دورية أكاديمية
Actively replicating gut bacteria identified by 5-ethynyl-2'-deoxyuridine (EdU) click chemistry and cell sorting.
العنوان: | Actively replicating gut bacteria identified by 5-ethynyl-2'-deoxyuridine (EdU) click chemistry and cell sorting. |
---|---|
المؤلفون: | Beauchemin ET; Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada., Hunter C; Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada., Maurice CF; Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada.; McGill Centre for Microbiome Research, McGill University, Montreal, Quebec, Canada. |
المصدر: | Gut microbes [Gut Microbes] 2023 Jan-Dec; Vol. 15 (1), pp. 2180317. |
نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
اللغة: | English |
بيانات الدورية: | Publisher: Taylor & Francis Country of Publication: United States NLM ID: 101495343 Publication Model: Print Cited Medium: Internet ISSN: 1949-0984 (Electronic) Linking ISSN: 19490976 NLM ISO Abbreviation: Gut Microbes Subsets: MEDLINE |
أسماء مطبوعة: | Publication: 2015- : Philadelphia, PA : Taylor & Francis Original Publication: Austin, Tex. : Landes Bioscience |
مواضيع طبية MeSH: | Click Chemistry*/methods , Gastrointestinal Microbiome*, Humans ; Mice ; Animals ; Deoxyuridine/chemistry ; Deoxyuridine/metabolism ; Bacteria/metabolism |
مستخلص: | The composition of the intestinal bacterial community is well described, but recent research suggests that the metabolism of these bacteria plays a larger role in health than which species are present. One fundamental aspect of gut bacterial metabolism that remains understudied is bacterial replication. Indeed, there exist few techniques which can identify actively replicating gut bacteria. In this study, we aimed to address this gap by adapting 5-ethynyl-2'-deoxyuridine (EdU) click chemistry (EdU-click), a metabolic labeling method, coupled with fluorescence-activated cell sorting and sequencing (FACS-Seq) to characterize replicating gut bacteria. We first used EdU-click with human gut bacterial isolates and show that many of them are amenable to this technique. We then optimized EdU-click and FACS-Seq for murine fecal bacteria and reveal that Prevotella UCG-001 and Ileibacterium are enriched in the replicating fraction. Finally, we labeled the actively replicating murine gut bacteria during exposure to cell wall-specific antibiotics in vitro . We show that regardless of the antibiotic used, the actively replicating bacteria largely consist of Ileibacterium , suggesting the resistance of this taxon to perturbations. Overall, we demonstrate how combining EdU-click and FACSeq can identify the actively replicating gut bacteria and their link with the composition of the whole community in both homeostatic and perturbed conditions. This technique will be instrumental in elucidating in situ bacterial replication dynamics in a variety of other ecological states, including colonization and species invasion, as well as for investigating the relationship between the replication and abundance of bacteria in complex communities. |
References: | Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):E2329-38. (PMID: 24843156) PLoS One. 2020 Feb 27;15(2):e0229740. (PMID: 32106263) Nat Microbiol. 2017 Jun 26;2:17099. (PMID: 28650431) Mol Biol Evol. 2021 Dec 9;38(12):5825-5829. (PMID: 34597405) Cell Host Microbe. 2017 Apr 12;21(4):433-442. (PMID: 28407481) Proc Natl Acad Sci U S A. 2021 Mar 23;118(12):. (PMID: 33723043) Bioinformatics. 2016 Oct 1;32(19):3047-8. (PMID: 27312411) J Appl Microbiol. 2000 Nov;89(5):815-24. (PMID: 11119156) Appl Environ Microbiol. 1990 May;56(5):1367-72. (PMID: 2160223) Proc Natl Acad Sci U S A. 2008 Feb 19;105(7):2415-20. (PMID: 18272492) J Nutr. 2018 Apr 1;148(4):562-572. (PMID: 29659960) Cell Metab. 2014 Jan 7;19(1):162-171. (PMID: 24374218) BMC Microbiol. 2021 Apr 23;21(1):125. (PMID: 33888068) FEMS Microbiol Ecol. 2011 Oct;78(1):17-30. (PMID: 21470255) Methods. 2009 May;48(1):8-13. (PMID: 19245839) Cell Host Microbe. 2019 Feb 13;25(2):195-209. (PMID: 30763534) Genome Res. 2022 Mar;32(3):558-568. (PMID: 34987055) Can J Infect Dis. 2001 Jul;12(4):254-6. (PMID: 18159347) Nucleic Acids Res. 2020 Jan 8;48(D1):D517-D525. (PMID: 31665441) Nat Biotechnol. 2016 Dec;34(12):1256-1263. (PMID: 27819664) Front Microbiol. 2017 Nov 07;8:2114. (PMID: 29163406) Nature. 2010 Mar 4;464(7285):59-65. (PMID: 20203603) Nat Methods. 2012 Jun 28;9(7):676-82. (PMID: 22743772) Nat Microbiol. 2018 Mar;3(3):337-346. (PMID: 29311644) Inflamm Bowel Dis. 2015 Jan;21(1):139-53. (PMID: 25248007) Nat Rev Microbiol. 2019 Aug;17(8):497-511. (PMID: 31249397) Mucosal Immunol. 2016 Jan;9(1):83-97. (PMID: 25943272) Nat Microbiol. 2019 Feb;4(2):293-305. (PMID: 30531976) Arch Biochem Biophys. 2021 Dec 15;714:109080. (PMID: 34742934) Sci Adv. 2020 Sep 4;6(36):. (PMID: 32917613) Nat Rev Microbiol. 2017 Jul;15(7):397-408. (PMID: 28461690) J Physiol. 2021 Mar;599(5):1487-1511. (PMID: 33450094) Nat Rev Microbiol. 2020 Apr;18(4):241-256. (PMID: 32055027) J Biol Chem. 2021 Nov;297(5):101345. (PMID: 34717955) Science. 2015 Sep 4;349(6252):1101-1106. (PMID: 26229116) Sci Rep. 2018 Nov 22;8(1):17278. (PMID: 30467421) BMC Microbiol. 2014 Jul 02;14:176. (PMID: 24993343) Ecology. 2017 Feb;98(2):555-564. (PMID: 27882545) J Struct Biol. 2014 Mar;185(3):243-9. (PMID: 24473063) Genome Med. 2016 Apr 27;8(1):51. (PMID: 27122046) Nature. 2012 Sep 13;489(7415):220-30. (PMID: 22972295) Sci Rep. 2021 May 10;11(1):9841. (PMID: 33972615) mSystems. 2020 Aug 4;5(4):. (PMID: 32753501) Genome Res. 2015 Jul;25(7):1043-55. (PMID: 25977477) Int J Mol Sci. 2020 Sep 10;21(18):. (PMID: 32927807) Nat Commun. 2019 Mar 21;10(1):1317. (PMID: 30899006) Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20404-9. (PMID: 22143759) Int J Syst Evol Microbiol. 2017 May;67(5):1247-1254. (PMID: 28100298) Nat Commun. 2019 Oct 11;10(1):4665. (PMID: 31604953) Nat Commun. 2015 Oct 29;6:8487. (PMID: 26511661) Nat Commun. 2015 Nov 30;6:10039. (PMID: 26615910) ISME J. 2021 Jan;15(1):183-195. (PMID: 32939027) Gut Microbes. 2021 Jan-Dec;13(1):1-15. (PMID: 33779505) Science. 2006 Jun 2;312(5778):1355-9. (PMID: 16741115) Nat Biotechnol. 2019 Aug;37(8):852-857. (PMID: 31341288) J Biol Chem. 2020 May 1;295(18):5871-5890. (PMID: 32205447) Environ Microbiol. 2010 Jan;12(1):74-82. (PMID: 19725866) |
معلومات مُعتمدة: | PJT-149098 Canada CIHR |
فهرسة مساهمة: | Keywords: 5-ethynyl-2‘-deoxyuridine; Click chemistry; EdU; bacterial physiology; bacterial replication; cell sorting; flow cytometry; gut microbiota Local Abstract: [plain-language-summary] The bacteria that live in our guts are known to influence our intestinal and overall health. Though we know a lot about which kinds of bacteria are in our guts, we still don’t know much about which bacteria are actually alive and growing. This is important to know, because bacteria that are growing, or replicating, are more likely to impact our health than bacteria which are not replicating. Our research group aimed to address this issue by developing a new technique that can identify which gut bacteria are actively replicating. We first tested this technique on specific gut bacteria, and then we made sure the technique worked when it was used on the gut bacteria of mice. By using this technique, we identified several types of mouse gut bacteria that were actively replicating. We also demonstrated one possible application of this technique by using it to identify mouse gut bacteria that were able to replicate after they were grown with antibiotics. Overall, we have introduced a new technique to identify replicating gut bacteria and show how it can be used to increase our knowledge on which bacteria are growing in the gut. This technique will help us identify which bacteria may be more important to our health due to their active growth. |
سلسلة جزيئية: | figshare 10.6084/m9.figshare.c.6103014.v1 |
المشرفين على المادة: | G373S00W2J (5-ethynyl-2'-deoxyuridine) W78I7AY22C (Deoxyuridine) |
تواريخ الأحداث: | Date Created: 20230223 Date Completed: 20230227 Latest Revision: 20230304 |
رمز التحديث: | 20231215 |
مُعرف محوري في PubMed: | PMC9980609 |
DOI: | 10.1080/19490976.2023.2180317 |
PMID: | 36823031 |
قاعدة البيانات: | MEDLINE |
تدمد: | 1949-0984 |
---|---|
DOI: | 10.1080/19490976.2023.2180317 |