Monitoring Perinatal Gut Microbiota in Mouse Models by Mass Spectrometry Approaches: Parental Genetic Background and Breastfeeding Effects.

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Among a variety of different feeding patterns, breastfeeding represents the best modality. In fact, the capacity of breast milk to modulate the composition of infants' gut microbiota leads to beneficial effects on their health. In this study, we used newborn mice as a model to evaluate the effect of parental genetic background (i.e., IgA-producing mice and IgA-deficient mice) and feeding modulation (i.e., maternal feeding and cross-feeding) on the onset and shaping of gut microbiota after birth. To investigate these topics, we used either a culturomic approach that employed Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MS), or bottom-up Liquid Chromatography, with subsequent MSMS shotgun metaproteomic analysis that compared and assembled results of the two techniques. We found that the microbial community was enriched by lactic acid bacteria when pups were breastfed by wild-type (WT) mothers, while IgA-deficient milk led to an increase in the opportunistic bacterial pathogen (OBP) population. Cross-feeding results suggested that IgA supplementation promoted the exclusion of some OBPs and the temporary appearance of beneficial species in pups fed by WT foster mothers. Our results show that both techniques yield a picture of microbiota from different angles and with varying depths. In particular, our metaproteomic pipeline was found to be a reliable tool in the description of microbiota. Data from these studies are available via ProteomeXchange, with identifier PXD004033.", "claims": [{"id": "claim-method", "statement": "The Shannon–Wiener index was calculated by the formula:", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27725814", "locator": "sections[5] \"Metaproteomic Procedures\" paragraph 6", "quote": "The Shannon–Wiener index was calculated by the formula:"}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data from these studies are available via ProteomeXchange, with identifier PXD004033.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27725814", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data from these studies are available via ProteomeXchange, with identifier PXD004033."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using the Shannon–Wiener index to assess alpha diversity, the study found that WT-mother milk enriched lactic acid bacteria whereas IgA-deficient milk increased opportunistic bacterial pathogens; the source data are available through ProteomeXchange under identifier PXD004033.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27725814", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We found that the microbial community was enriched by lactic acid bacteria when pups were breastfed by wild-type (WT) mothers, while IgA-deficient milk led to an increase in the opportunistic bacterial pathogen (OBP) population."}, {"asset": "source:pmid:27725814", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data from these studies are available via ProteomeXchange, with identifier PXD004033."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using the Shannon–Wiener index to assess alpha diversity, the study found that WT-mother milk enriched lactic acid bacteria whereas IgA-deficient milk increased opportunistic bacterial pathogens; the source data are available through ProteomeXchange under identifier PXD004033.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:27725814"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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