f Exogenous Engraftment: Host-specificity in Probiotic Administration

References

1. ParfreyL.W. MoreauC.S. RussellJ.A. Introduction: The host‐associated microbiome: Pattern, process and function.Mol. Ecol.20182781749176510.1111/mec.1470629727917
   [Google Scholar]
2. NIH Office of Dietary Supplements2022Available from: https://ods.od.nih.gov/factsheets/Probiotics-HealthProfessional/
3. GibbonsS.M. Defining microbiome health through a host lens.mSystems201943e00155e1910.1128/mSystems.00155‑1931120028
   [Google Scholar]
4. LongT.J. Home-field advantage: Why host-specificity is important for therapeutic microbial engraftment.Microbiol. Biotechnol. Lett.20235112412710.48022/mbl.2212.12002
   [Google Scholar]
5. WalterJ. Murine gut microbiota-diet trumps genes.Cell Host Microbe20151713510.1016/j.chom.2014.12.00425590753
   [Google Scholar]
6. WalterJ. Maldonado-GómezM.X. MartínezI. To engraft or not to engraft: An ecological framework for gut microbiome modulation with live microbes.Curr. Opin. Biotechnol.20184912913910.1016/j.copbio.2017.08.00828866242
   [Google Scholar]
7. SzajewskaH. GuarinoA. HojsakI. Use of probiotics for management of acute gastroenteritis: A position paper by the ESPGHAN working group for probiotics and prebiotics.J. pediatr. gastroenterol. nutr.201458453153910.1097/MPG.000000000000032024614141
   [Google Scholar]
8. KangD.W. AdamsJ.B. GregoryA.C. Microbiota transfer therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study.Microbiome2017511010.1186/s40168‑016‑0225‑728122648
   [Google Scholar]
9. LiS.S. ZhuA. BenesV. Durable coexistence of donor and recipient strains after fecal microbiota transplantation.Science2016352628558658910.1126/science.aad885227126044
   [Google Scholar]
10. ChungH. PampS.J. HillJ.A. Gut immune maturation depends on colonization with a host-specific microbiota.Cell201214971578159310.1016/j.cell.2012.04.03722726443
    [Google Scholar]
11. MallottE.K. AmatoK.R. Host specificity of the gut microbiome.Nat. Rev. Microbiol.2021191063965310.1038/s41579‑021‑00562‑334045709
    [Google Scholar]
12. BruckerR.M. BordensteinS.R. The hologenomic basis of speciation: Gut bacteria cause hybrid lethality in the genus Nasonia.Science2013341614666766910.1126/science.124065923868918
    [Google Scholar]
13. BronP.A. van BaarlenP. KleerebezemM. Emerging molecular insights into the interaction between probiotics and the host intestinal mucosa.Nat. Rev. Microbiol.2012101667810.1038/nrmicro269022101918
    [Google Scholar]
14. LiH. LimenitakisJ.P. FuhrerT. The outer mucus layer hosts a distinct intestinal microbial niche.Nat. Commun.201561829210.1038/ncomms929226392213
    [Google Scholar]
15. SmillieC.S. SaukJ. GeversD. Strain-tracking reveals the determinants of bacterial engraftment in the human gut following fecal microbiota transplantation.Cell Host Microbe2018232229240.e510.1016/j.chom.2018.01.00329447696
    [Google Scholar]
16. ChangC.Y. BajićD. VilaJ.C.C. EstrelaS. SanchezA. Emergent coexistence in multispecies microbial communities.Science2023381665534334810.1126/science.adg072737471535
    [Google Scholar]
17. IaniroG. PunčochářM. KarcherN. Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases.Nat. Med.20222891913192310.1038/s41591‑022‑01964‑336109637
    [Google Scholar]
18. KristensenN.B. BryrupT. AllinK.H. NielsenT. HansenT.H. PedersenO. Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: A systematic review of randomized controlled trials.Genome Med.2016815210.1186/s13073‑016‑0300‑527159972
    [Google Scholar]
19. Maldonado-GómezM.X. MartínezI. BottaciniF. Stable engraftment of Bifidobacterium longum AH1206 in the human gut depends on individualized features of the resident microbiome.Cell Host Microbe201620451552610.1016/j.chom.2016.09.00127693307
    [Google Scholar]
20. UyenoY. ShigemoriS. ShimosatoT. Effect of probiotics/prebiotics on cattle health and productivity.Microbes Environ.201530212613210.1264/jsme2.ME1417626004794
    [Google Scholar]
21. RameshD. VinothkannaA. RaiA.K. VigneshV.S. Isolation of potential probiotic Bacillus spp. and assessment of their subcellular components to induce immune responses in Labeo rohita against Aeromonas hydrophila.Fish Shellfish Immunol.201545226827610.1016/j.fsi.2015.04.01825917974
    [Google Scholar]
22. CostelloE.K. StagamanK. DethlefsenL. BohannanB.J.M. RelmanD.A. The application of ecological theory toward an understanding of the human microbiome.Science201233660861255126210.1126/science.122420322674335
    [Google Scholar]
23. SeedorfH. GriffinN.W. RidauraV.K. Bacteria from diverse habitats colonize and compete in the mouse gut.Cell2014159225326610.1016/j.cell.2014.09.00825284151
    [Google Scholar]
24. FaithJ.J. GurugeJ.L. CharbonneauM. The long-term stability of the human gut microbiota.Science20133416141123743910.1126/science.123743923828941
    [Google Scholar]
25. BiavatiB. MattarelliP. Bifidobacterium. in Bergey’s Manual of Systematic Bacteriology In: The Actinobacteria.Springer Science & Business Media20125171206
    [Google Scholar]
26. WalterJ. Ecological role of lactobacilli in the gastrointestinal tract: Implications for fundamental and biomedical research.Appl. Environ. Microbiol.200874164985499610.1128/AEM.00753‑0818539818
    [Google Scholar]
27. SornplangP. PiyadeatsoontornS. Probiotic isolates from unconventional sources: A review.J. Anim. Sci. Technol.20165812610.1186/s40781‑016‑0108‑227437119
    [Google Scholar]
28. CumminsJ. HoM-W. Genetically modified probiotics should be banned.Microb. Ecol. Health Dis.2005176668
    [Google Scholar]
29. US Food and Drug Administration. Draft guidance for industry: Policy regarding quantitative labeling of dietary supplements containing live microbials.2018Available from: https://www.fda.gov/regulatory-information/search-fda-guidance-documents/draft-guidance-industry-policy-regarding-quantitative-labeling-dietary-supplements-containing-live
30. VenugopalanV. ShrinerK.A. Wong-BeringerA. Regulatory oversight and safety of probiotic use.Emerg. Infect. Dis.201016111661166510.3201/eid1611.10057421029521
    [Google Scholar]
31. US Food and Drug AdministrationDrugs Development & Approval Process. FDA.2023Available from: https://www.fda.gov/drugs/development-approval-process-drugs
32. OlleB. Medicines from microbiota.Nat. Biotechnol.201331430931510.1038/nbt.254823563425
    [Google Scholar]
33. PEDICINIEuropean Parliament. Parliamentary Question E-004201/2017: Use of the term ‘probiotic’ and nutrition claims.2017Available from: https://www.europarl.europa.eu/doceo/document/E-8-2017-004201_EN.html
34. WrightA. Regulating the safety of probiotics-the European approach.Curr. Pharm. Des.2005111172310.2174/138161205338232215638749
    [Google Scholar]
35. TurckD. BohnT. CastenmillerJ. Safety of pasteurised Akkermansia muciniphila as a novel food pursuant to Regulation (EU) 2015/2283.EFSA J.2021199e0678034484452
    [Google Scholar]
36. European Food Safety AuthorityGuidance on the characterisation of microorganisms used as feed additives or as production organisms.2018Available from: https://www.efsa.europa.eu/en/efsajournal/pub/5206
    [Google Scholar]
37. Directive 2001/18/EC of the European Parliament and of the Council of 12 March 2001 on the deliberate release into the environment of genetically modified organisms and repealing Council Directive 90/220/EEC - Commission Declaration.OJ L2001106
    [Google Scholar]
38. CharbonneauM.R. IsabellaV.M. LiN. KurtzC.B. Developing a new class of engineered live bacterial therapeutics to treat human diseases.Nat. Commun.2020111173810.1038/s41467‑020‑15508‑132269218
    [Google Scholar]
39. ShenT.C.D. ChehoudC. NiJ. Dietary regulation of the gut microbiota engineered by a minimal defined bacterial consortium.PLoS One2016115e015562010.1371/journal.pone.015562027176607
    [Google Scholar]
40. ShenH. ZhaoZ. ZhaoZ. ChenY. ZhangL. Native and engineered probiotics: Promising agents against related systemic and intestinal diseases.Int. J. Mol. Sci.202223259410.3390/ijms2302059435054790
    [Google Scholar]
41. RussellB.J. BrownS.D. SiguenzaN. Intestinal transgene delivery with native E. coli chassis allows persistent physiological changes.Cell20221851732633277.e1510.1016/j.cell.2022.06.05035931082
    [Google Scholar]
42. SlomskiA. Postantibiotic microbiome therapeutic reduces C difficile recurrence.JAMA202232712111810.1001/jama.2022.375335315889
    [Google Scholar]
43. XiaJ.Y. HeplerC. TranP. WaldeckN.J. BassJ. PrindleA. Engineered calprotectin-sensing probiotics for IBD surveillance in humans.Proc. Natl. Acad. Sci. USA202312032e222112112010.1073/pnas.222112112037523538
    [Google Scholar]
44. van de WijgertJ.H.H.M. VerwijsM.C. GillA.C. BorgdorffH. van der VeerC. MayaudP. Pathobionts in the vaginal microbiota: Individual participant data meta-analysis of three sequencing studies.Front. Cell. Infect. Microbiol.20201012910.3389/fcimb.2020.0012932351902
    [Google Scholar]
45. MaJ. LyuY. LiuX. Engineered probiotics.Microb. Cell Fact.20222117210.1186/s12934‑022‑01799‑035477497
    [Google Scholar]
46. MazharS.F. AfzalM. AlmatroudiA. The prospects for the therapeutic implications of genetically engineered probiotics.J. Food Qual.2020202011110.1155/2020/9676452
    [Google Scholar]
47. AggarwalN. BreedonA.M.E. DavisC.M. HwangI.Y. ChangM.W. Engineering probiotics for therapeutic applications: Recent examples and translational outlook.Curr. Opin. Biotechnol.20206517117910.1016/j.copbio.2020.02.01632304955
    [Google Scholar]
48. RottinghausA.G. AmrofellM.B. MoonT.S. Biosensing in smart engineered probiotics.Biotechnol. J.20201510190031910.1002/biot.20190031931860168
    [Google Scholar]
49. ZhouY. HanY. Engineered bacteria as drug delivery vehicles: Principles and prospects.Engineering Microbiology20222310003410.1016/j.engmic.2022.100034
    [Google Scholar]