Personalized B cell response to the Lactobacillus rhamnosus GG probiotic in healthy human subjects: a randomized trial
Jette Bornholdt, Christa Broholm, Yun Chen, Alfredo Rago, Stine Sloth, Jakob Hendel, Cathrine Melsæther, Christina V Müller, Maria Juul Nielsen, Jesper Strickertsson, Lars Engelholm, Kristoffer Vitting-Seerup, Kim B Jensen, Adam Baker, Albin Sandelin, Jette Bornholdt, Christa Broholm, Yun Chen, Alfredo Rago, Stine Sloth, Jakob Hendel, Cathrine Melsæther, Christina V Müller, Maria Juul Nielsen, Jesper Strickertsson, Lars Engelholm, Kristoffer Vitting-Seerup, Kim B Jensen, Adam Baker, Albin Sandelin
Abstract
The specific effects of administering live probiotics in the human gut are not well characterized. To this end, we investigated the immediate effect of Lactobacillus rhamnosus GG (LGG) in the jejunum of 27 healthy volunteers 2 h after ingestion using a combination of global RNA sequencing of human biopsies and bacterial DNA sequencing in a multi-visit, randomized, cross-over design (ClinicalTrials.gov number NCT03140878). While LGG was detectable in jejunum after 2 h in treated subjects, the gene expression response vs. placebo was subtle if assessed across all subjects. However, clustering analysis revealed that one-third of subjects exhibited a strong and consistent LGG response involving hundreds of genes, where genes related to B cell activation were upregulated, consistent with prior results in mice. Immunohistochemistry and single cell-based deconvolution analyses showed that this B cell signature likely is due to activation and proliferation of existing B cells rather than B cell immigration to the tissue. Our results indicate that the LGG strain has an immediate effect in the human gut in a subpopulation of individuals. In extension, our data strongly suggest that studies on in vivo probiotic effects in humans require large cohorts and must take individual variation into account.
Keywords: Lactobacillus rhamnosus GG; B cell activation; human transcriptomics; immediate in vivo effect; probiotics.
Figures
References
- Clarke TC, Black LI, Stussman BJ, Barnes PM, Nahin RL.. Trends in the use of complementary health approaches among adults: United States, 2002–2012. Natl Health Stat Report. 2015;79:1–16.
- Draper K, Ley C, Parsonnet J. Probiotic guidelines and physician practice: a cross-sectional survey and overview of the literature. Benef Microbes. 2017;8:507–519. doi:10.3920/BM2016.0146.
- Hao Q, Dong BR, Wu T. Probiotics for preventing acute upper respiratory tract infections. Cochrane Database Syst Rev. 2015;2:CD006895.
- Guo Q, Goldenberg JZ, Humphrey C, El Dib R, Johnston BC. Probiotics for the prevention of pediatric antibiotic-associated diarrhea. Cochrane Database Syst Rev. 2019;4:CD004827.
- Kleerebezem M, Binda S, Bron PA, Gross G, Hill C, van Hylckama Vlieg JE, Lebeer S, Satokari R, Ouwehand AC. Understanding mode of action can drive the translational pipeline towards more reliable health benefits for probiotics. Curr Opin Biotechnol. 2019;56:55–60. doi:10.1016/j.copbio.2018.09.007.
- Shen NT, Maw A, Tmanova LL, Pino A, Ancy K, Crawford CV, Simon MS, Evans AT. Timely use of probiotics in hospitalized adults prevents clostridium difficile infection: a systematic review with meta-regression analysis. Gastroenterology. 2017;152:1889–900.e9. doi:10.1053/j.gastro.2017.02.003.
- Zmora N, Zeevi D, Korem T, Segal E, Elinav E. Taking it personally: personalized utilization of the human microbiome in health and disease. Cell Host Microbe. 2016;19:12–20. doi:10.1016/j.chom.2015.12.016.
- Zmora N, Zilberman-Schapira G, Suez J, Mor U, Dori-Bachash M, Bashiardes S, Kotler E, Zur M, Regev-Lehavi D, Brik RB-Z, et al. Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell. 2018;174:1388–405.e21. doi:10.1016/j.cell.2018.08.041.
- Hojsak I, Abdović S, Szajewska H, Milosević M, Krznarić Z, Kolacek S. Lactobacillus GG in the prevention of nosocomial gastrointestinal and respiratory tract infections. Pediatrics. 2010;125:e1171–7. doi:10.1542/peds.2009-2568.
- Hojsak I, Snovak N, Abdović S, Szajewska H, Misak Z, Kolacek S. Lactobacillus GG in the prevention of gastrointestinal and respiratory tract infections in children who attend day care centers: a randomized, double-blind, placebo-controlled trial. Clin Nutr. 2010;29:312–316. doi:10.1016/j.clnu.2009.09.008.
- Capurso L. Thirty years of Lactobacillus rhamnosus GG: a review. J Clin Gastroenterol. 2019;53(Suppl 1):S1–41. doi:10.1097/MCG.0000000000001170.
- Davidson LE, Fiorino A-M, Snydman DR, Hibberd PL. Lactobacillus GG as an immune adjuvant for live-attenuated influenza vaccine in healthy adults: a randomized double-blind placebo-controlled trial. Eur J Clin Nutr. 2011;65:501–507. doi:10.1038/ejcn.2010.289.
- Miettinen M, Veckman V, Latvala S, Sareneva T, Matikainen S, Julkunen I. Live Lactobacillus rhamnosus and Streptococcus pyogenes differentially regulate Toll-like receptor (TLR) gene expression in human primary macrophages. J Leukoc Biol. 2008;84:1092–1100. doi:10.1189/jlb.1206737.
- Miettinen M, Lehtonen A, Julkunen I, Matikainen S. Lactobacilli and Streptococci activate NF-kappa B and STAT signaling pathways in human macrophages. J Immunol. 2000;164:3733–3740. doi:10.4049/jimmunol.164.7.3733.
- Pagnini C, Corleto VD, Martorelli M, Lanini C, D’Ambra G, Di Giulio E, Delle Fave G. Mucosal adhesion and anti-inflammatory effects of GG in the human colonic mucosa: a proof-of-concept study. World J Gastroenterol. 2018;24:4652–4662. doi:10.3748/wjg.v24.i41.4652.
- van Baarlen P, Troost F, van der Meer C, Hooiveld G, Boekschoten M, Brummer RJM, Kleerebezem M. Human mucosal in vivo transcriptome responses to three lactobacilli indicate how probiotics may modulate human cellular pathways. Proc Natl Acad Sci U S A. 2011;108(Suppl 1):4562–4569. doi:10.1073/pnas.1000079107.
- Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550. doi:10.1186/s13059-014-0550-8.
- Kanehisa M, Sato Y, Furumichi M, Morishima K, Tanabe M. New approach for understanding genome variations in KEGG. Nucleic Acids Res. 2019;47:D590–5. doi:10.1093/nar/gky962.
- Jassal B, Matthews L, Viteri G, Gong C, Lorente P, Fabregat A, Sidiropoulos K, Cook J, Gillespie M, Haw R, et al. The reactome pathway knowledgebase. Nucleic Acids Res. 2020;48:D498–503.
- Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47:D607–13. doi:10.1093/nar/gky1131.
- Suzuki C, Aoki-Yoshida A, Aoki R, Sasaki K, Takayama Y, Mizumachi K. The distinct effects of orally administered Lactobacillus rhamnosus GG and Lactococcus lactis subsp. lactis C59 on gene expression in the murine small intestine. PLoS One. 2017;12:e0188985. doi:10.1371/journal.pone.0188985.
- Richards S, Watanabe C, Santos L, Craxton A, Clark EA. Regulation of B-cell entry into the cell cycle. Immunol Rev. 2008;224:183–200. doi:10.1111/j.1600-065X.2008.00652.x.
- Cragg MS, Walshe CA, Ivanov AO, Glennie MJ. The biology of CD20 and its potential as a target for mAb therapy. Curr Dir Autoimmun. 2005;8:140–174.
- Robichaud GA, Nardini M, Laflamme M, Cuperlovic-Culf M, Ouellette RJ. Human Pax-5 C-terminal isoforms possess distinct transactivation properties and are differentially modulated in normal and malignant B cells. J Biol Chem. 2004;279:49956–49963. doi:10.1074/jbc.M407171200.
- Kandasamy S, Chattha KS, Vlasova AN, Rajashekara G, Saif LJ. Lactobacilli and Bifidobacteria enhance mucosal B cell responses and differentially modulate systemic antibody responses to an oral human rotavirus vaccine in a neonatal gnotobiotic pig disease model. Gut Microbes. 2014;5:639–651. doi:10.4161/19490976.2014.969972.
- Vlasova AN, Chattha KS, Kandasamy S, Liu Z, Esseili M, Shao L, Rajashekara G, Saif LJ. Lactobacilli and bifidobacteria promote immune homeostasis by modulating innate immune responses to human rotavirus in neonatal gnotobiotic pigs. PLoS One. 2013;8:e76962. doi:10.1371/journal.pone.0076962.
- Boyd M, Thodberg M, Vitezic M, Bornholdt J, Vitting-Seerup K, Chen Y, Coskun M, Li Y, Lo BZS, Klausen P, et al. Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies. Nat Commun. 2018;9:1661. doi:10.1038/s41467-018-03766-z.
- Boztepe T, Gulec S. Investigation of the influence of high glucose on molecular and genetic responses: an study using a human intestine model. Genes Nutr. 2018;13:11. doi:10.1186/s12263-018-0602-x.
- Jeong Y-S, Kim D, Lee YS, Kim H-J, Han J-Y, Im -S-S, Chong HK, Kwon J-K, Cho Y-H, Kim WK, et al. Integrated expression profiling and genome-wide analysis of ChREBP targets reveals the dual role for ChREBP in glucose-regulated gene expression. PLoS One. 2011;6:e22544. doi:10.1371/journal.pone.0022544.
- Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, Tett A, Huttenhower C, Segata N. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods. 2015;12:902–903. doi:10.1038/nmeth.3589.
- Baselga A, Orme CDL. betapart: an R package for the study of beta diversity: betapart package. Methods Ecol Evol. 2012;3:808–812. doi:10.1111/j.2041-210X.2012.00224.x.
- Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;14:417–419. doi:10.1038/nmeth.4197.
- Reimand J, Arak T, Adler P, Kolberg L, Reisberg S, Peterson H, Vilo J. g: Profiler-a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Res. 2016;44:W83–9. doi:10.1093/nar/gkw199.
- Luo W, Brouwer C. Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Bioinformatics. 2013;29:1830–1831. doi:10.1093/bioinformatics/btt285.
- NCBI Resource Coordinators . Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2016;44:D7–19. doi:10.1093/nar/gkv1290.
- Hunt GJ, Freytag S, Bahlo M, Gagnon-Bartsch JA. dtangle: accurate and robust cell type deconvolution. Bioinformatics. 2019;35:2093–2099. doi:10.1093/bioinformatics/bty926.
- Smillie CS, Biton M, Ordovas-Montanes J, Sullivan KM, Burgin G, Graham DB, Herbst RH, Rogel N, Slyper M, Waldman J, et al. Intra- and inter-cellular rewiring of the human colon during ulcerative colitis. Cell. 2019;178:714–30.e22. doi:10.1016/j.cell.2019.06.029.
- Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43:e47. doi:10.1093/nar/gkv007.
Source: PubMed