Volume 5; Issue 3

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mSystems
Volume 5; Issue 3

mSystems

Volume 5; Issue 3

1

SARS-CoV-2 and ORF3a: Nonsynonymous Mutations, Functional Domains, and Viral Pathogenesis

Issa, Elio, Merhi, Georgi, Panossian, Balig, Salloum, Tamara, Tokajian, Sima, Gilbert, Jack A.

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Year:

2020

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PDF, 1.16 MB

2020

2

Isolation and Characterization of the Novel Phage JD032 and Global Transcriptomic Response during JD032 Infection of Clostridioides difficile Ribotype 078

Li, Tinghua, Zhang, Yan, Dong, Ke, Kuo, Chih-Jung, Li, Chong, Zhu, Yong-Qiang, Qin, Jinhong, Li, Qing-Tian, Chang, Yung-Fu, Guo, Xiaokui, Zhu, Yongzhang, Bordenstein, Seth

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2020

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PDF, 4.11 MB

2020

3

Phages Actively Challenge Niche Communities in Antarctic Soils

Bezuidt, Oliver K. I., Lebre, Pedro Humberto, Pierneef, Rian, LeÃ³n-Sobrino, Carlos, Adriaenssens, Evelien M., Cowan, Don A., Van de Peer, Yves, Makhalanyane, Thulani P., Flynn, Theodore M.

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2020

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PDF, 2.95 MB

2020

4

Automated Cell-Free Multiprotein Synthesis Facilitates the Identification of a Secretory, Oligopeptide Elicitor-Like, Immunoreactive Protein of the Oomycete Pythium insidiosum

Sae-Chew, Pattarana, Rujirawat, Thidarat, Kumsang, Yothin, Payattikul, Penpan, Lohnoo, Tassanee, Yingyong, Wanta, Jaturapaktrarak, Chalisa, Rotchanapreeda, Tiwa, Reamtong, Onrapak, Srisuk, Tanawut, Ki

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2020

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PDF, 2.96 MB

2020

5

Space Is More Important than Season when Shaping Soil Microbial Communities at a Large Spatial Scale

Zhang, Kaoping, Delgado-Baquerizo, Manuel, Zhu, Yong-Guan, Chu, Haiyan, Medema, Marnix

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2020

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PDF, 2.19 MB

2020

6

Recombinant HcGAPDH Protein Expressed on Probiotic Bacillus subtilis Spores Protects Sheep from Haemonchus contortus Infection by Inducing both Humoral and Cell-Mediated Responses

Yang, Yi, Zhang, Guiheng, Wu, Jie, Chen, Xueqiu, Tong, Danni, Yang, Yimin, Shi, Hengzhi, Yao, Chaoqun, Zhuang, Lenan, Wang, Jianbin, Du, Aifang, Bulman, Zackery

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2020

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PDF, 4.94 MB

2020

7

Continental-Scale Microbiome Study Reveals Different Environmental Characteristics Determining Microbial Richness, Composition, and Quantity in Hotel Rooms

Fu, Xi, Li, Yanling, Yuan, Qianqian, Cai, Gui-hong, Deng, Yiqun, Zhang, Xin, NorbÃ¤ck, Dan, Sun, Yu, Beiko, Robert G.

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2020

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PDF, 1.07 MB

2020

8

Emergence of mcr-9.1 in Extended-Spectrum-Î²-Lactamase-Producing Clinical Enterobacteriaceae in Pretoria, South Africa: Global Evolutionary Phylogenomics, Resistome, and Mobilome

Osei Sekyere, John, Maningi, Nontuthuko E., Modipane, Lesedi, Mbelle, Nontombi Marylucy, Greene, Casey S.

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2020

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PDF, 14.87 MB

2020

9

Combined RNAseq and ChIPseq Analyses of the BvgA Virulence Regulator of Bordetella pertussis

Coutte, LoÃ¯c, Antoine, Rudy, Slupek, Stephanie, Solans, Luis, Derop, Julien, Bonnefond, Amelie, Hot, David, Locht, Camille, Mandel, Mark J.

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2020

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PDF, 1.14 MB

2020

10

Administration of Exogenous Melatonin Improves the Diurnal Rhythms of the Gut Microbiota in Mice Fed a High-Fat Diet

Yin, Jie, Li, Yuying, Han, Hui, Ma, Jie, Liu, Gang, Wu, Xin, Huang, Xingguo, Fang, Rejun, Baba, Kenkichi, Bin, Peng, Zhu, Guoqiang, Ren, Wenkai, Tan, Bie, Tosini, Gianluca, He, Xi, Li, Tiejun, Yin, Yu

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2020

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PDF, 3.72 MB

2020

11

Mucosal Microbiota and Metabolome along the Intestinal Tract Reveal a Location-Specific Relationship

Yuan, Ce, Graham, Melanie, Staley, Christopher, Subramanian, Subbaya, Gibbons, Sean M.

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2020

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PDF, 989 KB

2020

12

The Killing Mechanism of Teixobactin against Methicillin-Resistant Staphylococcus aureus : an Untargeted Metabolomics Study

Hussein, Maytham, Karas, John A., Schneider-Futschik, Elena K., Chen, Fan, Swarbrick, James, Paulin, Olivia K. A., Hoyer, Daniel, Baker, Mark, Zhu, Yan, Li, Jian, Velkov, Tony, Lloyd, Karen G.

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2020

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PDF, 3.80 MB

2020

13

Predicting Phenotypic Polymyxin Resistance in Klebsiella pneumoniae through Machine Learning Analysis of Genomic Data

Macesic, Nenad, Bear Donât Walk, Oliver J., Peâer, Itsik, Tatonetti, Nicholas P., Peleg, Anton Y., Uhlemann, Anne-Catrin, Yang, Yu-Liang

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2020

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PDF, 1.46 MB

2020

14

PqsE Is Essential for RhlR-Dependent Quorum Sensing Regulation in Pseudomonas aeruginosa

Groleau, Marie-Christine, de Oliveira Pereira, Thays, Dekimpe, ValÃ©rie, DÃ©ziel, Eric, Shank, Elizabeth Anne

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2020

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PDF, 894 KB

2020

15

In Silico Analysis Highlights the Diversity and Novelty of Circular Bacteriocins in Sequenced Microbial Genomes

Xin, Bingyue, Liu, Hualin, Zheng, Jinshui, Xie, Chuanshuai, Gao, Ying, Dai, Dadong, Peng, Donghai, Ruan, Lifang, Chen, Huanchun, Sun, Ming, Methe, Barbara

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2020

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PDF, 3.23 MB

2020

16

Comparative Genomics and Metabolomics in the Genus Nocardia

MÃ¤nnle, Daniel, McKinnie, Shaun M. K., Mantri, Shrikant S., Steinke, Katharina, Lu, Zeyin, Moore, Bradley S., Ziemert, Nadine, Kaysser, Leonard, Savage, David F.

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2020

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PDF, 4.97 MB

2020

17

Increasing the Hindgut Carbohydrate/Protein Ratio by Cecal Infusion of Corn Starch or Casein Hydrolysate Drives Gut Microbiota-Related Bile Acid Metabolism To Stimulate Colonic Barrier Function

Pi, Yu, Mu, Chunlong, Gao, Kan, Liu, Zhuang, Peng, Yu, Zhu, Weiyun, Langille, Morgan G. I.

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Year:

2020

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PDF, 4.17 MB

2020

18

Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks

Arrieta-Ortiz, Mario L., Hafemeister, Christoph, Shuster, Bentley, Baliga, Nitin S., Bonneau, Richard, Eichenberger, Patrick, Typas, Athanasios

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2020

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PDF, 3.67 MB

2020

19

Plugging Small RNAs into the Network

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2020

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PDF, 217 KB

2020

20

Coexistence of Antibiotic Resistance Genes and Virulence Factors Deciphered by Large-Scale Complete Genome Analysis

Pan, Yu, Zeng, Jiaxiong, Li, Liguan, Yang, Jintao, Tang, Ziyun, Xiong, Wenguang, Li, Yafei, Chen, Sheng, Zeng, Zhenling, Gilbert, Jack A.

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2020

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PDF, 2.83 MB

2020

21

The Inactivation of Enzymes Belonging to the Central Carbon Metabolism Is a Novel Mechanism of Developing Antibiotic Resistance

Gil-Gil, Teresa, Corona, Fernando, MartÃnez, JosÃ© Luis, Bernardini, Alejandra, Marshall, Christopher W.

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2020

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PDF, 1.67 MB

2020

22

Spatial Compartmentalization of the Microbiome between the Lumen and Crypts Is Lost in the Murine Cecum following the Process of Surgery, Including Overnight Fasting and Exposure to Antibiotics

Zaborin, Alexander, Penalver Bernabe, Beatriz, Keskey, Robert, Sangwan, Naseer, Hyoju, Sanjiv, Gottel, Neil, Gilbert, Jack A., Zaborina, Olga, Alverdy, John C., Cotter, Paul D.

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2020

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PDF, 8.77 MB

2020

23

Cellular and Structural Basis of Synthesis of the Unique Intermediate Dehydro-F 420 -0 in Mycobacteria

Grinter, Rhys, Ney, Blair, Brammananth, Rajini, Barlow, Christopher K., Cordero, Paul R. F., Gillett, David L., IzorÃ©, Thierry, Cryle, Max J., Harold, Liam K., Cook, Gregory M., Taiaroa, George, Will

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2020

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PDF, 2.18 MB

2020

24

Roles of Organohalide-Respiring Dehalococcoidia in Carbon Cycling

Yang, Yi, Sanford, Robert, Yan, Jun, Chen, Gao, CÃ¡piro, Natalie L., Li, Xiuying, LÃ¶ffler, Frank E., Bouskill, Nick

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2020

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PDF, 736 KB

2020

25

Human Milk Oligosaccharides Modulate the Risk for Preterm Birth in a Microbiome-Dependent and -Independent Manner

Pausan, Manuela-Raluca, Kolovetsiou-Kreiner, Vassiliki, Richter, Gesa Lucia, Madl, Tobias, Giselbrecht, Elisabeth, Obermayer-Pietsch, Barbara, Weiss, Eva-Christine, Jantscher-Krenn, Evelyn, Moissl-Eic

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2020

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PDF, 4.97 MB

2020

26

Coupling Bacterial Community Assembly to Microbial Metabolism across Soil Profiles

Luan, Lu, Liang, Chao, Chen, Lijun, Wang, Haotian, Xu, Qinsong, Jiang, Yuji, Sun, Bo, Bouskill, Nick

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2020

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PDF, 4.62 MB

2020

27

Shifts in the Bacterial Population and Ecosystem Functions in Response to Vegetation in the Yellow River Delta Wetlands

Wang, Jianing, Wang, Jingjing, Zhang, Zheng, Li, Zhifeng, Zhang, Zhiguo, Zhao, Decun, Wang, Lidong, Lu, Feng, Li, Yue-zhong, Flynn, Theodore M.

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2020

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PDF, 2.64 MB

2020

28

Alteromonas Myovirus V22 Represents a New Genus of Marine Bacteriophages Requiring a Tail Fiber Chaperone for Host Recognition

Gonzalez-Serrano, Rafael, Dunne, Matthew, Rosselli, Riccardo, Martin-Cuadrado, Ana-Belen, Grosboillot, Virginie, Zinsli, LÃ©a V., Roda-Garcia, Juan J., Loessner, Martin J., Rodriguez-Valera, Francisco

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Year:

2020

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PDF, 3.57 MB

2020

29

Citrobacter Species Increase Energy Harvest by Modulating Intestinal Microbiota in Fish: Nondominant Species Play Important Functions

Zhang, Mei-Ling, Li, Miao, Sheng, Yi, Tan, Fang, Chen, Liqiao, Cann, Isaac, Du, Zhen-Yu, Rawls, John F.

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2020

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PDF, 1.68 MB

2020

30

Alterations in the Gut Microbiome in the Progression of Cirrhosis to Hepatocellular Carcinoma

Lapidot, Yelena, Amir, Amnon, Nosenko, Rita, Uzan-Yulzari, Atara, Veitsman, Ella, Cohen-Ezra, Oranit, Davidov, Yana, Weiss, Peretz, Bradichevski, Tanya, Segev, Shlomo, Koren, Omry, Safran, Michal, Ben

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2020

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PDF, 1.65 MB

2020

31

Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function

Niccum, Brittany A., Kastman, Erik K., Kfoury, Nicole, Robbat, Albert, Wolfe, Benjamin E., Cotter, Paul D.

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2020

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PDF, 2.92 MB

2020

32

Synthetic Symbiosis under Environmental Disturbances

Denton, Jai A., Gokhale, Chaitanya S., Del Vecchio, Domitilla

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2020

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PDF, 3.39 MB

2020

33

Differential Ecosystem Function Stability of Ammonia-Oxidizing Archaea and Bacteria following Short-Term Environmental Perturbation

Zhao, Jun, Meng, Yiyu, Drewer, Julia, Skiba, Ute M., Prosser, James I., Gubry-Rangin, CÃ©cile, Neufeld, Josh D.

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Year:

2020

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PDF, 2.28 MB

2020

34

Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean

Aylward, Frank O., Santoro, Alyson E., Bouskill, Nick

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2020

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PDF, 3.54 MB

2020

35

Initial Mapping of the New York City Wastewater Virome

Gulino, K., Rahman, J., Badri, M., Morton, J., Bonneau, R., Ghedin, E., Gilbert, Jack A.

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Year:

2020

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PDF, 1.92 MB

2020

36

High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy

Raghuvanshi, Ruma, Vasco, Karla, VÃ¡zquez-Baeza, Yoshiki, Jiang, Lingjing, Morton, James T., Li, Danxun, Gonzalez, Antonio, DeRight Goldasich, Lindsay, Humphrey, Gregory, Ackermann, Gail, Swafford, Au

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Year:

2020

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PDF, 1.47 MB

2020

37

Stool Samples of Acute Diarrhea Inpatients as a Reservoir of ST11 Hypervirulent KPC-2-Producing Klebsiella pneumoniae

Zheng, Beiwen, Xu, Hao, Lv, Tao, Guo, Lihua, Xiao, Yu, Huang, Chen, Zhang, Shuntian, Chen, Yunbo, Han, Huiming, Shen, Ping, Xiao, Yonghong, Li, Lanjuan, Baranzini, Sergio

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2020

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PDF, 3.96 MB

2020

38

Advantages and Limits of Metagenomic Assembly and Binning of a Giant Virus

Schulz, Frederik, Andreani, Julien, Francis, Rania, Boudjemaa, Hadjer, Bou Khalil, Jacques Yaacoub, Lee, Janey, La Scola, Bernard, Woyke, Tanja, Cristea, Ileana M.

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2020

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PDF, 1.14 MB

2020

39

Soil Carbon, Nitrogen, and Phosphorus Cycling Microbial Populations and Their Resistance to Global Change Depend on Soil C:N:P Stoichiometry

Luo, Gongwen, Xue, Chao, Jiang, Qianhong, Xiao, Yan, Zhang, Fengge, Guo, Shiwei, Shen, Qirong, Ling, Ning, Stegen, James C.

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2020

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PDF, 5.84 MB

2020

40

Viral Ecogenomics of Arctic Cryopeg Brine and Sea Ice

Zhong, Zhi-Ping, Rapp, Josephine Z., Wainaina, James M., Solonenko, Natalie E., Maughan, Heather, Carpenter, Shelly D., Cooper, Zachary S., Jang, Ho Bin, Bolduc, Benjamin, Deming, Jody W., Sullivan, M

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2020

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PDF, 2.92 MB

2020

41

Metabolomics and Machine Learning Approaches Combined in Pursuit for More Accurate Paracoccidioidomycosis Diagnoses

Lima, Estela de Oliveira, Navarro, Luiz Claudio, Morishita, Karen Noda, Kamikawa, Camila Mika, Rodrigues, Rafael Gustavo Martins, Dabaja, Mohamed Ziad, de Oliveira, Diogo Noin, Delafiori, Jeany, Dias-

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2020

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PDF, 2.11 MB

2020

42

Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture

Villa, Max M., Bloom, Rachael J., Silverman, Justin D., Durand, Heather K., Jiang, Sharon, Wu, Anchi, Dallow, Eric P., Huang, Shuqiang, You, Lingchong, David, Lawrence A., Thaiss, Christoph A.

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2020

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PDF, 3.08 MB

2020

43

Master Sculptor at Work: Enteropathogenic Escherichia coli Infection Uniquely Modifies Mitochondrial Proteolysis during Its Control of Human Cell Death

Marshall, Natalie C., Thejoe, Maichael, Klein, Theo, Serapio-Palacios, Antonio, Santos, Andrew S., von Krosigk, Niklas, Kizhakkedathu, Jayachandran N., Stoynov, Nikolay, Foster, Leonard J., Overall, C

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2020

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PDF, 5.65 MB

2020

44

Plant Hosts Modify Belowground Microbial Community Response to Extreme Drought

Veach, Allison M., Chen, Huaihai, Yang, Zamin K., Labbe, Audrey D., Engle, Nancy L., Tschaplinski, Timothy J., Schadt, Christopher W., Cregger, Melissa A., Mackelprang, Rachel

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Year:

2020

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PDF, 1.97 MB

2020

45

Impact of the Novel Prophage ÏSA169 on Persistent Methicillin-Resistant Staphylococcus aureus Endovascular Infection

Li, Liang, Wang, Genzhu, Li, Yi, Francois, Patrice, Bayer, Arnold S., Chen, Liang, Seidl, Kati, Cheung, Ambrose, Xiong, Yan Q., Byndloss, Mariana X.

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Year:

2020

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PDF, 1.06 MB

2020

46

Secondary Metabolism in the Gill Microbiota of Shipworms (Teredinidae) as Revealed by Comparison of Metagenomes and Nearly Complete Symbiont Genomes

Altamia, Marvin A., Lin, Zhenjian, Trindade-Silva, Amaro E., Uy, Iris Diana, Shipway, J. Reuben, Wilke, Diego Veras, Concepcion, Gisela P., Distel, Daniel L., Schmidt, Eric W., Haygood, Margo G., Pete

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Year:

2020

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PDF, 3.53 MB

2020

47

Siderophore-Mediated Interactions Determine the Disease Suppressiveness of Microbial Consortia

Gu, Shaohua, Yang, Tianjie, Shao, Zhengying, Wang, Tao, Cao, Kehao, Jousset, Alexandre, Friman, Ville-Petri, Mallon, Cyrus, Mei, Xinlan, Wei, Zhong, Xu, Yangchun, Shen, Qirong, Pommier, Thomas, Collin

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2020

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PDF, 1.49 MB

2020

48

High-Throughput Stool Metaproteomics: Method and Application to Human Specimens

Gonzalez, Carlos G., Wastyk, Hannah C., Topf, Madeline, Gardner, Christopher D., Sonnenburg, Justin L., Elias, Joshua E., Dorrestein, Pieter C.

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Year:

2020

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PDF, 3.19 MB

2020

49

Characterizing the Mechanism of Action of an Ancient Antimicrobial, Manuka Honey, against Pseudomonas aeruginosa Using Modern Transcriptomics

Bouzo, Daniel, Cokcetin, Nural N., Li, Liping, Ballerin, Giulia, Bottomley, Amy L., Lazenby, James, Whitchurch, Cynthia B., Paulsen, Ian T., Hassan, Karl A., Harry, Elizabeth J., Van Laar, Tricia A.

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Year:

2020

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PDF, 4.17 MB

2020

50

Genetic Variation Bias toward Noncoding Regions and Secreted Proteins in the Rice Blast Fungus Magnaporthe oryzae

Zhong, Zhenhui, Chen, Meilian, Lin, Lianyu, Chen, Ruiqi, Liu, Dan, Norvienyeku, Justice, Zheng, Huakun, Wang, Zonghua, Heck, Michelle

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Year:

2020

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PDF, 697 KB

2020

51

Reply to McDonald, âProtections against the Risk of Airborne SARS-CoV-2 Infectionâ

Dietz, Leslie, Horve, Patrick F., Coil, David A., Fretz, Mark, Eisen, Jonathan A., Van Den Wymelenberg, Kevin

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2020

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PDF, 227 KB

2020

52

Nitrogen Source Governs Community Carbon Metabolism in a Model Hypersaline Benthic Phototrophic Biofilm

Anderton, Christopher R., Mobberley, Jennifer M., Cole, Jessica K., Nunez, Jamie R., Starke, Robert, Boaro, Amy A., Yesiltepe, Yasemin, Morton, Beau R., Cory, Alexandra B., Cardamone, Hayley C., Hofmo

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2020

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PDF, 1.84 MB

2020

53

GapMind: Automated Annotation of Amino Acid Biosynthesis

Price, Morgan N., Deutschbauer, Adam M., Arkin, Adam P., Hallam, Steven J.

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Year:

2020

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PDF, 2.06 MB

2020

54

The Gut Microbiota Communities of Wild Arboreal and Ground-Feeding Tropical Primates Are Affected Differently by Habitat Disturbance

Barelli, Claudia, Albanese, Davide, Stumpf, Rebecca M., Asangba, Abigail, Donati, Claudio, Rovero, Francesco, Hauffe, Heidi C., Sharpton, Thomas J.

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2020

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PDF, 2.42 MB

2020

55

Emergence of Metabolite Provisioning as a By-Product of Evolved Biological Functions

Gude, Sebastian, Pherribo, Gordon J., Taga, Michiko E., Wolfe, Benjamin E.

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2020

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PDF, 1.17 MB

2020

56

SynBio and the Boundaries between Functional and Pathogenic RepA-WH1 Bacterial Amyloids

Giraldo, Rafael, Bernstein, Hans C.

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2020

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PDF, 1.01 MB

2020

57

Biofilm Structure Promotes Coexistence of Phage-Resistant and Phage-Susceptible Bacteria

Simmons, Emilia L., Bond, Matthew C., Koskella, Britt, Drescher, Knut, Bucci, Vanni, Nadell, Carey D., Bordenstein, Seth

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Year:

2020

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PDF, 2.18 MB

2020