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Metaproteomics of Human Breast Milk and Formula-fed Neonatal Piglets

ABSTRACT: The benefits of breastfeeding infants are well characterized, including those on the immune system. However, determining the mechanism by which human breast milk (HBM) elicits effects on immune response requires investigation in an appropriate animal model. In the current study we used neonatal piglets and compared their gut microbiome using mass spectrometry based metaproteomics

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Sus Scrofa Domesticus (domestic Pig)

TISSUE(S): Cecum

SUBMITTER: Boris Zybailov

LAB HEAD: Boris Zybailov

PROVIDER: PXD025432 | Pride | 2021-11-03

REPOSITORIES: Pride

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			Action	DRS
	35peptides_1_1_0.mzid.gz	Mzid
	36peptides_1_1_0.mzid.gz	Mzid
	37peptides_1_1_0.mzid.gz	Mzid
	38peptides_1_1_0.mzid.gz	Mzid
	39peptides_1_1_0.mzid.gz	Mzid

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Publications

Milk Formula Diet Alters Bacterial and Host Protein Profile in Comparison to Human Milk Diet in Neonatal Piglet Model.

Rosa Fernanda F Zybailov Boris L BL Glazko Galina V GV Rahmatallah Yasir Y Byrum Stephanie S Mackintosh Samuel G SG Bowlin Anne K AK Yeruva Laxmi L

Nutrients 20211022 11

The metaproteome profiling of cecal contents collected from neonatal piglets fed pasteurized human milk (HM) or a dairy-based infant formula (MF) from postnatal day (PND) 2 to 21 were assessed. At PND 21, a subset of piglets from each group (<i>n</i> = 11/group) were euthanized, and cecal contents were collected for further metaproteome analysis. Cecal microbiota composition showed predominantly more Firmicutes phyla and <i>Lachnospiraceae</i> family in the lumen of cecum of HM-fed piglets in co ...[more]

PMID: 34835974

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Investigation of Resistant Starch effect on gut microbiome in 5/6 nephrectomy mouse model of Chronic Kidney Disease

Project description:Background. Resistant Starch (RS) improves CKD outcomes. In this report we study how RS modulates host-microbiome interactions in CKD by measuring changes in abundance of proteins and bacteria in the gut. In addition, we demonstrate RS-mediated reduction in CKD-induced kidney damage. Methods. Eight mice underwent 5/6 nephrectomy to induce CKD and 8 served as healthy controls. CKD and Healthy (H) groups were further split into those receiving RS (CKDRS, n=4; HRS, n=4) and those on normal diet (CKD, n=4, H, n=4). Kidney injury was evaluated by measuring BUN/creatinine and by most-mortem histopathological evaluation. Cecal contents were analyzed mass spectrometry-based metaproteomics. PEAKS Studio was used to identify peptides via de novo sequencing. A set of R/Bioconductor packages and in house written scripts was further used to infer bacteria present, to evaluate changes in proteins and bacterial abundances, and to perform statistical analysis and hierarchical clustering. Results. The 5/6 nephrectomy compromised kidney function as seen by an increase in creatinine and BUN. Representative photomicrographs of trichrome-stained kidney sections showed reduced tubulointerstitial injury in CKD mice fed HAM-RS2 diet comparing to CKD mice fed normal diet. Identified organisms and proteins point toward a higher population of butyrate-producing bacteria, and reduced abundance of mucin-degrading bacteria. Conclusion. Resistant starch slows the progression of chronic kidney disease. Gut barrier function through maintenance of the mucin barrier plays a role in RS-associated improvements in CKD phenotype. Resistant starch supplementation leads to the active bacterial proliferation and the reduction of harmful bacterial metabolites.

2020-10-19 | PXD019623 | Pride

Venomics reveals an ant venom peptidome

Project description:In this study, we used a venomics strategy to identify the molecular diversity of the venom peptidome from the myrmicine ant Tetramorium bicarinatum.

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Immune response disfunction in chronic lymphocytic leukemia: Dissecting molecular mechanism by multipronged functional proteomics approaches. Crucial parameters for the evaluation of Immunopeptidomic analysis.

Project description:The main goal of the current project is to design and develop a multipronged functional proteomics strategy, with translation into the clinic, for deciphering all the microenvironment protein factors involved in the dysfunction of the immune system in MBLhi and CLL patients in order to understand the disease better and design effective treatment and management strategies. This novel strategy will be performed by a systematic and comprehensive integration of complementary functional proteomics approaches which include antigen presentation and recognition by Immunopeptidomics. In this work, different protein extraction methods (Protocol A and Protocol B) and different immunoprecipitation (IP) solid supports (Protocol #1 and Protocol #2) are performed, using four tumor cell lines as a model. The study samples will be identified by the name of the cell line, followed by the number of the IP protocol used, followed by the letter corresponding to the protein extraction protocol used. H460_1A: 0520_1_2 H460_1B: 0520_2_1 JURKAT_1A: 0520_3_1 JURKAT_1B: 0520_4_1 H460_2B: 0520_5_1 CACO-2_2B: 0520_6_1 MDA-MB-231_2B: 0520_7_1

2024-10-17 | PXD038165 | Pride

A draft genome sequence of the elusive giant squid, Architeuthis dux

Project description:We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long-reads and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from three different tissue types from three other species of squid species (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein coding genes supported by evidence and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.

2019-12-16 | PXD016522 | Pride

Shot-gun proteomic analysis of S Cerevisiae, Candidatus Accumulibacter and Clostridium sacch.

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2021-03-15 | PXD016992 | Pride

A novel peptide from Bothrops cotiara peptidome

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2023-10-20 | PXD041473 | Pride

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2023-10-23 | PXD045732 | Pride

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