Summary of Study ST002994

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 PR001864. The data can be accessed directly via it's Project DOI: 10.21228/M8S425 This work is supported by NIH grant, U2C- DK119886.

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Study IDST002994
Study TitleIntegrating uterine microbiome and metabolome to advance the understanding of the uterine environment in dairy cows with metritis
Study SummaryBackground: Metritis is a prevalent uterine disease that affects the welfare, fertility, and survival of dairy cows. The uterine microbiome from cows that develop metritis and those that remain healthy do not differ from calving until 2 days after calving, after which there is a dysbiosis of the uterine microbiome characterized by a shift towards opportunistic pathogens such as Fusobacteriota and Bacteroidota. Whether these opportunistic pathogens proliferate and overtake the uterine commensals could be determined by the type of substrates present in the uterus. The objective of this study was to integrate uterine metabolome and microbiome data to advance the understanding of metritis development in dairy cows. Holstein cows (n = 104) had uterine fluid collected at calving and at the day of metritis diagnosis. Cows with metritis (n = 52) were paired with cows without metritis (n = 52) based on days after calving. First, the uterine metabolome and microbiome were evaluated individually, and then integrated using network analyses. Results: The uterine metabolome differed both at calving and on the day of metritis diagnosis between cows with and without metritis. The uterine microbiome did not differ at calving but differed on the day of metritis diagnosis between cows with and without metritis. Omics integration was performed between 153 significant metabolites and 6 significant bacteria genera on the day of metritis diagnosis. A total of 49 metabolites were correlated with 3 bacteria genera (i.e. Fusobacteria, Porphyromonas and Bacteroides) on the day of metritis diagnosis. The main metabolites have been associated with attenuation of biofilm formation by commensal bacteria, pathogenic bacterial overgrowth, defense mechanisms against the immune system, tissue damage and inflammation, and immune dysregulation. Conclusions: The data integration presented herein helps advance the understanding of metritis development in dairy cows. The identified metabolites may be promising targets for future interventions aiming to reduce pathogenic bacterial growth in the uterus, and therefore, reducing the incidence of metritis.
Institute
University of Florida
Last NameCasaro
First NameSegundo
Address117 Deriso Hall, 2015 SW 16th Ave., Gainesville, FL 32610
Emailsegundocasaro@ufl.edu
Phone3522844016
Submit Date2023-11-30
Analysis Type DetailGC-MS
Release Date2024-03-01
Release Version1
Segundo Casaro Segundo Casaro
https://dx.doi.org/10.21228/M8S425
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001864
Project DOI:doi: 10.21228/M8S425
Project Title:Integrating uterine microbiome and metabolome to advance the understanding of the uterine environment in dairy cows with metritis
Project Summary:Background: Metritis is a prevalent uterine disease that affects the welfare, fertility, and survival of dairy cows. The uterine microbiome from cows that develop metritis and those that remain healthy do not differ from calving until 2 days after calving, after which there is a dysbiosis of the uterine microbiome characterized by a shift towards opportunistic pathogens such as Fusobacteriota and Bacteroidota. Whether these opportunistic pathogens proliferate and overtake the uterine commensals could be determined by the type of substrates present in the uterus. The objective of this study was to integrate uterine metabolome and microbiome data to advance the understanding of metritis development in dairy cows. Holstein cows (n = 104) had uterine fluid collected at calving and at the day of metritis diagnosis. Cows with metritis (n = 52) were paired with cows without metritis (n = 52) based on days after calving. First, the uterine metabolome and microbiome were evaluated individually, and then integrated using network analyses. Results: The uterine metabolome differed both at calving and on the day of metritis diagnosis between cows with and without metritis. The uterine microbiome did not differ at calving but differed on the day of metritis diagnosis between cows with and without metritis. Omics integration was performed between 153 significant metabolites and 6 significant bacteria genera on the day of metritis diagnosis. A total of 49 metabolites were correlated with 3 bacteria genera (i.e. Fusobacteria, Porphyromonas and Bacteroides) on the day of metritis diagnosis. The main metabolites have been associated with attenuation of biofilm formation by commensal bacteria, pathogenic bacterial overgrowth, defense mechanisms against the immune system, tissue damage and inflammation, and immune dysregulation. Conclusions: The data integration presented herein helps advance the understanding of metritis development in dairy cows. The identified metabolites may be promising targets for future interventions aiming to reduce pathogenic bacterial growth in the uterus, and therefore, reducing the incidence of metritis.
Institute:University of Florida
Department:Large Animal Clinical Sciences
Last Name:Segundo
First Name:Casaro
Address:117 Deriso Hall, 2015 SW 16th Ave., Gainesville, FL 32610
Email:segundocasaro@ufl.edu
Phone:3522844016

Subject:

Subject ID:SU003107
Subject Type:Mammal
Subject Species:Bos taurus
Taxonomy ID:9913
Gender:Female
Animal Housing:Free-stalls
Animal Feed:TMR

Factors:

Subject type: Mammal; Subject species: Bos taurus (Factor headings shown in green)

mb_sample_id local_sample_id Group Time Parity
SA3259459971_Calving_ConCon Calving Mult
SA3259469918_Calving_ConCon Calving Mult
SA3259479917_Calving_ConCon Calving Mult
SA3259489907_Calving_ConCon Calving Mult
SA3259499979_Calving_ConCon Calving Mult
SA3259509924_Calving_ConCon Calving Mult
SA3259519966_Calving_ConCon Calving Mult
SA3259529956_Calving_ConCon Calving Mult
SA3259539927_Calving_ConCon Calving Mult
SA3259549957_Calving_ConCon Calving Mult
SA3259559925_Calving_ConCon Calving Mult
SA3259569944_Calving_ConCon Calving Mult
SA3259579904_Calving_ConCon Calving Mult
SA3259589872_Calving_ConCon Calving Mult
SA3259599823_Calving_ConCon Calving Mult
SA3259609804_Calving_ConCon Calving Mult
SA32596110038_Calving_ConCon Calving Mult
SA32596210001_Calving_ConCon Calving Mult
SA3259639992_Calving_ConCon Calving Mult
SA3259649876_Calving_ConCon Calving Mult
SA3259659985_Calving_ConCon Calving Mult
SA3259669987_Calving_ConCon Calving Mult
SA3259679875_Calving_ConCon Calving Mult
SA3259689509_Calving_ConCon Calving Mult
SA3259699942_Calving_ConCon Calving Mult
SA3259709268_Calving_ConCon Calving Mult
SA3259719536_Calving_ConCon Calving Mult
SA3259729778_Calving_ConCon Calving Mult
SA3259739794_Calving_ConCon Calving Mult
SA3259749280_Calving_ConCon Calving Mult
SA3259759802_Calving_ConCon Calving Mult
SA3259769954_Calving_ConCon Calving Mult
SA3259779945_Calving_ConCon Calving Mult
SA3259789950_Calving_ConCon Calving Mult
SA32597910311_Calving_ConCon Calving Prim
SA32598010165_Calving_ConCon Calving Prim
SA32598110290_Calving_ConCon Calving Prim
SA32598210171_Calving_ConCon Calving Prim
SA32598310229_Calving_ConCon Calving Prim
SA32598410303_Calving_ConCon Calving Prim
SA32598510274_Calving_ConCon Calving Prim
SA32598610199_Calving_ConCon Calving Prim
SA32598710246_Calving_ConCon Calving Prim
SA32598810245_Calving_ConCon Calving Prim
SA32598910212_Calving_ConCon Calving Prim
SA32599010268_Calving_ConCon Calving Prim
SA32599110194_Calving_ConCon Calving Prim
SA32599210264_Calving_ConCon Calving Prim
SA32599310262_Calving_ConCon Calving Prim
SA32599410189_Calving_ConCon Calving Prim
SA32599510261_Calving_ConCon Calving Prim
SA32599610254_Calving_ConCon Calving Prim
SA3259979924_Diagnosis_ConCon Diagnosis Mult
SA3259989804_Diagnosis_ConCon Diagnosis Mult
SA3259999536_Diagnosis_ConCon Diagnosis Mult
SA3260009802_Diagnosis_ConCon Diagnosis Mult
SA3260019945_Diagnosis_ConCon Diagnosis Mult
SA3260029778_Diagnosis_ConCon Diagnosis Mult
SA3260039509_Diagnosis_ConCon Diagnosis Mult
SA3260049794_Diagnosis_ConCon Diagnosis Mult
SA3260059872_Diagnosis_ConCon Diagnosis Mult
SA3260069907_Diagnosis_ConCon Diagnosis Mult
SA3260079904_Diagnosis_ConCon Diagnosis Mult
SA3260089268_Diagnosis_ConCon Diagnosis Mult
SA3260099985_Diagnosis_ConCon Diagnosis Mult
SA3260109823_Diagnosis_ConCon Diagnosis Mult
SA3260119280_Diagnosis_ConCon Diagnosis Mult
SA3260129875_Diagnosis_ConCon Diagnosis Mult
SA3260139876_Diagnosis_ConCon Diagnosis Mult
SA3260149954_Diagnosis_ConCon Diagnosis Mult
SA3260159917_Diagnosis_ConCon Diagnosis Mult
SA3260169918_Diagnosis_ConCon Diagnosis Mult
SA3260179971_Diagnosis_ConCon Diagnosis Mult
SA3260189966_Diagnosis_ConCon Diagnosis Mult
SA3260199979_Diagnosis_ConCon Diagnosis Mult
SA3260209987_Diagnosis_ConCon Diagnosis Mult
SA32602110001_Diagnosis_ConCon Diagnosis Mult
SA3260229992_Diagnosis_ConCon Diagnosis Mult
SA3260239957_Diagnosis_ConCon Diagnosis Mult
SA3260249956_Diagnosis_ConCon Diagnosis Mult
SA3260259927_Diagnosis_ConCon Diagnosis Mult
SA3260269925_Diagnosis_ConCon Diagnosis Mult
SA3260279942_Diagnosis_ConCon Diagnosis Mult
SA3260289944_Diagnosis_ConCon Diagnosis Mult
SA3260299950_Diagnosis_ConCon Diagnosis Mult
SA32603010038_Diagnosis_ConCon Diagnosis Mult
SA32603110165_Diagnosis_ConCon Diagnosis Prim
SA32603210212_Diagnosis_ConCon Diagnosis Prim
SA32603310229_Diagnosis_ConCon Diagnosis Prim
SA32603410245_Diagnosis_ConCon Diagnosis Prim
SA32603510311_Diagnosis_ConCon Diagnosis Prim
SA32603610246_Diagnosis_ConCon Diagnosis Prim
SA32603710189_Diagnosis_ConCon Diagnosis Prim
SA32603810199_Diagnosis_ConCon Diagnosis Prim
SA32603910268_Diagnosis_ConCon Diagnosis Prim
SA32604010290_Diagnosis_ConCon Diagnosis Prim
SA32604110254_Diagnosis_ConCon Diagnosis Prim
SA32604210264_Diagnosis_ConCon Diagnosis Prim
SA32604310274_Diagnosis_ConCon Diagnosis Prim
SA32604410303_Diagnosis_ConCon Diagnosis Prim
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Collection:

Collection ID:CO003100
Collection Summary:All cows had uterine fluid collected at calving (first 24h after calving), and at diagnosis (day of metritis diagnosis). Briefly, cows’ cervix was stabilized by rectal palpation, the vulva was rinsed with alcohol 70% and dried with paper towels. Subsequently, a single-use plastic round-tip pipette (UterFlush pipettes, Van Beek) was introduced into the vagina at a 45° angle and manipulated through the cervix. A total of 50 mL of sterile saline solution (0.9% sodium chloride irrigation, Baxter) was infused into the uterine lumen using a 60-mL syringe (Covidien) attached to the end of the pipette. Uterine contents were homogenized, retrieved into the same 60-mL syringe, and transferred to a sterile 15-mL conical tube (VWR). After collection, tubes were placed on ice and transported to the laboratory within 2 hours. Once in the laboratory, uterine fluid samples were aliquoted into 2-mL microcentrifuge tubes (Eppendorf) and stored at -80 oC until essayed. One frozen uterine fluid aliquot was submitted to the University of California’s West Coast Metabolomics Center in Davis, CA for metabolome analysis.
Sample Type:Uterine fluid

Treatment:

Treatment ID:TR003116
Treatment Summary:This was a case-control study, hence, there were not treatments applied. Cows were self-assigned to the groups. Cows that developed metritis were paired with healthy cows by days in milk.

Sample Preparation:

Sampleprep ID:SP003113
Sampleprep Summary:Uterine fluid samples were aliquoted into 2-mL microcentrifuge tubes (Eppendorf) and stored at -80 oC until essayed.

Combined analysis:

Analysis ID AN004918
Analysis type MS
Chromatography type GC
Chromatography system Leco Pegasus IV GC
Column Restek Rtx-5Sil MS (30m x 0.25mm, 0.25um)
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus IV TOF
Ion Mode POSITIVE
Units peak heights

Chromatography:

Chromatography ID:CH003713
Instrument Name:Leco Pegasus IV GC
Column Name:Restek Rtx-5Sil MS (30m x 0.25mm, 0.25um)
Column Temperature:50-330
Flow Gradient:.
Flow Rate:1 mL min-1
Solvent A:.
Solvent B:.
Chromatography Type:GC

MS:

MS ID:MS004661
Analysis ID:AN004918
Instrument Name:Leco Pegasus IV TOF
Instrument Type:GC-TOF
MS Type:EI
MS Comments:Data are acquired using the following chromatographic parameters, with more details to be found in Fiehn O. et al. Plant J. 53 (2008) 691–704. Column: Restek corporation Rtx-5Sil MS (30 m length x 0.25 mm internal diameter with 0.25 μm film made of 95% dimethyl/5%diphenylpolysiloxane) Mobile phase: Helium Column temperature: 50-330°C Flow- rate: 1 mL min-1 Injection volume: 0.5 μL Injection: 25 splitless time into a multi-baffled glass liner Injection temperature: 50°C ramped to 250°C by 12°C s-1 Oven temperature program: 50°C for 1 min, then ramped at 20°C min-1 to 330°C, held constant for 5 min. The analytical GC column is protected by a 10 m long empty guard column which is cut by 20 cm intervals whenever the reference mixture QC samples indicate problems caused by column contaminations. We have validated that at this sequence of column cuts, no detrimental effects are detected with respect to peak shapes, absolute or relative metabolite retention times or reproducibility of quantifications. This chromatography method yields excellent retention and separation of primary metabolite classes (amino acids, hydroxyl acids, carbohydrates, sugar acids, sterols, aromatics, nucleosides, amines and miscellaneous compounds) with narrow peak widths of 2–3 s and very good within-series retention time reproducibility of better than 0.2 s absolute deviation of retention times. We use automatic liner exchanges after each set of 10 injections which we could show to reduce sample carryover for highly lipophilic compounds such as free fatty acids. Mass spectrometry parameters are used as follows: a Leco Pegasus IV mass spectrometer is used with unit mass resolution at 17 spectra s-1 from 80-500 Da at - 70 eV ionization energy and 1800 V detector voltage with a 230°C transfer line and a 250°C ion source.
Ion Mode:POSITIVE
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