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Ambrosio MR, Niccolai E, Petrelli F, Di Gloria L, Bertacca G, Giusti A, Baldi S, Cavazzana A, Palmeri M, Perotti B, Ramazzotti M, Arganini M, Amedei A. Immune landscape and oncobiota in HPV-Associated Colorectal Cancer: an explorative study. Clin Exp Med 2023; 23:5101-5112. [PMID: 37612430 PMCID: PMC10725376 DOI: 10.1007/s10238-023-01165-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/07/2023] [Indexed: 08/25/2023]
Abstract
Worldwide more than 550,000 new patients suffering from malignant tumors are associated with human papillomaviruses (HPV) infection. However, only a small portion of patients infected progress to cancer, suggesting that other factors other than HPV may play a role. Some studies have investigated HPV infection in colorectal cancer (CRC) with discordant results; moreover, the role of HPV in CRC development is still unknown. We investigated HPV infection in 50 CRC from different regions, excluding the anal one, by immunohistochemistry (IHC), real-time PCR and RNA-seq. For each patient, we studied the tumor microenvironment in neoplastic and matched non-neoplastic samples, and we compared the tumor-infiltrating immune cell phenotypes among HPV-positive and negative samples. Finally, we compared the CRC-associated microbiota in HPV-positive and negative neoplastic samples by 16S rRNA sequencing. HPV infection was identified in 20% of CRC from the right side (caecum, ascending and transverse colon) and in 40% from the left side (descending colon and rectum). In all HPV-positive CRCs we found no expression of p53 and RB, thus suggesting HPV involvement in tumorigenesis. As far as the tumor microenvironment is concerned, in HPV-related cancers we observed a neoplastic environment with a reduced immune surveillance but an enhanced cytotoxic response by lymphocytes. HPV-positive and -negative CRC showed a different microbiota with lack of species normally found in CRC in the HPV-positive ones. Our results support the carcinogenic significance of HPV in CRC, suggesting a role of HPV in modulating the tumor immune microenvironment.
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Affiliation(s)
| | - Elena Niccolai
- Department of Clinical and Experimental Medicine, University of Florence, Largo Brambilla 3, 50134, Florence, Italy
| | | | - Leandro Di Gloria
- Department of Biomedical, Experimental and Clinical Sciences, "Mario Serio" University of Florence, Florence, Italy
| | - Gloria Bertacca
- Clinical Chemical Analysis and Immuno Allergology Department, Azienda USL Toscana Nord Ovest, Pisa, Italy
| | - Andrea Giusti
- Pathology Unit, Azienda USL Toscana Nord Ovest, Pisa, Italy
| | - Simone Baldi
- Department of Clinical and Experimental Medicine, University of Florence, Largo Brambilla 3, 50134, Florence, Italy
| | | | - Matteo Palmeri
- Surgery Unit, Ospedale Unico Versilia, Azienda USL Toscana Nord Ovest, Pisa, Italy
| | - Bruno Perotti
- Surgery Unit, Ospedale Unico Versilia, Azienda USL Toscana Nord Ovest, Pisa, Italy
| | - Matteo Ramazzotti
- Department of Biomedical, Experimental and Clinical Sciences, "Mario Serio" University of Florence, Florence, Italy
| | - Marco Arganini
- Surgery Unit, Ospedale Unico Versilia, Azienda USL Toscana Nord Ovest, Pisa, Italy
| | - Amedeo Amedei
- Department of Clinical and Experimental Medicine, University of Florence, Largo Brambilla 3, 50134, Florence, Italy.
- Internal Interdisciplinary Medicine Unit, Careggi University Hospital, 50134, Florence, Italy.
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Minot SS, Garb B, Roldan A, Tang AS, Oskotsky TT, Rosenthal C, Hoffman NG, Sirota M, Golob JL. MaLiAmPi enables generalizable and taxonomy-independent microbiome features from technically diverse 16S-based microbiome studies. CELL REPORTS METHODS 2023; 3:100639. [PMID: 37939711 PMCID: PMC10694490 DOI: 10.1016/j.crmeth.2023.100639] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/01/2023] [Accepted: 10/17/2023] [Indexed: 11/10/2023]
Abstract
For studies using microbiome data, the ability to robustly combine data from technically and biologically distinct microbiome studies is a crucial means of supporting more robust and clinically relevant inferences. Formidable technical challenges arise when attempting to combine data from technically diverse 16S rRNA gene variable region amplicon sequencing (16S) studies. Closed operational taxonomic units and taxonomy are criticized as being heavily dependent upon reference sets and with limited precision relative to the underlying biology. Phylogenetic placement has been demonstrated to be a promising taxonomy-free manner of harmonizing microbiome data, but it has lacked a validated count-based feature suitable for use in machine learning and association studies. Here we introduce a phylogenetic-placement-based, taxonomy-independent, compositional feature of microbiota: phylotypes. Phylotypes were predictive of clinical outcomes such as obesity or pre-term birth on technically diverse independent validation sets harmonized post hoc. Thus, phylotypes enable the rigorous cross-validation of 16S-based clinical prognostic models and associative microbiome studies.
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Affiliation(s)
- Samuel S Minot
- Data Core, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Bailey Garb
- Bioinformatics Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Alennie Roldan
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Alice S Tang
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Tomiko T Oskotsky
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Christopher Rosenthal
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Noah G Hoffman
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan L Golob
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
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Nowicki C, Ray L, Engen P, Madrigrano A, Witt T, Lad T, Cobleigh M, Mutlu EA. Comparison of gut microbiome composition in colonic biopsies, endoscopically-collected and at-home-collected stool samples. Front Microbiol 2023; 14:1148097. [PMID: 37323911 PMCID: PMC10264612 DOI: 10.3389/fmicb.2023.1148097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Aim The goal of this study is to compare microbiome composition in three different sample types in women, namely stool brought from home vs. solid stool samples obtained at the time of an unprepped sigmoidoscopy vs. biopsies of the colonic mucosa at the time of an unprepped sigmoidoscopy, using alpha- and beta-diversity metrics following bacterial 16S rRNA sequencing. The findings may have relevance to health and disease states in which bacterial metabolism has a significant impact on molecules/metabolites that are recirculated between the gut lumen and mucosa and systemic circulation, such as estrogens (as in breast cancer) or bile acids. Methods Concomitant at-home-collected stool, endoscopically-collected stool, and colonic biopsy samples were collected from 48 subjects (24 breast cancer, 24 control.) After 16S rRNA sequencing, an amplicon sequence variant (ASV) based approach was used to analyze the data. Alpha diversity metrics (Chao1, Pielou's Evenness, Faith PD, Shannon, and Simpson) and beta diversity metrics (Bray-Curtis, Weighted and Unweighted Unifrac) were calculated. LEfSe was used to analyze differences in the abundance of various taxa between sample types. Results Alpha and beta diversity metrics were significantly different between the three sample types. Biopsy samples were different than stool samples in all metrics. The highest variation in microbiome diversity was noted in the colonic biopsy samples. At-home and endoscopically-collected stool showed more similarities in count-based and weighted beta diversity metrics. There were significant differences in rare taxa and phylogenetically-diverse taxa between the two types of stool samples. Generally, there were higher levels of Proteobacteria in biopsy samples, with significantly more Actinobacteria and Firmicutes in stool (all p < 0.001, q-value < 0.05). Overall, there was a significantly higher relative abundance of Lachnospiraceae and Ruminococcaceae in stool samples (at-home collected and endoscopically-collected) and higher abundances of Tisserellaceae in biopsy samples (all p < 0.001, q-value < 0.05). Conclusion Our data shows that different sampling methods can impact results when looking at the composition of the gut microbiome using ASV-based approaches.
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Affiliation(s)
- Christina Nowicki
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL, United States
| | - Lucille Ray
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL, United States
| | - Philip Engen
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Andrea Madrigrano
- Department of Surgery, Rush Medical College, Rush University Medical Center, Chicago, IL, United States
| | - Thomas Witt
- Department of Surgery, Rush Medical College, Rush University Medical Center, Chicago, IL, United States
| | - Thomas Lad
- Department of Oncology, Cook County Health and Hospital Systems, Chicago, IL, United States
| | - Melody Cobleigh
- Department of Internal Medicine, Division of Hematology, Oncology, and Cell Therapy, Rush University Medical Center, Chicago, IL, United States
| | - Ece A. Mutlu
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL, United States
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Di Pierro F. Special Issue "Gut Microbioma Structure and Functions in Human Health and Disease": Editorial. Microorganisms 2023; 11:1220. [PMID: 37317194 DOI: 10.3390/microorganisms11051220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/13/2023] [Accepted: 05/05/2023] [Indexed: 06/16/2023] Open
Abstract
The human gut microbiota is an integral component of the human body that can strike a delicate balance between health and disease [...].
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Aberrant HMGA2 Expression Sustains Genome Instability That Promotes Metastasis and Therapeutic Resistance in Colorectal Cancer. Cancers (Basel) 2023; 15:cancers15061735. [PMID: 36980621 PMCID: PMC10046046 DOI: 10.3390/cancers15061735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/06/2023] [Accepted: 03/11/2023] [Indexed: 03/16/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most lethal cancers worldwide, accounting for nearly ~10% of all cancer diagnoses and deaths. Current therapeutic approaches have considerably increased survival for patients diagnosed at early stages; however, ~20% of CRC patients are diagnosed with late-stage, metastatic CRC, where 5-year survival rates drop to 6–13% and treatment options are limited. Genome instability is an enabling hallmark of cancer that confers increased acquisition of genetic alterations, mutations, copy number variations and chromosomal rearrangements. In that regard, research has shown a clear association between genome instability and CRC, as the accumulation of aberrations in cancer-related genes provides subpopulations of cells with several advantages, such as increased proliferation rates, metastatic potential and therapeutic resistance. Although numerous genes have been associated with CRC, few have been validated as predictive biomarkers of metastasis or therapeutic resistance. A growing body of evidence suggests a member of the High-Mobility Group A (HMGA) gene family, HMGA2, is a potential biomarker of metastatic spread and therapeutic resistance. HMGA2 is expressed in embryonic tissues and is frequently upregulated in aggressively growing cancers, including CRC. As an architectural, non-histone chromatin binding factor, it initiates chromatin decompaction to facilitate transcriptional regulation. HMGA2 maintains the capacity for stem cell renewal in embryonic and cancer tissues and is a known promoter of epithelial-to-mesenchymal transition in tumor cells. This review will focus on the known molecular mechanisms by which HMGA2 exerts genome protective functions that contribute to cancer cell survival and chemoresistance in CRC.
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Rudar J, Golding GB, Kremer SC, Hajibabaei M. Decision Tree Ensembles Utilizing Multivariate Splits Are Effective at Investigating Beta Diversity in Medically Relevant 16S Amplicon Sequencing Data. Microbiol Spectr 2023; 11:e0206522. [PMID: 36877086 PMCID: PMC10100742 DOI: 10.1128/spectrum.02065-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 02/11/2023] [Indexed: 03/07/2023] Open
Abstract
Developing an understanding of how microbial communities vary across conditions is an important analytical step. We used 16S rRNA data isolated from human stool samples to investigate whether learned dissimilarities, such as those produced using unsupervised decision tree ensembles, can be used to improve the analysis of the composition of bacterial communities in patients suffering from Crohn's disease and adenomas/colorectal cancers. We also introduce a workflow capable of learning dissimilarities, projecting them into a lower dimensional space, and identifying features that impact the location of samples in the projections. For example, when used with the centered log ratio transformation, our new workflow (TreeOrdination) could identify differences in the microbial communities of Crohn's disease patients and healthy controls. Further investigation of our models elucidated the global impact amplicon sequence variants (ASVs) had on the locations of samples in the projected space and how each ASV impacted individual samples in this space. Furthermore, this approach can be used to integrate patient data easily into the model and results in models that generalize well to unseen data. Models employing multivariate splits can improve the analysis of complex high-throughput sequencing data sets because they are better able to learn about the underlying structure of the data set. IMPORTANCE There is an ever-increasing level of interest in accurately modeling and understanding the roles that commensal organisms play in human health and disease. We show that learned representations can be used to create informative ordinations. We also demonstrate that the application of modern model introspection algorithms can be used to investigate and quantify the impacts of taxa in these ordinations, and that the taxa identified by these approaches have been associated with immune-mediated inflammatory diseases and colorectal cancer.
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Affiliation(s)
- Josip Rudar
- Department of Integrative Biology & Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - G. Brian Golding
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Stefan C. Kremer
- School of Computer Science, University of Guelph, Guelph, Ontario, Canada
| | - Mehrdad Hajibabaei
- Department of Integrative Biology & Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
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Cobo F, Pérez-Carrasco V, García-Salcedo JA, Navarro-Marí JM. New anaerobic bacteria causing infection: Bacteremia due to Murdochiellaasaccharolytica. Anaerobe 2023; 79:102697. [PMID: 36649886 DOI: 10.1016/j.anaerobe.2023.102697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/15/2023]
Abstract
Murdochiella asaccharolytica is a Gram-positive anaerobic coccus firstly isolated from wound specimens, since then, it was very rarely isolated from human infections. We report the first case of bloodstream infection due to this bacterium in a 90 years-old-man. The patient had a history of B-cell lymphoma and presented with pain and induration of the base of penis along with fever. A blood culture was obtained yielding M. asaccharolytica in pure culture. Only resistance to clindamycin was demonstrated. Treatment with metronidazole was started and the clinical evolution improved with antimicrobial treatment, being discharged after 6 days.
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Affiliation(s)
- Fernando Cobo
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain.
| | - Virginia Pérez-Carrasco
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
| | - José A García-Salcedo
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
| | - José María Navarro-Marí
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
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Levitan O, Ma L, Giovannelli D, Burleson DB, McCaffrey P, Vala A, Johnson DA. The gut microbiome–Does stool represent right? Heliyon 2023; 9:e13602. [PMID: 37101508 PMCID: PMC10123208 DOI: 10.1016/j.heliyon.2023.e13602] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Many stool-based gut microbiome studies have highlighted the importance of the microbiome. However, we hypothesized that stool is a poor proxy for the inner-colonic microbiome and that studying stool samples may be inadequate to capture the true inner-colonic microbiome. To test this hypothesis, we conducted prospective clinical studies with up to 20 patients undergoing an FDA-cleared gravity-fed colonic lavage without oral purgative pre-consumption. The objective of this study was to present the analysis of inner-colonic microbiota obtained non-invasively during the lavage and how these results differ from stool samples. The inner-colonic samples represented the descending, transverse, and ascending colon. All samples were analyzed for 16S rRNA and shotgun metagenomic sequences. The taxonomic, phylogenetic, and biosynthetic gene cluster analyses showed a distinctive biogeographic gradient and revealed differences between the sample types, especially in the proximal colon. The high percentage of unique information found only in the inner-colonic effluent highlights the importance of these samples and likewise the importance of collecting them using a method that can preserve these distinctive signatures. We proposed that these samples are imperative for developing future biomarkers, targeted therapeutics, and personalized medicine.
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Diluted Fecal Community Transplant Restores Clostridioides difficile Colonization Resistance to Antibiotic-Perturbed Murine Communities. mBio 2022; 13:e0136422. [PMID: 35913161 PMCID: PMC9426422 DOI: 10.1128/mbio.01364-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fecal communities transplanted into individuals can eliminate recurrent Clostridioides difficile infection (CDI) with high efficacy. However, this treatment is only used once CDI becomes resistant to antibiotics or has recurred multiple times. We sought to investigate whether a fecal community transplant (FCT) pretreatment could be used to prevent CDI altogether. We treated male C57BL/6 mice with either clindamycin, cefoperazone, or streptomycin and then inoculated them with the microbial community from untreated mice before challenge with C. difficile. We measured colonization and sequenced the V4 region of the 16S rRNA gene to understand the dynamics of the murine fecal community in response to the FCT and C. difficile challenge. Clindamycin-treated mice became colonized with C. difficile but cleared it naturally and did not benefit from the FCT. Cefoperazone-treated mice became colonized by C. difficile, but the FCT enabled clearance of C. difficile. In streptomycin-treated mice, the FCT was able to prevent C. difficile from colonizing. We then diluted the FCT and repeated the experiments. Cefoperazone-treated mice no longer cleared C. difficile. However, streptomycin-treated mice colonized with 1:102 dilutions resisted C. difficile colonization. Streptomycin-treated mice that received an FCT diluted 1:103 became colonized with C. difficile but later cleared the infection. In streptomycin-treated mice, inhibition of C. difficile was associated with increased relative abundance of a group of bacteria related to Porphyromonadaceae and Lachnospiraceae. These data demonstrate that C. difficile colonization resistance can be restored to a susceptible community with an FCT as long as it complements the missing populations.
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Shute A, Bihan DG, Lewis IA, Nasser Y. Metabolomics: The Key to Unraveling the Role of the Microbiome in Visceral Pain Neurotransmission. Front Neurosci 2022; 16:917197. [PMID: 35812241 PMCID: PMC9260117 DOI: 10.3389/fnins.2022.917197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/30/2022] [Indexed: 11/29/2022] Open
Abstract
Inflammatory bowel disease (IBD), comprising Crohn’s disease and Ulcerative colitis, is a relapsing and remitting disease of the gastrointestinal tract, presenting with chronic inflammation, ulceration, gastrointestinal bleeding, and abdominal pain. Up to 80% of patients suffering from IBD experience acute pain, which dissipates when the underlying inflammation and tissue damage resolves. However, despite achieving endoscopic remission with no signs of ongoing intestinal inflammation or damage, 30–50% of IBD patients in remission experience chronic abdominal pain, suggesting altered sensory neuronal processing in this disorder. Furthermore, effective treatment for chronic pain is limited such that 5–25% of IBD outpatients are treated with narcotics, with associated morbidity and mortality. IBD patients commonly present with substantial alterations to the microbial community structure within the gastrointestinal tract, known as dysbiosis. The same is also true in irritable bowel syndrome (IBS), a chronic disorder characterized by altered bowel habits and abdominal pain, in the absence of inflammation. An emerging body of literature suggests that the gut microbiome plays an important role in visceral hypersensitivity. Specific microbial metabolites have an intimate relationship with host receptors that are highly expressed on host cell and neurons, suggesting that microbial metabolites play a key role in visceral hypersensitivity. In this review, we will discuss the techniques used to analysis the metabolome, current potential metabolite targets for visceral hypersensitivity, and discuss the current literature that evaluates the role of the post-inflammatory microbiota and metabolites in visceral hypersensitivity.
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Affiliation(s)
- Adam Shute
- Department of Medicine, Cumming School of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - Dominique G. Bihan
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Ian A. Lewis
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Yasmin Nasser
- Department of Medicine, Cumming School of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
- *Correspondence: Yasmin Nasser,
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Katsaounou K, Nicolaou E, Vogazianos P, Brown C, Stavrou M, Teloni S, Hatzis P, Agapiou A, Fragkou E, Tsiaoussis G, Potamitis G, Zaravinos A, Andreou C, Antoniades A, Shiammas C, Apidianakis Y. Colon Cancer: From Epidemiology to Prevention. Metabolites 2022; 12:metabo12060499. [PMID: 35736432 PMCID: PMC9229931 DOI: 10.3390/metabo12060499] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 02/01/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most prevalent cancers affecting humans, with a complex genetic and environmental aetiology. Unlike cancers with known environmental, heritable, or sex-linked causes, sporadic CRC is hard to foresee and has no molecular biomarkers of risk in clinical use. One in twenty CRC cases presents with an established heritable component. The remaining cases are sporadic and associated with partially obscure genetic, epigenetic, regenerative, microbiological, dietary, and lifestyle factors. To tackle this complexity, we should improve the practice of colonoscopy, which is recommended uniformly beyond a certain age, to include an assessment of biomarkers indicative of individual CRC risk. Ideally, such biomarkers will be causal to the disease and potentially modifiable upon dietary or therapeutic interventions. Multi-omics analysis, including transcriptional, epigenetic as well as metagenomic, and metabolomic profiles, are urgently required to provide data for risk analyses. The aim of this article is to provide a perspective on the multifactorial derailment of homeostasis leading to the initiation of CRC, which may be explored via multi-omics and Gut-on-Chip analysis to identify much-needed predictive biomarkers.
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Affiliation(s)
- Kyriaki Katsaounou
- Department of Biological Sciences, University of Cyprus, Nicosia 2109, Cyprus; (K.K.); (S.T.)
| | | | - Paris Vogazianos
- Stremble Ventures Ltd., Limassol 4042, Cyprus; (P.V.); (C.B.); (A.A.)
| | - Cameron Brown
- Stremble Ventures Ltd., Limassol 4042, Cyprus; (P.V.); (C.B.); (A.A.)
| | - Marios Stavrou
- Department of Electrical and Computer Engineering, University of Cyprus, Nicosia 2109, Cyprus; (M.S.); (C.A.)
| | - Savvas Teloni
- Department of Biological Sciences, University of Cyprus, Nicosia 2109, Cyprus; (K.K.); (S.T.)
| | - Pantelis Hatzis
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, Vari 16672, Greece;
| | - Agapios Agapiou
- Department of Chemistry, University of Cyprus, Nicosia 2109, Cyprus;
| | | | | | | | - Apostolos Zaravinos
- Department of Life Sciences, European University Cyprus, Nicosia 1516, Cyprus;
- Basic and Translational Cancer Research Center, Nicosia 1516, Cyprus
| | - Chrysafis Andreou
- Department of Electrical and Computer Engineering, University of Cyprus, Nicosia 2109, Cyprus; (M.S.); (C.A.)
| | - Athos Antoniades
- Stremble Ventures Ltd., Limassol 4042, Cyprus; (P.V.); (C.B.); (A.A.)
| | | | - Yiorgos Apidianakis
- Department of Biological Sciences, University of Cyprus, Nicosia 2109, Cyprus; (K.K.); (S.T.)
- Correspondence:
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Giovannucci E. Molecular Biologic and Epidemiologic Insights for Preventability of Colorectal Cancer. J Natl Cancer Inst 2022; 114:645-650. [PMID: 34978574 PMCID: PMC9086743 DOI: 10.1093/jnci/djab229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/30/2021] [Accepted: 12/16/2021] [Indexed: 11/12/2022] Open
Abstract
The etiology of colorectal cancer (CRC) has been informed from both a molecular biology perspective, which concerns the study of the nature, timing, and consequences of mutations in driver genes, and epidemiology, which focuses on identifying risk factors for cancer. For the most part, these fields have developed independently, and it is thus important to consider them in a more integrated manner. The molecular mutational perspective has stressed the importance of mutations due to replication of adult stem cells, and the molecular fingerprint of most CRCs does not suggest the importance of direct carcinogens. Epidemiology has identified numerous modifiable risk factors that account for most CRCs, most of which are not direct mutagens. The distribution of CRCs across the large bowel is not uniform, which is possibly caused by regional differences in the microbiota. Some risk factors are likely to act through or interact with the microbiota. The mutational perspective informs when risk factors may begin to operate in life and when they may cease to operate. Evidence from the mutational model and epidemiology supports that CRC risk factors begin early in life and may contribute to the risk of early-onset CRC. Later in carcinogenesis, there may be a "point of no return" when sufficient mutations have accumulated, and some risk factors do not affect cancer risk. This period may be at least 5-15 years for some risk factors. A more precise knowledge of timing of risk factor to cancer is required to inform preventive efforts.
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Affiliation(s)
- Edward Giovannucci
- Correspondence to: Edward Giovannucci, ScD, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA 02115, USA (e-mail: )
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13
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Eisenhofer R, D’Agnese E, Taggart D, Carver S, Penrose B. Microbial biogeography of the wombat gastrointestinal tract. PeerJ 2022; 10:e12982. [PMID: 35228910 PMCID: PMC8881912 DOI: 10.7717/peerj.12982] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/01/2022] [Indexed: 01/11/2023] Open
Abstract
Most herbivorous mammals have symbiotic microbes living in their gastrointestinal tracts that help with harvesting energy from recalcitrant plant fibre. The bulk of research into these microorganisms has focused on samples collected from faeces, representing the distal region of the gastrointestinal (GI) tract. However, the GI tract in herbivorous mammals is typically long and complex, containing different regions with distinct physico-chemical properties that can structure resident microbial communities. Little work has been done to document GI microbial communities of herbivorous animals at these sites. In this study, we use 16S rRNA gene sequencing to characterize the microbial biogeography along the GI tract in two species of wombats. Specifically, we survey the microbes along four major gut regions (stomach, small intestine, proximal colon, distal colon) in a single bare-nosed wombat (Vombatus ursinus) and a single southern hairy-nosed wombat (Lasiorhinus latifrons). Our preliminary results show that GI microbial communities of wombats are structured by GI region. For both wombat individuals, we observed a trend of increasing microbial diversity from stomach to distal colon. The microbial composition in the first proximal colon region was more similar between wombat species than the corresponding distal colon region in the same species. We found several microbial genera that were differentially abundant between the first proximal colon (putative site for primary plant fermentation) and distal colon regions (which resemble faecal samples). Surprisingly, only 10.6% (98) and 18.8% (206) of amplicon sequence variants (ASVs) were shared between the first proximal colon region and the distal colon region for the bare-nosed and southern hairy-nosed wombat, respectively. These results suggest that microbial communities in the first proximal colon region-the putative site of primary plant fermentation in wombats-are distinct from the distal colon, and that faecal samples may have limitations in capturing the diversity of these communities. While faeces are still a valuable and effective means of characterising the distal colon microbiota, future work seeking to better understand how GI microbiota impact the energy economy of wombats (and potentially other hindgut-fermenting mammals) may need to take gut biogeography into account.
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Affiliation(s)
- Raphael Eisenhofer
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia
| | - Erin D’Agnese
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia,School of Marine and Environmental Affairs, University of Washington, Seattle, WA, United States of America
| | - David Taggart
- School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, South Australia, Australia,FAUNA Research Alliance, Institute for Land, Water and Society, Kahibah, New South Wales, Australia
| | - Scott Carver
- Department of Biological Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Beth Penrose
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
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14
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Chikina AS, Matic Vignjevic D, Lennon-Dumenil AM. Roles of the macrophages in colon homeostasis. C R Biol 2021; 344:337-356. [DOI: 10.5802/crbiol.67] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 11/24/2022]
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15
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Saa P, Urrutia A, Silva-Andrade C, Martín AJ, Garrido D. Modeling approaches for probing cross-feeding interactions in the human gut microbiome. Comput Struct Biotechnol J 2021; 20:79-89. [PMID: 34976313 PMCID: PMC8685919 DOI: 10.1016/j.csbj.2021.12.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/03/2021] [Accepted: 12/04/2021] [Indexed: 12/16/2022] Open
Abstract
Microbial communities perform emergent activities that are essentially different from those carried by their individual members. The gut microbiome and its metabolites have a significant impact on the host, contributing to homeostasis or disease. Food molecules shape this community, being fermented through cross-feeding interactions of metabolites such as lactate, acetate, and amino acids, or products derived from macromolecule degradation. Mathematical and experimental approaches have been applied to understand and predict the interactions between microorganisms in complex communities such as the gut microbiota. Rational and mechanistic understanding of microbial interactions is essential to exploit their metabolic activities and identify keystone taxa and metabolites. The latter could be used in turn to modulate or replicate the metabolic behavior of the community in different contexts. This review aims to highlight recent experimental and modeling approaches for studying cross-feeding interactions within the gut microbiome. We focus on short-chain fatty acid production and fiber fermentation, which are fundamental processes in human health and disease. Special attention is paid to modeling approaches, particularly kinetic and genome-scale stoichiometric models of metabolism, to integrate experimental data under different diet and health conditions. Finally, we discuss limitations and challenges for the broad application of these modeling approaches and their experimental verification for improving our understanding of the mechanisms of microbial interactions.
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Affiliation(s)
- Pedro Saa
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute for Mathematical and Computational Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna, 4860 Santiago, Chile
| | - Arles Urrutia
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Claudia Silva-Andrade
- Laboratorio de Biología de Redes, Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Alberto J. Martín
- Laboratorio de Biología de Redes, Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
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16
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Turjeman S, Koren O. ARGuing the case for (or against) probiotics. Trends Microbiol 2021; 29:959-960. [PMID: 34563432 DOI: 10.1016/j.tim.2021.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/05/2021] [Accepted: 09/10/2021] [Indexed: 11/17/2022]
Abstract
Antibiotic resistance is one of the leading medical challenges with which we are currently faced. Antibiotics, while powerful medical tools, also wreak havoc on the endogenous microbiota. Many believe that probiotics can restore the microbiota following antibiotic treatment and might even suppress the spread of antibiotic-resistance genes, but a recent study (Montassier et al.) suggests otherwise.
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Affiliation(s)
- Sondra Turjeman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel. @biu.ac.il
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17
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Pennycook JH, Scanlan PD. Ecological and Evolutionary responses to Antibiotic Treatment in the Human Gut Microbiota. FEMS Microbiol Rev 2021; 45:fuab018. [PMID: 33822937 PMCID: PMC8498795 DOI: 10.1093/femsre/fuab018] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/25/2021] [Indexed: 12/16/2022] Open
Abstract
The potential for antibiotics to affect the ecology and evolution of the human gut microbiota is well recognised and has wide-ranging implications for host health. Here, we review the findings of key studies that surveyed the human gut microbiota during antibiotic treatment. We find several broad patterns including the loss of diversity, disturbance of community composition, suppression of bacteria in the Actinobacteria phylum, amplification of bacteria in the Bacteroidetes phylum, and promotion of antibiotic resistance. Such changes to the microbiota were often, but not always, recovered following the end of treatment. However, many studies reported unique and/or contradictory results, which highlights our inability to meaningfully predict or explain the effects of antibiotic treatment on the human gut microbiome. This problem arises from variation between existing studies in three major categories: differences in dose, class and combinations of antibiotic treatments used; differences in demographics, lifestyles, and locations of subjects; and differences in measurements, analyses and reporting styles used by researchers. To overcome this, we suggest two integrated approaches: (i) a top-down approach focused on building predictive models through large sample sizes, deep metagenomic sequencing, and effective collaboration; and (ii) a bottom-up reductionist approach focused on testing hypotheses using model systems.
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Affiliation(s)
- Joseph Hugh Pennycook
- APC Microbiome Ireland, Biosciences Institute, University College Cork, College Road, Cork, T12 YT20, Ireland
- School of Mirobiology, Food Science & Technology Building, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | - Pauline Deirdre Scanlan
- APC Microbiome Ireland, Biosciences Institute, University College Cork, College Road, Cork, T12 YT20, Ireland
- School of Mirobiology, Food Science & Technology Building, University College Cork, College Road, Cork, T12 K8AF, Ireland
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18
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Association of Fusobacterium nucleatum infection and colorectal cancer: A Mexican study. REVISTA DE GASTROENTEROLOGÍA DE MÉXICO 2021; 87:277-284. [PMID: 34312118 DOI: 10.1016/j.rgmxen.2021.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/09/2020] [Indexed: 12/26/2022]
Abstract
INTRODUCTION AND AIMS Colorectal cancer (CRC) is the third most prevalent cancer worldwide. Many risk factors are involved, and current evidence links the gut microbiota and colorectal carcinogenesis. Fusobacterium nucleatum (F. nucleatum) is proposed as one of the risk factors at the onset and during the progression of CRC, due to immune system and inflammatory modulation. MATERIALS AND METHODS Ninety samples from three different regions of the colon were collected through colonoscopy in patients with CRC, and qPCR TagMan® was conducted to detect F. nucleatum and cytokines (IL-17, IL-23, and IL-10) in tumor, peritumor, and normal samples. The differences between them were analyzed and correlated. RESULTS The abundance of F. nucleatum determined through the 2-ΔΔCt method in CRC (7.750 [5.790-10.469]) was significantly higher than in the normal control (0.409 [0.251-0.817]) (p < 0.05). There was no significant association between F. nucleatum and the cytokines (p > 0.05). CONCLUSIONS CRC is a heterogeneous disease that presents and progresses in a complex microenvironment, partially due to gut microbiome imbalance. F. nucleatum was enriched in CRC tissue, but whether that is a cause of the pathology or a consequence, has not yet been clearly defined.
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19
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Cuellar-Gómez H, Ocharán-Hernández ME, Calzada-Mendoza CC, Comoto-Santacruz DA. Association of Fusobacterium nucleatum infection and colorectal cancer: A Mexican study. REVISTA DE GASTROENTEROLOGIA DE MEXICO (ENGLISH) 2021; 87:S0375-0906(21)00035-5. [PMID: 34210555 DOI: 10.1016/j.rgmx.2020.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/19/2020] [Accepted: 12/09/2020] [Indexed: 12/24/2022]
Abstract
INTRODUCTION AND AIMS Colorectal cancer (CRC) is the third most prevalent cancer worldwide. Many risk factors are involved, and current evidence links the gut microbiota and colorectal carcinogenesis. Fusobacterium nucleatum is proposed as one of the risk factors at the onset and during the progression of CRC, due to immune system and inflammatory modulation. MATERIALS AND METHODS Ninety samples from three different regions of the colon were collected through colonoscopy in patients with CRC, and qPCR TagMan® was conducted to detect F. nucleatum and cytokines (IL-17, IL-23, and IL-10) in tumor, peritumor, and normal samples. The differences between them were analyzed and correlated. RESULTS The abundance of F. nucleatum determined through the 2-ΔΔCt method in CRC (7.750 [5.790-10.469]) was significantly higher than in the normal control (0.409 [0.251-0.817]) (p<0.05). There was no significant association between F. nucleatum and the cytokines (p>0.05). CONCLUSIONS CRC is a heterogeneous disease that presents and progresses in a complex microenvironment, partially due to gut microbiome imbalance. F. nucleatum was enriched in CRC tissue, but whether that is a cause of the pathology or a consequence, has not yet been clearly defined.
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Affiliation(s)
- H Cuellar-Gómez
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina Instituto Politécnico Nacional, Ciudad de México, CDMX, México
| | - M E Ocharán-Hernández
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina Instituto Politécnico Nacional, Ciudad de México, CDMX, México.
| | - C C Calzada-Mendoza
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina Instituto Politécnico Nacional, Ciudad de México, CDMX, México
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20
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Strobbe F, Bénard MV, Rossen NG, de Vos WM, Kumar N, Lawley TD, Zoetendal EG, Hugenholtz F, Ponsioen CY. A novel technique capable of taking 'protected' biopsies for reliable assessment of the distribution of microbiota along the colonic mucosa. J Microbiol Methods 2021; 185:106204. [PMID: 33872639 DOI: 10.1016/j.mimet.2021.106204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 02/24/2021] [Accepted: 03/13/2021] [Indexed: 11/18/2022]
Abstract
We evaluated a novel 'protected' biopsy method to reliably ascertain the spatial distribution of the mucosa-adherent colonic microbiota. Apart from minor differences at genus level, overall similarities along the colon were high between the various areas, irrespective of protected or unprotected sampling.
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Affiliation(s)
- Floortje Strobbe
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam Medical Center, Amsterdam, the Netherlands
| | - Mèlanie V Bénard
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam Medical Center, Amsterdam, the Netherlands
| | - Noortje G Rossen
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam Medical Center, Amsterdam, the Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands; Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Finland
| | - Nitin Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Sanger institute, Hinxton, United Kingdom
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger institute, Hinxton, United Kingdom
| | - Erwin G Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Floor Hugenholtz
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Amsterdam Medical Center, Amsterdam Infection & Immunity Institute, Amsterdam, the Netherlands
| | - Cyriel Y Ponsioen
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam Medical Center, Amsterdam, the Netherlands.
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21
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Čaja F, Stakheev D, Chernyavskiy O, Křížan J, Dvořák J, Rossmann P, Štěpánková R, Makovický P, Makovický P, Kozáková H, Vannucci L. Immune activation by microbiome shapes the colon mucosa: Comparison between healthy rat mucosa under conventional and germ-free conditions. J Immunotoxicol 2021; 18:37-49. [PMID: 33749490 DOI: 10.1080/1547691x.2021.1887412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Germ-free animals (GF) are those without a microbiome since birth. This particular biological model has become one of special interest with the growing evidence of importance of the microbiome in the life, development, adaptation, and immunity of humans and animals in the environments in which they live. Anatomical differences observed in GF compared with conventionally-reared animals (CV) has given rise to the question of the influence of commensal microflora on the development of structure and function (even immunological) of the bowel. Only recently, thanks to achievements in microscopy and associated methods, structural differences can be better evaluated and put in perspective with the immunological characteristics of GF vs. CV animals. This study, using a GF rat model, describes for the first time the possible influence that the presence of commensal microflora, continuously stimulating mucosal immunity, has on the collagen scaffold organization of the colon mucosa. Significant differences were found between CV and GF mucosa structure with higher complexity in the CV rats associated to a more activated immune environment. The immunological data suggest that, in response to the presence of a microbiome, an effective homeostatic regulation in developed by the CV rats in healthy conditions to avoid inflammation and maintain cytokine levels near the spontaneous production found in the GF animals. The results indicated that collagen scaffold adapted to the immune microenvironment; therefore, it is apparent that the microbiome was able to condition the structure of the colon mucosa.
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Affiliation(s)
- Fabián Čaja
- Laboratory of Immunotherapy, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.,Department of Cellular Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Dmitry Stakheev
- Laboratory of Immunotherapy, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Oleksander Chernyavskiy
- Department of Biomathematics, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Křížan
- Laboratory of Immunotherapy, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Dvořák
- Laboratory of Cellular and Molecular Immunology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Pavel Rossmann
- Laboratory of Cellular and Molecular Immunology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Renata Štěpánková
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Nový Hrádek, Czech Republic
| | - Peter Makovický
- Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Pavol Makovický
- Department of Biology, Faculty of Education, J. Selye University, Komárno, Slovakia
| | - Hana Kozáková
- Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Luca Vannucci
- Laboratory of Immunotherapy, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
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22
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Shanahan ER, McMaster JJ, Staudacher HM. Conducting research on diet-microbiome interactions: A review of current challenges, essential methodological principles, and recommendations for best practice in study design. J Hum Nutr Diet 2021; 34:631-644. [PMID: 33639033 DOI: 10.1111/jhn.12868] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/07/2021] [Accepted: 01/19/2021] [Indexed: 12/21/2022]
Abstract
Diet is one of the strongest modulators of the gut microbiome. However, the complexity of the interactions between diet and the microbial community emphasises the need for a robust study design and continued methodological development. This review aims to summarise considerations for conducting high-quality diet-microbiome research, outline key challenges unique to the field, and provide advice for addressing these in a practical manner useful to dietitians, microbiologists, gastroenterologists and other diet-microbiome researchers. Searches of databases and references from relevant articles were conducted using the primary search terms 'diet', 'diet intervention', 'dietary analysis', 'microbiome' and 'microbiota', alone or in combination. Publications were considered relevant if they addressed methods for diet and/or microbiome research, or were a human study relevant to diet-microbiome interactions. Best-practice design in diet-microbiome research requires appropriate consideration of the study population and careful choice of trial design and data collection methodology. Ongoing challenges include the collection of dietary data that accurately reflects intake at a timescale relevant to microbial community structure and metabolism, measurement of nutrients in foods pertinent to microbes, improving ability to measure and understand microbial metabolic and functional properties, adequately powering studies, and the considered analysis of multivariate compositional datasets. Collaboration across the disciplines of nutrition science and microbiology is crucial for high-quality diet-microbiome research. Improvements in our understanding of the interaction between nutrient intake and microbial metabolism, as well as continued methodological innovation, will facilitate development of effective evidence-based personalised dietary treatments.
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Affiliation(s)
- Erin R Shanahan
- School of Life and Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | | | - Heidi M Staudacher
- IMPACT (The Institute for Mental and Physical Health and Clinical Translation) Food & Mood Centre, Deakin University, Geelong, VIC, Australia
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23
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Fekete E, Allain T, Siddiq A, Sosnowski O, Buret AG. Giardia spp. and the Gut Microbiota: Dangerous Liaisons. Front Microbiol 2021; 11:618106. [PMID: 33510729 PMCID: PMC7835142 DOI: 10.3389/fmicb.2020.618106] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
Alteration of the intestinal microbiome by enteropathogens is commonly associated with gastrointestinal diseases and disorders and has far-reaching consequences for overall health. Significant advances have been made in understanding the role of microbial dysbiosis during intestinal infections, including infection with the protozoan parasite Giardia duodenalis, one of the most prevalent gut protozoa. Altered species composition and diversity, functional changes in the commensal microbiota, and changes to intestinal bacterial biofilm structure have all been demonstrated during the course of Giardia infection and have been implicated in Giardia pathogenesis. Conversely, the gut microbiota has been found to regulate parasite colonization and establishment and plays a critical role in immune modulation during mono and polymicrobial infections. These disruptions to the commensal microbiome may contribute to a number of acute, chronic, and post-infectious clinical manifestations of giardiasis and may account for variations in disease presentation within and between infected populations. This review discusses recent advances in characterizing Giardia-induced bacterial dysbiosis in the gut and the roles of dysbiosis in Giardia pathogenesis.
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Affiliation(s)
- Elena Fekete
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
- Inflammation Research Network, University of Calgary, Calgary, AB, Canada
- Host-Parasite Interactions, University of Calgary, Calgary, AB, Canada
| | - Thibault Allain
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
- Inflammation Research Network, University of Calgary, Calgary, AB, Canada
- Host-Parasite Interactions, University of Calgary, Calgary, AB, Canada
| | - Affan Siddiq
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
- Inflammation Research Network, University of Calgary, Calgary, AB, Canada
- Host-Parasite Interactions, University of Calgary, Calgary, AB, Canada
| | - Olivia Sosnowski
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
- Inflammation Research Network, University of Calgary, Calgary, AB, Canada
- Host-Parasite Interactions, University of Calgary, Calgary, AB, Canada
| | - Andre G. Buret
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
- Inflammation Research Network, University of Calgary, Calgary, AB, Canada
- Host-Parasite Interactions, University of Calgary, Calgary, AB, Canada
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24
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Song J, Li Y, Li J, Wang H, Zhang Y, Suo H. Lactobacillus rhamnosus 2016SWU.05.0601 regulates immune balance in ovalbumin-sensitized mice by modulating expression of the immune-related transcription factors and gut microbiota. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:4930-4939. [PMID: 32478427 DOI: 10.1002/jsfa.10554] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/13/2020] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Probiotics regulate host immune balance, which may reduce immune-related diseases. The effects and mechanisms of Lactobacillus rhamnosus 2016SWU.05.0601 (Lr-0601) on the immune response in ovalbumin (OVA)-sensitized mice were explored. RESULTS Lr-0601 reduced serum immunoglobulin (Ig)E and OVA-IgE and attenuated the alteration in lung pathology in OVA-sensitized mice. Lr-0601 blocked OVA-induced up-regulation in serum T helper (Th) 2 and Th17 cytokines but increased the serum levels of Th1 and regulatory T (Treg) cytokines in OVA-sensitized mice. OVA also markedly reduced the protein levels of spleen T-box transcription factor and forkhead/winged helix transcription factor p3, leading to the reduced mRNA expression of interferon-γ and interleukin (IL)-10. By contrast, OVA markedly increased the protein expression of spleen GATA-binding protein 3 and retinoid-related orphan receptor γt, as well as the mRNA expression of spleen IL-4 and IL-17. These changes induced by OVA were reversed by Lr-0601. Moreover, Lr-0601 helped alleviate OVA-induced intestinal microbiota dysbiosis. A correlation was found between specific genera and immune-associated cytokines. CONCLUSION The combined results indicate that Lr-0601 modulated the balance of Th1/Th2 and Treg/Th17 in OVA-sensitized mice, which was associated with the regulation of immune-related transcription factors and gut microbiota. Lr-0601 can potentially be used as a probiotic for preventing immune-related diseases. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Jiajia Song
- College of Food Science, Southwest University, Chongqing, China
| | - Yang Li
- College of Food Science, Southwest University, Chongqing, China
| | - Jian Li
- College of Life Science and Technology, Southwest Minzu University, Chengdu, China
| | - Hongwei Wang
- College of Food Science, Southwest University, Chongqing, China
| | - Yu Zhang
- College of Food Science, Southwest University, Chongqing, China
| | - Huayi Suo
- College of Food Science, Southwest University, Chongqing, China
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25
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Chikina AS, Nadalin F, Maurin M, San-Roman M, Thomas-Bonafos T, Li XV, Lameiras S, Baulande S, Henri S, Malissen B, Lacerda Mariano L, Barbazan J, Blander JM, Iliev ID, Matic Vignjevic D, Lennon-Duménil AM. Macrophages Maintain Epithelium Integrity by Limiting Fungal Product Absorption. Cell 2020; 183:411-428.e16. [PMID: 32970988 PMCID: PMC7646275 DOI: 10.1016/j.cell.2020.08.048] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/27/2020] [Accepted: 08/26/2020] [Indexed: 12/14/2022]
Abstract
The colon is primarily responsible for absorbing fluids. It contains a large number of microorganisms including fungi, which are enriched in its distal segment. The colonic mucosa must therefore tightly regulate fluid influx to control absorption of fungal metabolites, which can be toxic to epithelial cells and lead to barrier dysfunction. How this is achieved remains unknown. Here, we describe a mechanism by which the innate immune system allows rapid quality check of absorbed fluids to avoid intoxication of colonocytes. This mechanism relies on a population of distal colon macrophages that are equipped with "balloon-like" protrusions (BLPs) inserted in the epithelium, which sample absorbed fluids. In the absence of macrophages or BLPs, epithelial cells keep absorbing fluids containing fungal products, leading to their death and subsequent loss of epithelial barrier integrity. These results reveal an unexpected and essential role of macrophages in the maintenance of colon-microbiota interactions in homeostasis. VIDEO ABSTRACT.
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Affiliation(s)
- Aleksandra S Chikina
- Institut Curie, PSL Research University, CNRS UMR 144, F-75005 Paris, France; Institut Curie, PSL Research University, INSERM U932, F-75005 Paris, France
| | - Francesca Nadalin
- Institut Curie, PSL Research University, INSERM U932, F-75005 Paris, France
| | - Mathieu Maurin
- Institut Curie, PSL Research University, INSERM U932, F-75005 Paris, France
| | - Mabel San-Roman
- Institut Curie, PSL Research University, INSERM U932, F-75005 Paris, France
| | | | - Xin V Li
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Sonia Lameiras
- Institut Curie, PSL Research University, Next Generation Sequencing Facility, F-75005 Paris, France
| | - Sylvain Baulande
- Institut Curie, PSL Research University, Next Generation Sequencing Facility, F-75005 Paris, France
| | - Sandrine Henri
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Bernard Malissen
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France; Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | | | - Jorge Barbazan
- Institut Curie, PSL Research University, CNRS UMR 144, F-75005 Paris, France
| | - J Magarian Blander
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
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Jung Y, Tagele SB, Son H, Ibal JC, Kerfahi D, Yun H, Lee B, Park CY, Kim ES, Kim SJ, Shin JH. Modulation of Gut Microbiota in Korean Navy Trainees following a Healthy Lifestyle Change. Microorganisms 2020; 8:microorganisms8091265. [PMID: 32825401 PMCID: PMC7569816 DOI: 10.3390/microorganisms8091265] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/11/2020] [Accepted: 08/19/2020] [Indexed: 12/13/2022] Open
Abstract
Environmental factors can influence the composition of gut microbiota, but understanding the combined effect of lifestyle factors on adult gut microbiota is limited. Here, we investigated whether changes in the modifiable lifestyle factors, such as cigarette smoking, alcohol consumption, sleep duration, physical exercise, and body mass index affected the gut microbiota of Korean navy trainees. The navy trainees were instructed to stop smoking and alcohol consumption and follow a sleep schedule and physical exercise regime for eight weeks. For comparison, healthy Korean civilians, who had no significant change in lifestyles for eight weeks were included in this study. A total of 208 fecal samples were collected from navy trainees (n = 66) and civilians (n = 38) at baseline and week eight. Gut flora was assessed by sequencing the highly variable region of the 16S rRNA gene. The α-and β -diversity of gut flora of both the test and control groups were not significantly changed after eight weeks. However, there was a significant difference among individuals. Smoking had a significant impact in altering α-diversity. Our study showed that a healthy lifestyle, particularly cessation of smoking, even in short periods, can affect the gut microbiome by enhancing the abundance of beneficial taxa and reducing that of harmful taxa.
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Affiliation(s)
- YeonGyun Jung
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
| | - Setu Bazie Tagele
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
- Department of Applied Plant Sciences, University of Gondar, Gondar 196, Ethiopia
| | - HyunWoo Son
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
| | - Jerald Conrad Ibal
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
| | - Dorsaf Kerfahi
- Department of Biological Sciences, Keimyung University, Daegu 42601, Korea;
| | - Hyunju Yun
- Department of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea; (H.Y.); (B.L.); (C.Y.P.)
| | - Bora Lee
- Department of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea; (H.Y.); (B.L.); (C.Y.P.)
| | - Clara Yongjoo Park
- Department of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea; (H.Y.); (B.L.); (C.Y.P.)
| | - Eun Soo Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu 41944, Korea;
| | - Sang-Jun Kim
- Department of Natural Sciences, Republic of Korea Naval Academy, Changwon 51702, Korea;
| | - Jae-Ho Shin
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
- Correspondence: ; Tel.: +82-53-950-5716; Fax: +82-53-953-7233
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González-Mercado VJ, Henderson WA, Sarkar A, Lim J, Saligan LN, Berk L, Dishaw L, McMillan S, Groer M, Sepehri F, Melkus GD. Changes in Gut Microbiome Associated With Co-Occurring Symptoms Development During Chemo-Radiation for Rectal Cancer: A Proof of Concept Study. Biol Res Nurs 2020; 23:31-41. [PMID: 32700552 DOI: 10.1177/1099800420942830] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PURPOSE To examine a) whether there are significant differences in the severity of symptoms of fatigue, sleep disturbance, or depression between patients with rectal cancer who develop co-occurring symptoms and those with no symptoms before and at the end of chemotherapy and radiation therapy (CRT); b) differences in gut microbial diversity between those with co-occurring symptoms and those with no symptoms; and c) whether before-treatment diversity measurements and taxa abundances can predict co-occurrence of symptoms. METHODS Stool samples and symptom ratings were collected from 31 patients with rectal cancer prior to and at the end of (24-28 treatments) CRT. Descriptive statistics were computed and the Mann-Whitney U test was performed for symptoms. Gut microbiome data were analyzed using R's vegan package software. RESULTS Participants with co-occurring symptoms reported greater severity of fatigue at the end of CRT than those with no symptoms. Bacteroides and Blautia2 abundances differed between participants with co-occurring symptoms and those with no symptoms. Our random forest classification (unsupervised learning algorithm) predicted participants who developed co-occurring symptoms with 74% accuracy, using specific phylum, family, and genera abundances as predictors. CONCLUSION Our preliminary results point to an association between the gut microbiota and co-occurring symptoms in rectal cancer patients and serves as a first step in potential identification of a microbiota-based classifier.
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Affiliation(s)
- Velda J González-Mercado
- NYU Rory Meyers College of Nursing, New York, NY, USA.,College of Nursing, 7831University of South Florida, Tampa, FL, USA
| | | | - Anujit Sarkar
- College of Nursing and College of Public Health, 7831University of South Florida, Tampa, FL, USA
| | - Jean Lim
- 96722Rosenstiel School of Marine and Atmosphereic Science, University of Miami, FL, USA
| | - Leorey N Saligan
- Symptom Science Center, Symptom Biology Unit, Division of Intramural Research, NINR, NIH, DHHS, Bethesda, MD, USA
| | - Lawrence Berk
- College of Medicine Radiology, 7831University of South Florida, Tampa, FL, USA
| | - Larry Dishaw
- Department of Pediatrics, Molecular Genetics Children's Research Institute, 7831University of South Florida, St. Petersburg, FL, USA
| | - Susan McMillan
- College of Nursing, 7831University of South Florida, Tampa, FL, USA
| | - Maureen Groer
- College of Nursing, 7831University of South Florida, Tampa, FL, USA
| | - Farrah Sepehri
- College of Nursing, 7831University of South Florida, Tampa, FL, USA
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Wang L, Lo CH, He X, Hang D, Wang M, Wu K, Chan AT, Ogino S, Giovannucci EL, Song M. Risk Factor Profiles Differ for Cancers of Different Regions of the Colorectum. Gastroenterology 2020; 159:241-256.e13. [PMID: 32247020 PMCID: PMC7387153 DOI: 10.1053/j.gastro.2020.03.054] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/11/2020] [Accepted: 03/23/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND & AIMS The molecular features of colorectal tumors differ with their anatomic location. Colorectal tumors are usually classified as proximal or distal. We collected data from 3 cohorts to identify demographic, clinical, anthropometric, lifestyle, and dietary risk factors for colorectal cancer (CRC) at 7 anatomic subsites. We examined whether the associations differ among refined subsites and whether there are trends in associations from cecum to rectum. METHODS We collected data from the Nurses' Health Study, Nurses' Health Study 2, and Health Professionals Follow-up Study (45,351 men and 178,016 women, followed for a median 23 years) on 24 risk factors in relation to risk of cancer in cecum, ascending colon, transverse colon, descending colon, sigmoid colon, rectosigmoid junction, and rectum. Hazard ratios were estimated using Cox proportional hazards regression. We tested for linear and nonlinear trends in associations with CRC among subsites and within proximal colon, distal colon, and rectum. RESULTS We documented 3058 cases of CRC (474 in cecum, 633 in ascending colon, 250 in transverse colon, 221 in descending colon, 750 in sigmoid colon, 202 in rectosigmoid junction, and 528 in rectum). The positive associations with cancer risk decreased, from cecum to rectum, for age and family history of CRC. In contrast, the inverse associations with cancer risk increased, from cecum to rectum, for endoscopic screening and intake of whole grains, cereal fiber, and processed red meat. There was a significant nonlinear trend in the association between CRC and female sex, with hazard ratios ranging from 1.73 for ascending colon cancer to 0.54 for sigmoid colon cancer. For proximal colon cancers, the association with alcohol consumption and smoking before age 30 years increased from the cecum to transverse colon. For distal colon cancers, the positive association with waist circumference in men was greater for descending vs sigmoid colon cancer. CONCLUSIONS In an analysis of 3058 cases of CRC, we found that risk factor profiles differed for cancers along the colorectum. Proximal vs distal classifications are not sufficient to encompass the regional variations in colorectal tumor features and risk factors.
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Affiliation(s)
- Liang Wang
- Center of Gastrointestinal Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Chun-Han Lo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Xiaosheng He
- Department of Colorectal Surgery, the Six Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Dong Hang
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, P.R. China
| | - Molin Wang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kana Wu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Andrew T. Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA,Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edward L. Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Mingyang Song
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.
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Guilloux CA, Lamoureux C, Beauruelle C, Héry-Arnaud G. Porphyromonas: A neglected potential key genus in human microbiomes. Anaerobe 2020; 68:102230. [PMID: 32615270 DOI: 10.1016/j.anaerobe.2020.102230] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/11/2020] [Accepted: 06/14/2020] [Indexed: 01/16/2023]
Abstract
Anaerobes form a large part of microbial communities, and have begun to be specifically studied in both healthy and pathologic contexts. Porphyromonas is one of the top ten anaerobic taxa in the microbiome (anaerobiome) in healthy subjects. However, to date, most studies focused on the deleterious role of P. gingivalis, the most widely described species. Interestingly, targeted metagenomics reveals Porphyromonas other than gingivalis (POTG), highlighting other species such as P. catoniae or P. pasteri as potential biomarkers in disease progression or pathogen colonization susceptibility. From the sparse data, it appears that the Porphyromonas genus may also be a relevant target of investigation in several pulmonary diseases. Moreover, deciphering cutaneous, gastric and oral microbiomes hint that Porphyromonas may be a genus of interest in non-pulmonary diseases. This review aims to summarize the major data on POTG and to report their impact on the various human microbiomes in different clinical states.
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Affiliation(s)
| | - Claudie Lamoureux
- Unité de Bactériologie, Pôle de Biologie-Pathologie, Centre Hospitalier Régional et Universitaire de Brest, Hôpital de la Cavale Blanche, Boulevard Tanguy Prigent, Brest, France.
| | - Clémence Beauruelle
- Univ Brest, Inserm, EFS, UMR, 1078, GGB, F-29200, Brest, France; Unité de Bactériologie, Pôle de Biologie-Pathologie, Centre Hospitalier Régional et Universitaire de Brest, Hôpital de la Cavale Blanche, Boulevard Tanguy Prigent, Brest, France.
| | - Geneviève Héry-Arnaud
- Univ Brest, Inserm, EFS, UMR, 1078, GGB, F-29200, Brest, France; Unité de Bactériologie, Pôle de Biologie-Pathologie, Centre Hospitalier Régional et Universitaire de Brest, Hôpital de la Cavale Blanche, Boulevard Tanguy Prigent, Brest, France.
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30
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Um CY, McCullough ML, Guinter MA, Campbell PT, Jacobs EJ, Gapstur SM. Coffee consumption and risk of colorectal cancer in the Cancer Prevention Study-II Nutrition Cohort. Cancer Epidemiol 2020; 67:101730. [PMID: 32526644 DOI: 10.1016/j.canep.2020.101730] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND The association between coffee consumption and colorectal cancer risk generally appears null, but recent evidence suggests that risk may vary by coffee type. We examined associations of caffeinated and decaffeinated coffee intake with colorectal cancer risk overall and with colon and rectum separately, among older U.S. men and women. METHODS In 1999, 47,010 men and 60,051 women with no previous diagnosis of cancer, aged 47-96 years, in the Cancer Prevention Study-II Nutrition Cohort completed a food frequency questionnaire that assessed caffeinated and decaffeinated coffee intake; consumption was updated in 2003. A total of 1829 colorectal cancer cases were verified through June 2015. Cox proportional hazards regression was used to estimate multivariable-adjusted hazard rate ratios (HRs) and 95% confidence intervals (CIs), adjusting for smoking history, alcohol, caffeinated/decaffeinated coffee intake (depending on the model), and other colorectal cancer risk factors. RESULTS Consumption of ≥2 cups/day of decaffeinated coffee, compared to no decaffeinated coffee, was associated with lower risk of overall colorectal cancer (HR = 0.82, 95% CI: 0.69-0.96, P-trend = 0.04), colon cancer (HR = 0.82, 95% CI: 0.69-0.99, P-trend = 0.05) and rectal cancer (HR = 0.63, 95% CI: 0.40-0.99, P-trend = 0.17). Consumption of ≥2 cups/day of caffeinated coffee was associated with higher risk of rectal cancer (HR = 1.37, 95% CI: 0.99-1.89, P-trend = 0.04), but not with colorectal or colon cancer. CONCLUSION In this prospective study, higher intake of decaffeinated coffee was associated with lower risk of colorectal, colon, and rectal cancers. Further study on associations of caffeinated and decaffeinated coffee with colorectal cancer risk by subsite is needed.
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Affiliation(s)
- Caroline Y Um
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, United States.
| | - Marjorie L McCullough
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, United States
| | - Mark A Guinter
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, United States
| | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, United States
| | - Eric J Jacobs
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, United States
| | - Susan M Gapstur
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, United States
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Hugerth LW, Andreasson A, Talley NJ, Forsberg AM, Kjellström L, Schmidt PT, Agreus L, Engstrand L. No distinct microbiome signature of irritable bowel syndrome found in a Swedish random population. Gut 2020; 69:1076-1084. [PMID: 31601615 PMCID: PMC7282555 DOI: 10.1136/gutjnl-2019-318717] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 09/11/2019] [Accepted: 09/16/2019] [Indexed: 12/14/2022]
Abstract
OBJECTIVE The ethiopathogenesis of irritable bowel syndrome (IBS) is unknown. While a link to the gut microbiome is postulated, the heterogeneity of the healthy gut makes it difficult to draw definitive conclusions. We aimed to describe the faecal and mucosa-associated microbiome (MAM) and health correlates on a community cohort of healthy and IBS individuals with no colonoscopic findings. DESIGN The PopCol study recruited a random sample of 3556 adults; 745 underwent colonoscopy. IBS was defined by Rome IV criteria and organic disease excluded. 16S rRNA gene sequencing was conducted on sigmoid biopsy samples from 376 representative individuals (63 IBS cases) and faecal samples from 185 individuals (32 IBS cases). RESULTS While sigmoid MAM was dominated by Lachnospiraceae, faeces presented a higher relative abundance of Ruminococcaceae. Microbial richness in MAM was linearly correlated to that in faeces from the same individual (R²=0.255, p<3E-11) as was diversity (R²=0.06, p=0.0022). MAM diversity decreased with increasing body mass index (BMI; Pearson's r=-0.1, p=0.08) and poorer self-rated health (r=-0.15, p=0.007), but no other health correlates. Faecal microbiome diversity was correlated to stool consistency (r=-0.16, p=0.043). Several taxonomic groups were correlated to age, BMI, depression and self-reported health, including Coprococcus catus associated with lower levels of depression (r=-0.003, p=0.00017). The degree of heterogeneity observed between IBS patients is higher than that observed between healthy individuals. CONCLUSIONS No distinct microbial signature was observed in IBS. Individuals presenting with low self-rated health or high BMI have lower gut microbiome richness.
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Affiliation(s)
- Luisa W Hugerth
- Center for Translational Microbiome Research, CTMR, Department of Microbiology, Tumour and Cell Biology (MTC), Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Anna Andreasson
- Stress Research Institute, Stockholm University, Stockholm, Sweden,Department of Medicine, Karolinska University Hospital, Solna, Sweden,Department of Psychology, Macquarie University, Sydney, New South Wales, Australia
| | - Nicholas J Talley
- Health, University of Newcastle, Callaghan, New South Wales, Australia
| | - Anna M Forsberg
- Department of Medicine, Karolinska University Hospital, Solna, Sweden
| | | | | | - Lars Agreus
- Center for Family and Community Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lars Engstrand
- Center for Translational Microbiome Research, CTMR, Department of Microbiology, Tumour and Cell Biology (MTC), Karolinska Institutet, Science for Life Laboratory, Solna, Sweden .,Bacteriology, Swedish Institute for Communicable Disease Control, Stockholm, Sweden
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Sun W, Wang L, Zhang Q, Dong Q. Microbial Biomarkers for Colorectal Cancer Identified with Random Forest Model. EXPLORATORY RESEARCH AND HYPOTHESIS IN MEDICINE 2020; 000:1-000. [DOI: 10.14218/erhm.2019.00026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Ternes D, Karta J, Tsenkova M, Wilmes P, Haan S, Letellier E. Microbiome in Colorectal Cancer: How to Get from Meta-omics to Mechanism? Trends Microbiol 2020; 28:401-423. [PMID: 32298617 DOI: 10.1016/j.tim.2020.01.001] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/20/2019] [Accepted: 01/10/2020] [Indexed: 02/07/2023]
Abstract
Mounting evidence from metagenomic analyses suggests that a state of pathological microbial imbalance or dysbiosis is prevalent in the gut of patients with colorectal cancer. Several bacterial taxa have been identified of which representative isolate cultures interact with human cancer cells in vitro and trigger disease pathways in animal models. However, how the complex interrelationships in dysbiotic communities may be involved in cancer pathogenesis remains a crucial question. Here, we provide a survey of current knowledge of the gut microbiome in colorectal cancer. Moving beyond observational studies, we outline new experimental approaches for gaining ecosystem-level mechanistic understanding of the gut microbiome's role in cancer pathogenesis.
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Affiliation(s)
- Dominik Ternes
- Molecular Disease Mechanisms Group, Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jessica Karta
- Molecular Disease Mechanisms Group, Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Mina Tsenkova
- Molecular Disease Mechanisms Group, Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Eco-Systems Biology group, Luxembourg Center for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Serge Haan
- Molecular Disease Mechanisms Group, Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Elisabeth Letellier
- Molecular Disease Mechanisms Group, Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
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Baxter BA, Parker KD, Nosler MJ, Rao S, Craig R, Seiler C, Ryan EP. Metabolite profile comparisons between ascending and descending colon tissue in healthy adults. World J Gastroenterol 2020; 26:335-352. [PMID: 31988593 PMCID: PMC6969882 DOI: 10.3748/wjg.v26.i3.335] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/11/2019] [Accepted: 12/22/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Obesity is a risk factor for colorectal cancer, yet metabolic distinctions between healthy right and left colon tissue, before cancer is diagnosed, remains largely unknown. This study compared right-ascending and left-descending colon tissue metabolomes to identify differences from the stool metabolome in normal weight, overweight, and obese adults.
AIM To examine right and left colon tissue metabolites according to body mass index that may serve as mechanistic targets for interventions and biomarkers for colon cancer risk.
METHODS Global, non-targeted metabolomics was applied to assess right-ascending and left-descending colon tissue collected from healthy adults undergoing screening colonoscopies to test the hypothesis that BMI differentially impacts colon tissue metabolite profiles. The colon tissue and stool metabolome of healthy adults (n = 24) was analyzed for metabolite signatures and metabolic pathway networks implicated in progression of colorectal cancer.
RESULTS Ascending and descending colon contained 504 host, food, and microbiota-derived metabolites from normal weight, overweight and obese adults grouped according to body mass index. Amino acids, lipids, and nucleotides were among the chemical types that further differentiated from the stool metabolite profiles. Normal weight adults had 46 significantly different metabolites between ascending and descending colon tissue locations, whereas there were 37 metabolite differences in overweight and 28 metabolite differences for obese adults (P < 0.05). Obese adults had trimethylamine N-oxide, endocannabinoids and monoacylglycerols with different relative abundances identified between ascending and descending colon. Primary and secondary bile acids, vitamins, and fatty acids also showed marked relative abundance differences in colon tissue from overweight/obese adults.
CONCLUSION There were metabolite profile differences between right-ascending and left-descending colon tissue in healthy adults. Colon lipids and other metabolites in obese and overweight adults were distinguished from normal weight participants and associated with gut inflammation, nutrient absorption, and products of microbiota metabolism.
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Affiliation(s)
- Bridget A Baxter
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Fort Collins, CO 80523, United States
| | - Kristopher D Parker
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Fort Collins, CO 80523, United States
| | - Michael J Nosler
- University of Colorado Health Gastroenterology Clinic, Fort Collins, CO 80524, United States
| | - Sangeeta Rao
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523, United States
| | - Rebecca Craig
- Harmony Surgery Center, Fort Collins, CO 80528, United States
| | - Catherine Seiler
- Director of Clinical Operations, Harmony Surgery Center, Fort Collins, CO 80523, United States
| | - Elizabeth P Ryan
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Fort Collins, CO 80523, United States
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Li S, Peppelenbosch MP, Smits R. Bacterial biofilms as a potential contributor to mucinous colorectal cancer formation. Biochim Biophys Acta Rev Cancer 2019; 1872:74-79. [DOI: 10.1016/j.bbcan.2019.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 05/31/2019] [Accepted: 05/31/2019] [Indexed: 02/07/2023]
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Seekatz AM, Schnizlein MK, Koenigsknecht MJ, Baker JR, Hasler WL, Bleske BE, Young VB, Sun D. Spatial and Temporal Analysis of the Stomach and Small-Intestinal Microbiota in Fasted Healthy Humans. mSphere 2019; 4:e00126-19. [PMID: 30867328 PMCID: PMC6416366 DOI: 10.1128/msphere.00126-19] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 02/23/2019] [Indexed: 02/07/2023] Open
Abstract
Although the microbiota in the proximal gastrointestinal (GI) tract have been implicated in health and disease, much about these microbes remains understudied compared to those in the distal GI tract. This study characterized the microbiota across multiple proximal GI sites over time in healthy individuals. As part of a study of the pharmacokinetics of oral mesalamine administration, healthy, fasted volunteers (n = 8; 10 observation periods total) were orally intubated with a four-lumen catheter with multiple aspiration ports. Samples were taken from stomach, duodenal, and multiple jejunal sites, sampling hourly (≤7 h) to measure mesalamine (administered at t = 0), pH, and 16S rRNA gene-based composition. We observed a predominance of Firmicutes across proximal GI sites, with significant variation compared to stool. The microbiota was more similar within individuals over time than between subjects, with the fecal microbiota being unique from that of the small intestine. The stomach and duodenal microbiota displayed highest intraindividual variability compared to jejunal sites, which were more stable across time. We observed significant correlations in the duodenal microbial composition with changes in pH; linear mixed models identified positive correlations with multiple Streptococcus operational taxonomic units (OTUs) and negative correlations with multiple Prevotella and Pasteurellaceae OTUs. Few OTUs correlated with mesalamine concentration. The stomach and duodenal microbiota exhibited greater compositional dynamics than the jejunum. Short-term fluctuations in the duodenal microbiota were correlated with pH. Given the unique characteristics and dynamics of the proximal GI tract microbiota, it is important to consider these local environments in health and disease states.IMPORTANCE The gut microbiota are linked to a variety of gastrointestinal diseases, including inflammatory bowel disease. Despite this importance, microbiota dynamics in the upper gastrointestinal tract are understudied. Our article seeks to understand what factors impact microbiota dynamics in the healthy human upper gut. We found that the upper gastrointestinal tract contains consistently prevalent bacterial OTUs that dominate the overall community. Microbiota variability is highest in the stomach and duodenum and correlates with pH.
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Affiliation(s)
- Anna M Seekatz
- Department of Internal Medicine, Division of Infectious Disease, University of Michigan, Ann Arbor, Michigan, USA
| | - Matthew K Schnizlein
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Mark J Koenigsknecht
- Department of Internal Medicine, Division of Infectious Disease, University of Michigan, Ann Arbor, Michigan, USA
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason R Baker
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan, USA
| | - William L Hasler
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Barry E Bleske
- Department of Pharmacy Practice and Administrative Sciences, University of New Mexico, Albuquerque, New Mexico, USA
| | - Vincent B Young
- Department of Internal Medicine, Division of Infectious Disease, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Duxin Sun
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
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The Developing Story of Predictive Biomarkers in Colorectal Cancer. J Pers Med 2019; 9:jpm9010012. [PMID: 30736475 PMCID: PMC6463186 DOI: 10.3390/jpm9010012] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/28/2019] [Accepted: 02/04/2019] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common malignancy worldwide. Surgery remains the most important treatment for non-metastatic CRC, and the administration of adjuvant chemotherapy depends mainly on the disease stage, which is still the strongest prognostic factor. A refined understanding of the genomics of CRC has recently been achieved thanks to the widespread use of next generation sequencing with potential future therapeutic implications. Microsatellite instability (MSI) has been suggested as a predictive marker for response to anti-programmed-cell-death protein 1 (PD-1) therapy in solid tumors, including CRC. It should be noted that not all cancers with MSI phenotype respond to anti-PD-1 immunotherapy, highlighting the urgent need for even better predictive biomarkers. Mitogen-Activated Protein Kinase (MAPK) pathway genes KRAS, NRAS, and BRAF represent important molecular targets and could serve as independent prognostic biomarkers in CRC, and identify those who potentially benefit from anti-epidermal growth factor receptor (EGFR) treatment. Emerging evidence has attributed a significant role to inflammatory markers including blood cell ratios in the prognosis and survival of CRC patients; these biomarkers can be easily assessed in routine blood exams and be used to identify high-risk patients or those more likely to benefit from chemotherapy, targeted therapies and potentially immunotherapy. Analysis of cell-free DNA (cfDNA), circulating tumor cells (CTC) and/or micro RNAs (miRNAs) could provide useful information for the early diagnosis of CRC, the identification of minimal residual disease and, the evaluation of the risk of recurrence in early CRC patients. Even the selection of patients suitable for the new targeted therapy is becoming possible with the use of predictive miRNA biomarkers. Finally, the development of treatment resistance with the emergence of chemo-resistance clones after treatment remains the most important challenge in the clinical practice. In this context it is crucial to identify potential biomarkers and therapeutic targets which could lead to development of new and more effective treatments.
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Abstract
PURPOSE OF REVIEW The recent rise of young individuals under age 50 with colorectal cancer (CRC) is a startling trend in need of greater focus and research. The etiology of young-onset CRC is unexplained as efforts to blame obesity or diabetes as causative factors are simplistic and inadequate. RECENT FINDINGS We describe the epidemiologic shifts of CRC incidence and mortality across age groups as well as the differences in clinicopathologic, molecular, treatment, and survival characteristics between young and older patients. Novel studies of the microbiome may elucidate bacterial causes of CRC carcinogenesis in younger individuals. Moving up the colonoscopy screening to age 45 in normal-risk individuals should prove beneficial in detecting more patients with early-onset CRC. We favor the development of risk-adaptive screening decision algorithms and flexible sigmoidoscopy screening at age 40 given the predilection for left-sided primaries in this age group. More awareness and attention to young-onset CRC will be critical to improve outcomes in this patient population.
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Affiliation(s)
- Benjamin A Weinberg
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 3800 Reservoir Road NW, Washington, D.C, 20007, USA.
| | - John L Marshall
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 3800 Reservoir Road NW, Washington, D.C, 20007, USA
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Sze MA, Schloss PD. Leveraging Existing 16S rRNA Gene Surveys To Identify Reproducible Biomarkers in Individuals with Colorectal Tumors. mBio 2018; 9:e00630-18. [PMID: 29871916 PMCID: PMC5989068 DOI: 10.1128/mbio.00630-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/10/2018] [Indexed: 12/20/2022] Open
Abstract
An increasing body of literature suggests that both individual and collections of bacteria are associated with the progression of colorectal cancer. As the number of studies investigating these associations increases and the number of subjects in each study increases, a meta-analysis to identify the associations that are the most predictive of disease progression is warranted. We analyzed previously published 16S rRNA gene sequencing data collected from feces and colon tissue. We quantified the odds ratios (ORs) for individual bacterial taxa that were associated with an individual having tumors relative to a normal colon. Among the fecal samples, there were no taxa that had significant ORs associated with adenoma and there were 8 taxa with significant ORs associated with carcinoma. Similarly, among the tissue samples, there were no taxa that had a significant OR associated with adenoma and there were 3 taxa with significant ORs associated with carcinoma. Among the significant ORs, the association between individual taxa and tumor diagnosis was equal to or below 7.11. Because individual taxa had limited association with tumor diagnosis, we trained Random Forest classification models using only the taxa that had significant ORs, using the entire collection of taxa found in each study, and using operational taxonomic units defined based on a 97% similarity threshold. All training approaches yielded similar classification success as measured using the area under the curve. The ability to correctly classify individuals with adenomas was poor, and the ability to classify individuals with carcinomas was considerably better using sequences from feces or tissue.IMPORTANCE Colorectal cancer is a significant and growing health problem in which animal models and epidemiological data suggest that the colonic microbiota have a role in tumorigenesis. These observations indicate that the colonic microbiota is a reservoir of biomarkers that may improve our ability to detect colonic tumors using noninvasive approaches. This meta-analysis identifies and validates a set of 8 bacterial taxa that can be used within a Random Forest modeling framework to differentiate individuals as having normal colons or carcinomas. When models trained using one data set were tested on other data sets, the models performed well. These results lend support to the use of fecal biomarkers for the detection of tumors. Furthermore, these biomarkers are plausible candidates for further mechanistic studies into the role of the gut microbiota in tumorigenesis.
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Affiliation(s)
- Marc A Sze
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Patrick D Schloss
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
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