Dataset Information

Linking Intestinal Microorganisms to their Diet-derived Growth Substrates Using Protein Stable Isotope Fingerprinting (Protein-SIF)

ABSTRACT: The aim of this study was to directly link intestinal microorganisms to their diet-derived in vivo growth substrates using protein stable isotope fingerprinting (“Protein-SIF”)(Kleiner et al. 2018, PNAS 115(24)). We conducted studies in gnotobiotic mice (C57BL/6J) colonized with a community of 13 human-derived bacterial strains (Desai et al. 2016, Cell 167(5)). There were two groups of mice: group 1 consisted of 5 mice, and group 2 of 6 mice. All mice were fed defined diets modeled on the AIN-93G (EnvigoTeklad) varying in one ingredient source, and a “standard chow” (LabDiet 5010) as a baseline diet before and after the defined diets. Group 1 mice were fed diets differing in protein source (casein, egg whites, soy protein). Group 2 mice were fed diets differing in fiber source (cellulose, inulin, corn fiber), and fat source (corn oil, soybean oil, sunflower oil). Stable carbon isotope ratios for each dietary component were measured using IRMS (table with values is included in submission). Each diet was introduced for 7 days, and fecal samples were collected on the 7th day. We processed samples from the group 1 mice and the group 2 mice as two separate batches. We analyzed the samples by LC-MS/MS. Each sample was run in four consecutive technical replicates to increase the available number of MS1 spectra for SIF calculations. Data were analyzed with Proteome Discoverer followed by the calis-p software for Protein-SIF (https://sourceforge.net/projects/calis-p/). Additionally, this dataset includes diet samples and purified dietary components that were extracted using the same approach as the fecal samples, as well as LC-MS/MS runs of human hair derived peptides used for SIF calibration.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Bacteroides Uniformis Atcc 8492 Bacteroides Caccae Atcc 43185 Zea Mays Subsp. Mays (maize) Helianthus Annuus (common Sunflower) Akkermansia Muciniphila Atcc Baa-835 Beta Vulgaris (sugar Beet) Barnesiella Intestinihominis Yit 11860 Agathobacter Rectalis Dsm 17629 Glycine Max Faecalibacterium Prausnitzii M21/2 [clostridium] Symbiosum Wal-14163 Bacteroides Ovatus Atcc 8483 Bos Taurus (bovine) Gallus Gallus (chicken) Roseburia Intestinalis L1-82 Collinsella Aerofaciens Atcc 25986 Marvinbryantia Formatexigens Dsm 14469 Bacteroides Thetaiotaomicron (strain Atcc 29148 / Dsm 2079 / Nctc 10582 / E50 / Vpi-5482) Escherichia Coli Hs Mus Musculus (mouse)

TISSUE(S): Feces

SUBMITTER: J. Alfredo Blakeley Ruiz

LAB HEAD: Manuel Kleiner

PROVIDER: PXD046928 | Pride | 2024-12-16

REPOSITORIES: Pride

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			Action	DRS
	10_BAS_140min_600ng_Rep.msf	Msf
	10_BAS_140min_600ng_Rep1_Run5.raw	Raw
	10_BAS_140min_600ng_Rep2_Run5.raw	Raw
	10_BAS_140min_600ng_Rep3_Run5.raw	Raw
	10_BAS_140min_600ng_Rep4_Run5.raw	Raw

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Project description:The aim of this experiment was to explore transcriptomic changes in the distal gut of Altantic salmon fed five experimental and two control diets. The experimental diets were isonitrogenous, isolipidic and isocaloric. They had similar content of fish meal (~22%) and similar total plant protein content (~45%), but differed in the contents of soya protein concentrate (SPC) and bean protein concentrate (BPC). These two ingredients were used to replace each other (either partially or fully) at the levels of incorporation ranging from 0 to 45%, with ~11% increments. As a result, the experimental diets contained either 45% SPC and 0% BPC (S45), 34% SPC and 11% BPC (S34B11), 22% SPC and 22% BPC (S22B22), 11% SPC and 34% BPC (S11B34) or 0% SPC and 45% BPC (B45). The S45 and B45 diets were single plant protein diets, while the others (S34B11, S22B22 and S11B34) were mixed plant protein diets. The control diets were enriched with fish meal (FM diet) or soybean meal (SBM diet) to provide negative and positive controls for gut inflammation (enteritis), respectively. The study was conducted at EWOS Innovation Research Facility in Dirdal (Norway) Atlantic salmon (Salmo salar L.) of the SalmoBreed strain were supplied as fertilized eggs and hatched on site. Mixed-sex juvenile salmon in groups of ~150 fish were transferred to 26 indoor tanks (0.6 x 0.6 x 0.6 m), with ~60 L of freshwater flowing at a rate of 3.9 L/min and continuous aeration. The temperature of water was regulated at 13°C and all animals were exposed to a constant light regime (24 h light/day). Fish were fed a commercial EWOS Start 1 diet and acclimated to the experimental conditions for 2 weeks, after which (at body mass ~1.5 g) they were subjected to a 56-day feeding trial. Tanks were randomly assigned to the dietary treatments, with 4 replicate tanks per each experimental diet (S45, S34B11, S22B22, S11B34 and B45) and 3 replicate tanks per each control diet (FM and SBM diets). Fish were fed to satiation prior to the feeding trial and during the dietary manipulation using automatic band feeders (Holland Technology, Norway). During the feeding trial, all fish in each tank had their biomass recorded on days 0 (start of experiment), 14, 28, 42 and 56 (end of experiment) for evaluation of growth performance.

Dataset Information

Linking Intestinal Microorganisms to their Diet-derived Growth Substrates Using Protein Stable Isotope Fingerprinting (Protein-SIF)

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