Abstract:
:Chronic lung infections in cystic fibrosis (CF) could be treated more effectively if the effects of antimicrobials on pathogens in situ were known. Here, we compared changes in the microbial community composition and pathogen growth rates in longitudinal studies of seven pediatric CF patients undergoing intravenous antibiotic administration during pulmonary exacerbations. The microbial community composition was determined by counting rRNA with NanoString DNA analysis, and growth rates were obtained by incubating CF sputum with heavy water and tracing incorporation of deuterium into two branched-chain ("anteiso") fatty acids (a-C15:0 and a-C17:0) using gas chromatography-mass spectrometry (GC/MS). Prior to this study, both lipids were thought to be specific for Staphylococcaceae; hence, their isotopic enrichment was interpreted as a growth proxy for Staphylococcus aureus Our experiments revealed, however, that Prevotella is also a relevant microbial producer of a-C17:0 fatty acid in some CF patients; thus, deuterium incorporation into these lipids is better interpreted as a more general pathogen growth rate proxy. Even accounting for a small nonmicrobial background source detected in some patient samples, a-C15:0 fatty acid still appears to be a relatively robust proxy for CF pathogens, revealing a median generation time of ∼1.5 days, similar to prior observations. Contrary to our expectation, pathogen growth rates remained relatively stable throughout exacerbation treatment. We suggest two straightforward "best practices" for application of stable-isotope probing to CF sputum metabolites: (i) parallel determination of microbial community composition in CF sputum using culture-independent tools and (ii) assessing background levels of the diagnostic metabolite.IMPORTANCE In chronic lung infections, populations of microbial pathogens change and mature in ways that are often unknown, which makes it challenging to identify appropriate treatment options. A promising tool to better understand the physiology of microorganisms in a patient is stable-isotope probing, which we previously developed to estimate the growth rates of S. aureus in cystic fibrosis (CF) sputum. Here, we tracked microbial communities in a cohort of CF patients and found that anteiso fatty acids can also originate from other sources in CF sputum. This awareness led us to develop a new workflow for the application of stable-isotope probing in this context, improving our ability to estimate pathogen generation times in clinical samples.
journal_name
J Bacterioljournal_title
Journal of bacteriologyauthors
Neubauer C,Kasi AS,Grahl N,Sessions AL,Kopf SH,Kato R,Hogan DA,Newman DKdoi
10.1128/JB.00365-18subject
Has Abstractpub_date
2018-11-26 00:00:00issue
24eissn
0021-9193issn
1098-5530pii
JB.00365-18journal_volume
200pub_type
杂志文章abstract::The bacteriophage Mu genome contains a centrally located strong gyrase site (SGS) that is required for efficient prophage replication. To aid in studying the unusual properties of the SGS, we sought other gyrase sites that might be able to substitute for the SGS in Mu replication. Five candidate sites were obtained by...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.186.14.4575-4584.2004
更新日期:2004-07-01 00:00:00
abstract::Acyl carrier protein (ACP coli) was isolated from commercially grown Escherichia coli B and was acetylated by chemical methods. Biological activity of the synthesized acetyl-ACP coli was checked in an in vitro fatty acid-synthesizing system isolated from E. coli B. Since acetyl-ACP is preferred over acetyl-coenzyme A ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.96.4.1281-1284.1968
更新日期:1968-10-01 00:00:00
abstract::Enhancement of the production of soluble recombinant penicillin acylase in Escherichia coli via coexpression of a periplasmic protease/chaperone, DegP, was demonstrated. Coexpression of DegP resulted in a shift of in vivo penicillin acylase (PAC) synthesis flux from the nonproductive pathway to the productive one when...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.185.10.3020-3030.2003
更新日期:2003-05-01 00:00:00
abstract::The PRO1 gene of Saccharomyces cerevisiae encodes the 428-amino-acid protein gamma-glutamyl kinase (ATP:L-glutamate 5-phosphotransferase, EC 2.7.2.11), which catalyzes the first step in proline biosynthesis. Amino acid sequence comparison revealed significant homology between the yeast and Escherichia coli gamma-gluta...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.174.12.4148-4156.1992
更新日期:1992-06-01 00:00:00
abstract::The enzyme diversity of the cellulolytic system produced by Clostridium cellulolyticum grown on crystalline cellulose as a sole carbon and energy source was explored by two-dimensional electrophoresis. The cellulolytic system of C. cellulolyticum is composed of at least 30 dockerin-containing proteins (designated cell...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00917-06
更新日期:2007-03-01 00:00:00
abstract::The bacterial plant pathogen Pseudomonas syringae depends on a type III protein secretion system and the effector proteins that it translocates into plant cells to cause disease and to elicit the defense-associated hypersensitive response on resistant plants. The availability of the P. syringae pv. tomato DC3000 genom...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.186.11.3621-3630.2004
更新日期:2004-06-01 00:00:00
abstract::In Rhodobacter sphaeroides, MreB, MreC, MreD, PBP2, and RodA are encoded at the same locus. The localizations of PBP2, MreB, and MreC, which have all been implicated in the synthesis of the peptidoglycan layer, were investigated under different growth conditions to gain insight into the relationships between these pro...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.188.5.1691-1700.2006
更新日期:2006-03-01 00:00:00
abstract::Vibrio cholerae, the causative agent of the human diarrheal disease cholera, is a motile bacterium with a single polar flagellum. Motility has been implicated as a virulence determinant in some animal models of cholera, but the relationship between motility and virulence has not yet been clearly defined. We have begun...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.180.2.303-316.1998
更新日期:1998-01-01 00:00:00
abstract::Escherichia coli strain TP985, which has an insertional mutation in the gene for the periplasmic murein tripeptide binding protein MppA, was previously reported to overproduce MarA and exhibit a multiple-antibiotic resistance (Mar) phenotype (H. Li and J. T. Park, J. Bacteriol. 181:4842-4847, 1999). We found that TP98...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.185.4.1465-1469.2003
更新日期:2003-02-01 00:00:00
abstract::Anaerobic microbial toluene catabolism is initiated by addition of fumarate to the methyl group of toluene, yielding (R)-benzylsuccinate as first intermediate, which is further metabolized via beta-oxidation to benzoyl-coenzyme A (CoA) and succinyl-CoA. A specific succinyl-CoA:(R)-benzylsuccinate CoA-transferase activ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.183.14.4288-4295.2001
更新日期:2001-07-01 00:00:00
abstract::The three-dimensional structure of the nickel-containing hydrogenase from Thiocapsa roseopersicina has been determined at a resolution of 2 nm in the plane and 4 nm in the vertical direction by electron microscopy and computerized image processing on microcrystals of the enzyme. The enzyme forms a large ring-shaped co...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.173.8.2576-2580.1991
更新日期:1991-04-01 00:00:00
abstract::The nucleotide sequence of a region located downstream of the nifB gene, both in the cyanobacterium Anabaena sp. strain PCC 7120 and in Rhizobium meliloti, has been determined. This region contains a gene (fdxN) whose predicted polypeptide product strongly resembles typical bacterial ferredoxins. Cyanobacteria have no...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.170.9.4406-4410.1988
更新日期:1988-09-01 00:00:00
abstract::When Legionella pneumophila grows on agar plates, it secretes a surfactant that promotes flagellum- and pilus-independent "sliding" motility. We isolated three mutants that were defective for surfactant. The first two had mutations in genes predicted to encode cytoplasmic enzymes involved in lipid metabolism. These ge...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.05405-11
更新日期:2011-11-01 00:00:00
abstract::The Salmonella typhimurium pi-histidine episome was identified by Ames et al. (2) in an unstable partial revertant of a deletion mutation-containing strain, hisG203. HisG203 lacks the histidine operator, promoter, and part of the first structural gene. In this paper, we study some properties of pi factor and demonstra...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.109.3.993-1000.1972
更新日期:1972-03-01 00:00:00
abstract::Renaturable regions in the DNA strands of the N group plasmid pCU1 have been visualized as stem-loop structures by electron microscopy. Four such distinct structures are described, the smallest of which is within the loop of a larger one. The region of pCU1 in which these structures occur has several restriction sites...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.153.3.1502-1512.1983
更新日期:1983-03-01 00:00:00
abstract::The heat shock response of Bradyrhizobium japonicum is controlled by a complex network involving two known regulatory systems. While some heat shock genes are controlled by a highly conserved inverted-repeat structure (CIRCE), others depend on a sigma 32-type heat shock sigma factor. Using Western blot (immunoblot) an...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.178.18.5337-5346.1996
更新日期:1996-09-01 00:00:00
abstract::Escherichia coli K-12 deficient in galactose-1-phosphate uridyl transferase is capable of converting significant amounts of d-[1-(14)C]galactose to (14)CO(2), whereas strains deficient in other enzymes of the Leloir pathway cannot do so. ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.124.1.558-561.1975
更新日期:1975-10-01 00:00:00
abstract::The interaction of 12 phage strains with bacilli, protoplasts, and L forms of Bacillus subtilis 168 and with eight of its mutants and two of its lysogens is described qualitatively and quantitatively. After removal of the cell wall from B. subtilis 168, 11 of the 12 phage strains can still adsorb to the protoplasts, n...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.124.1.445-448.1975
更新日期:1975-10-01 00:00:00
abstract::The SecYEG heterotrimeric membrane protein complex functions as a channel for protein translocation across the Escherichia coli cytoplasmic membrane. SecY is the central subunit of the SecYEG complex and contains 10 transmembrane segments (TM1 to TM10). Previous mutation studies suggested that TM3 and TM4 are particul...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.186.12.3960-3969.2004
更新日期:2004-06-01 00:00:00
abstract::Kawakami, Masaya (Gunma University, Maebashi, Japan), Nobutaka Osawa, and Susumu Mitsuhashi. Experimental salmonellosis. VII. Comparison of the immunizing effect of live vaccine and materials extracted from Salmonella enteritidis. J. Bacteriol. 92:1585-1589. 1966.-Attempts were made to isolate the factors of live vacc...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.92.6.1585-1589.1966
更新日期:1966-12-01 00:00:00
abstract::We present the complete genome sequence of Listeria welshimeri, a nonpathogenic member of the genus Listeria. Listeria welshimeri harbors a circular chromosome of 2,814,130 bp with 2,780 open reading frames. Comparative genomic analysis of chromosomal regions between L. welshimeri, Listeria innocua, and Listeria monoc...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00758-06
更新日期:2006-11-01 00:00:00
abstract::Glycosylation is a common modulation of protein function in eukaryotes and is biologically important. However, in bacteria protein glycosylation is rare, and relatively few bacterial glycoproteins are known. In Escherichia coli only two glycoproteins have been described to date. Here we introduce a novel member to thi...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.188.5.1798-1807.2006
更新日期:2006-03-01 00:00:00
abstract::Burkholderia thailandensis is a soil saprophyte that is closely related to the pathogen Burkholderia pseudomallei, the etiological agent of melioidosis in humans. The environmental niches and infection sites occupied by these bacteria are thought to contain only limited concentrations of oxygen, where they can generat...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00304-20
更新日期:2020-11-04 00:00:00
abstract::The secretomes of a virulent Bacillus anthracis strain and of avirulent strains (cured of the virulence plasmids pXO1 and pXO2), cultured in rich and minimal media, were studied by a comparative proteomic approach. More than 400 protein spots, representing the products of 64 genes, were identified, and a unique patter...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.188.10.3551-3571.2006
更新日期:2006-05-01 00:00:00
abstract::The Escherichia coli plasmids pBR322 and pBR327 can be taken up by Haemophilus influenzae but do not replicate in this organism; however, integration of pBR into the H. influenzae chromosome was achieved by ligation to a fragment of the Haemophilus phage S2 that carried a phage attachment site (attP). Once these seque...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.171.4.1898-1903.1989
更新日期:1989-04-01 00:00:00
abstract::Dehority, B. A. (Ohio Agricultural Experiment Station, Wooster). Degradation and utilization of isolated hemicellulose by pure cultures of cellulolytic rumen bacteria. J. Bacteriol. 89:1515-1520. 1965.-Hemicelluloses isolated from flax, corn hulls, alfalfa, oat hulls, and fescue grass were used as sole energy sources ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.89.6.1515-1520.1965
更新日期:1965-06-01 00:00:00
abstract::Marchette, Nyven J. (University of Utah, Salt Lake City), and Paul S. Nicholes. Virulence and citrulline ureidase activity of Pasteurella tularensis. J. Bacteriol. 82:26-32. 1961.-The presence of a citrulline ureidase system in Pasteurella tularensis strains of high virulence, and its absence in avirulent strains and ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.82.1.26-32.1961
更新日期:1961-07-01 00:00:00
abstract::A segment of Escherichia coli DNA that contained a discontinuity of homology with Salmonella typhimurium DNA was isolated. The segment, 1,430 base pairs long, was derived from one end of the lac "loop," a region of about 12 kilobase pairs of E. coli DNA, including the lac operon which has no detectable homology with S...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.159.2.618-623.1984
更新日期:1984-08-01 00:00:00
abstract::Bishop, D. G. (University of Sydney, Sydney, Australia), and J. L. Still. Fatty acid metabolism in Serratia marcescens. J. Bacteriol. 82:370-375. 1961.-A study has been made of the oxidation of saturated fatty acids containing between two and 18 carbon atoms by whole cells of the bacterium, Serratia marcescens. This o...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.82.3.370-375.1961
更新日期:1961-09-01 00:00:00
abstract::We used primer extension and mutational analysis to identify a promoter upstream of ilvB, the first gene in the ilv-leu operon of Bacillus subtilis. Between the promoter and ilvB, there is a 482-bp leader region which contains a sequence that resembles a factor-independent transcription terminator. In in vitro transcr...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.174.10.3212-3219.1992
更新日期:1992-05-01 00:00:00