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Xu W, Brand VR, Suresh S, Jensen MA, Davis RW, Criddle CS, St Onge RP, Hyman RW. Community members in activated sludge as determined by molecular probe technology. WATER RESEARCH 2020; 168:115104. [PMID: 31639592 PMCID: PMC6873225 DOI: 10.1016/j.watres.2019.115104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 09/13/2019] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
The use of molecular probe technology is demonstrated for routine identification and tracking of cultured and uncultured microorganisms in an activated sludge bioreactor treating domestic wastewater. A key advantage of molecular probe technology is that it can interrogate hundreds of microbial species of interest in a single measurement. In environmental niches where a single genus (such as Competibacteraceae) dominates, it can be difficult and expensive to identify microorganisms that are present at low relative abundance. With molecular probe technology, it is straightforward. Members of the Competibacteraceae family, none of which have been grown in pure culture, are abundant in an activated sludge system in the San Francisco Bay Area, California, USA. Molecular probe ensembles with and without Competibacteraceae probes were constructed. Whereas the probe ensemble with Competibacteraceae probes identified a total of ten bacteria, the molecular probe ensemble without Competibacteraceae probes identified 29 bacteria, including many at low relative abundance and including some species of public health significance.
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Affiliation(s)
- Weihong Xu
- Stanford Genome Technology Center, Palo Alto, CA, 94304, USA; Precision Medicine Institute, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Veronica R Brand
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Sundari Suresh
- Stanford Genome Technology Center, Palo Alto, CA, 94304, USA
| | | | - Ronald W Davis
- Stanford Genome Technology Center, Palo Alto, CA, 94304, USA; Department of Biochemistry, Stanford University Medical College, Stanford, CA, 94305, USA; Department of Genetics, Stanford University Medical College, Stanford, CA, 94305, USA
| | - Craig S Criddle
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Robert P St Onge
- Stanford Genome Technology Center, Palo Alto, CA, 94304, USA; Department of Biochemistry, Stanford University Medical College, Stanford, CA, 94305, USA
| | - Richard W Hyman
- Stanford Genome Technology Center, Palo Alto, CA, 94304, USA; Department of Biochemistry, Stanford University Medical College, Stanford, CA, 94305, USA.
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Smith JD, Schlecht U, Xu W, Suresh S, Horecka J, Proctor MJ, Aiyar RS, Bennett RAO, Chu A, Li YF, Roy K, Davis RW, Steinmetz LM, Hyman RW, Levy SF, St Onge RP. A method for high-throughput production of sequence-verified DNA libraries and strain collections. Mol Syst Biol 2017; 13:913. [PMID: 28193641 PMCID: PMC5327727 DOI: 10.15252/msb.20167233] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The low costs of array‐synthesized oligonucleotide libraries are empowering rapid advances in quantitative and synthetic biology. However, high synthesis error rates, uneven representation, and lack of access to individual oligonucleotides limit the true potential of these libraries. We have developed a cost‐effective method called Recombinase Directed Indexing (REDI), which involves integration of a complex library into yeast, site‐specific recombination to index library DNA, and next‐generation sequencing to identify desired clones. We used REDI to generate a library of ~3,300 DNA probes that exhibited > 96% purity and remarkable uniformity (> 95% of probes within twofold of the median abundance). Additionally, we created a collection of ~9,000 individually accessible CRISPR interference yeast strains for > 99% of genes required for either fermentative or respiratory growth, demonstrating the utility of REDI for rapid and cost‐effective creation of strain collections from oligonucleotide pools. Our approach is adaptable to any complex DNA library, and fundamentally changes how these libraries can be parsed, maintained, propagated, and characterized.
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Affiliation(s)
- Justin D Smith
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ulrich Schlecht
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Weihong Xu
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - Sundari Suresh
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Joe Horecka
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael J Proctor
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Raeka S Aiyar
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Richard A O Bennett
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.,Department of Biochemistry and Cellular Biology, Stony Brook University, Stony Brook, NY, USA
| | - Angela Chu
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Yong Fuga Li
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Kevin Roy
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ronald W Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Richard W Hyman
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Sasha F Levy
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.,Department of Biochemistry and Cellular Biology, Stony Brook University, Stony Brook, NY, USA
| | - Robert P St Onge
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA .,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
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Chen H, Liu C, Chen D, Madrid K, Peng S, Dong X, Zhang M, Gu Y. Bacteria-Targeting Conjugates Based on Antimicrobial Peptide for Bacteria Diagnosis and Therapy. Mol Pharm 2015; 12:2505-16. [DOI: 10.1021/acs.molpharmaceut.5b00053] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Haiyan Chen
- Department of Biomedical Engineering, School of Engineering, State Key Laboratory of Natural Medicines, and ‡School of Pharmacy, China Pharmaceutical University, 24 Tongjia Lane, Gulou
District, Nanjing 210009, China
| | - Cuicui Liu
- Department of Biomedical Engineering, School of Engineering, State Key Laboratory of Natural Medicines, and ‡School of Pharmacy, China Pharmaceutical University, 24 Tongjia Lane, Gulou
District, Nanjing 210009, China
| | - Dan Chen
- Department of Biomedical Engineering, School of Engineering, State Key Laboratory of Natural Medicines, and ‡School of Pharmacy, China Pharmaceutical University, 24 Tongjia Lane, Gulou
District, Nanjing 210009, China
| | - Kyle Madrid
- Department of Chemistry, University of California, 900 University Avenue, Riverside, California 92521, United States
| | - Shuwen Peng
- Department of Biomedical Engineering, School of Engineering, State Key Laboratory of Natural Medicines, and ‡School of Pharmacy, China Pharmaceutical University, 24 Tongjia Lane, Gulou
District, Nanjing 210009, China
| | | | - Min Zhang
- Department of Biomedical Engineering, School of Engineering, State Key Laboratory of Natural Medicines, and ‡School of Pharmacy, China Pharmaceutical University, 24 Tongjia Lane, Gulou
District, Nanjing 210009, China
| | - Yueqing Gu
- Department of Biomedical Engineering, School of Engineering, State Key Laboratory of Natural Medicines, and ‡School of Pharmacy, China Pharmaceutical University, 24 Tongjia Lane, Gulou
District, Nanjing 210009, China
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