An exciting future for microbial molecular biology and physiology

被引:0
作者
Bridges, Andrew A. [1 ]
Guthrie, Leah [2 ]
Lehman, McKenzie [3 ]
Kellogg, Elizabeth H. [4 ]
Miranda, Samantha Wellington [5 ]
Pountain, Andrew [6 ]
Shiver, Anthony L. [7 ]
Varble, Andrew [8 ]
Kaplan, Heidi B. [6 ]
Shank, Elizabeth A. [9 ]
Storz, Gisela [10 ]
机构
[1] Carnegie Mellon Univ, Biol Sci, Pittsburgh, PA USA
[2] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA USA
[3] Univ Nebraska, Coll Med, Dept Pathol Microbiol & Immunol, Omaha, NE USA
[4] St Jude Childrens Res Hosp, Dept Struct Biol, Memphis, TN USA
[5] Univ Washington, Dept Microbiol, Seattle, WA USA
[6] Univ Texas Hlth Sci Ctr Houston, McGovern Med Sch, Dept Microbiol & Mol Genet, Houston, TX USA
[7] Stanford Univ, Dept Bioengn, Stanford, CA USA
[8] Univ Rochester, Med Ctr, Dept Microbiol & Immunol, Rochester, NY USA
[9] Univ Massachusetts, Dept Syst Biol, Chan Med Sch, Worcester, MA USA
[10] Eunice Kennedy Shriver Natl Inst Child Hlth & Huma, Div Mol & Cellular Biol, Bethesda, MD 20817 USA
来源
基金
美国国家卫生研究院;
关键词
multi-omic data; genome-scale mutagenesis; non-model microbes; microbial communities; single-cell sequencing; single-cell microscopy; macromolecular structures; HIGH-THROUGHPUT; ESCHERICHIA-COLI; GENETIC-DETERMINANTS; CRISPR; CONSTRUCTION; METABOLOMICS; EXPRESSION; LIBRARIES; GRIDS;
D O I
10.1128/mbio.00694-25
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
Continuous advances in technologies ranging from deep sequencing and genetic manipulation to mass spectrometry, single cell imaging, and structural biology have led to previously unimaginable advances in our understanding of microbial physiology and the molecular mechanisms underlying microbial responses in a multitude of environments. Simultaneously, these advances are revealing how much more there is to learn. At the 2024 virtual retreat of the Molecular Biology and Physiology (MBP) Community of the Council on Microbial Sciences (COMS) of the American Society for Microbiology (ASM), eight early-career investigators, along with retreat attendees, discussed some of these astounding advances, as well as the challenges and opportunities the developments raise. Motivated by these discussions, we review the state-of-the-art in molecular microbiology and provide an outlook on this field. Our hope is that the topics discussed here can serve as an inspiration for the development of future technologies, resources, and guidelines and for the training of the next generation of microbiologists.
引用
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页数:20
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共 170 条
[1]   Bacterial Quorum Sensing and Microbial Community Interactions [J].
Abisado, Rhea G. ;
Benomar, Saida ;
Klaus, Jennifer R. ;
Dandekar, Ajai A. ;
Chandler, Josephine R. .
MBIO, 2018, 9 (03)
[2]   Batch Production of High-Quality Graphene Grids for Cryo-EM: Cryo-EM Structure of Methylococcus capsulatus Soluble Methane Monooxygenase Hydroxylase [J].
Ahn, Eungjin ;
Kim, Byungchul ;
Park, Soyoung ;
Erwin, Amanda L. ;
Sung, Suk Hyun ;
Hovden, Robert ;
Mosalaganti, Shyamal ;
Cho, Uhn-Soo .
ACS NANO, 2023, 17 (06) :6011-6022
[3]   Super-resolution fluorescence microscopy for investigating bacterial cell biology [J].
Alexander, Carsten ;
Wolters, Manuel ;
Aepfelbacher, Martin .
MOLECULAR MICROBIOLOGY, 2024, 121 (04) :646-658
[4]   Rapid curation of gene disruption collections using Knockout Sudoku [J].
Anzai, Isao A. ;
Shaket, Lev ;
Adesina, Oluwakemi ;
Baym, Michael ;
Barstow, Buz .
NATURE PROTOCOLS, 2017, 12 (10) :2110-2137
[5]   Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits [J].
Ardalani, O. ;
Phaneuf, P. V. ;
Mohite, O. S. ;
Nielsen, L. K. ;
Palsson, B. O. .
MSYSTEMS, 2024, 9 (07)
[6]   Poly-omic risk scores predict inflammatory bowel disease diagnosis [J].
Arehart, Christopher H. ;
Sterrett, John D. ;
Garris, Rosanna L. ;
Quispe-Pilco, Ruth E. ;
Gignoux, Christopher R. ;
Evans, Luke M. ;
Stanislawski, Maggie A. .
MSYSTEMS, 2024, 9 (01)
[7]   Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron [J].
Arjes, Heidi A. ;
Sun, Jiawei ;
Liu, Hualan ;
Nguyen, Taylor H. ;
Culver, Rebecca N. ;
Celis, Arianna I. ;
Walton, Sophie Jean ;
Vasquez, Kimberly S. ;
Yu, Feiqiao Brian ;
Xue, Katherine S. S. ;
Newton, Daniel ;
Zermeno, Ricardo ;
Weglarz, Meredith ;
Deutschbauer, Adam ;
Huang, Kerwyn Casey ;
Shiver, Anthony L. .
BMC BIOLOGY, 2022, 20 (01)
[8]   KBase: The United States Department of Energy Systems Biology Knowledgebase [J].
Arkin, Adam P. ;
Cottingham, Robert W. ;
Henry, Christopher S. ;
Harris, Nomi L. ;
Stevens, Rick L. ;
Maslov, Sergei ;
Dehal, Paramvir ;
Ware, Doreen ;
Perez, Fernando ;
Canon, Shane ;
Sneddon, Michael W. ;
Henderson, Matthew L. ;
Riehl, William J. ;
Murphy-Olson, Dan ;
Chan, Stephen Y. ;
Kamimura, Roy T. ;
Kumari, Sunita ;
Drake, Meghan M. ;
Brettin, Thomas S. ;
Glass, Elizabeth M. ;
Chivian, Dylan ;
Gunter, Dan ;
Weston, David J. ;
Allen, Benjamin H. ;
Baumohl, Jason ;
Best, Aaron A. ;
Bowen, Ben ;
Brenner, Steven E. ;
Bun, Christopher C. ;
Chandonia, John-Marc ;
Chia, Jer-Ming ;
Colasanti, Ric ;
Conrad, Neal ;
Davis, James J. ;
Davison, Brian H. ;
DeJongh, Matthew ;
Devoid, Scott ;
Dietrich, Emily ;
Dubchak, Inna ;
Edirisinghe, Janaka N. ;
Fang, Gang ;
Faria, Jose P. ;
Frybarger, Paul M. ;
Gerlach, Wolfgang ;
Gerstein, Mark ;
Greiner, Annette ;
Gurtowski, James ;
Haun, Holly L. ;
He, Fei ;
Jain, Rashmi .
NATURE BIOTECHNOLOGY, 2018, 36 (07) :566-569
[9]   Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants:: the Keio collection [J].
Baba, Tomoya ;
Ara, Takeshi ;
Hasegawa, Miki ;
Takai, Yuki ;
Okumura, Yoshiko ;
Baba, Miki ;
Datsenko, Kirill A. ;
Tomita, Masaru ;
Wanner, Barry L. ;
Mori, Hirotada .
MOLECULAR SYSTEMS BIOLOGY, 2006, 2 (1) :2006.0008
[10]   Accurate prediction of protein structures and interactions using a three-track neural network [J].
Baek, Minkyung ;
DiMaio, Frank ;
Anishchenko, Ivan ;
Dauparas, Justas ;
Ovchinnikov, Sergey ;
Lee, Gyu Rie ;
Wang, Jue ;
Cong, Qian ;
Kinch, Lisa N. ;
Schaeffer, R. Dustin ;
Millan, Claudia ;
Park, Hahnbeom ;
Adams, Carson ;
Glassman, Caleb R. ;
DeGiovanni, Andy ;
Pereira, Jose H. ;
Rodrigues, Andria V. ;
van Dijk, Alberdina A. ;
Ebrecht, Ana C. ;
Opperman, Diederik J. ;
Sagmeister, Theo ;
Buhlheller, Christoph ;
Pavkov-Keller, Tea ;
Rathinaswamy, Manoj K. ;
Dalwadi, Udit ;
Yip, Calvin K. ;
Burke, John E. ;
Garcia, K. Christopher ;
Grishin, Nick V. ;
Adams, Paul D. ;
Read, Randy J. ;
Baker, David .
SCIENCE, 2021, 373 (6557) :871-+