The double-edged sword of probiotic supplementation on gut microbiota structure in Helicobacter pylori management

Ali Nabavi-Rad, Amir Sadeghi, Hamid Asadzadeh Aghdaei, Abbas Yadegar, Sinéad Marian Smith, Mohammad Reza Zali, Ali Nabavi-Rad, Amir Sadeghi, Hamid Asadzadeh Aghdaei, Abbas Yadegar, Sinéad Marian Smith, Mohammad Reza Zali

Abstract

As Helicobacter pylori management has become more challenging and less efficient over the last decade, the interest in innovative interventions is growing by the day. Probiotic co-supplementation to antibiotic therapies is reported in several studies, presenting a moderate reduction in drug-related side effects and a promotion in positive treatment outcomes. However, the significance of gut microbiota involvement in the competence of probiotic co-supplementation is emphasized by a few researchers, indicating the alteration in the host gastrointestinal microbiota following probiotic and drug uptake. Due to the lack of long-term follow-up studies to determine the efficiency of probiotic intervention in H. pylori eradication, and the delicate interaction of the gut microbiota with the host wellness, this review aims to discuss the gut microbiota alteration by probiotic co-supplementation in H. pylori management to predict the comprehensive effectiveness of probiotic oral administration.Abbreviations: acyl-CoA- acyl-coenzyme A; AMP- antimicrobial peptide; AMPK- AMP-activated protein kinase; AP-1- activator protein 1; BA- bile acid; BAR- bile acid receptor; BCAA- branched-chain amino acid; C2- acetate; C3- propionate; C4- butyrate; C5- valeric acid; CagA- Cytotoxin-associated gene A; cAMP- cyclic adenosine monophosphate; CD- Crohn's disease; CDI- C. difficile infection; COX-2- cyclooxygenase-2; DC- dendritic cell; EMT- epithelial-mesenchymal transition; FMO- flavin monooxygenases; FXR- farnesoid X receptor; GPBAR1- G-protein-coupled bile acid receptor 1; GPR4- G protein-coupled receptor 4; H2O2- hydrogen peroxide; HCC- hepatocellular carcinoma; HSC- hepatic stellate cell; IBD- inflammatory bowel disease; IBS- irritable bowel syndrome; IFN-γ- interferon-gamma; IgA immunoglobulin A; IL- interleukin; iNOS- induced nitric oxide synthase; JAK1- janus kinase 1; JAM-A- junctional adhesion molecule A; LAB- lactic acid bacteria; LPS- lipopolysaccharide; MALT- mucosa-associated lymphoid tissue; MAMP- microbe-associated molecular pattern; MCP-1- monocyte chemoattractant protein-1; MDR- multiple drug resistance; mTOR- mammalian target of rapamycin; MUC- mucin; NAFLD- nonalcoholic fatty liver disease; NF-κB- nuclear factor kappa B; NK- natural killer; NLRP3- NLR family pyrin domain containing 3; NOC- N-nitroso compounds; NOD- nucleotide-binding oligomerization domain; PICRUSt- phylogenetic investigation of communities by reconstruction of unobserved states; PRR- pattern recognition receptor; RA- retinoic acid; RNS- reactive nitrogen species; ROS- reactive oxygen species; rRNA- ribosomal RNA; SCFA- short-chain fatty acids; SDR- single drug resistance; SIgA- secretory immunoglobulin A; STAT3- signal transducer and activator of transcription 3; T1D- type 1 diabetes; T2D- type 2 diabetes; Th17- T helper 17; TLR- toll-like receptor; TMAO- trimethylamine N-oxide; TML- trimethyllysine; TNF-α- tumor necrosis factor-alpha; Tr1- type 1 regulatory T cell; Treg- regulatory T cell; UC- ulcerative colitis; VacA- Vacuolating toxin A.

Keywords: Helicobacter pylori; gastric cancer; gastrointestinal microbiota; gut metabolome; intestinal homeostasis; metabolic disorder; probiotic supplementation.

Conflict of interest statement

No potential conflict of interest was reported by the author(s).

Figures

Figure 1.
Figure 1.
The main genera and total abundance of bacteria vary along the gastrointestinal tract. The colon is characterized by low levels of oxygen as well as the presence of enormous numbers and species of bacteria. On the other hand, the microbial composition and metabolite concentration of stool samples are distinguished from gut biopsies, in which the bacteria and the fungi constitute the majority and minority of total fecal DNA, respectively. Fecal concentration of SCFAs are also demonstrated as they might be considered key regulators of the intestinal homeostasis.
Figure 2.
Figure 2.
The interplay between the gut metabolome, H. pylori, and the host immune system. H. pylori induces chronic gastric inflammation through the activation of transcriptional factors such as NF-κB. By stimulating the production of BCAA from the gut microbiota, H. pylori activates the mTORC1 complex and ultimately inhibits autophagic response. H. pylori further disrupts the integrity of the gastric epithelial barrier by suppressing the expression of tight junction proteins. On the other hand, microbiota production of SCFAs and secondary bile acids modulate gastric inflammation and immune system activation by reducing NF-κB activation, promoting the secretion of anti-inflammatory cytokines, AMPs, and IgA, and preserving the integrity of the gut barrier.
Figure 3.
Figure 3.
The progression of chronic gastritis toward gastric carcinoma has been characterized by the reduction in the Helicobacter genus, overgrowth of opportunistic bacteria, increased apoptosis, necrosis, and collagen production, changes in the cytoskeleton and polarity of the gastric epithelium, and gradual suppression of gastric acidity. The main mechanisms of action through which H. pylori virulence factors promote the risk of developing gastric cancer are further depicted.
Figure 4.
Figure 4.
The interplay between probiotic strains, H. pylori, and the host immune system. Several probiotic strains can directly eliminate H. pylori cells by producing bacteriocins, siderophore, hydrogen peroxide, biosurfactant, lactic acid, and SCFAs. Probiotic bacteria can retain the activity of the gut barrier by stimulating the production of mucin and tight junction proteins. Certain probiotic species preserve the inherent structure of the gut microbiota by increasing the concentration of AMPs, peptidoglycan hydrolase, and exopolysaccharides. Furthermore, several probiotic bacteria regulate the host inflammatory response and prevent the development of chronic inflammation.

References

    1. Miller AK, Williams SM.. Helicobacter pylori infection causes both protective and deleterious effects in human health and disease. Genes Immun. 2021;22(4):218–34. doi:10.1038/s41435-021-00146-4.
    1. Nabavi-Rad A, Azizi M, Jamshidizadeh S, Sadeghi A, Aghdaei HA, Yadegar A, Zali MR. The effects of vitamins and micronutrients on helicobacter pylori pathogenicity, survival, and eradication: a crosstalk between micronutrients and immune system. J Immunol Res. 2022;2022:4713684. doi:10.1155/2022/4713684.
    1. Senchukova MA, Tomchuk O, Shurygina EI. Helicobacter pylori in gastric cancer: features of infection and their correlations with long-term results of treatment. World J Gastroenterol. 2021;27(37):6290–6305. doi:10.3748/wjg.v27.i37.6290.
    1. Suzuki S, Gotoda T, Kusano C, Ikehara H, Ichijima R, Ohyauchi M, Ito H, Kawamura M, Ogata Y, Ohtaka M, et al. Seven-day vonoprazan and low-dose amoxicillin dual therapy as first-line Helicobacter pylori treatment: a multicentre randomised trial in Japan. Gut. 2020;69(6):1019. doi:10.1136/gutjnl-2019-319954.
    1. Malfertheiner P, Megraud F, O’Morain CA, Gisbert JP, Kuipers EJ, Axon AT, Bazzoli F, Gasbarrini A, Atherton J, Graham DY, et al. Management of Helicobacter pylori infection-the Maastricht V/Florence Consensus Report. Gut. 2017;66(1):6–30. doi:10.1136/gutjnl-2016-312288.
    1. Liu WZ, Xie Y, Lu H, Cheng H, Zeng ZR, Zhou LY, Chen Y, Wang JB, Du YQ, Lu NH, et al. Fifth Chinese national consensus report on the management of Helicobacter pylori infection. Helicobacter. 2018;23(2):e12475. doi:10.1111/hel.12475.
    1. Nyssen OP, Bordin D, Tepes B, Pérez-Aisa Á, Vaira D, Caldas M, Bujanda L, Castro-Fernandez M, Lerang F, Leja M, et al. European registry on Helicobacter pylori management (Hp-EuReg): patterns and trends in first-line empirical eradication prescription and outcomes of 5 years and 21 533 patients. Gut. 2021;70(1):40. doi:10.1136/gutjnl-2020-321372.
    1. McNicholl AG, Molina-Infante J, Lucendo AJ, Calleja JL, Pérez‐Aisa Á, Modolell I, Aldeguer X, Calafat M, Comino L, Ramas M, et al. Probiotic supplementation with lactobacillus plantarum and pediococcus acidilactici for Helicobacter pylori therapy: a randomized, double-blind, placebo-controlled trial. Helicobacter. 2018;23(5):e12529. doi:10.1111/hel.12529.
    1. Cunningham M, Azcarate-Peril MA, Barnard A. Shaping the Future of Probiotics and Prebiotics. Trends Microbiol. 2021;29(8):667–685.
    1. Goderska K, Agudo Pena S, Alarcon T. Helicobacter pylori treatment: antibiotics or probiotics. Appl Microbiol Biotechnol. 2018;102(1):1–7. doi:10.1007/s00253-017-8535-7.
    1. Ferraris C, Elli M, Tagliabue A. Gut microbiota for health: how can diet maintain a healthy gut microbiota? Nutrients. 2020;12(11):3596. doi:10.3390/nu12113596.
    1. de Vos WM, Tilg H, Van Hul M, Cani PD. Gut microbiome and health: mechanistic insights. Gut. 2022;71(5):1020–1032. doi:10.1136/gutjnl-2021-326789.
    1. Hillman ET, Lu H, Yao T, Nakatsu CH. Microbial ecology along the gastrointestinal tract. Microbes Environ. 2017;32(4):300–313. doi:10.1264/jsme2.ME17017.
    1. Shkoporov AN, Hill C. Bacteriophages of the human gut: the “known unknown” of the microbiome. Cell Host Microbe. 2019;25(2):195–209. doi:10.1016/j.chom.2019.01.017.
    1. O’Riordan KJ, Collins MK, Moloney GM, Knox EG, Aburto MR, Fülling C, Morley SJ, Clarke G, Schellekens H, Cryan JF, et al. Short chain fatty acids: microbial metabolites for gut-brain axis signalling. Mol Cell Endocrinol. 2022;546:111572. doi:10.1016/j.mce.2022.111572.
    1. Engevik M, Versalovic J. Taking a closer look at the biogeography of the human gastrointestinal microbiome. Gastroenterology. 2019;157(4):927–929. doi:10.1053/j.gastro.2019.08.006.
    1. Herath M, Hosie S, Bornstein JC, Franks AE, Hill-Yardin EL. The role of the gastrointestinal mucus system in intestinal homeostasis: implications for neurological disorders. Front Cell Infect Microbiol. 2020;10:248. doi:10.3389/fcimb.2020.00248.
    1. Martens EC, Neumann M, Desai MS. Interactions of commensal and pathogenic microorganisms with the intestinal mucosal barrier. Nat Rev Microbiol. 2018;16(8):457–470. doi:10.1038/s41579-018-0036-x.
    1. Mowat AM. To respond or not to respond - a personal perspective of intestinal tolerance. Nat Rev Immunol. 2018;18(6):405–415. doi:10.1038/s41577-018-0002-x.
    1. Yoo JY, Groer M, Dutra SVO, Sarkar A, McSkimming DI. Gut microbiota and immune system interactions. Microorganisms. 2020;8(10):1587. doi:10.3390/microorganisms8101587.
    1. Le Noci V, Bernardo G, Bianchi F, Tagliabue E, Sommariva M, Sfondrini L. Toll like receptors as sensors of the tumor microbial dysbiosis: implications in cancer progression. Front Cell Dev Biol. 2021;9:732192. doi:10.3389/fcell.2021.732192.
    1. Ferrand A, Al Nabhani Z, Tapias NS, Mas E, Hugot JP, Barreau F. NOD2 expression in intestinal epithelial cells protects toward the development of inflammation and associated carcinogenesis. Cell Mol Gastroenterol Hepatol. 2019;7(2):357–369. doi:10.1016/j.jcmgh.2018.10.009.
    1. Moltzau Anderson J, Lipinski S, Sommer F, Pan W-H, Boulard O, Rehman A, Falk-Paulsen M, Stengel ST, Aden K, Häsler R, et al. NOD2 influences trajectories of intestinal microbiota recovery after antibiotic perturbation. Cell Mol Gastroenterol Hepatol. 2020;10(2):365–389. doi:10.1016/j.jcmgh.2020.03.008.
    1. Fernández-García V, González-Ramos S, Martín-Sanz P, Portillo FG-D, Laparra JM, Boscá L. NOD1 in the interplay between microbiota and gastrointestinal immune adaptations. Pharmacological Research. 2021;171:105775. doi:10.1016/j.phrs.2021.105775.
    1. Irving AT, Mimuro H, Kufer TA, Lo C, Wheeler R, Turner L, Thomas B, Malosse C, Gantier M, Casillas L, et al. The immune receptor NOD1 and kinase RIP2 interact with bacterial peptidoglycan on early endosomes to promote autophagy and inflammatory signaling. Cell Host Microbe. 2014;15(5):623–635. doi:10.1016/j.chom.2014.04.001.
    1. Zheng D, Liwinski T, Elinav E. Interaction between microbiota and immunity in health and disease. Cell Res. 2020;30(6):492–506. doi:10.1038/s41422-020-0332-7.
    1. Zong X, Fu J, Xu B, Wang Y, Jin M. Interplay between gut microbiota and antimicrobial peptides. Animal Nutrition. 2020;6(4):389–396. doi:10.1016/j.aninu.2020.09.002.
    1. Lueschow SR, McElroy SJ. The paneth cell: the curator and defender of the immature small intestine. Front Immunol. 2020;11:587. doi:10.3389/fimmu.2020.00587.
    1. Liang W, Enee E, Andre-Vallee C, Falcone M, Sun J, Diana J. Intestinal cathelicidin antimicrobial peptide shapes a protective neonatal gut microbiota against pancreatic autoimmunity. Gastroenterology. 2021;162(4):1288–1302.e16. doi:10.1053/j.gastro.2021.12.272.
    1. Healy DB, Ryan CA, Ross RP, Stanton C, Dempsey EM. Clinical implications of preterm infant gut microbiome development. Nat Microbiol. 2022;7(1):22–33. doi:10.1038/s41564-021-01025-4.
    1. Lycke NY, Bemark M. The regulation of gut mucosal IgA B-cell responses: recent developments. Mucosal Immunol. 2017;10(6):1361–1374. doi:10.1038/mi.2017.62.
    1. Pabst O, Slack E. IgA and the intestinal microbiota: the importance of being specific. Mucosal Immunol. 2020;13(1):12–21. doi:10.1038/s41385-019-0227-4.
    1. Abokor AA, McDaniel GH, Golonka RM, Campbell C, Brahmandam S, Yeoh BS, Joe B, Vijay-Kumar M, Saha P. Immunoglobulin A, an active liaison for host-microbiota homeostasis. Microorganisms. 2021;9(10):2117. doi:10.3390/microorganisms9102117.
    1. Krishnaswamy JK, Alsen S, Yrlid U, Eisenbarth SC, Williams A. Determination of t follicular helper cell fate by dendritic cells. Front Immunol. 2018;9:2169. doi:10.3389/fimmu.2018.02169.
    1. Agus A, Clément K, Sokol H. Gut microbiota-derived metabolites as central regulators in metabolic disorders. Gut. 2021;70(6):1174–1182. doi:10.1136/gutjnl-2020-323071.
    1. Michaudel C, Sokol H. The gut microbiota at the service of immunometabolism. Cell Metab. 2020;32(4):514–523. doi:10.1016/j.cmet.2020.09.004.
    1. Liu KH, Owens JA, Saeedi B, Cohen CE, Bellissimo MP, Naudin C, Darby T, Druzak S, Maner-Smith K, Orr M, et al. Microbial metabolite delta-valerobetaine is a diet-dependent obesogen. Nature Metabolism. 2021;3(12):1694–1705. doi:10.1038/s42255-021-00502-8.
    1. Lavelle A, Sokol H. Gut microbiota-derived metabolites as key actors in inflammatory bowel disease. Nat Rev Gastroenterol Hepatol. 2020;17(4):223–237. doi:10.1038/s41575-019-0258-z.
    1. Portincasa P, Bonfrate L, Vacca M, De Angelis M, Farella I, Lanza E, Khalil M, Wang DQH, Sperandio M, Di Ciaula A, et al. Gut microbiota and short chain fatty acids: implications in glucose homeostasis. Int J Mol Sci. 2022;23(3):1105. doi:10.3390/ijms23031105.
    1. Dalile B, Van Oudenhove L, Vervliet B, Verbeke K. The role of short-chain fatty acids in microbiota-gut-brain communication. Nat Rev Gastroenterol Hepatol. 2019;16(8):461–478. doi:10.1038/s41575-019-0157-3.
    1. Nugent SG, Kumar D, Rampton DS, Evans DF. Intestinal luminal pH in inflammatory bowel disease: possible determinants and implications for therapy with aminosalicylates and other drugs. Gut. 2001;48(4):571–577. doi:10.1136/gut.48.4.571.
    1. Traxinger BR, Richert-Spuhler LE, Lund JM. Mucosal tissue regulatory T cells are integral in balancing immunity and tolerance at portals of antigen entry. Mucosal Immunol. 2021;15(3):398–407]. doi:10.1038/s41385-021-00471-x.
    1. Kim CH. Control of lymphocyte functions by gut microbiota-derived short-chain fatty acids. Cell Mol Immunol. 2021;18(5):1161–1171. doi:10.1038/s41423-020-00625-0.
    1. Liu P, Wang Y, Yang G, Zhang Q, Meng L, Xin Y, Jiang X. The role of short-chain fatty acids in intestinal barrier function, inflammation, oxidative stress, and colonic carcinogenesis. Pharmacol Res. 2021;165:105420. doi:10.1016/j.phrs.2021.105420.
    1. He J, Zhang P, Shen L, Niu L, Tan Y, Chen L, Zhao Y, Bai L, Hao X, Li X, et al. Short-chain fatty acids and their association with signalling pathways in inflammation, glucose and lipid metabolism. Int J Mol Sci. 2020;21(17):6356. doi:10.3390/ijms21176356.
    1. de Aguiar Vallim TQ, Tarling EJ, Edwards PA. Pleiotropic roles of bile acids in metabolism. Cell Metab. 2013;17(5):657–669. doi:10.1016/j.cmet.2013.03.013.
    1. Funabashi M, Grove TL, Wang M, Varma Y, McFadden ME, Brown LC, Guo C, Higginbottom S, Almo SC, Fischbach MA, et al. A metabolic pathway for bile acid dehydroxylation by the gut microbiome. Nature. 2020;582(7813):566–570. doi:10.1038/s41586-020-2396-4.
    1. Guzior DV, Quinn RA. Review: microbial transformations of human bile acids. Microbiome. 2021;9(1):140. doi:10.1186/s40168-021-01101-1.
    1. Jia X, Lu S, Zeng Z, Liu Q, Dong Z, Chen Y, Zhu Z, Hong Z, Zhang T, Du G, et al. Characterization of gut microbiota, bile acid metabolism, and cytokines in intrahepatic cholangiocarcinoma. Hepatology. 2020;71(3):893–906. doi:10.1002/hep.30852.
    1. Zhang M, Serna-Salas S, Damba T, Borghesan M, Demaria M, Moshage H. Hepatic stellate cell senescence in liver fibrosis: characteristics, mechanisms and perspectives. Mech Ageing Dev. 2021;199:111572. doi:10.1016/j.mad.2021.111572.
    1. Jia W, Xie G, Jia W. Bile acid-microbiota crosstalk in gastrointestinal inflammation and carcinogenesis. Nat Rev Gastroenterol Hepatol. 2018;15(2):111–128. doi:10.1038/nrgastro.2017.119.
    1. Roager HM, Licht TR. Microbial tryptophan catabolites in health and disease. Nat Commun. 2018;9(1):3294. doi:10.1038/s41467-018-05470-4.
    1. Peng H, Wang Y, Luo W. Multifaceted role of branched-chain amino acid metabolism in cancer. Oncogene. 2020;39(44):6747–6756. doi:10.1038/s41388-020-01480-z.
    1. Krautkramer KA, Fan J, Bäckhed F. Gut microbial metabolites as multi-kingdom intermediates. Nat Rev Microbiol. 2021;19(2):77–94. doi:10.1038/s41579-020-0438-4.
    1. Li X, Hong J, Wang Y, Pei M, Wang L, Gong Z. Trimethylamine-N-Oxide Pathway: a Potential Target for the Treatment of MAFLD. Front Mol Biosci. 2021;8:733507. doi:10.3389/fmolb.2021.733507.
    1. Brown JM, Hazen SL. Microbial modulation of cardiovascular disease. Nat Rev Microbiol. 2018;16(3):171–181. doi:10.1038/nrmicro.2017.149.
    1. Dalal N, Jalandra R, Bayal N. Gut microbiota-derived metabolites in CRC progression and causation. J Cancer Res Clin Oncol. 2021;147(11):3141–3155. doi:10.1007/s00432-021-03729-w.
    1. Li XS, Obeid S, Wang Z, Hazen BJ, Li L, Wu Y, Hurd AG, Gu X, Pratt A, Levison BS, et al. Trimethyllysine, a trimethylamine N-oxide precursor, provides near- and long-term prognostic value in patients presenting with acute coronary syndromes. Eur Heart J. 2019;40(32):2700–2709. doi:10.1093/eurheartj/ehz259.
    1. McBurney MI, Davis C, Fraser CM, Schneeman BO, Huttenhower C, Verbeke K, Walter J, Latulippe ME. Establishing what constitutes a healthy human gut microbiome: state of the science, regulatory considerations, and future directions. J Nutr. 2019;149(11):1882–1895. doi:10.1093/jn/nxz154.
    1. Levy M, Kolodziejczyk AA, Thaiss CA, Elinav E. Dysbiosis and the immune system. Nat Rev Immunol. 2017;17(4):219–232. doi:10.1038/nri.2017.7.
    1. Jochum L, Stecher B. Label or concept - what is a pathobiont? Trends Microbiol. 2020;28(10):789–792. doi:10.1016/j.tim.2020.04.011.
    1. Zeng MY, Inohara N, Nunez G. Mechanisms of inflammation-driven bacterial dysbiosis in the gut. Mucosal Immunol. 2017;10(1):18–26. doi:10.1038/mi.2016.75.
    1. Hiippala K, Jouhten H, Ronkainen A, Hartikainen A, Kainulainen V, Jalanka J, Satokari R. The potential of gut commensals in reinforcing intestinal barrier function and alleviating inflammation. Nutrients. 2018;10(8):988. doi:10.3390/nu10080988.
    1. Khan R, Petersen FC, Shekhar S. Commensal bacteria: an emerging player in defense against respiratory pathogens. Front Immunol. 2019;10:1203. doi:10.3389/fimmu.2019.01203.
    1. Carvalho AL, Fonseca S, Miquel-Clopes A, Cross K, Kok K-S, Wegmann U, Gil-Cardoso K, Bentley EG, Al Katy SHM, Coombes JL, et al. Bioengineering commensal bacteria-derived outer membrane vesicles for delivery of biologics to the gastrointestinal and respiratory tract. J Extracell Vesicles. 2019;8(1):1632100. doi:10.1080/20013078.2019.1632100.
    1. Mosca A, Leclerc M, Hugot JP. Gut microbiota diversity and human diseases: should we reintroduce key predators in our ecosystem? Front Microbiol. 2016;7:455. doi:10.3389/fmicb.2016.00455.
    1. Roswall J, Olsson LM, Kovatcheva-Datchary P, Nilsson S, Tremaroli V, Simon M-C, Kiilerich P, Akrami R, Krämer M, Uhlén M, et al. Developmental trajectory of the healthy human gut microbiota during the first 5 years of life. Cell Host Microbe. 2021;29(5):765–776 e763. doi:10.1016/j.chom.2021.02.021.
    1. Pellicano R, Ianiro G, Fagoonee S, Settanni CR, Gasbarrini A. Review: extragastric diseases and Helicobacter pylori. Helicobacter. 2020;25(Suppl 1):e12741. doi:10.1111/hel.12741.
    1. Ohno H, Satoh-Takayama N. Stomach microbiota, Helicobacter pylori, and group 2 innate lymphoid cells. Exp Mol Med. 2020;52(9):1377–1382. doi:10.1038/s12276-020-00485-8.
    1. Iino C, Shimoyama T. Impact of Helicobacter pylori infection on gut microbiota. World J Gastroenterol. 2021;27(37):6224–6230. doi:10.3748/wjg.v27.i37.6224.
    1. Engstrand L, Graham DY. Microbiome and Gastric Cancer. Dig Dis Sci. 2020;65(3):865–873. doi:10.1007/s10620-020-06101-z.
    1. Chen CC, Liou JM, Lee YC, Hong TC, El-Omar EM, Wu MS. The interplay between Helicobacter pylori and gastrointestinal microbiota. Gut Microbes. 2021;13(1):1–22. doi:10.1080/19490976.2021.1909459.
    1. Wadhwa R, Song S, Lee JS, Yao Y, Wei Q, Ajani JA. Gastric cancer-molecular and clinical dimensions. Nat Rev Clin Oncol. 2013;10(11):643–655. doi:10.1038/nrclinonc.2013.170.
    1. Martin-Nuñez GM, Cornejo-Pareja I, Clemente-Postigo M, Tinahones FJ. Gut microbiota: the missing link between helicobacter pylori infection and metabolic disorders? Front Endocrinol (Lausanne). 2021;12(657). doi:10.3389/fendo.2021.639856.
    1. Martinez JE, Kahana DD, Ghuman S, Wilson HP, Wilson J, Kim SCJ, Lagishetty V, Jacobs JP, Sinha-Hikim AP, Friedman TC, et al. unhealthy lifestyle and gut dysbiosis: a better understanding of the effects of poor diet and nicotine on the intestinal microbiome. Front Endocrinol (Lausanne). 2021;12:667066. doi:10.3389/fendo.2021.667066.
    1. Gaulke CA, Sharpton TJ. The influence of ethnicity and geography on human gut microbiome composition. Nat Med. 2018;24(10):1495–1496. doi:10.1038/s41591-018-0210-8.
    1. Vasapolli R, Schutte K, Schulz C, Vital M, Schomburg D, Pieper DH, Vilchez-Vargas R, Malfertheiner P. Analysis of transcriptionally active bacteria throughout the gastrointestinal tract of healthy individuals. Gastroenterology. 2019;157(4):1081–1092 e1083. doi:10.1053/j.gastro.2019.05.068.
    1. Bik EM, Eckburg PB, Gill SR. Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci U S A. 2006;103(3):732–737. doi:10.1073/pnas.0506655103.
    1. Li XX, Wong GL, To KF, Wong VWS, Lai LH, Chow DKL, Lau JYW, Sung JJY, Ding C. Bacterial microbiota profiling in gastritis without Helicobacter pylori infection or non-steroidal anti-inflammatory drug use. PLoS One. 2009;4(11):e7985. doi:10.1371/journal.pone.0007985.
    1. Chen X, Zhou X, Liao B, Zhou Y, Cheng L, Ren B. The cross-kingdom interaction between Helicobacter pylori and Candida albicans. PLoS Pathog. 2021;17(5):e1009515–e1009515. doi:10.1371/journal.ppat.1009515.
    1. Noto JM, Zackular JP, Varga MG, Delgado A, Romero-Gallo J, Scholz MB, Piazuelo MB, Skaar EP, Peek RM. Modification of the gastric mucosal microbiota by a strain-specific helicobacter pylori oncoprotein and carcinogenic histologic phenotype. mBio. 2019;10(3). doi:10.1128/mBio.00955-19.
    1. Wang L, Xin Y, Zhou J. Gastric mucosa-associated microbial signatures of early gastric cancer. Front Microbiol. 2020;11:1548. doi:10.3389/fmicb.2020.01548.
    1. Coker OO, Dai Z, Nie Y, Zhao G, Cao L, Nakatsu G, Wu WK, Wong SH, Chen Z, Sung JJY, et al. Mucosal microbiome dysbiosis in gastric carcinogenesis. Gut. 2018;67(6):1024–1032. doi:10.1136/gutjnl-2017-314281.
    1. Wang L, Zhou J, Xin Y. Bacterial overgrowth and diversification of microbiota in gastric cancer. Eur J Gastroenterol Hepatol. 2016;28(3):261–266. doi:10.1097/MEG.0000000000000542.
    1. Eun CS, Kim BK, Han DS, Kim SY, Kim KM, Choi BY, Song KS, Kim YS, Kim JF. Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods. Helicobacter. 2014;19(6):407–416. doi:10.1111/hel.12145.
    1. Aviles-Jimenez F, Vazquez-Jimenez F, Medrano-Guzman R, Mantilla A, Torres J. Stomach microbiota composition varies between patients with non-atrophic gastritis and patients with intestinal type of gastric cancer. Sci Rep. 2014;4(1):4202. doi:10.1038/srep04202.
    1. Ferreira RM, Pereira-Marques J, Pinto-Ribeiro I, Costa JL, Carneiro F, Machado JC, Figueiredo C. Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota. Gut. 2018;67(2):226–236. doi:10.1136/gutjnl-2017-314205.
    1. Dicksved J, Lindberg M, Rosenquist M, Enroth H, Jansson JK, Engstrand L. Molecular characterization of the stomach microbiota in patients with gastric cancer and in controls. J Med Microbiol. 2009;58(Pt 4):509–516. doi:10.1099/jmm.0.007302-0.
    1. Guo Y, Zhang Y, Gerhard M, Gao -J-J, Mejias-Luque R, Zhang L, Vieth M, Ma J-L, Bajbouj M, Suchanek S, et al. Effect of Helicobacter pylori on gastrointestinal microbiota: a population-based study in Linqu, a high-risk area of gastric cancer. Gut. 2020;69(9):1598–1607. doi:10.1136/gutjnl-2019-319696.
    1. Yang J, Zhou X, Liu X, Ling Z, Ji F. Role of the gastric microbiome in gastric cancer: from carcinogenesis to treatment. Front Microbiol. 2021;12:641322. doi:10.3389/fmicb.2021.641322.
    1. Navashenaq JG, Shabgah AG, Banach M, Jamialahmadi T, Penson PE, Johnston TP, Sahebkar A. The interaction of Helicobacter pylori with cancer immunomodulatory stromal cells: new insight into gastric cancer pathogenesis. Semin Cancer Biol. 2021. doi:10.1016/j.semcancer.2021.09.014.
    1. Bakhti SZ, Latifi-Navid S. Interplay and cooperation of Helicobacter pylori and gut microbiota in gastric carcinogenesis. BMC Microbiol. 2021;21(1):258. doi:10.1186/s12866-021-02315-x.
    1. Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma J-L, Bajbouj M, Suchanek S, Liu W-D, et al. Association between gut microbiota and helicobacter pylori-related gastric lesions in a high-risk population of gastric cancer. Front Cell Infect Microbiol. 2018;8:202. doi:10.3389/fcimb.2018.00202.
    1. He C, Peng C, Wang H, Ouyang Y, Zhu Z, Shu X, Zhu Y, Lu N. The eradication of Helicobacter pylori restores rather than disturbs the gastrointestinal microbiota in asymptomatic young adults. Helicobacter. 2019;24(4):e12590. doi:10.1111/hel.12590.
    1. Frost F, Kacprowski T, Ruhlemann M, Bang C, Franke A, Zimmermann K, Nauck M, Völker U, Völzke H, Biffar R, et al. Helicobacter pylori infection associates with fecal microbiota composition and diversity. Sci Rep. 2019;9(1):20100. doi:10.1038/s41598-019-56631-4.
    1. Lapidot Y, Reshef L, Cohen D, Muhsen K. Helicobacter pylori and the intestinal microbiome among healthy school-age children. Helicobacter. 2021;26(6):e12854. doi:10.1111/hel.12854.
    1. Heimesaat MM, Fischer A, Plickert R, Wiedemann T, Loddenkemper C, Göbel UB, Bereswill S, Rieder G. Helicobacter pylori induced gastric immunopathology is associated with distinct microbiota changes in the large intestines of long-term infected mongolian gerbils. PLOS ONE. 2014;9(6):e100362. doi:10.1371/journal.pone.0100362.
    1. Dash NR, Khoder G, Nada AM, Al Bataineh MT. Exploring the impact of Helicobacter pylori on gut microbiome composition. PLoS One. 2019;14(6):e0218274. doi:10.1371/journal.pone.0218274.
    1. Chen L, Xu W, Lee A, He J, Huang B, Zheng W, Su T, Lai S, Long Y, Chu H, et al. The impact of Helicobacter pylori infection, eradication therapy and probiotic supplementation on gut microenvironment homeostasis: an open-label, randomized clinical trial. EBioMedicine. 2018;35:87–96. doi:10.1016/j.ebiom.2018.08.028.
    1. Iino C, Shimoyama T, Chinda D, Sakuraba H, Fukuda S, Nakaji S. Influence of helicobacter pylori infection and atrophic gastritis on the gut microbiota in a Japanese population. Digestion. 2020;101:422–432.
    1. Cornejo-Pareja I, Martin-Nunez GM, Roca-Rodriguez MM. H. pylori eradication treatment alters gut microbiota and GLP-1 secretion in humans. J Clin Med. 2019;8(4). doi:10.3390/jcm8040451.
    1. Wang D, Li Y, Zhong H, Ding Q, Lin Y, Tang S, Zong Y, Wang Q, Zhang X, Yang H, et al. Alterations in the human gut microbiome associated with helicobacter pylori infection. FEBS Open Bio. 2019;9(9):1552–1560. doi:10.1002/2211-5463.12694.
    1. Yang L, Zhang J, Xu J, Wei X, Yang J, Liu Y, Li H, Zhao C, Wang Y, Zhang L, et al. Helicobacter pylori infection aggravates dysbiosis of gut microbiome in children with gastritis. Front Cell Infect Microbiol. 2019;9:375. doi:10.3389/fcimb.2019.00375.
    1. Zhou Y, Ye Z, Lu J, Miao S, Lu X, Sun H, Wu J, Wang Y, Huang Y. Long-term changes in the gut microbiota after 14-day bismuth quadruple therapy in penicillin-allergic children. Helicobacter. 2020;25(5):e12721. doi:10.1111/hel.12721.
    1. Munoz-Ramirez ZY, Pascoe B, Mendez-Tenorio A, Mourkas E, Sandoval-Motta S, Perez-Perez G, Morgan DR, Dominguez RL, Ortiz-Princz D, Cavazza ME, et al. A 500-year tale of co-evolution, adaptation, and virulence: helicobacter pylori in the Americas. ISME J. 2021;15(1):78–92. doi:10.1038/s41396-020-00758-0.
    1. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486(7402):222–227. doi:10.1038/nature11053.
    1. Lopetuso LR, Scaldaferri F, Franceschi F, Gasbarrini A. The gastrointestinal microbiome – functional interference between stomach and intestine. Best Pract Res Clin Gastroenterol. 2014;28(6):995–1002. doi:10.1016/j.bpg.2014.10.004.
    1. Kienesberger S, Cox LM, Livanos A, Zhang X-S, Chung J, Perez-Perez G, Gorkiewicz G, Zechner E, Blaser M. Gastric Helicobacter pylori infection affects local and distant microbial populations and host responses. Cell Rep. 2016;14(6):1395–1407. doi:10.1016/j.celrep.2016.01.017.
    1. Takahashi-Kanemitsu A, Knight CT, Hatakeyama M. Molecular anatomy and pathogenic actions of Helicobacter pylori CagA that underpin gastric carcinogenesis. Cell Mol Immunol. 2020;17(1):50–63. doi:10.1038/s41423-019-0339-5.
    1. Baj J, Forma A, Sitarz M, Portincasa P, Garruti G, Krasowska D, Maciejewski R. Helicobacter pylori virulence factors-mechanisms of bacterial pathogenicity in the gastric microenvironment. Cells. 2020;10(1):27. doi:10.3390/cells10010027.
    1. Huang Y, Ding Y, Xu H, Shen C, Chen X, Li C. Effects of sodium butyrate supplementation on inflammation, gut microbiota, and short-chain fatty acids in Helicobacter pylori-infected mice. Helicobacter. 2021;26(2):e12785. doi:10.1111/hel.12785.
    1. Zhang Z, Tang H, Chen P, Xie H, Tao Y. Demystifying the manipulation of host immunity, metabolism, and extraintestinal tumors by the gut microbiome. Signal Transduct Target Ther. 2019;4:41. doi:10.1038/s41392-019-0074-5.
    1. Wibowo H, Harbuwono DS, Tahapary DL, Kartika R, Pradipta S, Larasati RA. Impact of sodium butyrate treatment in LPS-stimulated peripheral blood mononuclear cells of poorly controlled type 2 DM. Front Endocrinol (Lausanne). 2021;12:652942. doi:10.3389/fendo.2021.652942.
    1. Campos-Perez W, Martinez-Lopez E. Effects of short chain fatty acids on metabolic and inflammatory processes in human health. Biochimica Et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. 2021;1866(5):158900. doi:10.1016/j.bbalip.2021.158900.
    1. Postler TS, Ghosh S. Understanding the Holobiont: how Microbial Metabolites Affect Human Health and Shape the Immune System. Cell Metab. 2017;26(1):110–130. doi:10.1016/j.cmet.2017.05.008.
    1. Sit WY, Chen YA, Chen YL, Lai CH, Wang WC. Cellular evasion strategies of Helicobacter pylori in regulating its intracellular fate. Semin Cell Dev Biol. 2020;101:59–67. doi:10.1016/j.semcdb.2020.01.007.
    1. Cuomo P, Papaianni M, Sansone C, Iannelli A, Iannelli D, Medaglia C, Paris D, Motta A, Capparelli R. an in vitro model to investigate the role of helicobacter pylori in type 2 diabetes, obesity, alzheimer’s disease and cardiometabolic disease. Int J Mol Sci. 2020;21(21):8369. doi:10.3390/ijms21218369.
    1. Farhangi MA, Vajdi M. Novel findings of the association between gut microbiota-derived metabolite trimethylamine N-oxide and inflammation: results from a systematic review and dose-response meta-analysis. Crit Rev Food Sci Nutr. 2020;60(16):2801–2823. doi:10.1080/10408398.2020.1770199.
    1. Wu D, Cao M, Peng J, Li N, Yi S, Song L, Wang X, Zhang M, Zhao J. The effect of trimethylamine N-oxide on Helicobacter pylori-induced changes of immunoinflammatory genes expression in gastric epithelial cells. Int Immunopharmacol. 2017;43:172–178. doi:10.1016/j.intimp.2016.11.032.
    1. Lynch SV, Pedersen O. The human intestinal microbiome in health and disease. N Engl J Med. 2016;375(24):2369–2379. doi:10.1056/NEJMra1600266.
    1. Fan Y, Pedersen O. Gut microbiota in human metabolic health and disease. Nat Rev Microbiol. 2021;19(1):55–71. doi:10.1038/s41579-020-0433-9.
    1. Ramirez J, Guarner F, Bustos Fernandez L, Maruy A, Sdepanian VL, Cohen H. Antibiotics as major disruptors of gut microbiota. Front Cell Infect Microbiol. 2020;10(731). doi:10.3389/fcimb.2020.572912.
    1. Blaser MJ. Antibiotic use and its consequences for the normal microbiome. Science. 2016;352(6285):544–545. doi:10.1126/science.aad9358.
    1. Palleja A, Mikkelsen KH, Forslund SK, Kashani A, Allin KH, Nielsen T, Hansen TH, Liang S, Feng Q, Zhang C, et al. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nat Microbiol. 2018;3(11):1255–1265. doi:10.1038/s41564-018-0257-9.
    1. Zarrinpar A, Chaix A, Xu ZZ, Chang MW, Marotz CA, Saghatelian A, Knight R, Panda S. Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism. Nat Commun. 2018;9(1):2872. doi:10.1038/s41467-018-05336-9.
    1. Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, Brochado AR, Fernandez KC, Dose H, Mori H, et al. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature. 2018;555(7698):623–628. doi:10.1038/nature25979.
    1. Rashidi A, Ebadi M, Rehman TU, Elhusseini H, Nalluri H, Kaiser T, Holtan SG, Khoruts A, Weisdorf DJ, Staley C, et al. Gut microbiota response to antibiotics is personalized and depends on baseline microbiota. Microbiome. 2021;9(1):211. doi:10.1186/s40168-021-01170-2.
    1. Salminen S, Collado MC, Endo A, Hill C, Lebeer S, Quigley EMM, Sanders ME, Shamir R, Swann JR, Szajewska H, et al. The international scientific association of probiotics and prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics. Nat Rev Gastroenterol Hepatol. 2021;18(9):649–667. doi:10.1038/s41575-021-00440-6.
    1. Veiga P, Suez J, Derrien M, Elinav E. Moving from probiotics to precision probiotics. Nat Microbiol. 2020;5(7):878–880. doi:10.1038/s41564-020-0721-1.
    1. Gao J, Li X, Zhang G, Sadiq FA, Simal‐Gandara J, Xiao J, Sang Y. Probiotics in the dairy industry-advances and opportunities. Compr Rev Food Sci Food Saf. 2021;20(4):3937–3982. doi:10.1111/1541-4337.12755.
    1. Suez J, Zmora N, Segal E, Elinav E. The pros, cons, and many unknowns of probiotics. Nat Med. 2019;25(5):716–729. doi:10.1038/s41591-019-0439-x.
    1. Wieërs G, Belkhir L, Enaud R, Leclercq S, Philippart de Foy J-M, Dequenne I, de Timary P, Cani PD. How probiotics affect the microbiota. Front Cell Infect Microbiol. 2020;9(454). doi:10.3389/fcimb.2019.00454.
    1. Hou Q, Zhao F, Liu W, Lv R, Khine WWT, Han J, Sun Z, Lee Y-K, Zhang H. Probiotic-directed modulation of gut microbiota is basal microbiome dependent. Gut Microbes. 2020;12(1):1736974. doi:10.1080/19490976.2020.1736974.
    1. Singh TP, Natraj BH. Next-generation probiotics: a promising approach towards designing personalized medicine. Crit Rev Microbiol. 2021;47(4):479–498. doi:10.1080/1040841X.2021.1902940.
    1. Zhai Q, Feng S, Arjan N, Chen W. A next generation probiotic, Akkermansia muciniphila. Crit Rev Food Sci Nutr. 2019;59(19):3227–3236. doi:10.1080/10408398.2018.1517725.
    1. Keshavarz Azizi Raftar S, Abdollahiyan S, Azimirad M, Yadegar A, Vaziri F, Moshiri A, Siadat SD, Zali MR. The anti-fibrotic effects of heat-killed akkermansia muciniphila muct on liver fibrosis markers and activation of hepatic stellate cells. Probiotics Antimicrob Proteins. 2021;13(3):776–787. doi:10.1007/s12602-020-09733-9.
    1. Depommier C, Everard A, Druart C, Plovier H, Van Hul M, Vieira-Silva S, Falony G, Raes J, Maiter D, Delzenne NM, et al. Supplementation with akkermansia muciniphila in overweight and obese human volunteers: a proof-of-concept exploratory study. Nat Med. 2019;25(7):1096–1103. doi:10.1038/s41591-019-0495-2.
    1. De Palma G, Nadal I, Medina M, Donat E, Ribes-Koninckx C, Calabuig M, Sanz Y. Intestinal dysbiosis and reduced immunoglobulin-coated bacteria associated with coeliac disease in children. BMC Microbiol. 2010;10(1):63. doi:10.1186/1471-2180-10-63.
    1. Rajilic-Stojanovic M, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S, de Vos WM. Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome. Gastroenterology. 2011;141(5):1792–1801. doi:10.1053/j.gastro.2011.07.043.
    1. Balamurugan R, Rajendiran E, George S, Samuel GV, Ramakrishna BS. Real-time polymerase chain reaction quantification of specific butyrate-producing bacteria, desulfovibrio and Enterococcus faecalis in the feces of patients with colorectal cancer. J Gastroenterol Hepatol. 2008;23(8 Pt 1):1298–1303. doi:10.1111/j.1440-1746.2008.05490.x.
    1. Furet J-P, Kong L-C, Tap J, Poitou C, Basdevant A, Bouillot J-L, Mariat D, Corthier G, Doré J, Henegar C, et al. Differential adaptation of human gut microbiota to bariatric surgery–induced weight loss. Diabetes. 2010;59(12):3049–3057. doi:10.2337/db10-0253.
    1. Martin R, Miquel S, Benevides L, Bridonneau C, Robert V, Hudault S, Chain F, Berteau O, Azevedo V, Chatel JM, et al. Functional characterization of novel faecalibacterium prausnitzii strains isolated from healthy volunteers: a step forward in the use of F. prausnitzii as a next-generation probiotic. Front Microbiol. 2017;8:1226. doi:10.3389/fmicb.2017.01226.
    1. Fei Y, Chen Z, Han S, Zhang S, Zhang T, Lu Y, Berglund B, Xiao H, Li L, Yao M, et al. Role of prebiotics in enhancing the function of next-generation probiotics in gut microbiota. Crit Rev Food Sci Nutr. pp.1–18. 2021. doi:10.1080/10408398.2021.1958744
    1. Min S, Kim S, Cho SW. Gastrointestinal tract modeling using organoids engineered with cellular and microbiota niches. Exp Mol Med. 2020;52(2):227–237. doi:10.1038/s12276-020-0386-0.
    1. Shah SC, Iyer PG, Moss SF. AGA clinical practice update on the management of refractory Helicobacter pylori infection: expert review. Gastroenterology. 2021;160(5):1831–1841. doi:10.1053/j.gastro.2020.11.059.
    1. Fallone CA, Chiba N, van Zanten SV, Fischbach L, Gisbert JP, Hunt RH, Jones NL, Render C, Leontiadis GI, Moayyedi P, et al. The Toronto consensus for the treatment of Helicobacter pylori infection in adults. Gastroenterology. 2016;151(1):51–69.e14. doi:10.1053/j.gastro.2016.04.006.
    1. Liou JM, Chen CC, Chang CM, Fang Y-J, Bair M-J, Chen P-Y, Chang C-Y, Hsu Y-C, Chen M-J, Chen -C-C, et al. Long-term changes of gut microbiota, antibiotic resistance, and metabolic parameters after Helicobacter pylori eradication: a multicentre, open-label, randomised trial. Lancet Infect Dis. 2019;19(10):1109–1120. doi:10.1016/S1473-3099(19)30272-5.
    1. Ford AC, Yuan Y, Moayyedi P. Helicobacter pylori eradication therapy to prevent gastric cancer: systematic review and meta-analysis. Gut. 2020;69(12):2113–2121. doi:10.1136/gutjnl-2020-320839.
    1. Tshibangu-Kabamba E, Yamaoka Y. Helicobacter pylori infection and antibiotic resistance - from biology to clinical implications. Nat Rev Gastroenterol Hepatol. 2021;18(9):613–629. doi:10.1038/s41575-021-00449-x.
    1. Cheung KS, Chan EW, Wong AYS, Chen L, Wong ICK, Leung WK. Long-term proton pump inhibitors and risk of gastric cancer development after treatment for Helicobacter pylori: a population-based study. Gut. 2018;67(1):28–35. doi:10.1136/gutjnl-2017-314605.
    1. Yuan J, He Q, Nguyen LH, Wong MCS, Huang J, Yu Y, Xia B, Tang Y, He Y, Zhang C, et al. Regular use of proton pump inhibitors and risk of type 2 diabetes: results from three prospective cohort studies. Gut. 2021;70(6):1070–1077. doi:10.1136/gutjnl-2020-322557.
    1. Ye Q, Shao X, Shen R, Chen D, Shen J. Changes in the human gut microbiota composition caused by Helicobacter pylori eradication therapy: a systematic review and meta-analysis. Helicobacter. 2020;25(4):e12713. doi:10.1111/hel.12713.
    1. Valdes AM, Walter J, Segal E, Spector TD. Role of the gut microbiota in nutrition and health. BMJ. 2018;361:k2179.
    1. Handa O, Naito Y, Osawa M. Nutrients and probiotics: current trends in their use to eradicate Helicobacter pylori. J Clin Biochem Nutr. 2020;67(1):26–28. doi:10.3164/jcbn.20-51.
    1. Montassier E, Valdes-Mas R, Batard E. Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner. Nat Microbiol. 2021;6(8):1043–1054. doi:10.1038/s41564-021-00920-0.
    1. Cifuentes SG, Prado MB, Fornasini M, Cohen H, Baldeon ME, Cardenas PA. Saccharomyces boulardii CNCM I-745 supplementation modifies the fecal resistome during Helicobacter pylori eradication therapy. Helicobacter. 2022;27(2):e12870. doi:10.1111/hel.12870.
    1. Zhang M, Zhang C, Zhao J, Zhang H, Zhai Q, Chen W. Meta-analysis of the efficacy of probiotic-supplemented therapy on the eradication of H. pylori and incidence of therapy-associated side effects. Microb Pathog. 2020;147:104403. doi:10.1016/j.micpath.2020.104403.
    1. Losurdo G, Cubisino R, Barone M, Principi M, Leandro G, Ierardi E, Leo AD. Probiotic monotherapy and Helicobacter pylori eradication: a systematic review with pooled-data analysis. World J Gastroenterol. 2018;24(1):139–149. doi:10.3748/wjg.v24.i1.139.
    1. Kori M, Daugule I, Urbonas V. Helicobacter pylori and some aspects of gut microbiota in children. Helicobacter. 2018;23(Suppl 1):e12524. doi:10.1111/hel.12524.
    1. Feng JR, Wang F, Qiu X, McFarland LV, Chen P-F, Zhou R, Liu J, Zhao Q, Li J. Efficacy and safety of probiotic-supplemented triple therapy for eradication of Helicobacter pylori in children: a systematic review and network meta-analysis. Eur J Clin Pharmacol. 2017;73(10):1199–1208. doi:10.1007/s00228-017-2291-6.
    1. Kamiya S, Yonezawa H, Osaki T. Role of probiotics in eradication therapy for Helicobacter pylori infection. Adv Exp Med Biol. 2019;1149:243–255.
    1. Fang HR, Zhang GQ, Cheng JY, Li ZY. Efficacy of lactobacillus-supplemented triple therapy for Helicobacter pylori infection in children: a meta-analysis of randomized controlled trials. Eur J Pediatr. 2019;178(1):7–16. doi:10.1007/s00431-018-3282-z.
    1. McElrath C, Espinosa V, Lin JD. Critical role of interferons in gastrointestinal injury repair. Nat Commun. 2021;12(1):2624. doi:10.1038/s41467-021-22928-0.
    1. George S, Lucero Y, Torres JP, Lagomarcino AJ, O’Ryan M. Gastric damage and cancer-associated biomarkers in Helicobacter pylori-infected children. Front Microbiol. 2020;11(90). doi:10.3389/fmicb.2020.00090.
    1. Paone P, Cani PD. Mucus barrier, mucins and gut microbiota: the expected slimy partners? Gut. 2020;69(12):2232–2243. doi:10.1136/gutjnl-2020-322260.
    1. Ghosh S, Whitley CS, Haribabu B, Jala VR. Regulation of intestinal barrier function by microbial metabolites. Cell Mol Gastroenterol Hepatol. 2021;11(5):1463–1482. doi:10.1016/j.jcmgh.2021.02.007.
    1. Qureshi N, Li P, Gu Q. Probiotic therapy in Helicobacter pylori infection: a potential strategy against a serious pathogen? Appl Microbiol Biotechnol. 2019;103(4):1573–1588. doi:10.1007/s00253-018-09580-3.
    1. Azimirad M, Krutova M, Yadegar A, Shahrokh S, Olfatifar M, Aghdaei HA, Fawley WN, Wilcox MH, Zali MR. Clostridioides difficile ribotypes 001 and 126 were predominant in Tehran healthcare settings from 2004 to 2018: a 14-year-long cross-sectional study. Emerg Microbes Infect. 2020;9(1):1432–1443. doi:10.1080/22221751.2020.1780949.
    1. Cristofori F, Dargenio VN, Dargenio C, Miniello VL, Barone M, Francavilla R. Anti-inflammatory and immunomodulatory effects of probiotics in gut inflammation: a door to the body. Front Immunol. 2021;12:578386. doi:10.3389/fimmu.2021.578386.
    1. Marques MS, Costa AC, Osório H, Pinto ML, Relvas S, Dinis-Ribeiro M, Carneiro F, Leite M, Figueiredo C. Helicobacter pylori PqqE is a new virulence factor that cleaves junctional adhesion molecule A and disrupts gastric epithelial integrity. Gut Microbes. 2021;13(1):1921928. doi:10.1080/19490976.2021.1921928.
    1. Rose EC, Odle J, Blikslager AT, Ziegler AL. Probiotics, prebiotics and epithelial tight junctions: a promising approach to modulate intestinal barrier function. Int J Mol Sci. 2021;22(13):6729. doi:10.3390/ijms22136729.
    1. Llewellyn A, Foey A. Probiotic Modulation of Innate Cell Pathogen Sensing and Signaling Events. Nutrients. 2017;9(10):1156. doi:10.3390/nu9101156.
    1. Ji J, Yang H. Using probiotics as supplementation for helicobacter pylori antibiotic therapy. Int J Mol Sci. 2020;21(3):1136. doi:10.3390/ijms21031136.
    1. Feng T, Wang J. Oxidative stress tolerance and antioxidant capacity of lactic acid bacteria as probiotic: a systematic review. Gut Microbes. 2020;12(1):1801944. doi:10.1080/19490976.2020.1801944.
    1. van Zyl WF, Deane SM, Dicks LMT. Molecular insights into probiotic mechanisms of action employed against intestinal pathogenic bacteria. Gut Microbes. 2020;12(1):1831339. doi:10.1080/19490976.2020.1831339.
    1. Sanders ME, Merenstein DJ, Reid G, Gibson GR, Rastall RA. Probiotics and prebiotics in intestinal health and disease: from biology to the clinic. Nat Rev Gastroenterol Hepatol. 2019;16(10):605–616. doi:10.1038/s41575-019-0173-3.
    1. van Baarlen P, Troost FJ, van Hemert S, van der Meer C, de Vos WM, de Groot PJ, Hooiveld GJEJ, Brummer RJM, Kleerebezem M. Differential NF-κB pathways induction by Lactobacillus plantarum in the duodenum of healthy humans correlating with immune tolerance. Proc Natl Acad Sci U S A. 2009;106(7):2371–2376. doi:10.1073/pnas.0809919106.
    1. Fong W, Li Q, Yu J. Gut microbiota modulation: a novel strategy for prevention and treatment of colorectal cancer. Oncogene. 2020;39(26):4925–4943. doi:10.1038/s41388-020-1341-1.
    1. Hrdý J, Alard J, Couturier-Maillard A, Boulard O, Boutillier D, Delacre M, Lapadatescu C, Cesaro A, Blanc P, Pot B, et al. Lactobacillus reuteri 5454 and Bifidobacterium animalis ssp. lactis 5764 improve colitis while differentially impacting dendritic cells maturation and antimicrobial responses. Sci Rep. 2020;10(1):5345. doi:10.1038/s41598-020-62161-1.
    1. Lu K, Dong S, Wu X, Jin R, Chen H. Probiotics in Cancer. Front Oncol. 2021;11:638148. doi:10.3389/fonc.2021.638148.
    1. Tezuka H, Ohteki T. Regulation of IgA Production by Intestinal Dendritic Cells and Related Cells. Front Immunol. 2019;10:1891. doi:10.3389/fimmu.2019.01891.
    1. Eslami M, Yousefi B, Kokhaei P, Jazayeri Moghadas A, Sadighi Moghadam B, Arabkari V, Niazi Z. Are probiotics useful for therapy of Helicobacter pylori diseases? Comp Immunol Microbiol Infect Dis. 2019;64:99–108. doi:10.1016/j.cimid.2019.02.010.
    1. Motta JP, Wallace JL, Buret AG, Deraison C, Vergnolle N. Gastrointestinal biofilms in health and disease. Nat Rev Gastroenterol Hepatol. 2021;18(5):314–334. doi:10.1038/s41575-020-00397-y.
    1. Oh B, Kim BS, Kim JW, Kim JS, Koh S-J, Kim BG, Lee KL, Chun J. The effect of probiotics on gut microbiota during the Helicobacter pylori eradication: randomized controlled trial. Helicobacter. 2016;21(3):165–174. doi:10.1111/hel.12270.
    1. Oh B, Kim JW, Kim BS. Changes in the functional potential of the gut microbiome following probiotic supplementation during Helicobacter Pylori treatment. Helicobacter. 2016;21:493–503.
    1. Wu L, Wang Z, Sun G. Effects of anti-H. pylori triple therapy and a probiotic complex on intestinal microbiota in duodenal ulcer. Sci Rep. 2019;9(1):12874. doi:10.1038/s41598-019-49415-3.
    1. Cárdenas PA, Garcés D, Prado-Vivar B, Flores N, Fornasini M, Cohen H, Salvador I, Cargua O, Baldeón ME. Effect of Saccharomyces boulardii CNCM I-745 as complementary treatment of Helicobacter pylori infection on gut microbiome. Eur J Clin Microbiol Infect Dis. 2020;39(7):1365–1372. doi:10.1007/s10096-020-03854-3.
    1. Kakiuchi T, Mizoe A, Yamamoto K, Imamura I, Hashiguchi K, Kawakubo H, Yamaguchi D, Fujioka Y, Nakayama A, Okuda M, et al. Effect of probiotics during vonoprazan-containing triple therapy on gut microbiota in Helicobacter pylori infection: a randomized controlled trial. Helicobacter. 2020;25(3):e12690. doi:10.1111/hel.12690.
    1. Tang B, Tang L, Huang C, Tian C, Chen L, He Z, Yang G, Zuo L, Zhao G, Liu E, et al. The effect of probiotics supplementation on gut microbiota after Helicobacter pylori eradication: a multicenter randomized controlled trial. Infect Dis Ther. 2021;10(1):317–333. doi:10.1007/s40121-020-00372-9.
    1. Guillemard E, Poirel M, Schäfer F, Quinquis L, Rossoni C, Keicher C, Wagner F, Szajewska H, Barbut F, Derrien M, et al. A randomised, controlled trial: effect of a multi-strain fermented milk on the gut microbiota recovery after helicobacter pylori therapy. Nutrients. 2021;13(9):3171. doi:10.3390/nu13093171.
    1. Yang C, Liang L, Lv P, Liu L, Wang S, Wang Z, Chen Y. Effects of non-viable Lactobacillus reuteri combining with 14-day standard triple therapy on Helicobacter pylori eradication: a randomized double-blind placebo-controlled trial. Helicobacter. 2021;26(6):e12856. doi:10.1111/hel.12856.
    1. Yuan Z, Xiao S, Li S, Suo B, Wang Y, Meng L, Liu Z, Yin Z, Xue Y, Zhou L, et al. The impact of Helicobacter pylori infection, eradication therapy, and probiotics intervention on gastric microbiota in young adults. Helicobacter. 2021;26(6):e12848. doi:10.1111/hel.12848.
    1. Stoeva MK, Garcia-So J, Justice N, Myers J, Tyagi S, Nemchek M, McMurdie PJ, Kolterman O, Eid J. Butyrate-producing human gut symbiont, Clostridium butyricum, and its role in health and disease. Gut Microbes. 2021;13(1):1–28. doi:10.1080/19490976.2021.1907272.
    1. Ariyoshi T, Hagihara M, Tomono S, Eguchi S, Minemura A, Miura D, Oka K, Takahashi M, Yamagishi Y, Mikamo H, et al. Clostridium butyricum MIYAIRI 588 modifies bacterial composition under antibiotic-induced dysbiosis for the activation of interactions via lipid metabolism between the gut microbiome and the host. Biomedicines. 2021;9(8):1065. doi:10.3390/biomedicines9081065.
    1. Wang Y, Huang JM, Zhou YL, Almeida A, Finn RD, Danchin A, He L-S. Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli. BMC Genomics. 2020;21(1):408. doi:10.1186/s12864-020-06807-4.
    1. Yuan X, Chen R, McCormick KL, Zhang Y, Lin X, Yang X. The role of the gut microbiota on the metabolic status of obese children. Microb Cell Fact. 2021;20(1):53. doi:10.1186/s12934-021-01548-9.
    1. Yeoh YK, Chen Z, Wong MCS, Hui M, Yu J, Ng SC, Sung JJY, Chan FKL, Chan PKS. Southern Chinese populations harbour non-nucleatum Fusobacteria possessing homologues of the colorectal cancer-associated FadA virulence factor. Gut. 2020;69(11):1998–2007. doi:10.1136/gutjnl-2019-319635.
    1. Harrandah AM, Chukkapalli SS, Bhattacharyya I, Progulske-Fox A, Chan EKL. Fusobacteria modulate oral carcinogenesis and promote cancer progression. J Oral Microbiol. 2020;13:1849493.
    1. Harding CM, Hennon SW, Feldman MF. Uncovering the mechanisms of Acinetobacter baumannii virulence. Nat Rev Microbiol. 2018;16(2):91–102. doi:10.1038/nrmicro.2017.148.
    1. Song WY, Kim HJ. Current biochemical understanding regarding the metabolism of acinetobactin, the major siderophore of the human pathogen Acinetobacter baumannii, and outlook for discovery of novel anti-infectious agents based thereon. Nat Prod Rep. 2020;37(4):477–487. doi:10.1039/C9NP00046A.
    1. Zhao X, Zhong X, Liu X, Wang X, Gao X. Therapeutic and improving function of lactobacilli in the prevention and treatment of cardiovascular-related diseases: a novel perspective from gut microbiota. Frontiers in Nutrition. 2021;8(299). doi:10.3389/fnut.2021.693412.
    1. Hanchi H, Mottawea W, Sebei K, Hammami R. The genus enterococcus: between probiotic potential and safety concerns—an update. Front Microbiol. 2018;9(1791). doi:10.3389/fmicb.2018.01791.
    1. Liu X, Mao B, Gu J, Wu J, Cui S, Wang G, Zhao J, Zhang H, Chen W. Blautia —a new functional genus with potential probiotic properties? Gut Microbes. 2021;13(1):1–21. doi:10.1080/19490976.2021.1875796.
    1. Xiang H, Gan J, Zeng D, Li J, Yu H, Zhao H, Yang Y, Tan S, Li G, Luo C, et al. Specific microbial taxa and functional capacity contribute to chicken abdominal fat deposition. Front Microbiol. 2021;12:643025. doi:10.3389/fmicb.2021.643025.
    1. Goris T, Cuadrat RRC, Braune A. Flavonoid-modifying capabilities of the human gut microbiome-an in silico study. Nutrients. 2021;13(8):2688. doi:10.3390/nu13082688.
    1. Engevik MA, Danhof HA, Ruan W, Engevik AC, Chang-Graham AL, Engevik KA, Shi Z, Zhao Y, Brand CK, Krystofiak ES, et al. Fusobacterium nucleatum Secretes outer membrane vesicles and promotes intestinal inflammation. mBio. 2021;12(2). doi:10.1128/mBio.02706-20.
    1. Ranjbar M, Salehi R, Haghjooy Javanmard S, Rafiee L, Faraji H, Jafarpor S, Ferns GA, Ghayour-Mobarhan M, Manian M, Nedaeinia R, et al. The dysbiosis signature of fusobacterium nucleatum in colorectal cancer-cause or consequences? A systematic review. Cancer Cell Int. 2021;21(1):194. doi:10.1186/s12935-021-01886-z.
    1. Murros KE, Huynh VA, Takala TM, Saris PEJ. Desulfovibrio bacteria are associated with parkinson’s disease. Front Cell Infect Microbiol. 2021;11:652617. doi:10.3389/fcimb.2021.652617.
    1. Rosario D, Bidkhori G, Lee S, Bedarf J, Hildebrand F, Le Chatelier E, Uhlen M, Ehrlich SD, Proctor G, Wüllner U, et al. Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson’s disease. Cell Rep. 2021;34(9):108807. doi:10.1016/j.celrep.2021.108807.
    1. Shao J, Li Z, Gao Y, Zhao K, Lin M, Li Y, Wang S, Liu Y, Chen L. Construction of a “Bacteria-Metabolites” co-expression network to clarify the anti-ulcerative colitis effect of flavonoids of sophora flavescens aiton by regulating the “Host-Microbe” interaction. Front Pharmacol. 2021;12:710052. doi:10.3389/fphar.2021.710052.
    1. Caulier S, Nannan C, Gillis A, Licciardi F, Bragard C, Mahillon J. Overview of the antimicrobial compounds produced by members of the Bacillus subtilis group. Front Microbiol. 2019;10:302. doi:10.3389/fmicb.2019.00302.
    1. Martin RM, Bachman MA. Colonization, infection, and the accessory genome of Klebsiella pneumoniae. Front Cell Infect Microbiol. 2018;8:4. doi:10.3389/fcimb.2018.00004.
    1. Dong S, Jiao J, Jia S, Li G, Zhang W, Yang K, Wang Z, Liu C, Li D, Wang X, et al. 16S rDNA full-length assembly sequencing technology analysis of intestinal microbiome in polycystic ovary syndrome. Front Cell Infect Microbiol. 2021;11:634981. doi:10.3389/fcimb.2021.634981.
    1. Yu X, Åvall-Jääskeläinen S, Koort J, Lindholm A, Rintahaka J, von Ossowski I, Palva A, Hynönen U. A comparative characterization of different host-sourced lactobacillus ruminis strains and their adhesive, inhibitory, and immunomodulating functions. Front Microbiol. 2017;8(657). doi:10.3389/fmicb.2017.00657.
    1. Yang J, Li Y, Wen Z, Liu W, Meng L, Huang H. Oscillospira - a candidate for the next-generation probiotics. Gut Microbes. 2021;13(1):1987783. doi:10.1080/19490976.2021.1987783.
    1. Bartley A, Yang T, Arocha R, Malphurs WL, Larkin R, Magee KL, Vickroy TW, Zubcevic J. Increased abundance of lactobacillales in the colon of beta-adrenergic receptor knock out mouse is associated with increased gut bacterial production of short chain fatty acids and reduced IL17 expression in circulating CD4+ immune cells. Front Physiol. 2018;9(1593). doi:10.3389/fphys.2018.01593.
    1. Chen Z, Xie Y, Zhou F, Zhang B, Wu J, Yang L, Xu S, Stedtfeld R, Chen Q, Liu J, et al. Featured Gut Microbiomes Associated With the Progression of Chronic Hepatitis B Disease. Front Microbiol. 2020;11:383. doi:10.3389/fmicb.2020.00383.
    1. Zhou Y, Chen C, Yu H, Yang Z. Fecal microbiota changes in patients with postpartum depressive disorder. Front Cell Infect Microbiol. 2020;10:567268. doi:10.3389/fcimb.2020.567268.
    1. Nagao-Kitamoto H, Leslie JL, Kitamoto S, Jin C, Thomsson KA, Gillilland MG, Kuffa P, Goto Y, Jenq RR, Ishii C, et al. Interleukin-22-mediated host glycosylation prevents clostridioides difficile infection by modulating the metabolic activity of the gut microbiota. Nat Med. 2020;26(4):608–617. doi:10.1038/s41591-020-0764-0.
    1. Tito RY, Cypers H, Joossens M, Varkas G, Van Praet L, Glorieus E, Van den Bosch F, De Vos M, Raes J, Elewaut D, et al. Brief report: dialister as a microbial marker of disease activity in spondyloarthritis. Arthritis & Rheumatology. 2017;69(1):114–121. doi:10.1002/art.39802.
    1. Kaakoush NO. Sutterella species, iga-degrading bacteria in ulcerative colitis. Trends Microbiol. 2020;28(7):519–522. doi:10.1016/j.tim.2020.02.018.
    1. Astbury S, Atallah E, Vijay A, Aithal GP, Grove JI, Valdes AM. Lower gut microbiome diversity and higher abundance of proinflammatory genus Collinsella are associated with biopsy-proven nonalcoholic steatohepatitis. Gut Microbes. 2020;11(3):569–580. doi:10.1080/19490976.2019.1681861.
    1. Bailen M, Bressa C, Martinez-Lopez S, González-Soltero R, Montalvo Lominchar MG, San Juan C, Larrosa M. Microbiota features associated with a high-fat/low-fiber diet in healthy adults. Front Nutr. 2020;7:583608. doi:10.3389/fnut.2020.583608.
    1. Zhang X, Coker OO, Chu ES, Fu K, Lau HCH, Wang Y-X, Chan AWH, Wei H, Yang X, Sung JJY, et al. Dietary cholesterol drives fatty liver-associated liver cancer by modulating gut microbiota and metabolites. Gut. 2021;70(4):761–774. doi:10.1136/gutjnl-2019-319664.
    1. Yuan C, Yin Z, Wang J, Qian C, Wei Y, Zhang S, Jiang L, Liu B. Comparative genomic analysis of citrobacter and key genes essential for the pathogenicity of Citrobacter koseri. Front Microbiol. 2019;10:2774. doi:10.3389/fmicb.2019.02774.
    1. Ma X, Ma L, Wang Z, Liu Y, Long L, Ma X, Chen H, Chen Z, Lin X, Si L, et al. Clinical features and gut microbial alterations in anti-leucine-rich glioma-inactivated 1 encephalitis-a pilot study. Front Neurol. 2020;11:585977. doi:10.3389/fneur.2020.585977.
    1. Cerqueira FM, Photenhauer AL, Pollet RM, Brown HA, Koropatkin NM. Starch Digestion by Gut Bacteria: crowdsourcing for Carbs. Trends Microbiol. 2020;28(2):95–108. doi:10.1016/j.tim.2019.09.004.
    1. Gurung M, Li Z, You H, Rodrigues R, Jump DB, Morgun A, Shulzhenko N. Role of gut microbiota in type 2 diabetes pathophysiology. EBioMedicine. 2020;51:102590. doi:10.1016/j.ebiom.2019.11.051.
    1. Schirmer M, Garner A, Vlamakis H, Xavier RJ. Microbial genes and pathways in inflammatory bowel disease. Nat Rev Microbiol. 2019;17(8):497–511. doi:10.1038/s41579-019-0213-6.
    1. Lordan C, Thapa D, Ross RP, Cotter PD. Potential for enriching next-generation health-promoting gut bacteria through prebiotics and other dietary components. Gut Microbes. 2020;11(1):1–20. doi:10.1080/19490976.2019.1613124.
    1. Tomova A, Bukovsky I, Rembert E, Yonas W, Alwarith J, Barnard ND, Kahleova H. The effects of vegetarian and vegan diets on gut microbiota. Front Nutr. 2019;6:47. doi:10.3389/fnut.2019.00047.
    1. Shimokawa C, Kato T, Takeuchi T, Ohshima N, Furuki T, Ohtsu Y, Suzue K, Imai T, Obi S, Olia A, et al. CD8(+) regulatory T cells are critical in prevention of autoimmune-mediated diabetes. Nat Commun. 2020;11(1):1922. doi:10.1038/s41467-020-15857-x.
    1. Carey MA, Medlock GL, Alam M, Kabir M, Uddin MJ, Nayak U, Papin J, Faruque ASG, Haque R, Petri WA, et al. Megasphaera in the stool microbiota is negatively associated with diarrheal cryptosporidiosis. Clin Infect Dis. 2021;73(6):e1242–e1251. doi:10.1093/cid/ciab207.
    1. Liu F, Li J, Guan Y, Lou Y, Chen H, Xu M, Deng D, Chen J, Ni B, Zhao L, et al. Dysbiosis of the gut microbiome is associated with tumor biomarkers in lung cancer. Int J Biol Sci. 2019;15(11):2381–2392. doi:10.7150/ijbs.35980.
    1. Vascellari S, Palmas V, Melis M, Pisanu S, Cusano R, Uva P, Perra D, Madau V, Sarchioto M, Oppo V, et al. Gut microbiota and metabolome alterations associated with parkinson’s disease. mSystems. 2020;5(5). doi:10.1128/mSystems.00561-20.
    1. Valles-Colomer M, Falony G, Darzi Y, Tigchelaar EF, Wang J, Tito RY, Schiweck C, Kurilshikov A, Joossens M, Wijmenga C, et al. The neuroactive potential of the human gut microbiota in quality of life and depression. Nat Microbiol. 2019;4(4):623–632. doi:10.1038/s41564-018-0337-x.
    1. Yin Z, Zhang S, Wei Y, Wang M, Ma S, Yang S, Wang J, Yuan C, Jiang L, Du Y, et al. Horizontal gene transfer clarifies taxonomic confusion and promotes the genetic diversity and pathogenicity of plesiomonas shigelloides. mSystems. 2020;5(5). doi:10.1128/mSystems.00448-20.
    1. Suez J, Zmora N, Elinav E. Probiotics in the next-generation sequencing era. Gut Microbes. 2020;11(1):77–93. doi:10.1080/19490976.2019.1586039.
    1. Zmora N, Zilberman-Schapira G, Suez J, Mor U, Dori-Bachash M, Bashiardes S, Kotler E, Zur M, Regev-Lehavi D, Brik RBZ, et al. Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell. 2018;174(6):1388–1405.e1321. doi:10.1016/j.cell.2018.08.041.
    1. Zafar H, Saier MH Jr. Gut bacteroides species in health and disease. Gut Microbes. 2021;13(1):1–20. doi:10.1080/19490976.2020.1848158.
    1. Zou Y, Lin X, Xue W. Characterization and description of Faecalibacterium butyricigenerans sp. nov. and F. longum sp. nov., isolated from human faeces. Sci Rep. 2021;11(1):11340. doi:10.1038/s41598-021-90786-3.
    1. Van Hul M, Le Roy T, Prifti E, Dao MC, Paquot A, Zucker J-D, Delzenne NM, Muccioli GG, Clément K, Cani PD, et al. From correlation to causality: the case of subdoligranulum. Gut Microbes. 2020;12(1):1–13. doi:10.1080/19490976.2020.1849998.
    1. Zhang X, Li N, Chen Q, Qin H. Fecal microbiota transplantation modulates the gut flora favoring patients with functional constipation. Front Microbiol. 2021;12:700718. doi:10.3389/fmicb.2021.700718.
    1. Ashida H, Suzuki T, Sasakawa C. Shigella infection and host cell death: a double-edged sword for the host and pathogen survival. Curr Opin Microbiol. 2021;59:1–7. doi:10.1016/j.mib.2020.07.007.
    1. Guerrant RL, Bolick DT, Swann JR. Modeling enteropathy or diarrhea with the top bacterial and protozoal pathogens: differential determinants of outcomes. ACS Infect Dis. 2021;7(5):1020–1031. doi:10.1021/acsinfecdis.0c00831.
    1. Diling C, Longkai Q, Yinrui G, Yadi L, Xiaocui T, Xiangxiang Z, Miao Z, Ran L, Ou S, Dongdong W, et al. CircNF1-419 improves the gut microbiome structure and function in AD-like mice. Aging (Albany NY). 2020;12(1):260–287. doi:10.18632/aging.102614.
    1. Mukherjee A, Lordan C, Ross RP, Cotter PD. Gut microbes from the phylogenetically diverse genus Eubacterium and their various contributions to gut health. Gut Microbes. 2020;12(1):1802866. doi:10.1080/19490976.2020.1802866.
    1. van Trijp MPH, Schutte S, Esser D. Minor changes in the composition and function of the gut microbiota during a 12-week whole grain wheat or refined wheat intervention correlate with liver fat in overweight and obese adults. J Nutr. 2021;151(3):491–502. doi:10.1093/jn/nxaa312.
    1. Wang Y, Zhang C, Hou S, Wu X, Liu J, Wan X. Analyses of potential driver and passenger bacteria in human colorectal cancer. Cancer Manag Res. 2020;12:11553–11561. doi:10.2147/CMAR.S275316.
    1. Fan X, Alekseyenko AV, Wu J, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Abnet CC, Stolzenberg-Solomon R, Miller G, et al. Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study. Gut. 2018;67(1):120–127. doi:10.1136/gutjnl-2016-312580.
    1. Schoilew K, Ueffing H, Dalpke A, Wolff B, Frese C, Wolff D, Boutin S. Bacterial biofilm composition in healthy subjects with and without caries experience. J Oral Microbiol. 2019;11(1):1633194. doi:10.1080/20002297.2019.1633194.
    1. Costa D, Iraola G. Pathogenomics of Emerging Campylobacter Species. Clin Microbiol Rev. 2019;32(4). doi:10.1128/CMR.00072-18.
    1. Gurwara S, Ajami NJ, Jang A, Hessel F, Chen L, Plew S, Wang Z, Graham D, Hair C, White D, et al. Dietary nutrients involved in one-carbon metabolism and colonic mucosa-associated gut microbiome in individuals with an endoscopically normal colon. Nutrients. 2019;11(3):613. doi:10.3390/nu11030613.
    1. Liu Y, Li W, Yang H. Leveraging 16S rRNA microbiome sequencing data to identify bacterial signatures for irritable bowel syndrome. Front Cell Infect Microbiol. 2021;11:645951. doi:10.3389/fcimb.2021.645951.
    1. Kim JM, Rim JH, Kim DH. Microbiome analysis reveals that ralstonia is responsible for decreased renal function in patients with ulcerative colitis. Clin Transl Med. 2021;11(3):e322. doi:10.1002/ctm2.322.
    1. Suárez-Jaramillo A, Baldeón ME, Prado B, Fornasini M, Cohen H, Flores N, Salvador I, Cargua O, Realpe J, Cárdenas PA, et al. Duodenal microbiome in patients with or without Helicobacter pylori infection. Helicobacter. 2020;25(6):e12753. doi:10.1111/hel.12753.
    1. Gareau MG, Sherman PM, Walker WA. Probiotics and the gut microbiota in intestinal health and disease. Nat Rev Gastroenterol Hepatol. 2010;7(9):503–514. doi:10.1038/nrgastro.2010.117.
    1. Sniffen JC, McFarland LV, Evans CT, Goldstein EJC. Choosing an appropriate probiotic product for your patient: an evidence-based practical guide. PLoS One. 2018;13(12):e0209205. doi:10.1371/journal.pone.0209205.
    1. Quin C, Estaki M, Vollman DM, Barnett JA, Gill SK, Gibson DL. Probiotic supplementation and associated infant gut microbiome and health: a cautionary retrospective clinical comparison. Sci Rep. 2018;8(1):8283. doi:10.1038/s41598-018-26423-3.
    1. Suez J, Zmora N, Zilberman-Schapira G, Mor U, Dori-Bachash M, Bashiardes S, Zur M, Regev-Lehavi D, Ben-Zeev Brik R, Federici S, et al. Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT. Cell. 2018;174(6):1406–1423.e1416. doi:10.1016/j.cell.2018.08.047.
    1. Donaldson GP, Lee SM, Mazmanian SK. Gut biogeography of the bacterial microbiota. Nat Rev Microbiol. 2016;14(1):20–32. doi:10.1038/nrmicro3552.
    1. Lau HCH, Kranenburg O, Xiao H, Yu J. Organoid models of gastrointestinal cancers in basic and translational research. Nat Rev Gastroenterol Hepatol. 2020;17(4):203–222. doi:10.1038/s41575-019-0255-2.
    1. Jalili-Firoozinezhad S, Gazzaniga FS, Calamari EL, Camacho DM, Fadel CW, Bein A, Swenor B, Nestor B, Cronce MJ, Tovaglieri A, et al. A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip. Nat Biomed Eng. 2019;3(7):520–531. doi:10.1038/s41551-019-0397-0.
    1. O’Toole PW, Marchesi JR, Hill C. Next-generation probiotics: the spectrum from probiotics to live biotherapeutics. Nat Microbiol. 2017;2(5):17057. doi:10.1038/nmicrobiol.2017.57.

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