antibiotic resistance genes (ARGs) has been increasingly conducted in environmental sectors to complement the surveys in human and animal sectors under the "One-Health"framework. However, there are substantial challenges in comparing and synthesizing the results of multiple studies that employ different test methods and approaches in bioinformatic analysis. In this article, we consider the commonly used quantification units (ARG copy per cell, ARG copy per genome, ARG density, ARG copy per 16S rRNA gene, RPKM, coverage, PPM, etc.) for profiling ARGs and suggest a universal unit (ARG copy per cell) for reporting such biological measurements of samples and improving the comparability of different surveillance efforts., Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public., BT/Environmental Biotechnology

Published
2023
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35. UvSMEK1, a Suppressor of MEK Null, Regulates Pathogenicity, Conidiation and Conidial Germination in Rice False Smut Fungus Ustilaginoidea virens

Author

Zhang Rongsheng, Cao Huijuan, Liu Yongfeng, Yong Mingli, Liang Dong, Yu Junjie, Du Yan, Qi Zhongqiang, Yu Mina, Song Tianqiao, Pan Xiayan, and Yin Xiaole

Subjects
biology, conidial germination, Wild type, Plant culture, food and beverages, Conidiation, Ustilaginoidea virens, suppressor, Plant Science, Fungus, conidiation, biology.organism_classification, SB1-1110, Microbiology, chemistry.chemical_compound, chemistry, Germination, Tryptone, MEK null, pathogenicity, Protein kinase A, Agronomy and Crop Science, Mycelium, Biotechnology
Abstract

Rice false smut, which is caused by Ustilaginoidea virens, is an emerging disease of rice spikelets in rice-growing areas worldwide. However, the infection mechanism of U. virens on rice spikelets is still unclear. Here, we characterized a suppressor of mitogen-activated protein kinase kinase or ERK kinase (MEK) null (UvSMEK1) in U. virens that is conserved among filamentous fungi. Compared with wild type U. virens strain P-1, UvSMEK1 deletion mutants were defective in pathogenicity and conidial germination. In addition, conidiation of UvSMEK1 deletion mutants was significantly reduced on yeast extract tryptone (YT) plates, but increased in YT broth compared with the wild type. Compared with UvSMEK1 expression level during the vegetative mycelia and conidiation stages, UvSMEK1 dramatically increased during infection of rice florets. Surprisingly, the UvSMEK1 deletion mutants exhibited higher tolerance to H2O2 and NaCl. In summary, presented evidence suggested that UvSMEK1 positively regulated pathogenicity, conidial germination and conidiation in YT broth, and negatively regulated conidiation on YT medium and tolerance to oxidative and osmotic stresses. The results enhance our understanding of the regulatory mechanism of pathogenicity of U. virens, and present a potential molecular target for blocking rice infection by U. virens.

Published
2021

37. An omics-based framework for assessing the health risk of antimicrobial resistance genes

Author

Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, Zhang, An-Ni, Gaston, Jeffry M., Dai, Chengzhen L., Zhao, Shijie, Poyet, Mathilde, Groussin, Mathieu, Yin, Xiaole, Li, Li-Guan, van Loosdrecht, Mark C. M., Topp, Edward, Gillings, Michael R., Hanage, William P., Tiedje, James M., Moniz, Katya, Alm, Eric J., Zhang, Tong, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, Zhang, An-Ni, Gaston, Jeffry M., Dai, Chengzhen L., Zhao, Shijie, Poyet, Mathilde, Groussin, Mathieu, Yin, Xiaole, Li, Li-Guan, van Loosdrecht, Mark C. M., Topp, Edward, Gillings, Michael R., Hanage, William P., Tiedje, James M., Moniz, Katya, Alm, Eric J., and Zhang, Tong

Abstract

AbstractAntibiotic resistance genes (ARGs) are widespread among bacteria. However, not all ARGs pose serious threats to public health, highlighting the importance of identifying those that are high-risk. Here, we developed an ‘omics-based’ framework to evaluate ARG risk considering human-associated-enrichment, gene mobility, and host pathogenicity. Our framework classifies human-associated, mobile ARGs (3.6% of all ARGs) as the highest risk, which we further differentiate as ‘current threats’ (Rank I; 3%) - already present among pathogens - and ‘future threats’ (Rank II; 0.6%) - novel resistance emerging from non-pathogens. Our framework identified 73 ‘current threat’ ARG families. Of these, 35 were among the 37 high-risk ARGs proposed by the World Health Organization and other literature; the remaining 38 were significantly enriched in hospital plasmids. By evaluating all pathogen genomes released since framework construction, we confirmed that ARGs that recently transferred into pathogens were significantly enriched in Rank II (‘future threats’). Lastly, we applied the framework to gut microbiome genomes from fecal microbiota transplantation donors. We found that although ARGs were widespread (73% of genomes), only 8.9% of genomes contained high-risk ARGs. Our framework provides an easy-to-implement approach to identify current and future antimicrobial resistance threats, with potential clinical applications including reducing risk of microbiome-based interventions.

Published
2022

43. Pyricularia sp. jiangsuensis , a new cryptic rice panicle blast pathogen from rice fields in Jiangsu Province, China

Author

Du, Yan, primary, Qi, Zhongqiang, additional, Liang, Dong, additional, Yu, Junjie, additional, Yu, Mina, additional, Zhang, Rongsheng, additional, Cao, Huijuan, additional, Yong, Mingli, additional, Pan, Xiayan, additional, Yin, Xiaole, additional, Qiao, Junqing, additional, Liu, Youzhou, additional, Chen, Zhiyi, additional, Song, Tianqiao, additional, Liu, Wende, additional, Zhang, Zhengguang, additional, and Liu, Yongfeng, additional

Published
2021
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46. MAT1-1-3, a Mating Type Gene in the Villosiclava virens, Is Required for Fruiting Bodies and Sclerotia Formation, Asexual Development and Pathogenicity

Author

Yong, Mingli, primary, Yu, Junjie, additional, Pan, Xiayan, additional, Yu, Mina, additional, Cao, Huijuan, additional, Qi, Zhongqiang, additional, Du, Yan, additional, Zhang, Rongsheng, additional, Song, Tianqiao, additional, Yin, Xiaole, additional, Chen, Zhiyi, additional, Liu, Wende, additional, and Liu, Yongfeng, additional

Published
2020
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49. CO 2 and CH 4 budgets and global warming potential modifications in Sphagnum -dominated peat mesocosms invaded by Molinia caerulea

Author

Leroy, Fabien, Gogo, Sébastien, Guimbaud, Christophe, Bernard-Jannin, Léonard, Yin, Xiaole, Belot, Guillaume, Shuguang, Wang, Laggoun-Défarge, Fatima, Institut des Sciences de la Terre d'Orléans - UMR7327 (ISTO), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS), Biogéosystèmes Continentaux - UMR7327, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Laboratoire de Physique et Chimie de l'Environnement et de l'Espace (LPC2E), Observatoire des Sciences de l'Univers en région Centre (OSUC), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), School of Environmental Science and Engineering, Shandong University, PIVOTS project by the Région Centre – Val de Loire (ARD 2020 program and CPER 2015–2020)., and ANR-10-LABX-0100,VOLTAIRE,Geofluids and Volatil elements – Earth, Atmosphere, Interfaces – Resources and Environment(2010)

Subjects
[SDU]Sciences of the Universe [physics], [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment
Abstract

International audience; Plant communities play a key role in regulating greenhouse gas (GHG) emissions in peatland ecosystems and therefore in their ability to act as carbon (C) sinks. However , in response to global change, a shift from Sphagnum-dominated to vascular-plant-dominated peatlands may occur , with a potential alteration in their C-sink function. To investigate how the main GHG fluxes (CO 2 and CH 4) are affected by a plant community change (shift from dominance of Sphagnum mosses to vascular plants, i.e., Molinia caerulea), a mesocosm experiment was set up. Gross primary production (GPP), ecosystem respiration (ER) and CH 4 emission models were used to estimate the annual C balance and global warming potential under both vegetation covers. While the ER and CH 4 emission models estimated an output of, respectively, 376 ± 108 and 7 ± 4 g C m −2 yr −1 in Sphagnum mesocosms, this reached 1018 ± 362 and 33 ± 8 g C m −2 yr −1 in mesocosms with Sphagnum rubellum and Molinia caerulea. Annual modeled GPP was estimated at −414±122 and −1273±482 g C m −2 yr −1 in Sphagnum and Sphagnum + Molinia plots, respectively, leading to an annual CO 2 and CH 4 budget of −30 g C m −2 yr −1 in Sphagnum plots and of −223 g C m −2 yr −1 in Sphagnum + Molinia ones (i.e., a C sink). Even if CH 4 emissions accounted for a small part of the gaseous C efflux (ca. 3 %), their global warming potential value makes both plant communities have a climate warming effect. The shift of vegetation from Sphagnum mosses to Molinia caerulea seems beneficial for C sequestra-tion at a gaseous level. However, roots and litter of Molinia caerulea could provide substrates for C emissions that were not taken into account in the short measurement period studied here.

Published
2019

50. CO<sub>2</sub> and CH<sub>4</sub> budgets and global warming potential modifications in <i>Sphagnum</i>-dominated peat mesocosms invaded by <i>Molinia caerulea</i>

Author

Leroy, Fabien, primary, Gogo, Sébastien, additional, Guimbaud, Christophe, additional, Bernard-Jannin, Léonard, additional, Yin, Xiaole, additional, Belot, Guillaume, additional, Shuguang, Wang, additional, and Laggoun-Défarge, Fatima, additional

Published
2019
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