Summary of Study ST003527

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002170. The data can be accessed directly via it's Project DOI: 10.21228/M84C19 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

Study ID	ST003527
Study Title	Combining antibiotics alters the longitudinal maturation of gut microbiota and its short chain fatty acid metabolites in extremely and very preterm infants
Study Summary	Antibiotics are routinely prescribed to extremely and very premature infants as a pre-emptive and prophylactic treatment to reduce the risk of acute neonatal illness (i.e. necrotizing enterocolitis, NEC) associated with morbidity. To investigate the effects of antibiotic types, combinations, and duration on the preterm gut microbiome and metabolome, we analyzed the microbiome compositions of 123 stool samples collected at 3 timepoints (postnatal day 1, 28 and 56) from extremely- and very-low-birthweight infants treated with 14 different antibiotics spanning across 5 classes. Targeted metabolomics were performed on 47 samples available, allowing us to quantify 649 metabolites including amino acids, bile acids, fatty acids, and lipids. As a result, we found that antibiotics exerted the most profound disruptive impact on the gut microbiota, while antibiotics and breastfeeding highly influence the gut metabolome. Short chain fatty acids were reduced in both antibiotic-treated and NEC group. Finally, we revealed that cephalosporins negatively impact conjugated bile acids due to a positive correlation with bile salt hydrolase-producing Staphylococcus.
Institute	Seoul National University
Last Name	Kyeong-Seog
First Name	Kim
Address	Jongno-Gu, South Korea
Email	92kkim@gmail.com
Phone	+8227408905
Submit Date	2024-09-23
Raw Data Available	Yes
Raw Data File Type(s)	d, wiff
Analysis Type Detail	GC/LC-MS
Release Date	2024-10-22
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002170
Project DOI:	doi: 10.21228/M84C19
Project Title:	Combining antibiotics alters the longitudinal maturation of gut microbiota and its short chain fatty acid metabolites in extremely and very preterm infants
Project Type:	Targeted metabolomics
Project Summary:	Antibiotics are routinely prescribed to extremely and very premature infants as a pre-emptive and prophylactic treatment to reduce the risk of acute neonatal illness (i.e. necrotizing enterocolitis, NEC) associated with morbidity. To investigate the effects of antibiotic types, combinations, and duration on the preterm gut microbiome and metabolome, we analyzed the microbiome compositions of 123 stool samples collected at 3 timepoints (postnatal day 1, 28 and 56) from extremely- and very-low-birthweight infants treated with 14 different antibiotics spanning across 5 classes. Targeted metabolomics were performed on 47 samples available, allowing us to quantify 649 metabolites including amino acids, bile acids, fatty acids, and lipids. As a result, we found that antibiotics exerted the most profound disruptive impact on the gut microbiota, while antibiotics and breastfeeding highly influence the gut metabolome. Short chain fatty acids were reduced in both antibiotic-treated and NEC group. Finally, we revealed that cephalosporins negatively impact conjugated bile acids due to a positive correlation with bile salt hydrolase-producing Staphylococcus.
Institute:	Seoul National University
Last Name:	Kyeong-Seog
First Name:	Kim
Address:	Jongno-Gu, South Korea
Email:	92kkim@gmail.com
Phone:	+8227408905

Subject:

Subject ID:	SU003656
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id	local_sample_id	Sample source	Group	Antibiotics
SA387219	NEC03_D1	Feces	1day	No
SA387220	PRE02_D1	Feces	1day	No
SA387221	PRE03_D1	Feces	1day	No
SA387222	PRE31_D1	Feces	1day	No
SA387223	PRE26_D1	Feces	1day	No
SA387224	PRE44_D1	Feces	1day	Yes
SA387225	PRE39_D1	Feces	1day	Yes
SA387226	PRE38_D1	Feces	1day	Yes
SA387227	PRE32_D1	Feces	1day	Yes
SA387228	PRE21_D1	Feces	1day	Yes
SA387229	PRE24_D1	Feces	1day	Yes
SA387230	PRE27_D1	Feces	1day	Yes
SA387231	NEC04_D1	Feces	1day	Yes
SA387232	NEC01_D1	Feces	1day	Yes
SA387233	PRE13_D1	Feces	1day	Yes
SA387234	PRE29_D1	Feces	1day	Yes
SA387235	PRE09_D1	Feces	1day	Yes
SA387236	PRE10_D1	Feces	1day	Yes
SA387237	PRE29_D28	Feces	28day	No
SA387238	PRE39_D28	Feces	28day	No
SA387239	PRE24_D28	Feces	28day	No
SA387240	PRE30_D28	Feces	28day	No
SA387241	PRE03_D28	Feces	28day	No
SA387242	PRE02_D28	Feces	28day	No
SA387243	PRE44_D28	Feces	28day	Yes
SA387244	PRE38_D28	Feces	28day	Yes
SA387245	NEC03_D28	Feces	28day	Yes
SA387246	PRE32_D28	Feces	28day	Yes
SA387247	PRE09_D28	Feces	28day	Yes
SA387248	PRE05_D28	Feces	28day	Yes
SA387249	PRE26_D28	Feces	28day	Yes
SA387250	NEC01_D28	Feces	28day	Yes
SA387251	NEC05_D28	Feces	28day	Yes
SA387252	PRE21_D28	Feces	28day	Yes
SA387253	NEC06_D28	Feces	28day	Yes
SA387254	PRE27_D28	Feces	28day	Yes
SA387255	PRE13_D56	Feces	56day	No
SA387256	PRE38_D56	Feces	56day	No
SA387257	PRE05_D56	Feces	56day	Yes
SA387258	PRE27_D56	Feces	56day	Yes
SA387259	NEC03_D56	Feces	56day	Yes
SA387260	PRE31_D56	Feces	56day	Yes
SA387261	PRE32_D56	Feces	56day	Yes
SA387262	NEC05_D56	Feces	56day	Yes
SA387263	PRE39_D56	Feces	56day	Yes
SA387264	PRE44_D56	Feces	56day	Yes
SA387265	PRE26_D56	Feces	56day	Yes

Showing results 1 to 47 of 47

Showing results 1 to 47 of 47

Collection:

Collection ID:	CO003649
Collection Summary:	All samples were obtained from infants who were born and admitted to the NICU at Samsung Medical Center in Seoul, after taking informed consent from parents. The institutional review board of Samsung Medical Center approved the collection of samples and clinical data (approval number 2021-02-038). The study was conducted in accordance with the principles outlined in the Declaration of Helsinki. A total of 47 stool samples from the patient cohort were collected on days 1, 28, and 56 after birth with a minimum of one sample per subject (Day in Study Design).
Sample Type:	Feces
Collection Method:	Using a sterile plastic spoon and adhering to aseptic protocols, approximately 1g of feces were collected
Collection Location:	NICU at Samsung Medical Center in Seoul
Collection Frequency:	NA
Collection Duration:	approx. 3 years
Volumeoramount Collected:	approx. 1g
Storage Conditions:	-80℃
Collection Vials:	2.0 mL cryovial
Storage Vials:	2.0 mL cryovial
Collection Tube Temp:	-80C
Additives:	NA

Treatment:

Treatment ID:	TR003665
Treatment Summary:	14 types of antibiotics were used for each preterm infant with the specific antibiotics varying based on the individual, namely gentamicin, cefazolin, vancomycin, meropenem, tazoferan, fluconazole, amphotericin, ampicillin, nafcillin, cefotaxime, teicoplanin, clarithromycin, cefepime, and amikacin. Of the 54 subjects, 38 received antibiotics treatment more than once (Antibiotics = Yes in Study Design).

Treatment ID:

TR003665

Treatment Summary:

14 types of antibiotics were used for each preterm infant with the specific antibiotics varying based on the individual, namely gentamicin, cefazolin, vancomycin, meropenem, tazoferan, fluconazole, amphotericin, ampicillin, nafcillin, cefotaxime, teicoplanin, clarithromycin, cefepime, and amikacin. Of the 54 subjects, 38 received antibiotics treatment more than once (Antibiotics = Yes in Study Design).

Sample Preparation:

Sampleprep ID:	SP003663
Sampleprep Summary:	For metabolome extraction from stool samples, 2-propanol was added at the 1 mg: 3 µL ratio. The mixture was vortexed vigorously until the stools are entirely homogenized, and then centrifuged to remove stool debris for 5 min at 18,341 × g and 4°C. Finally, the supernatant was collected for further analysis including targeted metabolomics using the MxP Quant 500 kit provided by Biocrates (Biocrates Life Science AG, Innsbruck, Austria), and for the analysis of SCFAs as described previously [10.3390/metabo12060525]. Briefly, for MxP Quant 500 kit assay, 10 µL of stool extract was used and the stool metabolome was derivatized with phenylisothiocyanate per manufacturer’s instruction. For the extraction of SCFAs, 10 µL of 10 µg/mL of acetic acid-d4, which was used for internal standard (IS) was added to the 30 µL of stool extract. Then, 0.1 mL of deionized water and 10 µL of 1.0 M hydrochloric acid was added to the sample, and further extracted SCFAs by adding 0.2 mL of methyl-tert butyl ether (MTBE). The MTBE phase was collected after vortex and centrifugation for gas chromatography–mass spectrometry (GC–MS) analysis.

Sampleprep ID:

SP003663

Sampleprep Summary:

For metabolome extraction from stool samples, 2-propanol was added at the 1 mg: 3 µL ratio. The mixture was vortexed vigorously until the stools are entirely homogenized, and then centrifuged to remove stool debris for 5 min at 18,341 × g and 4°C. Finally, the supernatant was collected for further analysis including targeted metabolomics using the MxP Quant 500 kit provided by Biocrates (Biocrates Life Science AG, Innsbruck, Austria), and for the analysis of SCFAs as described previously [10.3390/metabo12060525]. Briefly, for MxP Quant 500 kit assay, 10 µL of stool extract was used and the stool metabolome was derivatized with phenylisothiocyanate per manufacturer’s instruction. For the extraction of SCFAs, 10 µL of 10 µg/mL of acetic acid-d4, which was used for internal standard (IS) was added to the 30 µL of stool extract. Then, 0.1 mL of deionized water and 10 µL of 1.0 M hydrochloric acid was added to the sample, and further extracted SCFAs by adding 0.2 mL of methyl-tert butyl ether (MTBE). The MTBE phase was collected after vortex and centrifugation for gas chromatography–mass spectrometry (GC–MS) analysis.

Combined analysis:

Analysis ID	AN005792	AN005793	AN005794
Analysis type	MS	MS	MS
Chromatography type	GC	Reversed phase	None (Direct infusion)
Chromatography system	Agilent 7890B	Waters Acquity	Waters Acquity
Column	Agilent DB-FFAP (30m × 0.25mm, 0.25um)	Biocrates MxP Quant 500 (XL) PN 21117	NA (FIA mode)
MS Type	EI	ESI	ESI
MS instrument type	Triple quadrupole	Triple quadrupole	Triple quadrupole
MS instrument name	Agilent 7000B	ABI Sciex Triple Quad 5500+	ABI Sciex Triple Quad 5500+
Ion Mode	POSITIVE	UNSPECIFIED	UNSPECIFIED
Units	uM	uM	uM

Chromatography:

Chromatography ID:	CH004397
Chromatography Summary:	Selected Ion Monitoring (SIM) was applied to measure the short-chain fatty acid in feces. The m/z values at 60 (acetic acid, butyric acid, and isovaleric acid), 73 (isobutyric acid), and 74 (propionic acid) was applied.
Instrument Name:	Agilent 7890B
Column Name:	Agilent DB-FFAP (30m × 0.25mm, 0.25um)
Column Temperature:	an initial GC oven temperature was 40°C, held for 2 min, increased by 40°C/min to 200°C. The post-run time was 6 min at 240°C
Flow Gradient:	NA
Flow Rate:	NA
Solvent A:	NA
Solvent B:	NA
Chromatography Type:	GC

Chromatography ID:	CH004398
Instrument Name:	Waters Acquity
Column Name:	Biocrates MxP Quant 500 (XL) PN 21117
Column Temperature:	50
Flow Gradient:	Flow Gradient LC1: 0% B (0.25 min) -> 12% B (1.25 min) -> 17.5% B (1.2 min) -> 50% B (1.3 min) -> 100% B (0.5 min) -> stay at 100% B (0.5 min) -> 0% B (0.1 min) -> held at 0% B (0.7 min), total 5.8 min; Flow Gradient LC2: 0% B (0.25 min) -> 25% B (0.25 min) -> 50% B (1.5 min) -> 75% B (1.0 min) -> 100% B (0.5 min) -> stay at 100% B (1.5 min) -> 0% B (0.1 min) -> held at 0% B (0.7 min), total 5.8 min
Flow Rate:	0.8 mL/min, increased to 1.0 mL/min from minute 4.7 to 5.1
Solvent A:	100% water; 0.2% formic acid
Solvent B:	95% acetonitrile/5% water; 0.2% formic acid
Chromatography Type:	Reversed phase

Chromatography ID:	CH004399
Instrument Name:	Waters Acquity
Column Name:	NA (FIA mode)
Column Temperature:	NA
Flow Gradient:	100% B, 0-3min
Flow Rate:	0.03mL/min (0-1.6min), 0.2mL/min (1.6-2.8min), Back to 0.03mL/min (2.8-3.0min)
Solvent A:	100% water; 0.2% formic acid
Solvent B:	95% acetonitrile/5% water; 0.2% formic acid
Chromatography Type:	None (Direct infusion)

MS:

MS ID:	MS005512
Analysis ID:	AN005792
Instrument Name:	Agilent 7000B
Instrument Type:	Triple quadrupole
MS Type:	EI
MS Comments:	Selected Ion Monitoring (SIM) was applied to measure the short-chain fatty acid levels. The m/z values at 60 (acetic acid, butyric acid, valeric acid, and isovaleric acid), 63 (acetic acid-d4 which used as internal standard), 73 (isobutyric acid), and 74 (propionic acid) was applied.
Ion Mode:	POSITIVE

MS ID:	MS005513
Analysis ID:	AN005793
Instrument Name:	ABI Sciex Triple Quad 5500+
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	Samples were analyzed with four methods employing LC separation or flow injection analysis (FIA). LC1 used ionization in positive mode and scheduled MRM detection (125 transitions). LC2 used ionization in negative mode and scheduled MRM detection (69 transitions). Both FIA methods used ionization in positive mode and MRM detection (165 and 382 transitions). Data were analyzed employing the Biocrates MetIDQ software.
Ion Mode:	UNSPECIFIED

MS ID:	MS005514
Analysis ID:	AN005794
Instrument Name:	ABI Sciex Triple Quad 5500+
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	Samples were analyzed with four methods employing LC separation or flow injection analysis (FIA). LC1 used ionization in positive mode and scheduled MRM detection (125 transitions). LC2 used ionization in negative mode and scheduled MRM detection (69 transitions). Both FIA methods used ionization in positive mode and MRM detection (165 and 382 transitions). Data were analyzed employing the Biocrates MetIDQ software.
Ion Mode:	UNSPECIFIED