Inviting an author to review:
Find an author and click ‘Invite to review selected article’ near their name.
Search for authorsSearch for similar articles
11
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Indole-3-lactic acid associated with Bifidobacterium-dominated microbiota significantly decreases inflammation in intestinal epithelial cells

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Background

          Bifidobacterium longum subsp. infantis ( B. infantis) is a commensal bacterium that colonizes the gastrointestinal tract of breast-fed infants. B. infantis can efficiently utilize the abundant supply of oligosaccharides found in human milk (HMO) to help establish residence. We hypothesized that metabolites from B. infantis grown on HMO produce a beneficial effect on the host.

          Results

          In a previous study, we demonstrated that B. infantis routinely dominated the fecal microbiota of a breast fed Bangladeshi infant cohort (1). Characterization of the fecal metabolome of binned samples representing high and low B. infantis populations from this cohort revealed higher amounts of the tryptophan metabolite indole-3-lactic acid (ILA) in feces with high levels of B. infantis. Further in vitro analysis confirmed that B. infantis produced significantly greater quantities of the ILA when grown on HMO versus lactose, suggesting a growth substrate relationship to ILA production. The direct effects of ILA were assessed in a macrophage cell line and intestinal epithelial cell lines. ILA (1-10 mM) significantly attenuated lipopolysaccharide (LPS)-induced activation of NF-kB in macrophages. ILA significantly attenuated TNF-α- and LPS-induced increase in the pro-inflammatory cytokine IL-8 in intestinal epithelial cells. ILA increased mRNA expression of the aryl hydrogen receptor (AhR)-target gene CYP1A1 and nuclear factor erythroid 2–related factor 2 (Nrf2)-targeted genes glutathione reductase 2 (GPX2), superoxide dismutase 2 (SOD2), and NAD(P) H dehydrogenase (NQO1). Pretreatment with either the AhR antagonist or Nrf-2 antagonist inhibited the response of ILA on downstream effectors.

          Conclusions

          These findings suggest that ILA, a predominant metabolite from B. infantis grown on HMO and elevated in infant stool high in B. infantis, and protects gut epithelial cells in culture via activation of the AhR and Nrf2 pathway.

          Supplementary Information

          The online version contains supplementary material available at 10.1186/s12866-020-02023-y.

          Related collections

          Most cited references72

          • Record: found
          • Abstract: not found
          • Article: not found

          QIIME allows analysis of high-throughput community sequencing data.

            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

            Background The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data. Results Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research. Conclusions The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

              DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community amplicon sequencing on the HiSeq2000 and MiSeq Illumina platforms, and apply that protocol to sequence 24 microbial communities from host-associated and free-living environments. A critical question as more sequencing platforms become available is whether biological conclusions derived on one platform are consistent with what would be derived on a different platform. We show that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the HiSeq2000 versus the MiSeq) and across the sequenced regions of amplicons.
                Bookmark

                Author and article information

                Contributors
                heraybould@ucdavis.edu
                Journal
                BMC Microbiol
                BMC Microbiol
                BMC Microbiology
                BioMed Central (London )
                1471-2180
                23 November 2020
                23 November 2020
                2020
                : 20
                : 357
                Affiliations
                [1 ]GRID grid.27860.3b, ISNI 0000 0004 1936 9684, Department of Anatomy, Physiology and Cell Biology, , School of Veterinary Medicine, University of California, ; Davis, CA 95616 USA
                [2 ]GRID grid.27860.3b, ISNI 0000 0004 1936 9684, Foods for Health Institute, University of California, ; Davis, CA USA
                [3 ]GRID grid.27860.3b, ISNI 0000 0004 1936 9684, Department of Food Science and Technology, , University of CA, ; Davis, CA USA
                [4 ]GRID grid.27860.3b, ISNI 0000 0004 1936 9684, Department of Chemistry, , University of California, ; Davis, CA USA
                [5 ]GRID grid.414142.6, ISNI 0000 0004 0600 7174, Enteric and Respiratory Infections Unit, Infectious Diseases Division, icddr,b, ; Dhaka, Bangladesh
                [6 ]GRID grid.507310.0, US Department of Agriculture, Western Human Nutrition Research Center, ; Davis, CA USA
                [7 ]GRID grid.27860.3b, ISNI 0000 0004 1936 9684, Department of Nutrition, , University of California, ; Davis, CA USA
                Author information
                http://orcid.org/0000-0002-7501-8091
                Article
                2023
                10.1186/s12866-020-02023-y
                7681996
                33225894
                5f4d412e-1f69-45e0-be2a-4c203dbb84cc
                © The Author(s) 2020

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                : 11 May 2020
                : 27 October 2020
                Funding
                Funded by: National Institutes of Health (US)
                Award ID: AT006180
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: AT007079
                Award ID: AT008759
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100007917, Agricultural Research Service;
                Award ID: 2032-53000-001-00-D
                Award Recipient :
                Funded by: World Health Organization
                Award ID: 2010168947
                Award Recipient :
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2020

                Microbiology & Virology
                milk oligosaccharides,aryl-hydrocarbon receptor,nuclear factor erythroid 2–related factor 2,indole-3-lactic acid

                Comments

                Comment on this article

                scite_

                Similar content373

                Cited by65

                Most referenced authors1,411