Summary of Study ST004517

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 PR002846. The data can be accessed directly via it's Project DOI: 10.21228/M8SK18 This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

Study ID	ST004517
Study Title	Ruminococcoides intestinale Mitigates Ruminococcus gnavus–Associated Allergic Inflammation via Serotonin Metabolic Reprogramming
Study Summary	To strengthen the link between early-life gut microbiota metabolism and the development of allergic diseases, we established twin and singleton cohorts with longitudinal health monitoring from birth. Allergic diseases—primarily asthma and rhinitis—developed early (≤1 year of age) and showed a male predominance, with no significant differences in probiotic use between allergic and non-allergic groups. Fecal samples collected from both groups were subjected to untargeted metabolomic analysis using LC–MS. The results revealed a specific perturbation of the tryptophan (Trp) metabolism pathway. In particular, levels of downstream Trp metabolites, including tryptamine (TPA), phenylethylamine (PEA), and 5-hydroxytryptophan (5-HTP), were significantly elevated in children with allergic diseases, supporting a potential role for serotonergic mechanisms in allergic disease development.
Institute	National Taiwan University Hospital, National Taiwan University
Department	Department of Pediatrics,
Laboratory	Yen-Hsuan Ni's lab
Last Name	Huey-Huey
First Name	Chua
Address	No.8, Chung Shan S. Rd.（Zhongshan S. Rd.）, Zhongzheng Dist., Taipei City 10041, Taiwan
Email	hueyhueychua@gmail.com
Phone	+886-2-2312-3456 #71516
Submit Date	2025-12-30
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2026-01-12
Release Version	1

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Project:

Project ID:	PR002846
Project DOI:	doi: 10.21228/M8SK18
Project Title:	Ruminococcoides intestinale Mitigates Ruminococcus gnavus–Associated Allergic Inflammation via Serotonin Metabolic Reprogramming
Project Summary:	Host–microbe communication has been understood primarily through immune or metabolic pathways, yet neurotransmitters can also function as bidirectional signals. Here, we identify a serotonin (5-HT)-centered mechanism that integrates microbial competition with mucosal immunity. In the decade-long twin and singleton cohorts, allergic individuals were abundantly colonized by Ruminococcus gnavus, whereas healthy children were enriched in Ruminococcoides intestinale. We demonstrate that R. gnavus engages two complementary pathways: the bacterium expresses the chaperone allergen DnaK to activate pro-allergic IL-33 alarmin signaling, and concurrently enhances its own 5-HT biosynthesis. The combined actions of IL-33 and 5-HT generate a feed-forward loop that amplifies Th2 inflammation and promotes bacterial proliferation. Pharmacological screening further revealed that domperidone, which possesses ancillary 5-HT receptor–blocking activity, effectively inhibits these effects. In contrast, R. intestinale strain Ri-HJH consumes extracellular 5-HT and redirects tryptophan metabolism toward anti-inflammatory indoles, thereby restoring mucosal immune balance. These findings identify 5-HT as a shared metabolite mediating cross-kingdom communication and establish R. intestinale Ri-HJH as a defined probiotic capable of restoring 5-HT homeostasis.
Institute:	National Taiwan University Hospital, National Taiwan University
Department:	Department of Pediatrics
Laboratory:	Yen-Hsuan Ni's lab
Last Name:	Huey-Huey
First Name:	Chua
Address:	No.8, Chung Shan S. Rd.（Zhongshan S. Rd.）, Zhongzheng Dist., Taipei City 10041, Taiwan
Email:	hueyhueychua@gmail.com
Phone:	+886-2-2312-3456 #71516

Subject:

Subject ID:	SU004695
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	Treatment	Sample source	ESI Mode
SA536932	NEG_N110_B7_Allergy	Allergy	Feces	negative
SA536933	NEG_N90_B3_Allergy	Allergy	Feces	negative
SA536934	NEG_N101_B14_Allergy	Allergy	Feces	negative
SA536935	NEG_N106_B8_Allergy	Allergy	Feces	negative
SA536936	NEG_N107_B12_Allergy	Allergy	Feces	negative
SA536937	NEG_N109_B5_Allergy	Allergy	Feces	negative
SA536938	NEG_N77_B1_Allergy	Allergy	Feces	negative
SA536939	NEG_N78_B4_Allergy	Allergy	Feces	negative
SA536940	NEG_N99_B13_Allergy	Allergy	Feces	negative
SA536941	NEG_N113_B2_Allergy	Allergy	Feces	negative
SA536942	NEG_N81_B10_Allergy	Allergy	Feces	negative
SA536943	NEG_N114_B9_Allergy	Allergy	Feces	negative
SA536944	NEG_N95_B6_Allergy	Allergy	Feces	negative
SA536945	NEG_N102_B11_Allergy	Allergy	Feces	negative
SA536946	POS_N110_B7_Allergy	Allergy	Feces	positive
SA536947	POS_N77_B1_Allergy	Allergy	Feces	positive
SA536948	POS_N114_B9_Allergy	Allergy	Feces	positive
SA536949	POS_N113_B2_Allergy	Allergy	Feces	positive
SA536950	POS_N106_B8_Allergy	Allergy	Feces	positive
SA536951	POS_N109_B5_Allergy	Allergy	Feces	positive
SA536952	POS_N107_B12_Allergy	Allergy	Feces	positive
SA536953	POS_N102_B11_Allergy	Allergy	Feces	positive
SA536954	POS_N101_B14_Allergy	Allergy	Feces	positive
SA536955	POS_N99_B13_Allergy	Allergy	Feces	positive
SA536956	POS_N95_B6_Allergy	Allergy	Feces	positive
SA536957	POS_N90_B3_Allergy	Allergy	Feces	positive
SA536958	POS_N81_B10_Allergy	Allergy	Feces	positive
SA536959	POS_N78_B4_Allergy	Allergy	Feces	positive
SA536960	NEG_N111_A11_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	negative
SA536961	NEG_N112_A12_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	negative
SA536962	NEG_N97_A5_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	negative
SA536963	NEG_N94_A8_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	negative
SA536964	NEG_N93_A10_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	negative
SA536965	NEG_N76_A4_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	negative
SA536966	NEG_N89_A9_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	negative
SA536967	NEG_N88_A3_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	negative
SA536968	NEG_N87_A7_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	negative
SA536969	NEG_N86_A2_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	negative
SA536970	NEG_N80_A6_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	negative
SA536971	POS_N112_A12_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	positive
SA536972	POS_N111_A11_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	positive
SA536973	POS_N97_A5_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	positive
SA536974	POS_N94_A8_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	positive
SA536975	POS_N93_A10_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	positive
SA536976	POS_N89_A9_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	positive
SA536977	POS_N88_A3_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	positive
SA536978	POS_N87_A7_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	positive
SA536979	POS_N86_A2_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	positive
SA536980	POS_N80_A6_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	positive
SA536981	POS_N76_A4_HC-Ri-HJH-p	HC-Ri-HJH+	Feces	positive

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Showing results 1 to 50 of 50

Collection:

Collection ID:	CO004688
Collection Summary:	This study enrolled twins and age-matched singletons born at National Taiwan University Children’s Hospital (April 2011–December 2021) and followed from birth to 10 years. Allergic diseases were diagnosed based on clinical presentation according to the Taiwan Academy of Pediatric Allergy, Asthma, and Immunology criteria. Only symptoms persisting ≥6 months were classified as allergic. Non-allergic controls had no history of allergic sensitization as verified by three separate clinical evaluations conducted at 1, 2, and 3 years of age. The study was approved by the Institutional Review Board of National Taiwan University Hospital (201012049RB, 201901129RINA, and 202402101RIND). Fecal samples (0.5–1.0 g) were collected in sterile containers and stored at -80°C.
Sample Type:	Feces

Treatment:

Treatment ID:	TR004704
Treatment Summary:	Healthy control children colonized with Ruminococcoides intestinale strain Ri-HJH (HC–Ri-HJH+) and children with allergic disorders were enrolled, and fecal samples were collected for untargeted metabolomic analysis. Participants did not receive any study-specific interventions, and medication use among allergic participants was not considered in the analysis. Tryptophan metabolites were detected at higher levels in children with allergic disorders.

Treatment ID:

TR004704

Treatment Summary:

Healthy control children colonized with Ruminococcoides intestinale strain Ri-HJH (HC–Ri-HJH+) and children with allergic disorders were enrolled, and fecal samples were collected for untargeted metabolomic analysis. Participants did not receive any study-specific interventions, and medication use among allergic participants was not considered in the analysis. Tryptophan metabolites were detected at higher levels in children with allergic disorders.

Sample Preparation:

Sampleprep ID:	SP004701
Sampleprep Summary:	For fecal samples, 30 mg of lyophilized pellets were extracted with 750 µL ice-cold water by vortexing, ultrasonication (20 min), and centrifugation (15,000 rpm, 10 min, 4°C). Pellets were re-extracted with 750 µL methanol containing internal standard using the same procedure. Supernatants were combined (50% MeOH), diluted four-fold with ice-cold methanol, filtered (0.22 µm), and transferred to LC–MS vials.

Sampleprep ID:

SP004701

Sampleprep Summary:

For fecal samples, 30 mg of lyophilized pellets were extracted with 750 µL ice-cold water by vortexing, ultrasonication (20 min), and centrifugation (15,000 rpm, 10 min, 4°C). Pellets were re-extracted with 750 µL methanol containing internal standard using the same procedure. Supernatants were combined (50% MeOH), diluted four-fold with ice-cold methanol, filtered (0.22 µm), and transferred to LC–MS vials.

Combined analysis:

Analysis ID	AN007578	AN007579
Chromatography ID	CH005747	CH005747
MS ID	MS007275	MS007276
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Dionex Ultimate 3000	Thermo Dionex Ultimate 3000
Column	Waters ACQUITY UPLC HSS T3 (100 x 2.1 mm, 1.8 µm)	Waters ACQUITY UPLC HSS T3 (100 x 2.1 mm, 1.8 µm)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive Plus Orbitrap	Thermo Q Exactive Plus Orbitrap
Ion Mode	POSITIVE	NEGATIVE
Units	Peak area (𝑀𝑒𝑡𝑎𝑏𝑜𝑙𝑖𝑡𝑒 𝑃𝑒𝑎𝑘 𝐴𝑟𝑒𝑎/𝐼𝑛𝑡𝑒𝑟𝑛𝑎𝑙 𝑆𝑡𝑎𝑛𝑑𝑎𝑟𝑑 𝑃𝑒𝑎𝑘 𝐴𝑟𝑒𝑎)	Peak area (𝑀𝑒𝑡𝑎𝑏𝑜𝑙𝑖𝑡𝑒 𝑃𝑒𝑎𝑘 𝐴𝑟𝑒𝑎/𝐼𝑛𝑡𝑒𝑟𝑛𝑎𝑙 𝑆𝑡𝑎𝑛𝑑𝑎𝑟𝑑 𝑃𝑒𝑎𝑘 𝐴𝑟𝑒𝑎)

Chromatography:

Chromatography ID:	CH005747
Instrument Name:	Thermo Dionex Ultimate 3000
Column Name:	Waters ACQUITY UPLC HSS T3 (100 x 2.1 mm, 1.8 µm)
Column Temperature:	40°C
Flow Gradient:	The LC gradient profile was as following: 0-1.5 min, B 1%; 1.5-9.5 min, B 1-35%; 9.5-11.5 min, B 35-80%; 11.5-13.5 min, B 80-100%; 13.5-16.5 min, B 100%; 16.5-20.0 min, B 1%.
Flow Rate:	0.3 mL/min
Solvent A:	100% Water; 0.1% Formic acid
Solvent B:	100% Acetonitrile; 0.1% Formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS007275
Analysis ID:	AN007578
Instrument Name:	Thermo Q Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	MS spectra were obtained in positive ion mode. The Mass spectra were acquired using a top-5 data-dependent acquisition (DDA) method. Full MS scans were collected at a resolution of 70,000 (FWHM) over an m/z range of 80–1200. The data-dependent MS/MS (ddMS2) spectra were acquired with a spectral resolution of 17,500, isolation window of 1.5 m/z, stepped normalized CE with 15, 30, 45, and dynamic exclusion of 15.0 s. The AGC target for full MS and ddMS2 were set up as 3e6 and 5e5, respectively. Raw data were processed using Compound Discoverer 3.3 (Thermo Fisher Scientific), which included peak detection, retention time alignment (mass tolerance 5 ppm, max shift 0.2 min), isotopic grouping, background subtraction (sample/blank ratio ≥ 3), and compound annotation based on in-house LWHK library and online databases (mzCloud, Metabolika, ChemSpider).Normalization was performed using an internal standard to eliminate the matrix effect from different samples (𝑀𝑒𝑡𝑎𝑏𝑜𝑙𝑖𝑡𝑒 𝑃𝑒𝑎𝑘 𝐴𝑟𝑒𝑎/𝐼𝑛𝑡𝑒𝑟𝑛𝑎𝑙 𝑆𝑡𝑎𝑛𝑑𝑎𝑟𝑑 𝑃𝑒𝑎𝑘 𝐴𝑟𝑒𝑎).
Ion Mode:	POSITIVE

MS ID:	MS007276
Analysis ID:	AN007579
Instrument Name:	Thermo Q Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	MS spectra were obtained in negative ion mode. The Mass spectra were acquired using a top-5 data-dependent acquisition (DDA) method. Full MS scans were collected at a resolution of 70,000 (FWHM) over an m/z range of 80–1200. The data-dependent MS/MS (ddMS2) spectra were acquired with a spectral resolution of 17,500, isolation window of 1.5 m/z, stepped normalized CE with 15, 30, 45, and dynamic exclusion of 15.0 s. The AGC target for full MS and ddMS2 were set up as 3e6 and 5e5, respectively. Raw data were processed using Compound Discoverer 3.3 (Thermo Fisher Scientific), which included peak detection, retention time alignment (mass tolerance 5 ppm, max shift 0.2 min), isotopic grouping, background subtraction (sample/blank ratio ≥ 3), and compound annotation based on in-house LWHK library and online databases (mzCloud, Metabolika, ChemSpider).Normalization was performed using an internal standard to eliminate the matrix effect from different samples (𝑀𝑒𝑡𝑎𝑏𝑜𝑙𝑖𝑡𝑒 𝑃𝑒𝑎𝑘 𝐴𝑟𝑒𝑎/𝐼𝑛𝑡𝑒𝑟𝑛𝑎𝑙 𝑆𝑡𝑎𝑛𝑑𝑎𝑟𝑑 𝑃𝑒𝑎𝑘 𝐴𝑟𝑒𝑎).
Ion Mode:	NEGATIVE