Summary of Study ST001862

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 PR001175. The data can be accessed directly via it's Project DOI: 10.21228/M8TM5F 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	ST001862
Study Title	Cross-feeding between intestinal pathobionts promotes their overgrowth during undernutrition
Study Summary	Child undernutrition is a global health issue associated with a high burden of infectious disease. Undernourished children display an overabundance of intestinal pathogens and pathobionts, and these bacteria induce enteric dysfunction in undernourished mice; however, the cause of their overgrowth remains poorly defined. Here, we show that disease-inducing human isolates of Enterobacteriaceae and Bacteroidales spp. are capable of multi-species symbiotic cross-feeding, resulting in synergistic growth of a mixed community in vitro. Growth synergy occurs uniquely under malnourished conditions limited in protein and iron: in this context, Bacteroidales spp. liberate diet- and mucin-derived sugars and Enterobacteriaceae spp. enhance the bioavailability of iron. Analysis of human microbiota datasets reveals that Bacteroidaceae and Enterobacteriaceae are strongly correlated in undernourished children, but not in adequately nourished children, consistent with a diet-dependent growth synergy in the human gut. Together these data suggest that dietary cross-feeding fuels the overgrowth of pathobionts in undernutrition.
Institute	University of British Columbia
Department	Michael Smith Laboratories
Last Name	Huus
First Name	Kelsey
Address	3125 East Mall
Email	khuus@msl.ubc.ca
Phone	+1-604-822-2210
Submit Date	2021-07-11
Raw Data Available	Yes
Raw Data File Type(s)	d
Analysis Type Detail	LC-MS
Release Date	2021-11-06
Release Version	1

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Sample Preparation:

Sampleprep ID:	SP001945
Sampleprep Summary:	Sugars Analysis Low molecular weight sugars and NAc-sugar amines were quantified by LC-MRM/MS at The Metabolomics Innovation Centre (TMIC) commercial service (University of Victoria , Genome BC Proteomics Centre), according to previously published UPLC-MRM/MS methods (Han et al 2016, Electrophoresis), with necessary modifications. In brief, a mixed stock solution of 13 low-MW sugars and 4 N-acetyl sugar amines was prepared with the use of their standard substances in 80% methanol at 500µM for each compound. This solution was then serially diluted with the same solvent to prepare calibration solutions in a concentration range of 0.002 to 125µM. For chemical derivatization, 20µL of each medium sample or each calibration solution was mixed in turn with 20µL of an internal standard solution containing 13C6-glucose, 13C6-mannose, 13C6-fructose and 13C5-ribose in water, 40µL of 200-mM 3-nitrophenylhydrazine hydrochloride solution in 60% methanol and 40µL of 200-mM EDC.HCl solution prepared in a mixed solvent of methanol/water/pyridine (60:40:5, v/v/v). The mixture was allowed to react at 50ºC for 90 min. SCFA Analysis Quantification of short-chain fatty acids was performed in-house according to a method developed by Han et al., with minor modifications(Han et al 2015, Analytica Chimica Acta). Briefly, 500µL of supernatant were mixed with 500µL of 50 % acetonitrile, then the mixture was vortexed for 5 minutes and centrifuged at 7000 x g for 5 minutes. 50 µL of the organic phase were derivatized adding 20µL of 200mM 3NPH in 50 % acetonitrile and 20 µL 120 mM EDC solution of 6 % pyridine in 50 % acetonitrile. The mixture was left under agitation at 40ºC for 30 minutes. After this time reaction was stopped adding 100 µL of 0.1 % formic acid in 90 % acetonitrile.

Sampleprep ID:

SP001945

Sampleprep Summary:

Sugars Analysis Low molecular weight sugars and NAc-sugar amines were quantified by LC-MRM/MS at The Metabolomics Innovation Centre (TMIC) commercial service (University of Victoria , Genome BC Proteomics Centre), according to previously published UPLC-MRM/MS methods (Han et al 2016, Electrophoresis), with necessary modifications. In brief, a mixed stock solution of 13 low-MW sugars and 4 N-acetyl sugar amines was prepared with the use of their standard substances in 80% methanol at 500µM for each compound. This solution was then serially diluted with the same solvent to prepare calibration solutions in a concentration range of 0.002 to 125µM. For chemical derivatization, 20µL of each medium sample or each calibration solution was mixed in turn with 20µL of an internal standard solution containing 13C6-glucose, 13C6-mannose, 13C6-fructose and 13C5-ribose in water, 40µL of 200-mM 3-nitrophenylhydrazine hydrochloride solution in 60% methanol and 40µL of 200-mM EDC.HCl solution prepared in a mixed solvent of methanol/water/pyridine (60:40:5, v/v/v). The mixture was allowed to react at 50ºC for 90 min. SCFA Analysis Quantification of short-chain fatty acids was performed in-house according to a method developed by Han et al., with minor modifications(Han et al 2015, Analytica Chimica Acta). Briefly, 500µL of supernatant were mixed with 500µL of 50 % acetonitrile, then the mixture was vortexed for 5 minutes and centrifuged at 7000 x g for 5 minutes. 50 µL of the organic phase were derivatized adding 20µL of 200mM 3NPH in 50 % acetonitrile and 20 µL 120 mM EDC solution of 6 % pyridine in 50 % acetonitrile. The mixture was left under agitation at 40ºC for 30 minutes. After this time reaction was stopped adding 100 µL of 0.1 % formic acid in 90 % acetonitrile.