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Alivisatos AP, Blaser MJ, Brodie EL, Chun M, Dangl JL, Donohue TJ, Dorrestein PC, Gilbert JA, Green JL, Jansson JK, Knight R, Maxon ME, McFall-Ngai MJ, Miller JF, Pollard KS, Ruby EG, Taha SA. MICROBIOME. A unified initiative to harness Earth's microbiomes. Science 2015; 350:507-8. [PMID: 26511287 DOI: 10.1126/science.aac8480] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- A P Alivisatos
- See the supplementary materials for authors' affiliations
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2
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Lynch SV, Dixon L, Benoit MR, Brodie EL, Keyhan M, Hu P, Ackerley DF, Andersen GL, Matin A. Role of the rapA gene in controlling antibiotic resistance of Escherichia coli biofilms. Antimicrob Agents Chemother 2007; 51:3650-8. [PMID: 17664315 PMCID: PMC2043260 DOI: 10.1128/aac.00601-07] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
By using a high-throughput screening method, a mutant of a uropathogenic Escherichia coli strain affected in the rapA gene was isolated. The mutant formed normal-architecture biofilms but showed decreased penicillin G resistance, although the mutation did not affect planktonic cell resistance. Transcriptome analysis showed that 22 genes were down-regulated in the mutant biofilm. One of these genes was yhcQ, which encodes a putative multidrug resistance pump. Mutants with mutations in this gene also formed biofilms with decreased resistance, although the effect was less pronounced than that of the rapA mutation. Thus, an additional mechanism(s) controlled by a rapA-regulated gene(s) was involved in wild-type biofilm resistance. The search for this mechanism was guided by the fact that another down-regulated gene in rapA biofilms, yeeZ, is suspected to be involved in extra cell wall-related functions. A comparison of the biofilm matrix of the wild-type and rapA strains revealed decreased polysaccharide quantities and coverage in the mutant biofilms. Furthermore, the (fluorescent) functional penicillin G homologue Bocillin FL penetrated the mutant biofilms more readily. The results strongly suggest a dual mechanism for the wild-type biofilm penicillin G resistance, retarded penetration, and effective efflux. The results of studies with an E. coli K-12 strain pointed to the same conclusion. Since efflux and penetration can be general resistance mechanisms, tests were conducted with other antibiotics. The rapA biofilm was also more sensitive to norfloxacin, chloramphenicol, and gentamicin.
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Affiliation(s)
- S V Lynch
- Department of Microbiology and Immunology, Sherman Fairchild Science Building, Stanford University School of Medicine, Stanford, CA 94305-5124, USA
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Flanagan JL, Brodie EL, Weng L, Lynch SV, Garcia O, Brown R, Hugenholtz P, DeSantis TZ, Andersen GL, Wiener-Kronish JP, Bristow J. Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. J Clin Microbiol 2007; 45:1954-62. [PMID: 17409203 PMCID: PMC1933106 DOI: 10.1128/jcm.02187-06] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Management of airway infections caused by Pseudomonas aeruginosa is a serious clinical challenge, but little is known about the microbial ecology of airway infections in intubated patients. We analyzed bacterial diversity in endotracheal aspirates obtained from intubated patients colonized by P. aeruginosa by using 16S rRNA clone libraries and microarrays (PhyloChip) to determine changes in bacterial community compositions during antibiotic treatment. Bacterial 16S rRNA genes were absent from aspirates obtained from patients briefly intubated for elective surgery but were detected by PCR in samples from all patients intubated for longer periods. Sequencing of 16S rRNA clone libraries demonstrated the presence of many orally, nasally, and gastrointestinally associated bacteria, including known pathogens, in the lungs of patients colonized with P. aeruginosa. PhyloChip analysis detected the same organisms and many additional bacterial groups present at low abundance that were not detected in clone libraries. For each patient, both culture-independent methods showed that bacterial diversity decreased following the administration of antibiotics, and communities became dominated by a pulmonary pathogen. P. aeruginosa became the dominant species in six of seven patients studied, despite treatment of five of these six with antibiotics to which it was sensitive in vitro. Our data demonstrate that the loss of bacterial diversity under antibiotic selection is highly associated with the development of pneumonia in ventilated patients colonized with P. aeruginosa. Interestingly, PhyloChip analysis demonstrated reciprocal changes in abundance between P. aeruginosa and the class Bacilli, suggesting that these groups may compete for a similar ecological niche and suggesting possible mechanisms through which the loss of microbial diversity may directly contribute to pathogen selection and persistence.
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Affiliation(s)
- J L Flanagan
- Department of Anesthesia and Perioperative, University of California, San Francisco, CA, USA
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DeSantis TZ, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 2006; 34:W394-9. [PMID: 16845035 PMCID: PMC1538769 DOI: 10.1093/nar/gkl244] [Citation(s) in RCA: 711] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Microbiologists conducting surveys of bacterial and archaeal diversity often require comparative alignments of thousands of 16S rRNA genes collected from a sample. The computational resources and bioinformatics expertise required to construct such an alignment has inhibited high-throughput analysis. It was hypothesized that an online tool could be developed to efficiently align thousands of 16S rRNA genes via the NAST (Nearest Alignment Space Termination) algorithm for creating multiple sequence alignments (MSA). The tool was implemented with a web-interface at http://greengenes.lbl.gov/NAST. Each user-submitted sequence is compared with Greengenes' 'Core Set', comprising approximately 10,000 aligned non-chimeric sequences representative of the currently recognized diversity among bacteria and archaea. User sequences are oriented and paired with their closest match in the Core Set to serve as a template for inserting gap characters. Non-16S data (sequence from vector or surrounding genomic regions) are conveniently removed in the returned alignment. From the resulting MSA, distance matrices can be calculated for diversity estimates and organisms can be classified by taxonomy. The ability to align and categorize large sequence sets using a simple interface has enabled researchers with various experience levels to obtain bacterial and archaeal community profiles.
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Affiliation(s)
- T. Z. DeSantis
- Lawrence Berkeley National Laboratory, Center for Environmental BiotechnologyBerkeley, CA, USA
- Lawrence Berkeley National Laboratory, Virtual Institute for Microbial Stress and SurvivalBerkeley, CA, USA
- To whom correspondence should be addressed.
| | - P. Hugenholtz
- DOE Joint Genome Institute, Microbial Ecology ProgramWalnut Creek, CA, USA
| | - K. Keller
- Lawrence Berkeley National Laboratory, Virtual Institute for Microbial Stress and SurvivalBerkeley, CA, USA
- University of California, Quantitative Biomedical ResearchBerkeley, CA, USA
| | - E. L. Brodie
- Lawrence Berkeley National Laboratory, Center for Environmental BiotechnologyBerkeley, CA, USA
| | - N. Larsen
- Danish Genome InstituteAarhus, Denmark
| | - Y. M. Piceno
- Lawrence Berkeley National Laboratory, Center for Environmental BiotechnologyBerkeley, CA, USA
| | - R. Phan
- Lawrence Berkeley National Laboratory, Center for Environmental BiotechnologyBerkeley, CA, USA
- Lawrence Berkeley National Laboratory, Virtual Institute for Microbial Stress and SurvivalBerkeley, CA, USA
| | - G. L. Andersen
- Lawrence Berkeley National Laboratory, Center for Environmental BiotechnologyBerkeley, CA, USA
- Lawrence Berkeley National Laboratory, Virtual Institute for Microbial Stress and SurvivalBerkeley, CA, USA
- To whom correspondence should be addressed.
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DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006; 72:5069-72. [PMID: 16820507 PMCID: PMC1489311 DOI: 10.1128/aem.03006-05] [Citation(s) in RCA: 7193] [Impact Index Per Article: 399.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Accepted: 04/15/2006] [Indexed: 02/06/2023] Open
Abstract
A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.
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Affiliation(s)
- T Z DeSantis
- Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, CA 94720, USA
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DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006. [PMID: 16820507 DOI: 10.1128/aem.03006-05/asset/a1c681b7-c257-4c7c-8c7a-7f0a00dbed55/assets/graphic/zam0070668890002.jpeg] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.
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Affiliation(s)
- T Z DeSantis
- Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, CA 94720, USA
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7
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DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB. Appl Environ Microbiol 2006. [DOI: '10.1128/aem.03006-05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
Abstract
ABSTRACT
A 16S rRNA gene database (
http://greengenes.lbl.gov
) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the
Archaea
and
Bacteria
.
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Affiliation(s)
- T. Z. DeSantis
- Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, California 94720
| | - P. Hugenholtz
- Microbial Ecology Program, DOE Joint Genome Institute, 2800 Mitchell Drive, Bldg. 400-404, Walnut Creek, California 94598
| | - N. Larsen
- Danish Genome Institute, Gustav Wieds vej 10 C, DK-8000 Aarhus C, Denmark
| | - M. Rojas
- Department of Bioinformatics, Baylor University, P.O. Box 97356, 1311 S. 5th St., Waco, Texas 76798-7356
| | - E. L. Brodie
- Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, California 94720
| | - K. Keller
- Department of Bioengineering, University of California, Berkeley, California 94720
| | - T. Huber
- Departments of Biochemistry and Mathematics, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - D. Dalevi
- Department of Computer Science, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - P. Hu
- Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, California 94720
| | - G. L. Andersen
- Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, California 94720
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Abstract
ABSTRACT
Life on Earth evolved in the presence of gravity, and thus it is of interest from the perspective of space exploration to determine if diminished gravity affects biological processes. Cultivation of
Escherichia coli
under low-shear simulated microgravity (SMG) conditions resulted in enhanced stress resistance in both exponential- and stationary-phase cells, making the latter superresistant. Given that microgravity of space and SMG also compromise human immune response, this phenomenon constitutes a potential threat to astronauts. As low-shear environments are encountered by pathogens on Earth as well, SMG-conferred resistance is also relevant to controlling infectious disease on this planet. The SMG effect resembles the general stress response on Earth, which makes bacteria resistant to multiple stresses; this response is σ
s
dependent, irrespective of the growth phase. However, SMG-induced increased resistance was dependent on σ
s
only in stationary phase, being independent of this sigma factor in exponential phase. σ
s
concentration was some 30% lower in exponential-phase SMG cells than in normal gravity cells but was twofold higher in stationary-phase SMG cells. While SMG affected σ
s
synthesis at all levels of control, the main reasons for the differential effect of this gravity condition on σ
s
levels were that it rendered the sigma protein less stable in exponential phase and increased
rpoS
mRNA translational efficiency. Since σ
s
regulatory processes are influenced by mRNA and protein-folding patterns, the data suggest that SMG may affect these configurations.
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Affiliation(s)
- S V Lynch
- Department of Microbiology and Immunology, D317 Sherman Fairchild Science Building, Stanford University School of Medicine, 299 Campus Dr., Stanford, CA 94305, USA
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