The Application of SIMCA P+ in Shotgun Metabolomics Analysis of ZICⓇHILIC-MS Spectra of Human Urine - Experience with the Shimadzu IT-T of and Profiling Solutions Data Extraction Software

Trivedi, Drupad K.; Iles, Ray K.

doi:10.4172/2157-7064.1000145

Cited by 36 publications

(41 citation statements)

References 4 publications

(5 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Only OPLS-DA with R 2 > 0.8 and Q 2 > 0.5 were considered robust and predictive, respectively. The variable importance plot (VIP) was used to determine the five metabolites most associated with each class [38]. MiniTab 17 was used to generate box plots and determine the significance by Tukey’s method for multiple comparisons.…”

Section: Methodsmentioning

confidence: 99%

Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease

et al. 2016

View full text Add to dashboard Cite

BackgroundThe preterm microbiome is crucial to gut health and may contribute to necrotising enterocolitis (NEC), which represents the most significant pathology affecting preterm infants. From a cohort of 318 infants, <32 weeks gestation, we selected 7 infants who developed NEC (defined rigorously) and 28 matched controls. We performed detailed temporal bacterial (n = 641) and metabolomic (n = 75) profiling of the gut microbiome throughout the disease.ResultsA core community of Klebsiella, Escherichia, Staphyloccocus, and Enterococcus was present in all samples. Gut microbiota profiles grouped into six distinct clusters, termed preterm gut community types (PGCTs). Each PGCT reflected dominance by the core operational taxonomic units (OTUs), except of PGCT 6, which had high diversity and was dominant in bifidobacteria. While PGCTs 1–5 were present in infants prior to NEC diagnosis, PGCT 6 was comprised exclusively of healthy samples. NEC infants had significantly more PGCT transitions prior to diagnosis. Metabolomic profiling identified significant pathways associated with NEC onset, with metabolites involved in linoleate metabolism significantly associated with NEC diagnosis. Notably, metabolites associated with NEC were the lowest in PGCT 6.ConclusionsThis is the first study to integrate sequence and metabolomic stool analysis in preterm neonates, demonstrating that NEC does not have a uniform microbial signature. However, a diverse gut microbiome with a high abundance of bifidobacteria may protect preterm infants from disease. These results may inform biomarker development and improve understanding of gut-mediated mechanisms of NEC.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-016-0216-8) contains supplementary material, which is available to authorized users.

show abstract

Section: Methodsmentioning

confidence: 99%

Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease

et al. 2016

View full text Add to dashboard Cite

show abstract

“…To check that data was adhering to multivariate normalities, Hotelling's T 2 tolerance limits were calculated and set at 0.95. Only variables >1 in the variable importance plot were included from the important variables plot [16]. Analysis of variance was used to determine whether numbers of L. acidophilus and B. bifidum (qPCR) increased during probiotic treatment with post hoc Tukey's test applied for multiple pairwise comparisons (Minitab 16).…”

Section: Methodsmentioning

confidence: 99%

Routine Use of Probiotics in Preterm Infants: Longitudinal Impact on the Microbiome and Metabolome

Abdulkadir¹,

Nelson²,

Skeath³

et al. 2016

Neonatology

View full text Add to dashboard Cite

Background: Probiotics are live microbial supplements that colonize the gut and potentially exert health benefit to the host. Objectives: We aimed to determine the impact of a probiotic (Infloran®: Lactobacillus acidophilus-NCIMB701748 and Bifidobacterium bifidum-ATCC15696) on the bacterial and metabolic function of the preterm gut while in the neonatal intensive care unit (NICU) and following discharge. Methods: Stool samples (n = 88) were collected before, during, and after probiotic intake from 7 patients, along with time-matched controls from 3 patients. Samples were also collected following discharge home from the NICU. Samples underwent bacterial profiling analysis by 16S rRNA gene sequencing and quantitative PCR (qPCR), as well as metabolomic profiling using liquid chromatography mass spectrometry. Results: Bacterial profiling showed greater Bifidobacterium (15.1%) and Lactobacillus (4.2%) during supplementation compared to the control group (4.0% and 0%, respectively). While Lactobacillus became reduced after the probiotic had been stopped, Bifidobacterium remained high following discharge, suggestive of successful colonisation. qPCR analysis showed a significant increase (p ≤ 0.01) in B. bifidum in infants who received probiotic treatment compared to controls, but no significant increase was observed for L. acidophilus (p = 0.153). Metabolite profiling showed clustering based on receiving probiotic or matched controls, with distinct metabolites associated with probiotic administration. Conclusions: Probiotic species successfully colonise the preterm gut, reducing the relative abundance of potentially pathogenic bacteria, and effecting gut functioning. Bifidobacterium (but not Lactobacillus) colonised the gut in the long term, suggesting the possibility that therapeutically administered probiotics may continue to exert important functional effects on gut microbial communities in early infancy.

show abstract

“…On confirmation of one or more matching product ions, these standards were spiked to the pool of urine samples and change in intensity of precursor ion as well as retention time reproducibility were monitored for further confirmation. SIMCA P + (version 11.4) was used for multivariate analysis and Minitab version 14 was used for univariate statistics as described in Trivedi and Iles ().…”

Section: Methodsmentioning

confidence: 99%

“…The cases spanned the late first, and early and late second trimesters of pregnancy (see Table ). We have previously established a logical MS/MS identification methodology (Trivedi and Iles, ), a baseline for normal maternal urine metabolome (Trivedi and Iles, ), as well as describing statistical tools that can be used for exploring such complex data (Trivedi and Iles, ). This study builds on this platform for the analysis of the maternal urinary metabolome from women with and without an aneuploid pregnancy (predominantly Down syndrome).…”

Section: Introductionmentioning

confidence: 99%

Shotgun metabolomic profiles in maternal urine identify potential mass spectral markers of abnormal fetal biochemistry – dihydrouracil and progesterone in the metabolism of Down syndrome

Trivedi

Iles²

2014

Biomedical Chromatography

View full text Add to dashboard Cite

In Down syndrome (DS) in particular, the precise cellular mechanisms linking genotype to phenotype is not straightforward despite a clear mapping of the genetic cause. Metabolomic profiling might be more revealing in understanding molecular-cellular mechanisms of inborn errors of metabolism/syndromes than genomics alone and also result in new prenatal screening approaches. The urinary metabolome of 122 maternal urine from women with and without an aneuploid pregnancy (predominantly Down syndrome) were compared by both zwitterionic hydrophilic interaction chromatography (ZIC-HILIC) and reversed-phase liquid chromatography (RPLC) coupled to hybrid ion trap time of flight mass spectral analysis. ZIC-HILIC mass spectrometry resolved 10-fold more unique molecular ions than RPLC mass spectrometry, of which molecules corresponding to ions of m/z 114.07 and m/z 314.20 showed maternal urinary level changes that significantly coincided with the presence of a DS fetus. The ion of m/z 314.20 was identified as progesterone and m/z 114.07 as dihydrouracil. A metabolomics profiling-based maternal urinary screening test modelled from this separation data would detect approximately 87 and 60.87% (using HILIC-MS and RPLC-MS, respectively) of all DS pregnancies between 9 and 23 weeks of gestation with no false positives.

show abstract

The Application of SIMCA P+ in Shotgun Metabolomics Analysis of ZICⓇHILIC-MS Spectra of Human Urine - Experience with the Shimadzu IT-T of and Profiling Solutions Data Extraction Software

Cited by 36 publications

References 4 publications

Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease

Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease

Routine Use of Probiotics in Preterm Infants: Longitudinal Impact on the Microbiome and Metabolome

Shotgun metabolomic profiles in maternal urine identify potential mass spectral markers of abnormal fetal biochemistry – dihydrouracil and progesterone in the metabolism of Down syndrome

Contact Info

Product

Resources

About