Refining the Application of Microbial Lipids as Tracers of Staphylococcus aureus Growth Rates in Cystic Fibrosis Sputum.


: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.


J Bacteriol


Journal of bacteriology


Neubauer C,Kasi AS,Grahl N,Sessions AL,Kopf SH,Kato R,Hogan DA,Newman DK




Has Abstract


2018-11-26 00:00:00












  • The complex of Sphingomonas elodea ATCC 31461 glucose-1-phosphate uridylyltransferase with glucose-1-phosphate reveals a novel quaternary structure, unique among nucleoside diphosphate-sugar pyrophosphorylase members.

    abstract::Gellan gum is a widely used commercial material, available in many different forms. Its economic importance has led to studies into the biosynthesis of exopolysaccharide gellan gum, which is industrially prepared in high yields using Sphingomonas elodea ATCC 31461. Glucose-1-phosphate uridylyltransferase mediates the ...

    journal_title:Journal of bacteriology

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    authors: Aragão D,Fialho AM,Marques AR,Mitchell EP,Sá-Correia I,Frazão C

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    journal_title:Journal of bacteriology

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    authors: Miller JF,Johnson SA,Black WJ,Beattie DT,Mekalanos JJ,Falkow S

    更新日期:1992-02-01 00:00:00

  • Cloning, sequencing, and mapping of the bacterioferritin gene (bfr) of Escherichia coli K-12.

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    journal_title:Journal of bacteriology

    pub_type: 杂志文章


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    abstract::Primer extension analysis of transcripts of the Bacillus subtilis autolysin (cwlB) operon indicated that SigD-dependent transcripts from the Pd promoter are missing in the degU32(Hy) and degS200 (Hy) mutants. The degU32(Hy) mutation caused a 99% reduction in the expression of a sigD-lacZ translational fusion gene cons...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章


    authors: Tokunaga T,Rashid MH,Kuroda A,Sekiguchi J

    更新日期:1994-08-01 00:00:00

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    journal_title:Journal of bacteriology

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    更新日期:2001-07-01 00:00:00

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    journal_title:Journal of bacteriology

    pub_type: 杂志文章


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    更新日期:1985-01-01 00:00:00

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    journal_title:Journal of bacteriology

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    更新日期:1995-06-01 00:00:00

  • Decay of a model mRNA in Bacillus subtilis by a combination of RNase J1 5' exonuclease and RNase Y endonuclease activities.

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    journal_title:Journal of bacteriology

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    journal_title:Journal of bacteriology

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    更新日期:1962-07-01 00:00:00

  • Histidine-mediated control of tryptophan biosynthetic enzymes in Neurospora crassa.

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    journal_title:Journal of bacteriology

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    journal_title:Journal of bacteriology

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    journal_title:Journal of bacteriology

    pub_type: 杂志文章


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  • Repression of the Staphylococcus aureus accessory gene regulator in serum and in vivo.

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    journal_title:Journal of bacteriology

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    journal_title:Journal of bacteriology

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  • Structural elements required for replication and incompatibility of the Rhizobium etli symbiotic plasmid.

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    journal_title:Journal of bacteriology

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    authors: Ramírez-Romero MA,Soberón N,Pérez-Oseguera A,Téllez-Sosa J,Cevallos MA

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  • Regulation of the Salmonella typhimurium aroF gene in Escherichia coli.

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    journal_title:Journal of bacteriology

    pub_type: 杂志文章


    authors: Muday GK,Herrmann KM

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  • Resistance to arsenic compounds conferred by a plasmid transmissible between strains of Escherichia coli.

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    journal_title:Journal of bacteriology

    pub_type: 杂志文章


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    更新日期:1973-07-01 00:00:00

  • Identification of a single amino acid substitution in the diphtheria toxin A chain of CRM 228 responsible for the loss of enzymatic activity.

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    journal_title:Journal of bacteriology

    pub_type: 杂志文章


    authors: Johnson VG,Nicholls PJ

    更新日期:1994-08-01 00:00:00

  • Mu-like prophage strong gyrase site sequences: analysis of properties required for promoting efficient mu DNA replication.

    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


    authors: Oram M,Pato ML

    更新日期:2004-07-01 00:00:00

  • Residual polarity and transcription-translation coupling during recovery from chloramphenicol or fusidic acid.

    abstract::Fusidic acid or chloramphenicol was used to inhibit peptide synthesis to 1% of normal in Escherichia coli B, strain AS19. After 10 min of inhibition, peptide synthesis could be quickly restored to 80% of the normal rate after washing the bacteria on a filter. However, even in the presence of adenosine 3'-5'-cyclic-mon...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章


    authors: Pastushok C,Kennell D

    更新日期:1974-02-01 00:00:00

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    journal_title:Journal of bacteriology

    pub_type: 杂志文章


    authors: Hinton SM,Merritt B

    更新日期:1986-11-01 00:00:00

  • Thermally induced intracellular alteration of ribosomal ribonucleic acid.

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    journal_title:Journal of bacteriology

    pub_type: 杂志文章


    authors: Rosenthal LJ,Iandolo JJ

    更新日期:1970-09-01 00:00:00

  • Phenotypic and genotypic evidence for L-fucose utilization by Campylobacter jejuni.

    abstract::Campylobacter jejuni remains among the leading causes of bacterial food-borne illness. The current understanding of Campylobacter physiology suggests that it is asaccharolytic and is unable to catabolize exogenous carbohydrates. Contrary to this paradigm, we provide evidence for l-fucose utilization by C. jejuni. The ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章


    authors: Muraoka WT,Zhang Q

    更新日期:2011-03-01 00:00:00

  • Regulation and function of cytochrome c' in Rhodobacter sphaeroides 2.4.3.

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    journal_title:Journal of bacteriology

    pub_type: 杂志文章


    authors: Choi PS,Grigoryants VM,Abruña HD,Scholes CP,Shapleigh JP

    更新日期:2005-06-01 00:00:00

  • Structure, serological specificity, and synthesis of artificial glycoconjugates representing the genus-specific lipopolysaccharide epitope of Chlamydia spp.

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    journal_title:Journal of bacteriology

    pub_type: 杂志文章


    authors: Holst O,Brade L,Kosma P,Brade H

    更新日期:1991-03-01 00:00:00

  • Integration host factor increases the transpositional immunity conferred by gamma delta ends.

    abstract::The ends of the bacterial transposon gamma delta contain adjacent binding sites for gamma delta transposase and integration host factor (IHF). IHF+ and IHF- strains were used in conjunction with gamma delta transposon ends containing or lacking the site for IHF binding to determine the role that IHF plays in various g...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章


    authors: Wiater LA,Grindley ND

    更新日期:1990-09-01 00:00:00