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The Role of Microbiota in Gastrointestinal Cancer and Cancer Treatment: Chance or Curse?

  • Annemieke Smet
    Affiliations
    Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine and Health Sciences

    Infla-Med Research Consortium of Excellence, University of Antwerp, Antwerp, Belgium
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  • Juozas Kupcinskas
    Affiliations
    Institute for Digestive Research, Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
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  • Alexander Link
    Affiliations
    Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University, Magdeburg, Germany
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  • Author Footnotes
    § Authors share co-senior authorship.
    Georgina L. Hold
    Footnotes
    § Authors share co-senior authorship.
    Affiliations
    Microbiome Research Centre, St George and Sutherland Clinical School, University of New South Wales, Sydney, Australia
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  • Author Footnotes
    § Authors share co-senior authorship.
    Jan Bornschein
    Correspondence
    Correspondence Address correspondence to: Jan Bornschein, MD, Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, United Kingdom.
    Footnotes
    § Authors share co-senior authorship.
    Affiliations
    Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
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  • Author Footnotes
    § Authors share co-senior authorship.
Open AccessPublished:September 07, 2021DOI:https://doi.org/10.1016/j.jcmgh.2021.08.013
      The gastrointestinal (GI) tract is home to a complex and dynamic community of microorganisms, comprising bacteria, archaea, viruses, yeast, and fungi. It is widely accepted that human health is shaped by these microbes and their collective microbial genome. This so-called second genome plays an important role in normal functioning of the host, contributing to processes involved in metabolism and immune modulation. Furthermore, the gut microbiota also is capable of generating energy and nutrients (eg, short-chain fatty acids and vitamins) that are otherwise inaccessible to the host and are essential for mucosal barrier homeostasis. In recent years, numerous studies have pointed toward microbial dysbiosis as a key driver in many GI conditions, including cancers. However, comprehensive mechanistic insights on how collectively gut microbes influence carcinogenesis remain limited. In addition to their role in carcinogenesis, the gut microbiota now has been shown to play a key role in influencing clinical outcomes to cancer immunotherapy, making them valuable targets in the treatment of cancer. It also is becoming apparent that, besides the gut microbiota’s impact on therapeutic outcomes, cancer treatment may in turn influence GI microbiota composition. This review provides a comprehensive overview of microbial dysbiosis in GI cancers, specifically esophageal, gastric, and colorectal cancers, potential mechanisms of microbiota in carcinogenesis, and their implications in diagnostics and cancer treatment.

      Keywords

      Abbreviations used in this paper:

      CRC (colorectal cancer), EAC (esophageal adenocarcinoma), ESCC (esophageal squamous cell carcinoma), ETBF (enterotoxigenic Bacteroides fragilis), FMT (fecal microbiota transplantation), GC (gastric cancer), GERD (gastroesophageal reflux disease), GI (gastrointestinal), HFD (high-fat diet), ICI (immune checkpoint inhibitor), PD-1 (programmed cell death 1), PPI (proton pump inhibitor), RID (radiotherapy-induced diarrhea), Th (T-helper cell), TLR (Toll-like receptor)
      With the widely accepted concept that human health is shaped by microbes, we present an overview of the involvement of microbiota in gastrointestinal cancer biology. This includes mechanistic insights as well as the impact on diagnostics and cancer treatment.
      The gut microbiota has arguably become one of the most exciting frontiers in health in the past decade. Since the development of next-generation sequencing technologies and their application within clinical research, our understanding of the human microbiome and its role in health and disease has increased exponentially.
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      Microbially induced pro inflammatory cytokine level increases can lead to epithelial DNA damage including epigenetic regulatory changes, which in turn induce genetic instability. These factors influence cancer initiation, promotion, dissemination, and also impact treatment.
      In this review, we explore the contribution of gut microbes in esophageal, gastric, and colorectal cancers. We also offer a glimpse toward future developments in relation to microbial manipulation strategies in the context of cancer prevention and management.

      Esophageal Cancer

      Esophageal cancer is a major cause of global cancer mortality, with 2 distinct histologic types (ie, esophageal squamous cell carcinoma [ESCC] and esophageal adenocarcinoma [EAC]).
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      Figure thumbnail gr1
      Figure 1Overview on microbiota and cancers of the luminal GI tract. Bacterial genera/species abundantly present (blue arrow) or depleted (red arrow) in esophageal, gastric, and colorectal cancers.
      Studies investigating cancer risk stratification based on microbial composition analysis have highlighted that P gingivalis, Streptococcus, Neisseria, Actinomyces, and Atopobium are the main predictors for ESCC development,
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      It remains to be determined whether these microbial changes have a causative effect or represent merely a consequence of the cancer being present.
      Figure thumbnail gr2
      Figure 2Impact of the microbiota on GI cancers. The GI microbiota and its potential implications in cancer development, diagnostics, treatment interventions, and prevention by probiotics. CTLA-4, cytotoxic T-lymphocyte–associated protein 4; PD-L1, programmed cell death 1 ligand.

      The Curious Case of Helicobacter pylori in EAC

      Epidemiologic evidence suggests an inverse relationship between H pylori eradication and EAC incidence, potentially induced by a shift in the gastric microbiota.
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      Microbial Involvement in Esophageal Carcinogenesis: Mechanistic Insights

      Evidence from many preclinical models has shaped our mechanistic understanding of microbiota involvement in gastrointestinal carcinogenesis. Although the limitations of such models are extensive, it nevertheless remains that significant understanding and shaping of clinical studies has benefitted from these studies.
      Through the use of nude mice xenograft studies, using intraperitoneal injection of esophageal cancer cells, significant alterations have occurred in the microbiota structure including a depletion of Pasteurellales and enrichment of carbohydrate/lipid metabolic pathways in the esophageal microbiota. Furthermore, fecal microbiota transplantation (FMT) of “healthy” mouse stool to antibiotic-treated xenograft-bearing mice significantly improved liver metastases, highlighting a protective role of the gut microbiota.
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      Figure thumbnail gr3
      Figure 3Role of the microbiota in GI carcinogenesis. (A) A HFD impacts microbiota composition resulting in Clostridium abundance and Lactobacillus, Escherichia, and Shigella depletion and acceleration in esophageal tumor development.
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      CCL, chemokin (C-C motif) ligand; c-MYC, MYC proto-oncogene; CXCR2, C-X-C motif chemokine receptor 2; EMT, epithelial-mesenchymal transition; G-CSF, granulocyte colony-stimulating factor; Hp, H pylori; MUC4, mucin 4; PCWBR2, putative cell wall binding repeat 2; rASF, restricted altered Schaedler's flora; ROS, reactive oxygen species; STAT3, signal transducer and activator of transcription 3.
      Diet also has an impact on the microbiota composition in esophageal carcinogenesis. Sprague Dawley rats fed a high-fat diet (HFD) have an altered esophageal microbiota compared with rats fed a normal chow diet, with an increase in Clostridium species and depletion of Escherichia, Shigella, and Lactobacillus genera (Figure 3A).
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      Cross-talk among metabolic parameters, esophageal microbiota, and host gene expression following chronic exposure to an obesogenic diet.
      In addition, transgenic interleukin (IL)2–IL1β mice fed with a HFD developed esophageal tumors more rapidly than mice fed with a normal diet. This acceleration was associated with gut microbiota changes as well as immune alterations including Toll-like receptor (TLR) expression, an increased ratio of neutrophils:natural killer cells, and aberrant levels of T-cell recruiting factors (chemokin [C-C motif] ligands 6 and 12: CCL6, CCL12), granulocyte colony-stimulating factor (G-CSF), and chemokine (C-X-C motif) ligand 1 (CXCL1), leading to an increase of C-X-C motif chemokine receptor 2 (CXCR2)-positive immune cells (Figure 3A). Organoid studies further confirmed that CXCR2 stimulation initiated expansion of Lgr5 progenitor cells, causing initiation of metaplasia.
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      Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota.
      The proinflammatory effect of a HFD on the esophageal tract can be synergized further by the addition of deoxycholic acid to drinking water. Deoxycholic acid promotes the development of BE and chronic HFD + deoxycholic acid treatment results in a higher microbial diversity, an increase in inflammation, and a lipid tissue signature useful for early BE diagnosis.
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      Pathobiology of Helicobacter pylori-induced gastric cancer.
      Surgical alteration of the upper gastrointestinal (GI) tract leads to functional modification affecting host metabolism and mucosal homeostasis. Esophagojejunostomy to induce BE in rats affects both TLR expression and esophageal microbiota composition, characterized by a significant decrease of Lactobacillus and an increase of Clostridium, Enterococcus, and Streptococcus.
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      Other Helicobacters and the gastric microbiome.
      Furthermore, this effect is aggravated by the introduction of antibiotics but is reversed by the addition of rebamipide, a mucosal protective agent used for peptic ulcer disease.
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      The gastric microbiome is perturbed in advanced gastric adenocarcinoma identified through shotgun metagenomics.
      Another factor that can affect the balance between esophageal mucosal integrity and the gut microbiota is riboflavin. Riboflavin deficiency in rats is linked to esophageal epithelial atrophy and reduced activity of xenobiotic metabolic pathways. Riboflavin supplementation of riboflavin-deficient rats has a direct impact on gut microbiota composition with a reduction in Firmicutes abundance and an increase of Proteobacteria.
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      Stomach microbiota composition varies between patients with non-atrophic gastritis and patients with intestinal type of gastric cancer.

      Gastric Cancer

      Gastric cancer (GC) is a multifactorial disease with different genetic, molecular, and environmental factors influencing disease development, with the most frequent cause being H pylori infection.
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      This class I carcinogen plays a crucial role in initiating steps of gastric carcinogenesis by causing enhanced inflammation and progressive changes in the architecture and function of the gastric mucosa, resulting in a life-long infection unless an eradication strategy is implemented.
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      Different gastric microbiota compositions in two human populations with high and low gastric cancer risk in Colombia.
      ,
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      Increased abundance of Clostridium and Fusobacterium in gastric microbiota of patients with gastric cancer in Taiwan.
      Because of the acidic environment and other local antimicrobial factors, it was long thought that the stomach was inhabited exclusively by H pylori and was considered inhospitable to other microorganisms.
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      • Kaakoush N.O.
      Dysbiosis of the microbiome in gastric carcinogenesis.
      However, from a certain timepoint in the course of progression of mucosal changes, gastric carcinogenesis is H pylori–independent because colonization levels decrease in patients with intestinal metaplasia and dysplasia, and essentially is absent by the adenocarcinoma stage.
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      Different gastric microbiota compositions in two human populations with high and low gastric cancer risk in Colombia.
      H pylori thus may act by a hit-and-run mechanism, priming the gastric mucosa for further oncogenic changes, which are accomplished by other microbes.
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      Different gastric microbiota compositions in two human populations with high and low gastric cancer risk in Colombia.
      ,
      • Gao J.-J.
      • Zhang Y.
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      Association between gut microbiota and Helicobacter pylori-related gastric lesions in a high-risk population of gastric cancer.
      • Castaño-Rodríguez N.
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      • Fock K.M.
      • Mitchell H.M.
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      Dysbiosis of the microbiome in gastric carcinogenesis.
      • Coker O.O.
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      Mucosal microbiome dysbiosis in gastric carcinogenesis.
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      Molecular characterization of the stomach microbiota in patients with gastric cancer and in controls.
      Furthermore, stomach microhabitats are not always as uniform as previously thought. Local pH, mucin distribution, nutrients, ions, and chemical levels vary considerably in tumor and adjacent tumor-free tissue. These factors heavily influence microbial composition and diversity.
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      Association between gut microbiota and Helicobacter pylori-related gastric lesions in a high-risk population of gastric cancer.
      Recent advances in sequencing technologies have highlighted significant differences in the gastric microbiota compared with the oral and/or esophageal microbiota, with the stomach harboring a distinct microbial ecosystem comprising Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Fusobacteria.
      • Eun C.S.
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      Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods.
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      Comparison of the human gastric microbiota in hypochlorhydric states arising as a result of Helicobacter pylori-induced atrophic gastritis, autoimmune atrophic gastritis and proton pump inhibitor use.
      Studies also have shown the presence of a specific fungal consortium (mycobiome).
      • Sohn S.-H.
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      • Kim J.
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      Analysis of gastric body microbiota by pyrosequencing: possible role of bacteria other than Helicobacter pylori in the gastric carcinogenesis.
      One question that remains unanswered is related to transient vs persistent gastric colonization and its role in disease pathogenesis. Studies have tried to address this question, but the full potential of the gastric microbiota remains to be elucidated, including the contribution of the various gastric microbiota components and the extent of microbe:microbe crosstalk/interactions.
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      In vivo analysis of the viable microbiota and Helicobacter pylori transcriptome in gastric infection and early stages of carcinogenesis.

      Microbiota Diversity in Gastric Carcinogenesis

      Studies assessing human gastric microbiota profiles have shown significant differences between patients with chronic (atrophic) gastritis, metaplasia, and GC, highlighting that dysbiosis in the stomach is a dynamic process that correlates with cancer progression (Supplementary Table 2).
      • Yang I.
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      • Piazuelo M.B.
      • Bravo L.E.
      • Yepez M.C.
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      • Wilson K.T.
      • Peek R.M.
      • Correa P.
      • Josenhans C.
      • Fox J.G.
      • Suerbaum S.
      Different gastric microbiota compositions in two human populations with high and low gastric cancer risk in Colombia.
      ,
      • Gao J.-J.
      • Zhang Y.
      • Gerhard M.
      • Mejias-Luque R.
      • Zhang L.
      • Vieth M.
      • Ma J.-L.
      • Bajbouj M.
      • Suchanek S.
      • Liu W.-D.
      • Ulm K.
      • Quante M.
      • Li Z.-X.
      • Zhou T.
      • Schmid R.
      • Classen M.
      • Li W.-Q.
      • You W.-C.
      • Pan K.-F.
      Association between gut microbiota and Helicobacter pylori-related gastric lesions in a high-risk population of gastric cancer.
      ,
      • Coker O.O.
      • Dai Z.
      • Nie Y.
      • Zhao G.
      • Cao L.
      • Nakatsu G.
      • Wu W.K.
      • Wong S.H.
      • Chen Z.
      • Sung J.J.Y.
      • Yu J.
      Mucosal microbiome dysbiosis in gastric carcinogenesis.
      ,
      • Eun C.S.
      • Kim B.K.
      • Han D.S.
      • Kim S.Y.
      • Kim K.M.
      • Choi B.Y.
      • Song K.S.
      • Kim Y.S.
      • Kim J.F.
      Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods.
      ,
      • Sohn S.-H.
      • Kim N.
      • Jo H.J.
      • Kim J.
      • Park J.H.
      • Nam R.H.
      • Seok Y.-J.
      • Kim Y.-R.
      • Lee D.H.
      Analysis of gastric body microbiota by pyrosequencing: possible role of bacteria other than Helicobacter pylori in the gastric carcinogenesis.
      • Thorell K.
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      • Liu O.H.-F.
      • Palacios Gonzales R.V.
      • Nookaew I.
      • Rabeneck L.
      • Paszat L.
      • Graham D.Y.
      • Nielsen J.
      • Lundin S.B.
      • Å Sjöling
      In vivo analysis of the viable microbiota and Helicobacter pylori transcriptome in gastric infection and early stages of carcinogenesis.
      • Vuik F.
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      • van de Winkel A.
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      • Spaander M.
      • Peppelenbosch M.P.
      • Engstrand L.
      • Kuipers E.J.
      Composition of the mucosa-associated microbiota along the entire gastrointestinal tract of human individuals.
      • Miao R.
      • Wan C.
      • Wang Z.
      The relationship of gastric microbiota and Helicobacter pylori infection in pediatrics population.
      • Han H.S.
      • Lee S.-Y.
      • Oh S.Y.
      • Moon H.W.
      • Cho H.
      • Kim J.-H.
      Correlations of the gastric and duodenal microbiota with histological, endoscopic, and symptomatic gastritis.
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      • Bolor D.
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      Gastric mucosal microbiota in a Mongolian population with gastric cancer and precursor conditions.
      • Gantuya B.
      • El-Serag H.B.
      • Matsumoto T.
      • Ajami N.J.
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      • Uchida T.
      • Yamaoka Y.
      Gastric microbiota in Helicobacter pylori-negative and -positive gastritis among high incidence of gastric cancer area.
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      • Thon C.
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      Fusobacterium nucleatum is associated with worse prognosis in Lauren’s diffuse type gastric cancer patients.
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      • Gophna U.
      • Half E.E.
      Gastric microbiota is altered in oesophagitis and Barrett’s oesophagus and further modified by proton pump inhibitors.
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      The role of non-H. pylori bacteria in the development of gastric cancer.
      Microbiota profiles in patients with H pylori–induced superficial gastritis or even glandular atrophy are dominated by Helicobacter and, to a much lesser extent, Streptococcus, Prevotella, and Neisseria, resulting in decreased phylotype richness, diversity, and evenness compared with patients with a normal gastric mucosa (Supplementary Table 2).
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      Gastric colonisation with a restricted commensal microbiota replicates the promotion of neoplastic lesions by diverse intestinal microbiota in the Helicobacter pylori INS-GAS mouse model of gastric carcinogenesis.
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      High-fat-diet-induced modulations of leptin signaling and gastric microbiota drive precancerous lesions in the stomach.
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      A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses.
      The loss of specialized glandular tissue and decreased acid secretion in GC tissue results in H pylori loss and enrichment of intestinal commensals, including Lactobacillus, Enterococci, Carnobacterium, Parvimonas, Citrobacter, Clostridium, Achromobacter, and Rhodococcus,
      • Yang I.
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      • Wilson K.T.
      • Peek R.M.
      • Correa P.
      • Josenhans C.
      • Fox J.G.
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      Different gastric microbiota compositions in two human populations with high and low gastric cancer risk in Colombia.
      ,
      • Han H.S.
      • Lee S.-Y.
      • Oh S.Y.
      • Moon H.W.
      • Cho H.
      • Kim J.-H.
      Correlations of the gastric and duodenal microbiota with histological, endoscopic, and symptomatic gastritis.
      ,
      • Nakatsu G.
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      • Zhou H.
      • Sheng J.
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      • Wu W.K.K.
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      as well as oral species; Fusobacterium nucleatum, Veillonella, Leptotrichia, Haemophilus, and Campylobacter (Figure 1, Supplementary Table 2).
      • Coker O.O.
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      • Nie Y.
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      • Wu W.K.
      • Wong S.H.
      • Chen Z.
      • Sung J.J.Y.
      • Yu J.
      Mucosal microbiome dysbiosis in gastric carcinogenesis.
      ,
      • Vuik F.
      • Dicksved J.
      • Lam S.Y.
      • Fuhler G.M.
      • van der Laan L.
      • van de Winkel A.
      • Konstantinov S.R.
      • Spaander M.
      • Peppelenbosch M.P.
      • Engstrand L.
      • Kuipers E.J.
      Composition of the mucosa-associated microbiota along the entire gastrointestinal tract of human individuals.
      ,
      • Miao R.
      • Wan C.
      • Wang Z.
      The relationship of gastric microbiota and Helicobacter pylori infection in pediatrics population.
      ,
      • Gantuya B.
      • El Serag H.B.
      • Matsumoto T.
      • Ajami N.J.
      • Uchida T.
      • Oyuntsetseg K.
      • Bolor D.
      • Yamaoka Y.
      Gastric mucosal microbiota in a Mongolian population with gastric cancer and precursor conditions.
      • Gantuya B.
      • El-Serag H.B.
      • Matsumoto T.
      • Ajami N.J.
      • Oyuntsetseg K.
      • Azzaya D.
      • Uchida T.
      • Yamaoka Y.
      Gastric microbiota in Helicobacter pylori-negative and -positive gastritis among high incidence of gastric cancer area.
      • Boehm E.T.
      • Thon C.
      • Kupcinskas J.
      • Steponaitiene R.
      • Skieceviciene J.
      • Canbay A.
      • Malfertheiner P.
      • Link A.
      Fusobacterium nucleatum is associated with worse prognosis in Lauren’s diffuse type gastric cancer patients.
      • Amir I.
      • Konikoff F.M.
      • Oppenheim M.
      • Gophna U.
      • Half E.E.
      Gastric microbiota is altered in oesophagitis and Barrett’s oesophagus and further modified by proton pump inhibitors.
      ,
      • Feng Q.
      • Liang S.
      • Jia H.
      • Stadlmayr A.
      • Tang L.
      • Lan Z.
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      • Su L.
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      Gut microbiome development along the colorectal adenoma-carcinoma sequence.
      Furthermore, species, including F nucleatum, are associated with worse prognosis in Laurén's diffuse-type GC (Supplementary Table 2).
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      High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia.
      In addition to differences in microbial communities, metabolic pathways, including amino acid and nitrate metabolism, membrane transport, and carbohydrate digestion and absorption have been shown to be up-regulated in GC compared with healthy gastric tissue.
      • Yang I.
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      • Piazuelo M.B.
      • Bravo L.E.
      • Yepez M.C.
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      • Wilson K.T.
      • Peek R.M.
      • Correa P.
      • Josenhans C.
      • Fox J.G.
      • Suerbaum S.
      Different gastric microbiota compositions in two human populations with high and low gastric cancer risk in Colombia.
      Proton pump inhibitors (PPIs) frequently are used to treat GI disorders including erosive esophagitis and GERD. Although effective at improving GI symptoms, use of PPIs also promotes microbial growth that has genotoxic potential, with an increase in bacterial nitrate/nitrite reductase function, which is linked with cancer development.
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      • Kinross J.M.
      International Cancer Microbiome Consortium consensus statement on the role of the human microbiome in carcinogenesis.
      Moreover, the higher gastric pH, resulting from PPI use, can lead to an increase of Peptostreptococcus stomatis, Streptococcus anginosus, Parvimonas micra, Slackia exigua, and Dialister pneumosintes.
      • Castellarin M.
      • Warren R.L.
      • Freeman J.D.
      • Dreolini L.
      • Krzywinski M.
      • Strauss J.
      • Barnes R.
      • Watson P.
      • Allen-Vercoe E.
      • Moore R.A.
      • Holt R.A.
      Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma.
      It remains unclear whether microbiota changes resulting from PPI therapy influence an individual‘s gastric cancer risk.

      Microbial Involvement in Gastric Carcinogenesis: Mechanistic Insights

      The differential susceptibility to H pylori–induced GC development has been partly attributed to differences in virulence of H pylori isolates, but also to the involvement of non–H pylori bacteria. Gastric colonization of INS-GAS mice (insulin-gastrin mice, with constitutional expression of gastrin regulated by the insulin promotor) with different types of intestinal microbes, including restricted altered Schaedler's flora (ie, Clostridium, Lactobacillus, and Bacteroides species) and specific pathogen-free (with undefined complex intestinal flora) in combination with or without H pylori co-infection, showed that mice exposed to intestinal flora + H pylori co-infection show the strongest inflammatory responses, with 40% developing gastric cancer. This phenomenon also was seen in approximately 25% of mice exposed to restricted altered Schaedler's flora (ASF) + H pylori co-infection. Furthermore, H pylori colonization induced the expression of IL11 and cancer-related genes Ptger4 and Tgf-β (Figure 3B).
      • Münch N.S.
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      • Einwächter H.
      • Bolze F.
      • Klingenspor M.
      • Haller D.
      • Kavanagh M.
      • Lysaght J.
      • Friedman R.
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      • Pollak M.
      • Holt P.R.
      • Muthupalani S.
      • Fox J.G.
      • Whary M.T.
      • Lee Y.
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      • Elliot R.
      • Fitzgerald R.
      • Steiger K.
      • Schmid R.M.
      • Wang T.C.
      • Quante M.
      High-fat diet accelerates carcinogenesis in a mouse model of Barrett’s esophagus via interleukin 8 and alterations to the gut microbiome.
      In terms of host changes, ASF + H pylori co-infection colonization resulted in gastric mucosal changes including the development of spasmolytic polypeptide-expressing metaplasia accompanied by aberrant mucin 4 (MUC4) expression and the presence of Ulex europaeus lectin–positive foveolar hyperplasia.
      • Molendijk J.
      • Nguyen T.-M.-T.
      • Brown I.
      • Mohamed A.
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      • Krause L.
      • Morrison M.
      • Hill M.M.
      Chronic high-fat diet induces early Barrett’s esophagus in mice through lipidome remodeling.
      This further supports a role for H pylori in accelerating gastric cancer development with the yes-associated protein 1, a key effector of the Hippo pathway, also being implicated in the process (Figure 3B).
      • Kohata Y.
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      • Tanigawa T.
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      • Watanabe T.
      • Tominaga K.
      • Fujiwara Y.
      • Arakawa T.
      Rebamipide alters the esophageal microbiome and reduces the incidence of Barrett’s esophagus in a rat model.
      HFD also has been shown induce gastric dysbiotic changes including increased Lactobacillus abundance, intestinal metaplasia, expression of leptin, phosphorylated leptin receptor, and signal transducer and activator or transcription 3 (STAT3) and intracellular β-catenin accumulation (Figure 3B),
      • Zaidi A.H.
      • Kelly L.A.
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      • Gazarik K.E.
      • Heit M.I.
      • Nistico L.
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      • Spirk T.L.
      • Byers B.
      • Lloyd E.J.
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      • Jobe B.A.
      Associations of microbiota and toll-like receptor signaling pathway in esophageal adenocarcinoma.
      ,
      • Sawada A.
      • Fujiwara Y.
      • Nagami Y.
      • Tanaka F.
      • Yamagami H.
      • Tanigawa T.
      • Shiba M.
      • Tominaga K.
      • Watanabe T.
      • Gi M.
      • Wanibuchi H.
      • Arakawa T.
      Alteration of esophageal microbiome by antibiotic treatment does not affect incidence of rat esophageal adenocarcinoma.
      whereas loss of the leptin receptor attenuates the effect of HFD on dysbiosis and intestinal metaplasia.
      • Sawada A.
      • Fujiwara Y.
      • Nagami Y.
      • Tanaka F.
      • Yamagami H.
      • Tanigawa T.
      • Shiba M.
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      • Gi M.
      • Wanibuchi H.
      • Arakawa T.
      Alteration of esophageal microbiome by antibiotic treatment does not affect incidence of rat esophageal adenocarcinoma.

      Colorectal Cancer

      In comparison with GC, in which a single microbe plays the dominant role, defining carcinogenic culprits from within the colonic microbiota and defining their involvement in colorectal cancer (CRC) development is incredibly challenging. Alterations in gut microbiota signatures consistently are reported in CRC, with tumor signatures differing from adjacent normal tissue. Differences include reduced diversity and altered community structure, which increase as CRC progresses (Supplementary Table 3).
      • Arthur J.C.
      • Perez-Chanona E.
      • Mühlbauer M.
      • Tomkovich S.
      • Uronis J.M.
      • Fan T.-J.
      • Campbell B.J.
      • Abujamel T.
      • Dogan B.
      • Rogers A.B.
      • Rhodes J.M.
      • Stintzi A.
      • Simpson K.W.
      • Hansen J.J.
      • Keku T.O.
      • Fodor A.A.
      • Jobin C.
      Intestinal inflammation targets cancer-inducing activity of the microbiota.
      ,
      • Warren R.L.
      • Freeman D.J.
      • Pleasance S.
      • Watson P.
      • Moore R.A.
      • Cochrane K.
      • Allen-Vercoe E.
      • Holt R.A.
      Co-occurrence of anaerobic bacteria in colorectal carcinomas.
      • Bullman S.
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      • Sicinska E.
      • Clancy T.E.
      • Zhang X.
      • Cai D.
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      • Nelson T.
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      • Hagan T.
      • Walker M.
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      • Diosdado B.
      • Serna G.
      • Mulet N.
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      • Ramon Y.
      • Cajal S.
      • Fasani R.
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      • Ng K.
      • Élez E.
      • Ogino S.
      • Tabernero J.
      • Fuchs C.S.
      • Hahn W.C.
      • Nuciforo P.
      • Meyerson M.
      Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer.
      • Mori G.
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      • Barbieri G.
      • Passardi A.
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      • Ranzani G.N.
      • Calistri D.
      • Pasca M.R.
      Shifts of faecal microbiota during sporadic colorectal carcinogenesis.
      • Yang T.-W.
      • Lee W.-H.
      • Tu S.-J.
      • Huang W.-C.
      • Chen H.-M.
      • Sun T.-H.
      • Tsai M.-C.
      • Wang C.-C.
      • Chen H.-Y.
      • Huang C.-C.
      • Shiu B.-H.
      • Yang T.-L.
      • Huang H.-T.
      • Chou Y.-P.
      • Chou C.-H.
      • Huang Y.-R.
      • Sun Y.-R.
      • Liang C.
      • Lin F.-M.
      • Ho S.-Y.
      • Chen W.-L.
      • Yang S.-F.
      • Ueng K.-C.
      • Huang H.-D.
      • Huang C.-N.
      • Jong Y.-J.
      • Lin C.-C.
      Enterotype-based analysis of gut microbiota along the conventional adenoma-carcinoma colorectal cancer pathway.
      Lower numbers of beneficial, potentially protective taxa, including butyrate-producing species belonging to Clostridium clusters IV and XIV, repeatedly are documented in CRC, whereas increased pro-oncogenic capacity has been attributed to an increase in species including Fusobacterium, Bacteroides, Campylobacter, Escherichia, and Porphyromonas (Figure 1, Supplementary Table 3).
      • Kostic A.D.
      • Chun E.
      • Robertson L.
      • Glickman J.N.
      • Gallini C.A.
      • Michaud M.
      • Clancy T.E.
      • Chung D.C.
      • Lochhead P.
      • Hold G.L.
      • El-Omar E.M.
      • Brenner D.
      • Fuchs C.S.
      • Meyerson M.
      • Garrett W.S.
      Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment.
      ,
      • Arthur J.C.
      • Perez-Chanona E.
      • Mühlbauer M.
      • Tomkovich S.
      • Uronis J.M.
      • Fan T.-J.
      • Campbell B.J.
      • Abujamel T.
      • Dogan B.
      • Rogers A.B.
      • Rhodes J.M.
      • Stintzi A.
      • Simpson K.W.
      • Hansen J.J.
      • Keku T.O.
      • Fodor A.A.
      • Jobin C.
      Intestinal inflammation targets cancer-inducing activity of the microbiota.
      ,
      • Yu T.
      • Guo F.
      • Yu Y.
      • Sun T.
      • Ma D.
      • Han J.
      • Qian Y.
      • Kryczek I.
      • Sun D.
      • Nagarsheth N.
      • Chen Y.
      • Chen H.
      • Hong J.
      • Zou W.
      • Fang J.-Y.
      Fusobacterium nucleatum promotes chemoresistance to colorectal cancer by modulating autophagy.
      • Abed J.
      • Emgård J.E.M.
      • Zamir G.
      • Faroja M.
      • Almogy G.
      • Grenov A.
      • Sol A.
      • Naor R.
      • Pikarsky E.
      • Atlan K.A.
      • Mellul A.
      • Chaushu S.
      • Manson A.L.
      • Earl A.M.
      • Ou N.
      • Brennan C.A.
      • Garrett W.S.
      • Bachrach G.
      Fap2 mediates Fusobacterium nucleatum colorectal adenocarcinoma enrichment by binding to tumor-expressed Gal-GalNAc.
      • Purcell R.V.
      • Pearson J.
      • Aitchison A.
      • Dixon L.
      • Frizelle F.A.
      • Keenan J.I.
      Colonization with enterotoxigenic Bacteroides fragilis is associated with early-stage colorectal neoplasia.
      • Viljoen K.S.
      • Dakshinamurthy A.
      • Goldberg P.
      • Blackburn J.M.
      Quantitative profiling of colorectal cancer-associated bacteria reveals associations between fusobacterium spp., enterotoxigenic Bacteroides fragilis (ETBF) and clinicopathological features of colorectal cancer.
      Firmicutes and Actinobacteria phyla and the Lachnospiraceae family are detected more frequently in premalignant adenomas, Proteobacteria, Alcaligenaceae, Enterobacteriaceae, and Sutterella species are increased in CRC (Figure 1, Supplementary Table 3).
      • Boleij A.
      • Hechenbleikner E.M.
      • Goodwin A.C.
      • Badani R.
      • Stein E.M.
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      • Ellis B.
      • Carroll K.C.
      • Albesiano E.
      • Wick E.C.
      • Platz E.A.
      • Pardoll D.M.
      • Sears C.L.
      The Bacteroides fragilis toxin gene is prevalent in the colon mucosa of colorectal cancer patients.
      Studies also have suggested that specific species including Oscillospira are depleted in the transition from advanced adenoma to early CRC (Figure 1).
      • Bonnet M.
      • Buc E.
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      • Dubois D.
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      • Bonnet R.
      • Pezet D.
      • Darfeuille-Michaud A.
      Colonization of the human gut by E. coli and colorectal cancer risk.

      Key Players in Colorectal Carcinogenesis

      F nucleatum frequently is detected in CRC tissue, both at the adenoma and adenocarcinoma stages, in association with other oral commensal species, including Peptostreptococcus, Leptotrichia, and Campylobacter species (Figure 1, Supplementary Table 3).
      • Kostic A.D.
      • Chun E.
      • Robertson L.
      • Glickman J.N.
      • Gallini C.A.
      • Michaud M.
      • Clancy T.E.
      • Chung D.C.
      • Lochhead P.
      • Hold G.L.
      • El-Omar E.M.
      • Brenner D.
      • Fuchs C.S.
      • Meyerson M.
      • Garrett W.S.
      Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment.
      ,
      • Abed J.
      • Emgård J.E.M.
      • Zamir G.
      • Faroja M.
      • Almogy G.
      • Grenov A.
      • Sol A.
      • Naor R.
      • Pikarsky E.
      • Atlan K.A.
      • Mellul A.
      • Chaushu S.
      • Manson A.L.
      • Earl A.M.
      • Ou N.
      • Brennan C.A.
      • Garrett W.S.
      • Bachrach G.
      Fap2 mediates Fusobacterium nucleatum colorectal adenocarcinoma enrichment by binding to tumor-expressed Gal-GalNAc.
      ,
      • Purcell R.V.
      • Pearson J.
      • Aitchison A.
      • Dixon L.
      • Frizelle F.A.
      • Keenan J.I.
      Colonization with enterotoxigenic Bacteroides fragilis is associated with early-stage colorectal neoplasia.
      Its presence also is associated with an increased risk of CRC recurrence and development of chemoresistance.
      • Dejea C.M.
      • Wick E.C.
      • Hechenbleikner E.M.
      • White J.R.
      • Mark Welch J.L.
      • Rossetti B.J.
      • Peterson S.N.
      • Snesrud E.C.
      • Borisy G.G.
      • Lazarev M.
      • Stein E.
      • Vadivelu J.
      • Roslani A.C.
      • Malik A.A.
      • Wanyiri J.W.
      • Goh K.L.
      • Thevambiga I.
      • Fu K.
      • Wan F.
      • Llosa N.
      • Housseau F.
      • Romans K.
      • Wu X.
      • McAllister F.M.
      • Wu S.
      • Vogelstein B.
      • Kinzler K.W.
      • Pardoll D.M.
      • Sears C.L.
      Microbiota organization is a distinct feature of proximal colorectal cancers.
      F nucleatum impacts on CRC development in a number of ways: F nucleatum frequently is detected at higher levels in the tumor microenvironment through its ability to localize with tumor-enriched lectins via the outer membrane protein (fatty acid binding protein 2, Fap2),
      • Dejea C.M.
      • Fathi P.
      • Craig J.M.
      • Boleij A.
      • Taddese R.
      • Geis A.L.
      • Wu X.
      • DeStefano Shields C.E.
      • Hechenbleikner E.M.
      • Huso D.L.
      • Anders R.A.
      • Giardiello F.M.
      • Wick E.C.
      • Wang H.
      • Wu S.
      • Pardoll D.M.
      • Housseau F.
      • Sears C.L.
      Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria.
      and F nucleatum modifies the tumor microenvironment; blocking natural killer cell antitumor responses and directing myeloid cell recruitment. F nucleatum also influences microbial metastatic dissemination as microbiota signatures associated with Fusobacterium-enriched but not Fusobacterium-negative cancers detected in distant metastases.
      • Kostic A.D.
      • Chun E.
      • Robertson L.
      • Glickman J.N.
      • Gallini C.A.
      • Michaud M.
      • Clancy T.E.
      • Chung D.C.
      • Lochhead P.
      • Hold G.L.
      • El-Omar E.M.
      • Brenner D.
      • Fuchs C.S.
      • Meyerson M.
      • Garrett W.S.
      Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment.
      ,
      • Viljoen K.S.
      • Dakshinamurthy A.
      • Goldberg P.
      • Blackburn J.M.
      Quantitative profiling of colorectal cancer-associated bacteria reveals associations between fusobacterium spp., enterotoxigenic Bacteroides fragilis (ETBF) and clinicopathological features of colorectal cancer.
      Other bacteria that have been implicated in CRC pathogenesis include enterotoxigenic Bacteroides fragilis (ETBF) and Escherichia coli (shown to promote colon tumorigenesis in colitis-associated cancer rather than sporadic CRC), Streptococcus gallolyticus subspecies gallolyticus, and Enterococcus faecalis. The presence of B fragilis/ETBF in CRC tissue also is associated with a poorer prognostic outcome.
      • Buc E.
      • Dubois D.
      • Sauvanet P.
      • Raisch J.
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      • Darfeuille-Michaud A.
      • Pezet D.
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      High prevalence of mucosa-associated E. coli producing cyclomodulin and genotoxin in colon cancer.
      • Cuevas-Ramos G.
      • Petit C.R.
      • Marcq I.
      • Boury M.
      • Oswald E.
      • Nougayrède J.-P.
      Escherichia coli induces DNA damage in vivo and triggers genomic instability in mammalian cells.
      • Nougayrède J.-P.
      • Homburg S.
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      • Boury M.
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      • Gottschalk G.
      • Buchrieser C.
      • Hacker J.
      • Dobrindt U.
      • Oswald E.
      Escherichia coli induces DNA double-strand breaks in eukaryotic cells.
      Although studies consistently indicate an increased abundance of Enterobacteriaceae (particularly E coli) in inflamed colonic mucosa compared with uninflamed tissue, the evidence for E coli involvement in CRC is associated predominantly with data from preclinical studies. Higher numbers of E coli strains with the pks gene, which mediates production of the genotoxic colibactin, also have been found in the following: (1) CRC patients compared with controls, (2) CRC tissue compared with adjacent normal mucosa, and (3) late-stage compared with early stage CRC.
      • Pleguezuelos-Manzano C.
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      • Manders F.
      • Dalmasso G.
      • Stege P.B.
      • Paganelli F.L.
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      • Beumer J.
      • Mizutani T.
      • Miao Y.
      • van der Linden R.
      • van der Elst S.
      • Garcia K.C.
      • Top J.
      • Willems R.J.L.
      • Giannakis M.
      • Bonnet R.
      • Quirke P.
      • Meyerson M.
      • Cuppen E.
      • van Boxtel R.
      • Clevers H.
      Mutational signature in colorectal cancer caused by genotoxic pks(+) E. coli.

      Microbial Biofilms and CRC

      Bacterial biofilms have long been recognized as contributors to chronic infections and diseases in human beings, however, their role in intestinal cancers received limited consideration until seminal work by the Sears laboratory showed that invasive polymicrobial biofilms are present in many right-sided colonic tumors but only in a small proportion of left-sided tumors; findings that subsequently have been validated in other cohorts.
      • Yang T.-W.
      • Lee W.-H.
      • Tu S.-J.
      • Huang W.-C.
      • Chen H.-M.
      • Sun T.-H.
      • Tsai M.-C.
      • Wang C.-C.
      • Chen H.-Y.
      • Huang C.-C.
      • Shiu B.-H.
      • Yang T.-L.
      • Huang H.-T.
      • Chou Y.-P.
      • Chou C.-H.
      • Huang Y.-R.
      • Sun Y.-R.
      • Liang C.
      • Lin F.-M.
      • Ho S.-Y.
      • Chen W.-L.
      • Yang S.-F.
      • Ueng K.-C.
      • Huang H.-D.
      • Huang C.-N.
      • Jong Y.-J.
      • Lin C.-C.
      Enterotype-based analysis of gut microbiota along the conventional adenoma-carcinoma colorectal cancer pathway.
      ,
      • Lopès A.
      • Billard E.
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      • Villéger R.
      • Veziant J.
      • Roche G.
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      • Barnich N.
      • Dumas B.
      • Bonnet M.
      Colibactin-positive Escherichia coli induce a procarcinogenic immune environment leading to immunotherapy resistance in colorectal cancer.
      Biofilm-positive tissues (tumor and normal mucosa) show well-established features of carcinogenesis including loss of E-cadherin and increased IL6 expression. Elucidation of CRC tissue biofilm composition showed specific microbial scaffolds: polymicrobial, polymicrobial with Fusobacteria, and Proteobacterial predominant.
      • Yang T.-W.
      • Lee W.-H.
      • Tu S.-J.
      • Huang W.-C.
      • Chen H.-M.
      • Sun T.-H.
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      • Wang C.-C.
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      • Huang H.-T.
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      • Huang Y.-R.
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      • Chen W.-L.
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      • Ueng K.-C.
      • Huang H.-D.
      • Huang C.-N.
      • Jong Y.-J.
      • Lin C.-C.
      Enterotype-based analysis of gut microbiota along the conventional adenoma-carcinoma colorectal cancer pathway.
      ,
      • Lopès A.
      • Billard E.
      • Casse A.H.
      • Villéger R.
      • Veziant J.
      • Roche G.
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      • Briat A.
      • Pagès F.
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      • Pezet D.
      • Barnich N.
      • Dumas B.
      • Bonnet M.
      Colibactin-positive Escherichia coli induce a procarcinogenic immune environment leading to immunotherapy resistance in colorectal cancer.
      Biofilms also have been detected in familial adenomatous polyposis patients. In contrast to the sporadic CRC biofilms, familial adenomatous polyposis–associated biofilms were composed predominantly of ETBF and pks + E coli.
      • Tronnet S.
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      The genotoxin colibactin shapes gut microbiota in mice.

      Microbial Involvement in Colorectal Carcinogenesis: Mechanistic Insights

      In the context of CRC, intestinal microbes impact via various mechanisms, with certain microbes being able to produce toxins that can influence carcinogenic processes.
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      • Meyerson M.
      • Cuppen E.
      • van Boxtel R.
      • Clevers H.
      Mutational signature in colorectal cancer caused by genotoxic pks(+) E. coli.
      ,
      • Yang Y.
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      • Jobin C.
      Amending microbiota by targeting intestinal inflammation with TNF blockade attenuates development of colorectal cancer.
      E coli strains belonging to group B2 harbor a genomic island pks which encodes for the polyketide-peptide genotoxin colibactin (Figure 3C).
      • Long X.
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      Peptostreptococcus anaerobius promotes colorectal carcinogenesis and modulates tumour immunity.
      Infection with pks+ E coli can result in enterocyte DNA double-strand breaks and activation of DNA damage checkpoint pathways, cell-cycle arrest, and cell death.
      • Nougayrède J.-P.
      • Homburg S.
      • Taieb F.
      • Boury M.
      • Brzuszkiewicz E.
      • Gottschalk G.
      • Buchrieser C.
      • Hacker J.
      • Dobrindt U.
      • Oswald E.
      Escherichia coli induces DNA double-strand breaks in eukaryotic cells.
      ,
      • Pleguezuelos-Manzano C.
      • Puschhof J.
      • Rosendahl Huber A.
      • van Hoeck A.
      • Wood H.M.
      • Nomburg J.
      • Gurjao C.
      • Manders F.
      • Dalmasso G.
      • Stege P.B.
      • Paganelli F.L.
      • Geurts M.H.
      • Beumer J.
      • Mizutani T.
      • Miao Y.
      • van der Linden R.
      • van der Elst S.
      • Garcia K.C.
      • Top J.
      • Willems R.J.L.
      • Giannakis M.
      • Bonnet R.
      • Quirke P.
      • Meyerson M.
      • Cuppen E.
      • van Boxtel R.
      • Clevers H.
      Mutational signature in colorectal cancer caused by genotoxic pks(+) E. coli.
      Colibactin-positive E coli also can lead to impairment of antitumor T-cell responses including a decrease in CD3+ and CD8+ T cells and an increase in colonic inflammation in APCmin/+ mice (mice carrying a point mutation in the murine APC gene) (Figure 3C).
      • Juzėnas S.
      • Saltenienė V.
      • Kupcinskas J.
      • Link A.
      • Kiudelis G.
      • Jonaitis L.
      • Jarmalaite S.
      • Kupcinskas L.
      • Malfertheiner P.
      • Skieceviciene J.
      Analysis of deregulated microRNAs and their target genes in gastric cancer.
      Furthermore, colibactin can shape gut microbiota composition/function, highlighting how microbes can compete for gut niche utilization.
      • Park S.-R.
      • Kim D.-J.
      • Han S.-H.
      • Kang M.-J.
      • Lee J.-Y.
      • Jeong Y.-J.
      • Lee S.-J.
      • Kim T.-H.
      • Ahn S.-G.
      • Yoon J.-H.
      • Park J.-H.
      Diverse Toll-like receptors mediate cytokine production by Fusobacterium nucleatum and Aggregatibacter actinomycetemcomitans in macrophages.
      Interestingly, the carcinogenic effects of colibactin-producing E coli are reversed by tumor necrosis factor blockade.
      • Tsoi H.
      • Chu E.S.H.
      • Zhang X.
      • Sheng J.
      • Nakatsu G.
      • Ng S.C.
      • Chan A.W.H.
      • Chan F.K.L.
      • Sung J.J.Y.
      • Yu J.
      Peptostreptococcus anaerobius induces intracellular cholesterol biosynthesis in colon cells to induce proliferation and causes dysplasia in mice.
      F nucleatum and Peptostreptococcus anaerobius are 2 anaerobic pathogens linked to CRC development. Both organisms adhere to the colonic mucosa and accelerate tumor development in APCmin/+ mice through interaction between outer membrane protein Fap2 (F nucleatum) and putative cell wall binding repeat 2 protein and integrin α21 (P anaerobius). These interactions lead to increased cell proliferation and nuclear factor-κB activation, triggering proinflammatory responses including increased proinflammatory cytokine production and expansion of myeloid-derived suppressor cells, tumor-associated macrophages, and granulocytic tumor-associated neutrophils (Figure 3C).
      • Kostic A.D.
      • Chun E.
      • Robertson L.
      • Glickman J.N.
      • Gallini C.A.
      • Michaud M.
      • Clancy T.E.
      • Chung D.C.
      • Lochhead P.
      • Hold G.L.
      • El-Omar E.M.
      • Brenner D.
      • Fuchs C.S.
      • Meyerson M.
      • Garrett W.S.
      Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment.
      ,
      • Kupcinskas J.
      • Wex T.
      • Link A.
      • Bartuseviciute R.
      • Dedelaite M.
      • Kevalaite G.
      • Leja M.
      • Skieceviciene J.
      • Kiudelis G.
      • Jonaitis L.
      • Kupcinskas L.
      • Malfertheiner P.
      PSCA and MUC1 gene polymorphisms are associated with gastric cancer and pre-malignant gastric conditions [corrected].
      Furthermore, both pathogens interact with TLR2 and TLR4 on colonic epithelial cells, resulting in an increase of reactive oxygen species levels, further promoting cholesterol synthesis and cell proliferation (Figure 3C).
      • Kupcinskas L.
      • Wex T.
      • Kupcinskas J.
      • Leja M.
      • Ivanauskas A.
      • Jonaitis L.V.
      • Janciauskas D.
      • Kiudelis G.
      • Funka K.
      • Sudraba A.
      • Chiu H.-M.
      • Lin J.-T.
      • Malfertheiner P.
      Interleukin-1B and interleukin-1 receptor antagonist gene polymorphisms are not associated with premalignant gastric conditions: a combined haplotype analysis.
      ,
      • Sears C.L.
      Enterotoxigenic Bacteroides fragilis: a rogue among symbiotes.
      ETBF originally was proposed as a microbial initiator of CRC based on the mechanism of action of its virulence factor fragilysin, which is one of the most potent known proinflammatory enterotoxins.
      • Warren R.L.
      • Freeman D.J.
      • Pleasance S.
      • Watson P.
      • Moore R.A.
      • Cochrane K.
      • Allen-Vercoe E.
      • Holt R.A.
      Co-occurrence of anaerobic bacteria in colorectal carcinomas.
      ,
      • Goulas T.
      • Arolas J.L.
      • Gomis-Rüth F.X.
      Structure, function and latency regulation of a bacterial enterotoxin potentially derived from a mammalian adamalysin/ADAM xenolog.
      Fragilysin binds to colonic epithelial receptors activating nuclear factor-κB signaling pathways, inducing increased cell proliferation, proinflammatory cytokine production, and direct DNA damage (Figure 3C). Fragilysin also induces cleavage of E-cadherin, resulting in increased Wnt/β-catenin (Wnt: wingless/integrated) signaling, an increase in cell proliferation, and expression of the protooncogene c-MYC (Figure 3C).
      • Petkevicius V.
      • Salteniene V.
      • Juzenas S.
      • Wex T.
      • Link A.
      • Leja M.
      • Steponaitiene R.
      • Skieceviciene J.
      • Kupcinskas L.
      • Jonaitis L.
      • Kiudelis G.
      • Malfertheiner P.
      • Kupcinskas J.
      Polymorphisms of microRNA target genes IL12B, INSR, CCND1 and IL10 in gastric cancer.
      ,
      • Wu S.
      • Rhee K.-J.
      • Zhang M.
      • Franco A.
      • Sears C.L.
      Bacteroides fragilis toxin stimulates intestinal epithelial cell shedding and gamma-secretase-dependent E-cadherin cleavage.
      A strong correlation between S gallolyticus and CRC also has been reported. S gallolyticus has the ability to colonize the intestinal tract and to promote tumor development in an azoxymethane-induced mice model of CRC, underscoring its importance in the functional relevance of CRC.
      • Kumar R.
      • Herold J.L.
      • Taylor J.
      • Xu J.
      • Xu Y.
      Variations among Streptococcus gallolyticus subsp. gallolyticus strains in connection with colorectal cancer.
      However, more studies are needed to unravel the mechanisms involved.
      Mechanistic evaluation of colonic mucosal biofilms has been performed using microbial slurries from human biofilm-positive CRC mucosa, human biofilm-positive non-CRC mucosa, and biofilm-negative mucosa, inoculated into CRC-susceptible mice.
      • Tomkovich S.
      • Dejea C.M.
      • Winglee K.
      • Drewes J.L.
      • Chung L.
      • Housseau F.
      • Pope J.L.
      • Gauthier J.
      • Sun X.
      • Mühlbauer M.
      • Liu X.
      • Fathi P.
      • Anders R.A.
      • Besharati S.
      • Perez-Chanona E.
      • Yang Y.
      • Ding H.
      • Wu X.
      • Wu S.
      • White J.R.
      • Gharaibeh R.Z.
      • Fodor A.A.
      • Wang H.
      • Pardoll D.M.
      • Jobin C.
      • Sears C.L.
      Human colon mucosal biofilms from healthy or colon cancer hosts are carcinogenic.
      Biofilm-positive slurries induced robust invasive biofilm development, a phenomenon not seen in biofilm-negative slurries. Recruitment of immunosuppressive myeloid cells and associated IL17 production was seen within 1 week of biofilm-positive slurry inoculation, clearly showing the capacity of intestinal biofilms to drive intestinal mucosal changes and microbial architecture toward carcinogenesis. Further studies are needed to investigate biofilm-associated procarcinogenic and proinflammatory microbes as well as assessing their role in other gastrointestinal cancers.

      Impact of the Microbiota on Diagnostic Tests

      With altered microbiota signatures now being well accepted as a hallmark of progression in a number of gastrointestinal cancers, there is an ever-increasing interest in leveraging microbiota biomarker detection in cancer surveillance. Several studies have shown the value of including microbiota biomarker detection to complement existing screening tests and to improve early detection in CRC surveillance, with most success shown in the context of F nucleatum (Figure 2).
      • Baxter N.T.
      • Koumpouras C.C.
      • Rogers M.A.M.
      • Ruffin 4th, M.T.
      • Schloss P.D.
      DNA from fecal immunochemical test can replace stool for detection of colonic lesions using a microbiota-based model.
      • Taylor M.
      • Wood H.M.
      • Halloran S.P.
      • Quirke P.
      Examining the potential use and long-term stability of guaiac faecal occult blood test cards for microbial DNA 16S rRNA sequencing.
      • Baxter N.T.
      • Ruffin 4th, M.T.
      • Rogers M.A.M.
      • Schloss P.D.
      Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions.
      • Zeller G.
      • Tap J.
      • Voigt A.Y.
      • Sunagawa S.
      • Kultima J.R.
      • Costea P.I.
      • Amiot A.
      • Böhm J.
      • Brunetti F.
      • Habermann N.
      • Hercog R.
      • Koch M.
      • Luciani A.
      • Mende D.R.
      • Schneider M.A.
      • Schrotz-King P.
      • Tournigand C.
      • Tran Van Nhieu J.
      • Yamada T.
      • Zimmermann J.
      • Benes V.
      • Kloor M.
      • Ulrich C.M.
      • von Knebel Doeberitz M.
      • Sobhani I.
      • Bork P.
      Potential of fecal microbiota for early-stage detection of colorectal cancer.
      Inclusion of F nucleatum detection, in combination with the fecal immunochemical test (FIT), improved the sensitivity for CRC (92.3% vs 73.1%) and for advanced adenoma (38.6% vs 15.5%) compared with FIT alone, supporting F nucleatum as a valuable CRC marker that easily could be implemented in current practice (Figure 2).
      • Wong S.H.
      • Kwong T.N.Y.
      • Chow T.-C.
      • Luk A.K.C.
      • Dai R.Z.W.
      • Nakatsu G.
      • Lam T.Y.T.
      • Zhang L.
      • Wu J.C.Y.
      • Chan F.K.L.
      • Ng S.S.M.
      • Wong M.C.S.
      • Ng S.C.
      • Wu W.K.K.
      • Yu J.
      • Sung J.J.Y.
      Quantitation of faecal Fusobacterium improves faecal immunochemical test in detecting advanced colorectal neoplasia.
      Furthermore, combining tests for F nucleatum, P stomatis, and several other species associated with CRC allowed an accurate classification of CRC patients with an area under the curve (AUC) of 0.84 and an odds ratio (OR) of 23 (Figure 2).
      • Zeller G.
      • Tap J.
      • Voigt A.Y.
      • Sunagawa S.
      • Kultima J.R.
      • Costea P.I.
      • Amiot A.
      • Böhm J.
      • Brunetti F.
      • Habermann N.
      • Hercog R.
      • Koch M.
      • Luciani A.
      • Mende D.R.
      • Schneider M.A.
      • Schrotz-King P.
      • Tournigand C.
      • Tran Van Nhieu J.
      • Yamada T.
      • Zimmermann J.
      • Benes V.
      • Kloor M.
      • Ulrich C.M.
      • von Knebel Doeberitz M.
      • Sobhani I.
      • Bork P.
      Potential of fecal microbiota for early-stage detection of colorectal cancer.
      Other studies have shown that the presence of P micra, S anginosus, and Proteobacteria in CRC resulted in an area under the concentration-time curve of 0.76, which increased to 0.83 when clinical markers were included (Figure 2).
      • Villéger R.
      • Lopès A.
      • Veziant J.
      • Gagnière J.
      • Barnich N.
      • Billard E.
      • Boucher D.
      • Bonnet M.
      Microbial markers in colorectal cancer detection and/or prognosis.
      Efforts have been made to implement machine-learning models in predicting CRC based on the composition of the gut microbiota from stool samples.
      • Zeller G.
      • Tap J.
      • Voigt A.Y.
      • Sunagawa S.
      • Kultima J.R.
      • Costea P.I.
      • Amiot A.
      • Böhm J.
      • Brunetti F.
      • Habermann N.
      • Hercog R.
      • Koch M.
      • Luciani A.
      • Mende D.R.
      • Schneider M.A.
      • Schrotz-King P.
      • Tournigand C.
      • Tran Van Nhieu J.
      • Yamada T.
      • Zimmermann J.
      • Benes V.
      • Kloor M.
      • Ulrich C.M.
      • von Knebel Doeberitz M.
      • Sobhani I.
      • Bork P.
      Potential of fecal microbiota for early-stage detection of colorectal cancer.
      ,
      • Ai D.
      • Pan H.
      • Han R.
      • Li X.
      • Liu G.
      • Xia L.C.
      Using decision tree aggregation with random Forest model to identify gut microbes associated with colorectal cancer.
      • Ai L.
      • Tian H.
      • Chen Z.
      • Chen H.
      • Xu J.
      • Fang J.-Y.
      Systematic evaluation of supervised classifiers for fecal microbiota-based prediction of colorectal cancer.
      • Kharrat N.
      • Assidi M.
      • Abu-Elmagd M.
      • Pushparaj P.N.
      • Alkhaldy A.
      • Arfaoui L.
      • Naseer M.I.
      • El Omri A.
      • Messaoudi S.
      • Buhmeida A.
      • Rebai A.
      Data mining analysis of human gut microbiota links Fusobacterium spp. with colorectal cancer onset.
      • Thomas A.M.
      • Manghi P.
      • Asnicar F.
      • Pasolli E.
      • Armanini F.
      • Zolfo M.
      • Beghini F.
      • Manara S.
      • Karcher N.
      • Pozzi C.
      • Gandini S.
      • Serrano D.
      • Tarallo S.
      • Francavilla A.
      • Gallo G.
      • Trompetto M.
      • Ferrero G.
      • Mizutani S.
      • Shiroma H.
      • Shiba S.
      • Shibata T.
      • Yachida S.
      • Yamada T.
      • Wirbel J.
      • Schrotz-King P.
      • Ulrich C.M.
      • Brenner H.
      • Arumugam M.
      • Bork P.
      • Zeller G.
      • Cordero F.
      • Dias-Neto E.
      • Setubal J.C.
      • Tett A.
      • Pardini B.
      • Rescigno M.
      • Waldron L.
      • Naccarati A.
      • Segata N.
      Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.
      • Zackular J.P.
      • Rogers M.A.M.
      • Ruffin 4th, M.T.
      • Schloss P.D.
      The human gut microbiome as a screening tool for colorectal cancer.
      F nucleatum, E faecalis, Streptococcus bovis, B fragilis, Porphyromonas species, Citrobacter species, and Slakia were identified as potential biomarkers for the diagnosis of CRC and adenomatous polyps (Figure 2).
      • Ai D.
      • Pan H.
      • Han R.
      • Li X.
      • Liu G.
      • Xia L.C.
      Using decision tree aggregation with random Forest model to identify gut microbes associated with colorectal cancer.
      • Ai L.
      • Tian H.
      • Chen Z.
      • Chen H.
      • Xu J.
      • Fang J.-Y.
      Systematic evaluation of supervised classifiers for fecal microbiota-based prediction of colorectal cancer.
      • Kharrat N.
      • Assidi M.
      • Abu-Elmagd M.
      • Pushparaj P.N.
      • Alkhaldy A.
      • Arfaoui L.
      • Naseer M.I.
      • El Omri A.
      • Messaoudi S.
      • Buhmeida A.
      • Rebai A.
      Data mining analysis of human gut microbiota links Fusobacterium spp. with colorectal cancer onset.
      ,
      • Eklöf V.
      • Löfgren-Burström A.
      • Zingmark C.
      • Edin S.
      • Larsson P.
      • Karling P.
      • Alexeyev O.
      • Rutegård J.
      • Wikberg M.L.
      • Palmqvist R.
      Cancer-associated fecal microbial markers in colorectal cancer detection.
      • Mangifesta M.
      • Mancabelli L.
      • Milani C.
      • Gaiani F.
      • de’Angelis N.
      • de’Angelis G.L.
      • van Sinderen D.
      • Ventura M.
      • Turroni F.
      Mucosal microbiota of intestinal polyps reveals putative biomarkers of colorectal cancer.
      • Rezasoltani S.
      • Sharafkhah M.
      • Asadzadeh Aghdaei H.
      • Nazemalhosseini Mojarad E.
      • Dabiri H.
      • Akhavan Sepahi A.
      • Modarressi M.H.
      • Feizabadi M.M.
      • Zali M.R.
      Applying simple linear combination, multiple logistic and factor analysis methods for candidate fecal bacteria as novel biomarkers for early detection of adenomatous polyps and colon cancer.
      The combination of these bacterial candidates improved the diagnostic performance rather than assessment of each bacterium alone.
      • Rezasoltani S.
      • Sharafkhah M.
      • Asadzadeh Aghdaei H.
      • Nazemalhosseini Mojarad E.
      • Dabiri H.
      • Akhavan Sepahi A.
      • Modarressi M.H.
      • Feizabadi M.M.
      • Zali M.R.
      Applying simple linear combination, multiple logistic and factor analysis methods for candidate fecal bacteria as novel biomarkers for early detection of adenomatous polyps and colon cancer.
      In addition, microbe-derived metabolic signatures in stool or serum also have been considered as potential tools in CRC detection.
      • Yang Y.
      • Misra B.B.
      • Liang L.
      • Bi D.
      • Weng W.
      • Wu W.
      • Cai S.
      • Qin H.
      • Goel A.
      • Li X.
      • Ma Y.
      Integrated microbiome and metabolome analysis reveals a novel interplay between commensal bacteria and metabolites in colorectal cancer.
      ,
      • Tan B.
      • Qiu Y.
      • Zou X.
      • Chen T.
      • Xie G.
      • Cheng Y.
      • Dong T.
      • Zhao L.
      • Feng B.
      • Hu X.
      • Xu L.X.
      • Zhao A.
      • Zhang M.
      • Cai G.
      • Cai S.
      • Zhou Z.
      • Zheng M.
      • Zhang Y.
      • Jia W.
      Metabonomics identifies serum metabolite markers of colorectal cancer.
      There are less data on similar approaches for gastric or esophageal cancer. Profiling of microbiota coating the tongue has been assessed alongside serologic markers for early detection of GC.
      • Wu J.
      • Xu S.
      • Xiang C.
      • Cao Q.
      • Li Q.
      • Huang J.
      • Shi L.
      • Zhang J.
      • Zhan Z.
      Tongue coating microbiota community and risk effect on gastric cancer.
      A predictive model also was developed that includes serologic testing of IgG anti–H pylori antibody and pepsinogen, nitrosating/nitrate-reducing bacteria abundance, and type IV secretion system gene-contributing bacteria in the stomach.
      • Choi S.
      • Lee J.G.
      • Lee A.-R.
      • Eun C.S.
      • Han D.S.
      • Park C.H.
      Helicobacter pylori antibody and pepsinogen testing for predicting gastric microbiome abundance.
      Both approaches have clear limitations and currently remain within the development space.

      Impact on Cancer Treatment

      Recently, there has been increasing interest in defining the impact of the gut microbiota on cancer treatment. There is a bidirectional interaction because many drugs are metabolized by gut bacteria, resulting in interindividual differences in drug metabolism and, thus, huge implications for efficacy and side effects of drugs across multiple disease indications.
      • Zimmermann M.
      • Zimmermann-Kogadeeva M.
      • Wegmann R.
      • Goodman A.L.
      Mapping human microbiome drug metabolism by gut bacteria and their genes.
      On the other hand, systemic treatments also have an effect on the composition and functioning of the microbiota.
      • Kupcinskas J.
      • Petkevicius V.B.J.
      Cancer therapies and their impact on the gut microbiota.

      Chemotherapy

      Platinum-based cytotoxic compounds mediate their effects through causing DNA damage, including formation of DNA adducts and intrastrand cross-links, which induces apoptosis. Although the majority of the current evidence is still from preclinical models, there is increasing understanding that the gastrointestinal microbiota might serve as predictive indicators for treatment response. Commensal bacteria can influence therapeutic effects of oxaliplatin by modulating the production of reactive oxygen species in tumor-infiltrating myeloid cells, which can enhance tumor regression.
      • Iida N.
      • Dzutsev A.
      • Stewart C.A.
      • Smith L.
      • Bouladoux N.
      • Weingarten R.A.
      • Molina D.A.
      • Salcedo R.
      • Back T.
      • Cramer S.
      • Dai R.-M.
      • Kiu H.
      • Cardone M.
      • Naik S.
      • Patri A.K.
      • Wang E.
      • Marincola F.M.
      • Frank K.M.
      • Belkaid Y.
      • Trinchieri G.
      • Goldszmid R.S.
      Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment.
      In the presence of antibiotics, oxaliplatin and cisplatin treatment reduce this effect and result in poorer survival in various murine models, with mice lacking TLR pathway components not able to respond to oxaliplatin. Cyclophosphamide, an alkylating anticancer agent, induces a reduction in regulatory T cells and increases the number of T helper (Th1) and Th17 cells as well as intestinal permeability.
      • Ghiringhelli F.
      • Larmonier N.
      • Schmitt E.
      • Parcellier A.
      • Cathelin D.
      • Garrido C.
      • Chauffert B.
      • Solary E.
      • Bonnotte B.
      • Martin F.
      CD4+CD25+ regulatory T cells suppress tumor immunity but are sensitive to cyclophosphamide which allows immunotherapy of established tumors to be curative.
      ,
      • Schiavoni G.
      • Sistigu A.
      • Valentini M.
      • Mattei F.
      • Sestili P.
      • Spadaro F.
      • Sanchez M.
      • Lorenzi S.
      • D’Urso M.T.
      • Belardelli F.
      • Gabriele L.
      • Proietti E.
      • Bracci L.
      Cyclophosphamide synergizes with type I interferons through systemic dendritic cell reactivation and induction of immunogenic tumor apoptosis.
      Viaud et al
      • Viaud S.
      • Saccheri F.
      • Mignot G.
      • Yamazaki T.
      • Daillère R.
      • Hannani D.
      • Enot D.P.
      • Pfirschke C.
      • Engblom C.
      • Pittet M.J.
      • Schlitzer A.
      • Ginhoux F.
      • Apetoh L.
      • Chachaty E.
      • Woerther P.-L.
      • Eberl G.
      • Bérard M.
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      • Cerf-Bensussan N.
      • Opolon P.
      • Yessaad N.
      • Vivier E.
      • Ryffel B.
      • Elson C.O.
      • Doré J.
      • Kroemer G.
      • Lepage P.
      • Boneca I.G.
      • Ghiringhelli F.
      • Zitvogel L.
      The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide.
      reported a specific association between luminal microbial components and mucosal Th responses induced by cyclophosphamide treatment. Tumor-bearing mice with a reduced gut microbiota showed a reduction in Th17 cell numbers, with their tumors being refractory to cyclophosphamide treatment. Specifically, gram-positive bacteria Enterococcus hirae, Lactobacillus johnsonii, and Lactobacillus murinus, were shown to regulate cyclophosphamide efficacy (Figure 2); adoptive transfer of Th17 cells partially restored therapeutic efficacy. In the context of irinotecan treatment, targeted inhibition of gut bacterial β-glucuronidase enzymes improved cancer chemotherapeutic outcomes through a reduction in GI epithelial cell toxicity in preclinical models.
      Other common CRC chemotherapeutic agents, including 5-fluorouracil, have been shown to induce gut dysbiosis in multiple preclinical studies, but do not seem to be affected by the gut microbiota in terms of their efficacy. After 5-fluorouracil and irinotecan therapy, levels of Enterobacteriaceae increase, whereas treatment with 5-fluorouracil alone also resulted in an increase of Staphylococcus and Clostridium species and a decrease of Bacteroides and Lactobacillus abundance.
      • Carvalho R.
      • Vaz A.
      • Pereira F.L.
      • Dorella F.
      • Aguiar E.
      • Chatel J.-M.
      • Bermudez L.
      • Langella P.
      • Fernandes G.
      • Figueiredo H.
      • Goes-Neto A.
      • Azevedo V.
      Gut microbiome modulation during treatment of mucositis with the dairy bacterium Lactococcus lactis and recombinant strain secreting human antimicrobial PAP.
      ,
      • Bhatt A.P.
      • Pellock S.J.
      • Biernat K.A.
      • Walton W.G.
      • Wallace B.D.
      • Creekmore B.C.
      • Letertre M.M.
      • Swann J.R.
      • Wilson I.D.
      • Roques J.R.
      • Darr D.B.
      • Bailey S.T.
      • Montgomery S.A.
      • Roach J.M.
      • Azcarate-Peril M.A.
      • Sartor R.B.
      • Gharaibeh R.Z.
      • Bultman S.J.
      • Redinbo M.R.
      Targeted inhibition of gut bacterial β-glucuronidase activity enhances anticancer drug efficacy.

      Radiotherapy

      Radiation therapy is a core modality in cancer treatment and is associated with side effects including mucositis, dermatitis, and also bone marrow suppression.
      • Al-Qadami G.
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      • Le H.
      • Bowen J.
      Gut microbiota: implications for radiotherapy response and radiotherapy-induced mucositis.
      From both clinical and mechanistic studies, it is well documented that radiotherapy results in significant alteration of both gut microbiota abundance and diversity. Radiation treatment is associated with a reduction in Firmicutes and Bacteroidetes (although increases in Bacteroidetes also have been documented),
      • Gerassy-Vainberg S.
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      • Kashi Y.
      • Chowers Y.
      Radiation induces proinflammatory dysbiosis: transmission of inflammatory susceptibility by host cytokine induction.
      along with a consistent increase in Proteobacteria, most often Enterobacteriaceae.
      • Touchefeu Y.
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      • de La Cochetière M.F.
      Systematic review: the role of the gut microbiota in chemotherapy- or radiation-induced gastrointestinal mucositis - current evidence and potential clinical applications.
      Gerassy-Vainberg et al
      • Gerassy-Vainberg S.
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      • Dahan A.
      • Ziv O.
      • Dheer R.
      • Abreu M.T.
      • Koren O.
      • Kashi Y.
      • Chowers Y.
      Radiation induces proinflammatory dysbiosis: transmission of inflammatory susceptibility by host cytokine induction.
      showed that radiation treatment induced localized dysbiosis, which was associated with postradiation tissue damage. No studies have been published that assess the effect of the gut microbiota on the efficacy and outcome of radiotherapy, but there are data indicating that the gut microbiota impacts tissue radiosensitivity.
      • Crawford P.A.
      • Gordon J.I.
      Microbial regulation of intestinal radiosensitivity.
      • Cui M.
      • Xiao H.
      • Luo D.
      • Zhang X.
      • Zhao S.
      • Zheng Q.
      • Li Y.
      • Zhao Y.
      • Dong J.
      • Li H.
      • Wang H.
      • Fan S.
      Circadian rhythm shapes the gut microbiota affecting host radiosensitivity.
      • Paulos C.M.
      • Wrzesinski C.
      • Kaiser A.
      • Hinrichs C.S.
      • Chieppa M.
      • Cassard L.
      • Palmer D.C.
      • Boni A.
      • Muranski P.
      • Yu Z.
      • Gattinoni L.
      • Antony P.A.
      • Rosenberg S.A.
      • Restifo N.P.
      Microbial translocation augments the function of adoptively transferred self/tumor-specific CD8+ T cells via TLR4 signaling.
      Radiotherapy-induced diarrhea (RID) is a significant problem. Across the developed world, it is estimated that 150,000 to 300,000 patients require treatment for RID every year.
      • Andreyev J.
      Gastrointestinal complications of pelvic radiotherapy: are they of any importance?.
      The potential for ameliorating RID through probiotic supplementation has been a focus of recent studies.
      • Devaraj N.K.
      • Suppiah S.
      • Veettil S.K.
      • Ching S.M.
      • Lee K.W.
      • Menon R.K.
      • Soo M.J.
      • Deuraseh I.
      • Hoo F.K.
      • Sivaratnam D.
      The effects of probiotic supplementation on the incidence of diarrhea in cancer patients receiving radiation therapy: a systematic review with meta-analysis and trial sequential analysis of randomized controlled trials.
      In an analysis of 8 trials with a total of 1116 participants, probiotics were associated with a lower risk of RID (relative risk, 0.62; 95% CI, 0.46-0.83) compared with placebo, but the baseline characteristics of the patients included were diverse. This notion also has been supported by a systematic review showing the potential of probiotics containing Lactobacillus species for the prevention of RID (Figure 2). However, additional well-designed research in the field is required.
      • Bowen J.M.
      • Gibson R.J.
      • Coller J.K.
      • Blijlevens N.
      • Bossi P.
      • Al-Dasooqi N.
      • Bateman E.H.
      • Chiang K.
      • de Mooij C.
      • Mayo B.
      • Stringer A.M.
      • Tissing W.
      • Wardill H.R.
      • van Sebille Y.Z.A.
      • Ranna V.
      • Vaddi A.
      • Keefe D.M.
      • Lalla R.V.
      • Cheng K.K.F.
      • Elad S.
      Systematic review of agents for the management of cancer treatment-related gastrointestinal mucositis and clinical practice guidelines.

      Immunotherapy

      Multiple studies have highlighted the role of the gut microbiota in modulating immunotherapy efficacy across various cancers.
      • Frankel A.E.
      • Coughlin L.A.
      • Kim J.
      • Froehlich T.W.
      • Xie Y.
      • Frenkel E.P.
      • Koh A.Y.
      Metagenomic shotgun sequencing and unbiased metabolomic profiling identify specific human gut microbiota and metabolites associated with immune checkpoint therapy efficacy in melanoma patients.
      • Routy B.
      • Le Chatelier E.
      • Derosa L.
      • Duong C.P.M.
      • Alou M.T.
      • Daillère R.
      • Fluckiger A.
      • Messaoudene M.
      • Rauber C.
      • Roberti M.P.
      • Fidelle M.
      • Flament C.
      • Poirier-Colame V.
      • Opolon P.
      • Klein C.
      • Iribarren K.
      • Mondragón L.
      • Jacquelot N.
      • Qu B.
      • Ferrere G.
      • Clémenson C.
      • Mezquita L.
      • Masip J.R.
      • Naltet C.
      • Brosseau S.
      • Kaderbhai C.
      • Richard C.
      • Rizvi H.
      • Levenez F.
      • Galleron N.
      • Quinquis B.
      • Pons N.
      • Ryffel B.
      • Minard-Colin V.
      • Gonin P.
      • Soria J.-C.
      • Deutsch E.
      • Loriot Y.
      • Ghiringhelli F.
      • Zalcman G.
      • Goldwasser F.
      • Escudier B.
      • Hellmann M.D.
      • Eggermont A.
      • Raoult D.
      • Albiges L.
      • Kroemer G.
      • Zitvogel L.
      Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors.
      • Gopalakrishnan V.
      • Spencer C.N.
      • Nezi L.
      • Reuben A.
      • Andrews M.C.
      • Karpinets T.V.
      • Prieto P.A.
      • Vicente D.
      • Hoffman K.
      • Wei S.C.
      • Cogdill A.P.
      • Zhao L.
      • Hudgens C.W.
      • Hutchinson D.S.
      • Manzo T.
      • Petaccia de Macedo M.
      • Cotechini T.
      • Kumar T.
      • Chen W.S.
      • Reddy S.M.
      • Szczepaniak Sloane R.
      • Galloway-Pena J.
      • Jiang H.
      • Chen P.L.
      • Shpall E.J.
      • Rezvani K.
      • Alousi A.M.
      • Chemaly R.F.
      • Shelburne S.
      • Vence L.M.
      • Okhuysen P.C.
      • Jensen V.B.
      • Swennes A.G.
      • McAllister F.
      • Marcelo Riquelme Sanchez E.
      • Zhang Y.
      • Le Chatelier E.
      • Zitvogel L.
      • Pons N.
      • Austin-Breneman J.L.
      • Haydu L.E.
      • Burton E.M.
      • Gardner J.M.
      • Sirmans E.
      • Hu J.
      • Lazar A.J.
      • Tsujikawa T.
      • Diab A.
      • Tawbi H.
      • Glitza I.C.
      • Hwu W.J.
      • Patel S.P.
      • Woodman S.E.
      • Amaria R.N.
      • Davies M.A.
      • Gershenwald J.E.
      • Hwu P.
      • Lee J.E.
      • Zhang J.
      • Coussens L.M.
      • Cooper Z.A.
      • Futreal P.A.
      • Daniel C.R.
      • Ajami N.J.
      • Petrosino J.F.
      • Tetzlaff M.T.
      • Sharma P.
      • Allison J.P.
      • Jenq R.R.
      • Wargo J.A.
      Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients.
      • Matson V.
      • Fessler J.
      • Bao R.
      • Chongsuwat T.
      • Zha Y.
      • Alegre M.-L.
      • Luke J.J.
      • Gajewski T.F.
      The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients.
      Initial studies focused on understanding how the gut microbiota impacted CpG-oligonucleotide immunotherapy responses, which activates innate immune cells through TLR9.
      • Iida N.
      • Dzutsev A.
      • Stewart C.A.
      • Smith L.
      • Bouladoux N.
      • Weingarten R.A.
      • Molina D.A.
      • Salcedo R.
      • Back T.
      • Cramer S.
      • Dai R.-M.
      • Kiu H.
      • Cardone M.
      • Naik S.
      • Patri A.K.
      • Wang E.
      • Marincola F.M.
      • Frank K.M.
      • Belkaid Y.
      • Trinchieri G.
      • Goldszmid R.S.
      Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment.
      Subsequently, investigations assessed gut microbiota influence on immune-stimulatory cyclophosphamide chemotherapy treatment through shaping T-helper cell portfolios, namely the generation-specific subsets of Th17 and memory Th1 cells. More recently, the role of specific microbes was assessed in response to immune checkpoint inhibitor (ICI) therapies, including cytotoxic T-lymphocyte–associated protein 4 and programmed cell death 1 (PD-1)/PD-1 ligand inhibitors.
      Vétizou et al
      • Vétizou M.
      • Pitt J.M.
      • Daillère R.
      • Lepage P.
      • Waldschmitt N.
      • Flament C.
      • Rusakiewicz S.
      • Routy B.
      • Roberti M.P.
      • Duong C.P.M.
      • Poirier-Colame V.
      • Roux A.
      • Becharef S.
      • Formenti S.
      • Golden E.
      • Cording S.
      • Eberl G.
      • Schlitzer A.
      • Ginhoux F.
      • Mani S.
      • Yamazaki T.
      • Jacquelot N.
      • Enot D.P.
      • Bérard M.
      • Nigou J.
      • Opolon P.
      • Eggermont A.
      • Woerther P.-L.
      • Chachaty E.
      • Chaput N.
      • Robert C.
      • Mateus C.
      • Kroemer G.
      • Raoult D.
      • Boneca I.G.
      • Carbonnel F.
      • Chamaillard M.
      • Zitvogel L.
      Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota.
      showed that the efficacy of anti–cytotoxic T-lymphocyte–associated protein 4 therapy was dependent on B fragilis and/or Bacteroides thetaiotaomicron and Burkholderiales populations, with T-cell responses specific for B fragilis and B thetaiotaomicron associated with therapeutic efficacy. In addition, the re-introduction of B fragilis cells and/or polysaccharides or adoptive transfer of B fragilis–specific T cells restored therapeutic efficacy and reduced immune-mediated colitis through activation of Th1 cells with cross-reactivity to bacterial antigens and tumor neoantigens (Figure 2).
      • Vétizou M.
      • Pitt J.M.
      • Daillère R.
      • Lepage P.
      • Waldschmitt N.
      • Flament C.
      • Rusakiewicz S.
      • Routy B.
      • Roberti M.P.
      • Duong C.P.M.
      • Poirier-Colame V.
      • Roux A.
      • Becharef S.
      • Formenti S.
      • Golden E.
      • Cording S.
      • Eberl G.
      • Schlitzer A.
      • Ginhoux F.
      • Mani S.
      • Yamazaki T.
      • Jacquelot N.
      • Enot D.P.
      • Bérard M.
      • Nigou J.
      • Opolon P.
      • Eggermont A.
      • Woerther P.-L.
      • Chachaty E.
      • Chaput N.
      • Robert C.
      • Mateus C.
      • Kroemer G.
      • Raoult D.
      • Boneca I.G.
      • Carbonnel F.
      • Chamaillard M.
      • Zitvogel L.
      Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota.
      ,
      • Cramer P.
      • Bresalier R.S.
      Gastrointestinal and hepatic complications of immune checkpoint inhibitors.
      In terms of PD-1/PD-1 ligand acting agents, differences in clinical response have been linked to gut microbiota composition. In particular, an abundance of A muciniphila and E hirae have been shown to be more abundant in anti–PD-1 treatment responders compared with nonresponders (Figure 2).
      • Routy B.
      • Le Chatelier E.
      • Derosa L.
      • Duong C.P.M.
      • Alou M.T.
      • Daillère R.
      • Fluckiger A.
      • Messaoudene M.
      • Rauber C.
      • Roberti M.P.
      • Fidelle M.
      • Flament C.
      • Poirier-Colame V.
      • Opolon P.
      • Klein C.
      • Iribarren K.
      • Mondragón L.
      • Jacquelot N.
      • Qu B.
      • Ferrere G.
      • Clémenson C.
      • Mezquita L.
      • Masip J.R.
      • Naltet C.
      • Brosseau S.
      • Kaderbhai C.
      • Richard C.
      • Rizvi H.
      • Levenez F.
      • Galleron N.
      • Quinquis B.
      • Pons N.
      • Ryffel B.
      • Minard-Colin V.
      • Gonin P.
      • Soria J.-C.
      • Deutsch E.
      • Loriot Y.
      • Ghiringhelli F.
      • Zalcman G.
      • Goldwasser F.
      • Escudier B.
      • Hellmann M.D.
      • Eggermont A.
      • Raoult D.
      • Albiges L.
      • Kroemer G.
      • Zitvogel L.
      Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors.
      This responder/nonresponder phenotype also has been shown to be transmissible because mice receiving FMT subsequently acquire donor responder/nonresponder efficacy. The nonresponsive phenotype was rescued by addition of A muciniphila alone or in combination with E hirae.
      Taking the concept of the impact of the gut microbiota on ICI efficacy one step further, several studies investigated if FMT could safely and effectively improve response to ICI treatment in anti–PD-1–refractory patients.
      • Gopalakrishnan V.
      • Spencer C.N.
      • Nezi L.
      • Reuben A.
      • Andrews M.C.
      • Karpinets T.V.
      • Prieto P.A.
      • Vicente D.
      • Hoffman K.
      • Wei S.C.
      • Cogdill A.P.
      • Zhao L.
      • Hudgens C.W.
      • Hutchinson D.S.
      • Manzo T.
      • Petaccia de Macedo M.
      • Cotechini T.
      • Kumar T.
      • Chen W.S.
      • Reddy S.M.
      • Szczepaniak Sloane R.
      • Galloway-Pena J.
      • Jiang H.
      • Chen P.L.
      • Shpall E.J.
      • Rezvani K.
      • Alousi A.M.
      • Chemaly R.F.
      • Shelburne S.
      • Vence L.M.
      • Okhuysen P.C.
      • Jensen V.B.
      • Swennes A.G.
      • McAllister F.
      • Marcelo Riquelme Sanchez E.
      • Zhang Y.
      • Le Chatelier E.
      • Zitvogel L.
      • Pons N.
      • Austin-Breneman J.L.
      • Haydu L.E.
      • Burton E.M.
      • Gardner J.M.
      • Sirmans E.
      • Hu J.
      • Lazar A.J.
      • Tsujikawa T.
      • Diab A.
      • Tawbi H.
      • Glitza I.C.
      • Hwu W.J.
      • Patel S.P.
      • Woodman S.E.
      • Amaria R.N.
      • Davies M.A.
      • Gershenwald J.E.
      • Hwu P.
      • Lee J.E.
      • Zhang J.
      • Coussens L.M.
      • Cooper Z.A.
      • Futreal P.A.
      • Daniel C.R.
      • Ajami N.J.
      • Petrosino J.F.
      • Tetzlaff M.T.
      • Sharma P.
      • Allison J.P.
      • Jenq R.R.
      • Wargo J.A.
      Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients.
      ,
      • Baruch E.N.
      • Youngster I.
      • Ben-Betzalel G.
      • Ortenberg R.
      • Lahat A.
      • Katz L.
      • Adler K.
      • Dick-Necula D.
      • Raskin S.
      • Bloch N.
      • Rotin D.
      • Anafi L.
      • Avivi C.
      • Melnichenko J.
      • Steinberg-Silman Y.
      • Mamtani R.
      • Harati H.
      • Asher N.
      • Shapira-Frommer R.
      • Brosh-Nissimov T.
      • Eshet Y.
      • Ben-Simon S.
      • Ziv O.
      • Khan M.A.W.
      • Amit M.
      • Ajami N.J.
      • Barshack I.
      • Schachter J.
      • Wargo J.A.
      • Koren O.
      • Markel G.
      • Boursi B.
      Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients.
      ,
      • Davar D.
      • Dzutsev A.K.
      • McCulloch J.A.
      • Rodrigues R.R.
      • Chauvin J.-M.
      • Morrison R.M.
      • Deblasio R.N.
      • Menna C.
      • Ding Q.
      • Pagliano O.
      • Zidi B.
      • Zhang S.
      • Badger J.H.
      • Vetizou M.
      • Cole A.M.
      • Fernandes M.R.
      • Prescott S.
      • Costa R.G.F.
      • Balaji A.K.
      • Morgun A.
      • Vujkovic-Cvijin I.
      • Wang H.
      • Borhani A.A.
      • Schwartz M.B.
      • Dubner H.M.
      • Ernst S.J.
      • Rose A.
      • Najjar Y.G.
      • Belkaid Y.
      • Kirkwood J.M.
      • Trinchieri G.
      • Zarour H.M.
      Fecal microbiota transplant overcomes resistance to anti-PD-1 therapy in melanoma patients.
      Anti–PD-1–refractory patients were given oral antibiotics (vancomycin and neomycin) and bowel preparation to deplete their microbiota, followed by FMT from donors who had achieved a complete response with anti–PD-1 therapy. Microbiota analysis confirmed that recipient gut microbiota profiles resembled donor profiles, although no microbial features clearly differentiated between responders and those who remained refractory. FMT treatment was shown to induce antitumor changes in immune cell infiltrates and gene expression profiles in the gut lamina propria and the tumor microenvironment.

      Impact of Probiotics on Postsurgical Outcome

      Digestive surgery has a dramatic effect on the microbiota, usually causing surgery-induced dysbiosis. Many factors may alter the overall microbial numbers/composition: bowel preparation, antibiotics, anesthesia, surgical stress, parenteral nutrition, and surgical anatomic changes.
      • Komatsu S.
      • Yokoyama Y.
      • Nagino M.
      Gut microbiota and bacterial translocation in digestive surgery: the impact of probiotics.
      Loss of microbial diversity or abundance, an increase in potentially harmful species, and a decrease in beneficial species can slow wound healing and predispose patients undergoing abdominal surgery to infectious complications.
      • Stavrou G.
      • Kotzampassi K.
      Gut microbiome, surgical complications and probiotics.
      ,
      • Vaishnavi C.
      Translocation of gut flora and its role in sepsis.
      A recent systematic review (21 clinical trials with 1831 patients who were subjected to elective colorectal surgery) suggested that probiotics could significantly decrease inflammation, postoperative infectious complications, and the duration of antibiotic therapy.
      • Darbandi A.
      • Mirshekar M.
      • Shariati A.
      • Moghadam M.T.
      • Lohrasbi V.
      • Asadolahi P.
      • Talebi M.
      The effects of probiotics on reducing the colorectal cancer surgery complications: a periodic review during 2007-2017.
      A similar conclusion was made by another meta-analysis, concluding that probiotics may have an effect on preventing postoperative infections and related complications in cancer patients undergoing surgery.
      • Ouyang X.
      • Li Q.
      • Shi M.
      • Niu D.
      • Song W.
      • Nian Q.
      • Li X.
      • Ding Z.
      • Ai X.
      • Wang J.
      Probiotics for preventing postoperative infection in colorectal cancer patients: a systematic review and meta-analysis.
      A Chinese group studied the impact of a probiotic compound containing Bifidobacterium infantis, Lactobacillus acidophilus, E faecalis, and Bacillus cereus on serologic inflammatory markers induced by gastrectomy.
      • Zheng C.
      • Chen T.
      • Wang Y.
      • Gao Y.
      • Kong Y.
      • Liu Z.
      • Deng X.
      A randomised trial of probiotics to reduce severity of physiological and microbial disorders induced by partial gastrectomy for patients with gastric cancer.
      Probiotic supplementation significantly enhanced the immune response and reduced the severity of inflammation through modification of the gut microbiota (Figure 2). However, it remains unclear whether this results in an actual clinical benefit. Overall, there is a clear need for more evidence to draw conclusions about the efficacy of probiotics given before or after cancer surgery to provide evidence-based clinical recommendations.

      Summary and Glimpse to the Future

      We live in an increasingly microbiota-focused world, a world where we understand that microbes strongly shape health and disease, including cancer, although our appreciation is still in its infancy. With this knowledge comes the requirement to fully appreciate the mechanistic impact of the microbiota in cancer development as well as in therapeutic regimens including microbiota manipulation strategies. Please note, that supplementary tables 1-3 list a detailed overview of the current literature on the interaction of microbiota and esophageal, gastric and colorectal cancer.
      • Blackett K.L.
      • Siddhi S.S.
      • Cleary S.
      • Steed H.
      • Miller M.H.
      • Macfarlane S.
      • Macfarlane G.T.
      • Dillon J.F.
      Oesophageal bacterial biofilm changes in gastro-oesophageal reflux disease, Barrett’s and oesophageal carcinoma: association or causality?.
      • Cass S.
      • Hamilton C.
      • Miller A.
      • Jupiter D.
      • Khanipov K.
      • Booth A.
      • Pyles R.
      • Krill T.
      • Reep G.
      • Okereke I.
      Novel ex vivo model to examine the mechanism and relationship of esophageal microbiota and disease.
      • Deng Y.
      • Tang D.
      • Hou P.
      • Shen W.
      • Li H.
      • Wang T.
      • Liu R.
      Dysbiosis of gut microbiota in patients with esophageal cancer.
      • Deshpande N.P.
      • Riordan S.M.
      • Castaño-Rodríguez N.
      • Wilkins M.R.
      • Kaakoush N.O.
      Signatures within the esophageal microbiome are associated with host genetics, age, and disease.
      • Gall A.
      • Fero J.
      • McCoy C.
      • Claywell B.C.
      • Sanchez C.A.
      • Blount P.L.
      • Li X.
      • Vaughan T.L.
      • Matsen F.A.
      • Reid B.J.
      • Salama N.R.
      Bacterial composition of the human upper gastrointestinal tract microbiome is dynamic and associated with genomic instability in a Barrett’s esophagus cohort.
      • Gao S.
      • Li S.
      • Ma Z.
      • Liang S.
      • Shan T.
      • Zhang M.
      • Zhu X.
      • Zhang P.
      • Liu G.
      • Zhou F.
      • Yuan X.
      • Jia R.
      • Potempa J.
      • Scott D.A.
      • Lamont R.J.
      • Wang H.
      • Feng X.
      Presence of Porphyromonas gingivalis in esophagus and its association with the clinicopathological characteristics and survival in patients with esophageal cancer.
      • Narikiyo M.
      • Tanabe C.
      • Yamada Y.
      • Igaki H.
      • Tachimori Y.
      • Kato H.
      • Muto M.
      • Montesano R.
      • Sakamoto H.
      • Nakajima Y.
      • Sasaki H.
      Frequent and preferential infection of Treponema denticola, Streptococcus mitis, and Streptococcus anginosus in esophageal cancers.
      • Snider E.J.
      • Compres G.
      • Freedberg D.E.
      • Giddins M.J.
      • Khiabanian H.
      • Lightdale C.J.
      • Nobel Y.R.
      • Toussaint N.C.
      • Uhlemann A.-C.
      • Abrams J.A.
      Barrett’s esophagus is associated with a distinct oral microbiome.
      • Yamamura K.
      • Baba Y.
      • Nakagawa S.
      • Mima K.
      • Miyake K.
      • Nakamura K.
      • Sawayama H.
      • Kinoshita K.
      • Ishimoto T.
      • Iwatsuki M.
      • Sakamoto Y.
      • Yamashita Y.
      • Yoshida N.
      • Watanabe M.
      • Baba H.
      Human microbiome Fusobacterium nucleatum in esophageal cancer tissue is associated with prognosis.
      • Ahn J.
      • Sinha R.
      • Pei Z.
      • Dominianni C.
      • Wu J.
      • Shi J.
      • Goedert J.J.
      • Hayes R.B.
      • Yang L.
      Human gut microbiome and risk for colorectal cancer.
      • Allali I.
      • Delgado S.
      • Marron P.I.
      • Astudillo A.
      • Yeh J.J.
      • Ghazal H.
      • Amzazi S.
      • Keku T.
      • Azcarate-Peril M.A.
      Gut microbiome compositional and functional differences between tumor and non-tumor adjacent tissues from cohorts from the US and Spain.
      • Chang H.
      • Mishra R.
      • Cen C.
      • Tang Y.
      • Ma C.
      • Wasti S.
      • Wang Y.
      • Ou Q.
      • Chen K.
      • Zhang J.
      Metagenomic analyses expand bacterial and functional profiling biomarkers for colorectal cancer in a Hainan cohort, China.
      • Chen C.
      • Niu M.
      • Pan J.
      • Du N.
      • Liu S.
      • Li H.
      • He Q.
      • Mao J.
      • Duan Y.
      • Du Y.
      Bacteroides, butyric acid and t10,c12-CLA changes in colorectal adenomatous polyp patients.
      • Chen H.-M.
      • Yu Y.-N.
      • Wang J.-L.
      • Lin Y.-W.
      • Kong X.
      • Yang C.-Q.
      • Yang L.
      • Liu Z.-J.
      • Yuan Y.-Z.
      • Liu F.
      • Wu J.-X.
      • Zhong L.
      • Fang D.-C.
      • Zou W.
      • Fang J.-Y.
      Decreased dietary fiber intake and structural alteration of gut microbiota in patients with advanced colorectal adenoma.
      • Coker O.O.
      • Wu W.K.K.
      • Wong S.H.
      • Sung J.J.Y.
      • Yu J.
      Altered gut archaea composition and interaction with bacteria are associated with colorectal cancer.
      • Coker O.O.
      • Nakatsu G.
      • Dai R.Z.
      • Wu W.K.K.
      • Wong S.H.
      • Ng S.C.
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