1
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Zhao C, Chen F, Li Q, Zhang W, Peng L, Yue C. Causal relationship between oral microbiota and epilepsy risk: Evidence from Mendelian randomization analysis in East Asians. Epilepsia Open 2024. [PMID: 39382490 DOI: 10.1002/epi4.13074] [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: 08/19/2024] [Revised: 09/24/2024] [Accepted: 09/30/2024] [Indexed: 10/10/2024] Open
Abstract
OBJECTIVE Gut microbiota can traverse into the brain, activate the vagus nerve, and modulate immune responses and inflammatory processes, thereby influencing the onset of epileptic seizures. However, research on oral microbiota and epilepsy remains limited, and observational studies have been inconsistent. We aim to estimate the potential links between oral microbiota and epilepsy and elucidate which specific oral microbes may directly influence the pathogenesis of epilepsy. METHODS A two-sample MR analysis was conducted using genome-wide association study (GWAS) data specific to OM and epilepsy in East Asian individuals. Single nucleotide polymorphisms (SNPs) independent of confounders served as instrumental variables (IVs) to deduce causality. MR methodologies, including inverse variance weighted (IVW), MR-Egger, weighted median, and weighed mode methods, were utilized. Sensitivity analysis, including Cochrane's Q test, MR-Egger intercept test, and leave-one-out analysis, was applied to confirm the robustness of results. RESULTS Among the 3117 bacterial taxa examined, we observed that 14 OM, like s_Streptococcus_mitis, s_Streptococcus_pneumoniae, and s_Haemophilus, were positively associated with epilepsy, while 7 OM, like g_Fusobacterium and g_Aggregatibacter, were negatively related to epilepsy. The MR-Egger intercept suggested that no evidence of horizontal pleiotropy was observed (p > 0.05). The leave-one-out analysis validated the robustness of the results. SIGNIFICANCE This study underscores the effect of OM on epilepsy, suggesting potential mechanisms between the OM and epilepsy. Further investigation into the potential role of the OM is needed to enhance our in-depth understanding of the pathogenesis of epilepsy. PLAIN LANGUAGE SUMMARY Previous research has demonstrated that the microbiota may influence the onset of epileptic seizures. We applied 3117 oral microbiota from the newest publicly available database of East Asian populations. Mendelian randomization analysis was utilized to estimate the causal relationship between oral microbiota and epilepsy. Our results showed that a causal effect exists between 21 oral microbiota and epilepsy. We provided genetic evidence for risk assessment and early intervention in epilepsy.
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Affiliation(s)
- Chenyang Zhao
- The First People's Hospital of Chenzhou, Chenzhou, China
- The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Fei Chen
- Huadong Hospital, Fudan University, Shanghai, China
| | - Qiong Li
- The First People's Hospital of Chenzhou, Chenzhou, China
- The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Wei Zhang
- The First People's Hospital of Chenzhou, Chenzhou, China
| | - Lixiu Peng
- The First People's Hospital of Chenzhou, Chenzhou, China
- The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Chaoyan Yue
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
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Hong BY, Chhaya A, Robles A, Cervantes J, Tiwari S. The role of Fusobacterium nucleatum in the pathogenesis of colon cancer. J Investig Med 2024:10815589241277829. [PMID: 39175147 DOI: 10.1177/10815589241277829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
Previously, many studies have reported changes in the gut microbiota of patients with colorectal cancer (CRC). While CRC is a well-described disease, the relationship between its development and features of the intestinal microbiome is still being understood. Evidence linking Fusobacterium nucleatum enrichment in colorectal tumor tissue has prompted the elucidation of various molecular mechanisms and tumor-promoting attributes. In this review we highlight various aspects of our understanding of the relationship between the development of CRC and the alteration of intestinal microbiome, focusing specifically on the role of F. nucleatum. As the amount of F. nucleatum DNA in CRC tissue is associated with shorter survival, it may potentially serve as a prognostic biomarker, and most importantly may open the door for a role in CRC treatment.
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Affiliation(s)
- Bo-Young Hong
- Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Ajay Chhaya
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Alejandro Robles
- Department of Internal Medicine, Division of Gastroenterology, Texas Tech University Health Sciences Center El Paso, El Paso, TX, USA
| | - Jorge Cervantes
- Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Sangeeta Tiwari
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
- Biomedical Research Center, University of Texas at El Paso, El Paso, TX, USA
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3
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Bystrom LT, Wolthers KR. New Electron-Transfer Chain to a Flavodiiron Protein in Fusobacterium nucleatum Couples Butyryl-CoA Oxidation to O 2 Reduction. Biochemistry 2024; 63:2352-2368. [PMID: 39206807 DOI: 10.1021/acs.biochem.4c00279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Fusobacterium nucleatum, a Gram-negative obligate anaerobe, is common to the oral microbiota, but the species is known to infect other sites of the body where it is associated with a range of pathologies. At present, little is known about the mechanisms by which F. nucleatum mitigates against oxidative and nitrosative stress. Inspection of the F. nucleatum subsp. polymorphum ATCC 10953 genome reveals that it encodes a flavodiiron protein (FDP; FNP2073) that is known in other organisms to reduce NO to N2O and/or O2 to H2O. FNP2073 is dicistronic with a gene encoding a multicomponent enzyme termed BCR for butyryl-CoA reductase. BCR is composed of a butyryl-CoA dehydrogenase domain (BCD), the C-terminal domain of the α-subunit of the electron-transfer flavoprotein (Etfα), and a rubredoxin domain. We show that BCR and the FDP form an α4β4 heterotetramic complex and use butyryl-CoA to selectively reduce O2 to H2O. The FAD associated with the Etfα domain (α-FAD) forms red anionic semiquinone (FAD•-), whereas the FAD present in the BCD domain (δ-FAD) forms the blue-neutral semiquinone (FADH•), indicating that both cofactors participate in one-electron transfers. This was confirmed in stopped-flow studies where the reduction of oxidized BCR with an excess of butyryl-CoA resulted in rapid (<1.6 ms) interflavin electron transfer evidenced by the formation of the FAD•-. Analysis of bacterial genomes revealed that the dicistron is present in obligate anaerobic gut bacteria considered to be beneficial by virtue of their ability to produce butyrate. Thus, BCR-FDP may help to maintain anaerobiosis in the colon.
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Affiliation(s)
- Liam T Bystrom
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna V1 V 1 V7, Canada
| | - Kirsten R Wolthers
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna V1 V 1 V7, Canada
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4
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Selvaraj A, McManus G, Healy CM, Moran GP. Fusobacterium nucleatum induces invasive growth and angiogenic responses in malignant oral keratinocytes that are cell line- and bacterial strain-specific. Front Cell Infect Microbiol 2024; 14:1417946. [PMID: 39286811 PMCID: PMC11402903 DOI: 10.3389/fcimb.2024.1417946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 08/13/2024] [Indexed: 09/19/2024] Open
Abstract
Fusobacterium nucleatum is an anaerobic commensal of the oral cavity recently reported to be associated with cancers of the gastrointestinal tract and oral squamous cell carcinoma (OSCC). In this study, we investigate the impact on oral keratinocytes of infection with a genetically diverse set of strains of F. nucleatum subsp. polymorphum recovered from patients with oral dysplasia (n=6). We employed H357 oral keratinocytes derived from a stage 1 OSCC and H376 cells derived from a stage 3 OSCC. Adhesion phenotypes were strain specific, with 3/6 clinical isolates examined exhibiting higher adherence to the stage 3 H376 cell line. Conversely, intracellular invasion was greatest in the H357 cells and was associated with specific transcriptional responses including autophagy and keratinization. Infection of both H357 and H376 cell lines induced transcriptional and cytokine responses linked to cancer cell migration and angiogenesis. F. nucleatum infection induced greater levels of MMP9 secretion in the H376 cell line which was associated with enhanced motility and invasion phenotypes. Additionally, the degree of F. nucleatum induced invasive growth by H376 cells varied between different clinical isolates of F. nucleatum subsp. polymorphum. Blockage of CCL5 signalling using the inhibitor metCCL5 resulted in reduced keratinocyte invasion. F. nucleatum infection also induced expression of the pro-angiogenic chemokine MCP-1 and the angiogenic growth factor VEGF-A resulting in increased capillary-like tube formation in HUVEC cells, most significantly in H376 cells. Treatment of HUVEC cells with resveratrol, a VEGF-A signalling inhibitor, significantly attenuated F. nucleatum induced tube formation. Our data indicate that the outcomes of F. nucleatum-oral cell interactions can vary greatly depending on the bacterial genotype and the malignant phenotype of the host cell.
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Affiliation(s)
- Ajith Selvaraj
- Division of Oral Biosciences, Dublin Dental University Hospital and School of Dental Science, Trinity College Dublin, Dublin, Ireland
| | - Gavin McManus
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Claire M Healy
- Division of Oral and Maxillofacial Surgery, Oral Medicine and Oral Pathology, Dublin Dental University Hospital and School of Dental Science, Trinity College Dublin, Dublin, Ireland
| | - Gary P Moran
- Division of Oral Biosciences, Dublin Dental University Hospital and School of Dental Science, Trinity College Dublin, Dublin, Ireland
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5
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Valadbeigi H, Khoshnood S, Negahdari B, Maleki A, Mohammadinejat M, Haddadi MH. Mixed oral biofilms are controlled by the interspecies interactions of Fusobacterium nucleatum. Oral Dis 2024; 30:3582-3590. [PMID: 38009960 DOI: 10.1111/odi.14822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/10/2023] [Accepted: 10/20/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND Fusobacterium nucleatum (F. nucleatum) is an integral component of supra- and subgingival biofilms, especially more prevalent in subgingival areas during both periodontal health and disease. AIMS In this review, we explore the physical, metabolic, and genetic interactions that influence the role of F. nucleatum in the formation of mixed oral biofilms. The role of F. nucleatum in antibiotic resistance in oral biofilms was discussed and some therapeutic strategies were proposed. METHODS PubMed, Scopus, Google Scholar, and the Web of Science were extensively searched for English-language reports. RESULTS F. nucleatum-derived proteins such as RadD, Fap2, FomA, and CmpA are involved in direct interactions contributing to biofilm formation, while autoinducer-2 and putrescine are involved in metabolic interactions. Both groups are essential for the formation and persistence of oral biofilms. This study highlights the clinical relevance of targeted interactions of F. nucleatum in supra- and subgingival oral biofilms. CONCLUSIONS By focusing on these interactions, researchers and clinicians can develop more effective strategies to prevent biofilm-related disease and reduce the spread of antibiotic resistance. Further research in this area is warranted to explore the potential therapeutic interventions that can be derived from understanding the interactions of F. nucleatum in oral biofilm dynamics.
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Affiliation(s)
- Hassan Valadbeigi
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Saeed Khoshnood
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Babak Negahdari
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Maleki
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Medya Mohammadinejat
- Department of Medicinal Chemistry, Faculty of Chemistry, North-Tehran Branch, Islamic Azad University, Tehran, Iran
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Chen L, Kang Z, Shen J, Zhao R, Miao Y, Zhang L, Zheng Z, Zhang Z, Liu N, Wang C, Fang H, Zhou J, Wang Y, Liu Z, Yang Y, Chen Q. An emerging antibacterial nanovaccine for enhanced chemotherapy by selectively eliminating tumor-colonizing bacteria. Sci Bull (Beijing) 2024; 69:2565-2579. [PMID: 38918142 DOI: 10.1016/j.scib.2024.06.016] [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: 10/12/2023] [Revised: 04/22/2024] [Accepted: 06/11/2024] [Indexed: 06/27/2024]
Abstract
Fusobacterium nucleatum (F. nucleatum), an oral anaerobe, is prevalent in colorectal cancer and is closely related to increased cancer cell growth, metastasis, and poor treatment outcomes. Bacterial vaccines capable of selectively eliminating bacteria present a promising approach to targeting intratumor F. nucleatum, thereby enhancing cancer treatment. Although adjuvants have been employed to enhance the immune response, the vaccine's effectiveness is constrained by inadequate T-cell activation necessary for eradicating intracellular pathogens. In this study, we developed a minimalistic, biomimetic nanovaccine by integrating highly immunostimulatory adjuvant cholesterol-modified CpG oligonucleotides into the autologously derived F. nucleatum membranes. Compared to the traditional vaccines consisting of inactivated bacteria and Alum adjuvant, the nanovaccine coupled with bacterial membranes and adjuvants could remarkably improve multiple antigens and adjuvant co-delivery to dendritic cells, maximizing their ability to achieve effective antigen presentation and strong downstream immune progress. Notably, the nanovaccine exhibits outstanding selective prophylactic and therapeutic effects, eliminating F. nucleatum without affecting intratumoral and gut microbiota. It significantly enhances chemotherapy efficacy and reduces cancer metastasis in F. nucleatum-infected colorectal cancer. Overall, this work represents the rational application of bacterial nanovaccine and provides a blueprint for future development in enhancing the antitumor effect against bacterial-infected cancer.
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Affiliation(s)
- Linfu Chen
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Zheyu Kang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Jingjing Shen
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Rui Zhao
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Yu Miao
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Lin Zhang
- Department of Gynecologic Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Zixuan Zheng
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Zhemin Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Nanhui Liu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Cheng Wang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Huapan Fang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Jun Zhou
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Yudong Wang
- Department of Gynecologic Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Zhuang Liu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Yang Yang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Qian Chen
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China.
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7
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Zepeda-Rivera MA, Eisele Y, Baryiames A, Wu H, Mengoni C, Piccinno G, McMahon EF, LaCourse KD, Jones DS, Hauner H, Minot SS, Segata N, Dewhirst FE, Johnston CD, Bullman S. Fusobacterium sphaericum sp. nov. , isolated from a human colon tumor, adheres to colonic epithelial cells and induces IL-8 secretion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.16.545380. [PMID: 37398369 PMCID: PMC10312772 DOI: 10.1101/2023.06.16.545380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Cancerous tissue is a largely unexplored microbial niche that provides a unique environment for the colonization and growth of specific bacterial communities, and with it, the opportunity to identify novel bacterial species. Here, we report distinct features of a novel Fusobacterium species, F. sphaericum sp. nov. ( Fs ), isolated from primary colon adenocarcinoma tissue. We acquire the complete closed genome and associated methylome of this organism and phylogenetically confirm its classification into the Fusobacterium genus, with F. perfoetens as its closest neighbor. Fs is phenotypically and genetically distinct, with morphological analysis revealing its coccoid shape, that while similar to F. perfoetens is rare for most Fusobacterium members. Fs displays a metabolic profile and antibiotic resistance repertoire consistent with other Fusobacterium species. In vitro, Fs has adherent and immunomodulatory capabilities, as it intimately associates with human colon cancer epithelial cells and promotes IL-8 secretion. Analysis of the prevalence and abundance of Fs in >20,000 human metagenomic samples shows that it is a low-prevalence member within human stool with variable relative abundance, found in both healthy controls and patients with colorectal cancer (CRC). Our study sheds light on a novel bacterial species isolated directly from the human CRC tumor niche, and given its interaction with cancer epithelial cells suggests that its role in human health and disease warrants further investigation.
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8
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Onyeaghala GC, Sharma S, Oyenuga M, Staley CM, Milne GL, Demmer RT, Shaukat A, Thyagarajan B, Straka RJ, Church TR, Prizment AE. The Effects of Aspirin Intervention on Inflammation-Associated Lingual Bacteria: A Pilot Study from a Randomized Clinical Trial. Microorganisms 2024; 12:1609. [PMID: 39203451 PMCID: PMC11357305 DOI: 10.3390/microorganisms12081609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 08/02/2024] [Accepted: 08/04/2024] [Indexed: 09/03/2024] Open
Abstract
Several bacterial taxa enriched in inflammatory bowel diseases and colorectal cancer (CRC) are found in the oral cavity. We conducted a pilot study nested within a six-week aspirin intervention in a randomized placebo-controlled trial to test their response to aspirin intervention. Fifty healthy subjects, 50-75 years old, were randomized to receive 325 mg aspirin (n = 30) or placebo (n = 20) orally once daily for six weeks. Oral tongue swabs were collected at baseline and week six. We estimated the association between aspirin use and the temporal changes in the relative abundance of pre-specified genus level taxa from pre- to post-treatment. The temporal change in relative abundance differed for eight genus level taxa between the aspirin and placebo groups. In the aspirin group, there were significant increases in the relative abundances of Neisseria, Streptococcus, Actinomyces, and Rothia and significant decreases in Prevotella, Veillonella, Fusobacterium, and Porphyromonas relative to placebo. The log ratio of Neisseria to Fusobacterium declined more in the aspirin group than placebo, signaling a potential marker associated with aspirin intervention. These preliminary findings should be validated using metagenomic sequencing and may guide future studies on the role of aspirin on taxa in various oral ecological niches.
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Affiliation(s)
- Guillaume C. Onyeaghala
- Division of Nephrology, Hennepin Healthcare, University of Minnesota, Minneapolis, MN 55415, USA;
| | - Shweta Sharma
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN 55455, USA; (S.S.); (B.T.)
| | - Mosunmoluwa Oyenuga
- Department of Internal Medicine, SSM Health St. Mary’s Hospital—St. Louis, St. Louis, MO 63117, USA;
| | - Christopher M. Staley
- Department of Surgery, Medical School, University of Minnesota, Minneapolis, MN 55455, USA;
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Ginger L. Milne
- Department of Medicine, Vanderbilt School of Medicine, Nashville, TN 37232, USA;
| | - Ryan T. Demmer
- Mayo Clinic College of Medicine & Sciences, Rochester, MN 55905, USA;
| | - Aasma Shaukat
- Department of Population Health, New York University Grossman School of Medicine, New York University, New York, NY 10016, USA;
| | - Bharat Thyagarajan
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN 55455, USA; (S.S.); (B.T.)
- Department of Laboratory Medicine & Pathology, Medical School, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert J. Straka
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Timothy R. Church
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA;
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Saint Paul, MN 55108, USA
| | - Anna E. Prizment
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN 55455, USA; (S.S.); (B.T.)
- Department of Laboratory Medicine & Pathology, Medical School, University of Minnesota, Minneapolis, MN 55455, USA
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González A, Fullaondo A, Odriozola A. Microbiota-associated mechanisms in colorectal cancer. ADVANCES IN GENETICS 2024; 112:123-205. [PMID: 39396836 DOI: 10.1016/bs.adgen.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
Abstract
Colorectal cancer (CRC) is one of the most common cancers worldwide, ranking third in terms of incidence and second as a cause of cancer-related death. There is growing scientific evidence that the gut microbiota plays a key role in the initiation and development of CRC. Specific bacterial species and complex microbial communities contribute directly to CRC pathogenesis by promoting the neoplastic transformation of intestinal epithelial cells or indirectly through their interaction with the host immune system. As a result, a protumoural and immunosuppressive environment is created conducive to CRC development. On the other hand, certain bacteria in the gut microbiota contribute to protection against CRC. In this chapter, we analysed the relationship of the gut microbiota to CRC and the associations identified with specific bacteria. Microbiota plays a key role in CRC through various mechanisms, such as increased intestinal permeability, inflammation and immune system dysregulation, biofilm formation, genotoxin production, virulence factors and oxidative stress. Exploring the interaction between gut microbiota and tumourigenesis is essential for developing innovative therapeutic approaches in the fight against CRC.
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Affiliation(s)
- Adriana González
- Hologenomics Research Group, Department of Genetics, Physical Anthropology, and Animal Physiology, University of the Basque Country, Spain.
| | - Asier Fullaondo
- Hologenomics Research Group, Department of Genetics, Physical Anthropology, and Animal Physiology, University of the Basque Country, Spain
| | - Adrian Odriozola
- Hologenomics Research Group, Department of Genetics, Physical Anthropology, and Animal Physiology, University of the Basque Country, Spain
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10
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Kunath BJ, De Rudder C, Laczny CC, Letellier E, Wilmes P. The oral-gut microbiome axis in health and disease. Nat Rev Microbiol 2024:10.1038/s41579-024-01075-5. [PMID: 39039286 DOI: 10.1038/s41579-024-01075-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2024] [Indexed: 07/24/2024]
Abstract
The human body hosts trillions of microorganisms throughout many diverse habitats with different physico-chemical characteristics. Among them, the oral cavity and the gut harbour some of the most dense and diverse microbial communities. Although these two sites are physiologically distinct, they are directly connected and can influence each other in several ways. For example, oral microorganisms can reach and colonize the gastrointestinal tract, particularly in the context of gut dysbiosis. However, the mechanisms of colonization and the role that the oral microbiome plays in causing or exacerbating diseases in other organs have not yet been fully elucidated. Here, we describe recent advances in our understanding of how the oral and intestinal microbiota interplay in relation to their impact on human health and disease.
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Affiliation(s)
- Benoit J Kunath
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| | - Charlotte De Rudder
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Cedric C Laczny
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Elisabeth Letellier
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Belvaux, Luxembourg.
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11
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Acharya S, Hegde U, Acharya AB, Nitin P. Dysbiosis linking periodontal disease and oral squamous cell carcinoma-A brief narrative review. Heliyon 2024; 10:e32259. [PMID: 38947439 PMCID: PMC11214465 DOI: 10.1016/j.heliyon.2024.e32259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 05/12/2024] [Accepted: 05/30/2024] [Indexed: 07/02/2024] Open
Abstract
An association between periodontal disease and oral squamous cell carcinoma (OSCC) has been recognized. However, there is no causal relationship between the two. The polymicrobial etiology of periodontal disease is confirmed, and so are the proven etiological factors for OSCC. Inflammation lies at the core of periodontal pathogenesis induced by the putative microbes. OSCC has inflammatory overtures in its pathobiology. Bacterial species involved in periodontal disease have been extensively documented and validated. The microbial profile in OSCC has been explored with no specific conclusions. The scientific reasoning to link a common microbial signature that connects periodontal disease to OSCC has led to many studies but has not provided conclusive evidence. Therefore, it would be beneficial to know the status of any plausible microbiota having a similarity in periodontal disease and OSCC. This brief review attempted to clarify the existence of a dysbiotic "fingerprint" that may link these two diseases. The review examined the literature with a focused objective of identifying periodontal microbial profiles in OSCC that could provide insights into pathogen commonality. The review concluded that there is great diversity in microbial association, but important bacterial species that correlate with periodontal disease and OSCC are forthcoming.
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Affiliation(s)
- Swetha Acharya
- Department of Oral Pathology, JSS Dental College and Hospital, JSS Academy of Higher Education and Research (JSSAHER), Mysuru, 570004, Karnataka, India
| | - Usha Hegde
- Department of Oral Pathology, JSS Dental College and Hospital, JSS Academy of Higher Education and Research (JSSAHER), Mysuru, 570004, Karnataka, India
| | - Anirudh B. Acharya
- Department of Preventive and Restorative Dentistry, College of Dental Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Priyanka Nitin
- Department of Oral Pathology, JSS Dental College and Hospital, JSS Academy of Higher Education and Research (JSSAHER), Mysuru, 570004, Karnataka, India
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12
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Zheng S, Deng R, Huang G, Ou Z, Shen Z. Effects of honokiol combined with resveratrol on bacteria responsible for oral malodor and their biofilm. J Oral Microbiol 2024; 16:2361402. [PMID: 38860120 PMCID: PMC11164056 DOI: 10.1080/20002297.2024.2361402] [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] [Received: 12/12/2023] [Accepted: 05/23/2024] [Indexed: 06/12/2024] Open
Abstract
Background This study aimed to investigate the effect of honokiol combined with resveratrol on bacteria responsible for oral malodor and their biofilm. Method This study investigated drug's MIC, FICI and dynamic bactericidal susceptibility activities against Pg and Fn. The effects of drugs on biofilm metabolic activity, biofilm total amount, and biofilm microstructure were determined by CCK-8 experiment, semi-quantitative adhesion experiment and SEM, respectively. The effects of drugs on biofilm genes, extracellular polysaccharides, proteins and DNA content were determined by qRT-PCR, phenol-sulfuric acid method, BCA method and Nano Drop one C, respectively. Results The combination had synergistic antibacterial effect on Pg and Fn. 1/2×MIC and 1×MIC combination inhibit the whole process of Pg and Fn growth. The results showed that the combination effectively reduce biofilm metabolic activity and total amount, and destroy biofilm microstructure. The results showed that the combination downregulate the gene expression both Pg and Fn, reduce extracellular polysaccharides and DNA of Pg, and reduce extracellular proteins and DNA of Fn. Conclusion This study showed that the combination had a synergistic antibacterial effect on Pg and Fn, reduced the biofilm extracellular matrix, inhibited biofilm formation, and downregulated the expression of genes related to biofilm formation.
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Affiliation(s)
- Shiqian Zheng
- Research and Development Department (R&D), Guangdong Botanical Beauty Care Biotechnology Co. Ltd., Guangzhou, China
| | - Rongrong Deng
- Research and Development Department (R&D), Guangdong Botanical Beauty Care Biotechnology Co. Ltd., Guangzhou, China
| | - Gengjiu Huang
- Research and Development Department (R&D), Guangdong Botanical Beauty Care Biotechnology Co. Ltd., Guangzhou, China
| | - Zhiwen Ou
- Research and Development Department (R&D), Guangdong Botanical Beauty Care Biotechnology Co. Ltd., Guangzhou, China
| | - Zhibin Shen
- Research and Development Department (R&D), Guangdong Botanical Beauty Care Biotechnology Co. Ltd., Guangzhou, China
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13
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Afonso AC, Simões M, Saavedra MJ, Simões L, Lema JM, Trueba-Santiso A. Exploring coaggregation mechanisms involved in biofilm formation in drinking water through a proteomic-based approach. J Appl Microbiol 2024; 135:lxae143. [PMID: 38877639 DOI: 10.1093/jambio/lxae143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/06/2024] [Accepted: 06/13/2024] [Indexed: 06/16/2024]
Abstract
AIM Coaggregation, a highly specific cell-cell interaction mechanism, plays a pivotal role in multispecies biofilm formation. While it has been mostly studied in oral environments, its occurrence in aquatic systems is also acknowledged. Considering biofilm formation's economic and health-related implications in engineered water systems, it is crucial to understand its mechanisms. Here, we hypothesized that traceable differences at the proteome level might determine coaggregation ability. METHODS AND RESULTS Two strains of Delftia acidovorans, isolated from drinking water were studied. First, in vitro motility assays indicated more swarming and twitching motility for the coaggregating strain (C+) than non-coaggregating strain (C-). By transmission electronic microscopy, we confirmed the presence of flagella for both strains. By proteomics, we detected a significantly higher expression of type IV pilus twitching motility proteins in C+, in line with the motility assays. Moreover, flagellum ring proteins were more abundant in C+, while those involved in the formation of the flagellar hook (FlE and FilG) were only detected in C-. All the results combined suggested structural and conformational differences between stains in their cell appendages. CONCLUSION This study presents an alternative approach for identifying protein biomarkers to detect coaggregation abilities in uncharacterized strains.
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Affiliation(s)
- Ana C Afonso
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal
- ALiCE-Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal
- CITAB, Department of Veterinary Sciences, University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal
- CEB-LABBELS, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Manuel Simões
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal
- ALiCE-Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal
| | - Maria José Saavedra
- CITAB, Department of Veterinary Sciences, University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal
| | - Lúcia Simões
- CEB-LABBELS, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Juan M Lema
- CRETUS, Department of Chemical Engineering, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Alba Trueba-Santiso
- CRETUS, Department of Chemical Engineering, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
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14
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Cai L, Zhu H, Mou Q, Wong PY, Lan L, Ng CWK, Lei P, Cheung MK, Wang D, Wong EWY, Lau EHL, Yeung ZWC, Lai R, Meehan K, Fung S, Chan KCA, Lui VWY, Cheng ASL, Yu J, Chan PKS, Chan JYK, Chen Z. Integrative analysis reveals associations between oral microbiota dysbiosis and host genetic and epigenetic aberrations in oral cavity squamous cell carcinoma. NPJ Biofilms Microbiomes 2024; 10:39. [PMID: 38589501 PMCID: PMC11001959 DOI: 10.1038/s41522-024-00511-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 03/27/2024] [Indexed: 04/10/2024] Open
Abstract
Dysbiosis of the human oral microbiota has been reported to be associated with oral cavity squamous cell carcinoma (OSCC) while the host-microbiota interactions with respect to the potential impact of pathogenic bacteria on host genomic and epigenomic abnormalities remain poorly studied. In this study, the mucosal bacterial community, host genome-wide transcriptome and DNA CpG methylation were simultaneously profiled in tumors and their adjacent normal tissues of OSCC patients. Significant enrichment in the relative abundance of seven bacteria species (Fusobacterium nucleatum, Treponema medium, Peptostreptococcus stomatis, Gemella morbillorum, Catonella morbi, Peptoanaerobacter yurli and Peptococcus simiae) were observed in OSCC tumor microenvironment. These tumor-enriched bacteria formed 254 positive correlations with 206 up-regulated host genes, mainly involving signaling pathways related to cell adhesion, migration and proliferation. Integrative analysis of bacteria-transcriptome and bacteria-methylation correlations identified at least 20 dysregulated host genes with inverted CpG methylation in their promoter regions associated with enrichment of bacterial pathogens, implying a potential of pathogenic bacteria to regulate gene expression, in part, through epigenetic alterations. An in vitro model further confirmed that Fusobacterium nucleatum might contribute to cellular invasion via crosstalk with E-cadherin/β-catenin signaling, TNFα/NF-κB pathway and extracellular matrix remodeling by up-regulating SNAI2 gene, a key transcription factor of epithelial-mesenchymal transition (EMT). Our work using multi-omics approaches explored complex host-microbiota interactions and provided important insights into genetic and functional basis in OSCC tumorigenesis, which may serve as a precursor for hypothesis-driven study to better understand the causational relationship of pathogenic bacteria in this deadly cancer.
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Affiliation(s)
- Liuyang Cai
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hengyan Zhu
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Qianqian Mou
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Po Yee Wong
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Linlin Lan
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Cherrie W K Ng
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Pu Lei
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Man Kit Cheung
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Daijuanru Wang
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Eddy W Y Wong
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Eric H L Lau
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zenon W C Yeung
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ronald Lai
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Katie Meehan
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Sherwood Fung
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kwan Chee A Chan
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Vivian W Y Lui
- Georgia Cancer Center, Augusta, GA, 30912, USA
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Alfred S L Cheng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jun Yu
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Paul K S Chan
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jason Y K Chan
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China.
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15
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Darbyshire AL, Wolthers KR. Characterization of a Structurally Distinct ATP-Dependent Reactivating Factor of Adenosylcobalamin-Dependent Lysine 5,6-Aminomutase. Biochemistry 2024; 63:913-925. [PMID: 38471967 DOI: 10.1021/acs.biochem.3c00653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Several anaerobic bacterial species, including the Gram-negative oral bacterium Fusobacterium nucleatum, ferment lysine to produce butyrate, acetate, and ammonia. The second step of the metabolic pathway─isomerization of β-l-lysine to erythro-3,5-diaminohexanoate─is catalyzed by the adenosylcobalamin (AdoCbl) and pyridoxal 5'-phosphate (PLP)-dependent enzyme, lysine 5,6-aminomutase (5,6-LAM). Similar to other AdoCbl-dependent enzymes, 5,6-LAM undergoes mechanism-based inactivation due to loss of the AdoCbl 5'-deoxyadenosyl moiety and oxidation of the cob(II)alamin intermediate to hydroxocob(III)alamin. Herein, we identified kamB and kamC, two genes responsible for ATP-dependent reactivation of 5,6-LAM. KamB and KamC, which are encoded upstream of the genes corresponding to α and β subunits of 5,6-LAM (kamD and kamE), co-purified following coexpression of the genes in Escherichia coli. KamBC exhibited a basal level of ATP-hydrolyzing activity that was increased 35% in a reaction mixture that facilitated 5,6-LAM turnover with β-l-lysine or d,l-lysine. Ultraviolet-visible (UV-vis) spectroscopic studies performed under anaerobic conditions revealed that KamBC in the presence of ATP/Mg2+ increased the steady-state concentration of the cob(II)alamin intermediate in the presence of excess β-l-lysine. Using a coupled UV-visible spectroscopic assay, we show that KamBC is able to reactivate 5,6-LAM through exchange of the damaged hydroxocob(III)alamin for AdoCbl. KamBC is also specific for 5,6-LAM as it had no effect on the rate of substrate-induced inactivation of the homologue, ornithine 4,5-aminomutase. Based on sequence homology, KamBC is structurally distinct from previously characterized B12 chaperones and reactivases, and correspondingly adds to the list of proteins that have evolved to maintain the cellular activity of B12 enzymes.
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Affiliation(s)
- Amanda L Darbyshire
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna V1V 1V7, Canada
| | - Kirsten R Wolthers
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna V1V 1V7, Canada
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16
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Zepeda-Rivera M, Minot SS, Bouzek H, Wu H, Blanco-Míguez A, Manghi P, Jones DS, LaCourse KD, Wu Y, McMahon EF, Park SN, Lim YK, Kempchinsky AG, Willis AD, Cotton SL, Yost SC, Sicinska E, Kook JK, Dewhirst FE, Segata N, Bullman S, Johnston CD. A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche. Nature 2024; 628:424-432. [PMID: 38509359 PMCID: PMC11006615 DOI: 10.1038/s41586-024-07182-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 02/08/2024] [Indexed: 03/22/2024]
Abstract
Fusobacterium nucleatum (Fn), a bacterium present in the human oral cavity and rarely found in the lower gastrointestinal tract of healthy individuals1, is enriched in human colorectal cancer (CRC) tumours2-5. High intratumoural Fn loads are associated with recurrence, metastases and poorer patient prognosis5-8. Here, to delineate Fn genetic factors facilitating tumour colonization, we generated closed genomes for 135 Fn strains; 80 oral strains from individuals without cancer and 55 unique cancer strains cultured from tumours from 51 patients with CRC. Pangenomic analyses identified 483 CRC-enriched genetic factors. Tumour-isolated strains predominantly belong to Fn subspecies animalis (Fna). However, genomic analyses reveal that Fna, considered a single subspecies, is instead composed of two distinct clades (Fna C1 and Fna C2). Of these, only Fna C2 dominates the CRC tumour niche. Inter-Fna analyses identified 195 Fna C2-associated genetic factors consistent with increased metabolic potential and colonization of the gastrointestinal tract. In support of this, Fna C2-treated mice had an increased number of intestinal adenomas and altered metabolites. Microbiome analysis of human tumour tissue from 116 patients with CRC demonstrated Fna C2 enrichment. Comparison of 62 paired specimens showed that only Fna C2 is tumour enriched compared to normal adjacent tissue. This was further supported by metagenomic analysis of stool samples from 627 patients with CRC and 619 healthy individuals. Collectively, our results identify the Fna clade bifurcation, show that specifically Fna C2 drives the reported Fn enrichment in human CRC and reveal the genetic underpinnings of pathoadaptation of Fna C2 to the CRC niche.
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Affiliation(s)
- Martha Zepeda-Rivera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Samuel S Minot
- Data Core, Shared Resources, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Heather Bouzek
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hanrui Wu
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Aitor Blanco-Míguez
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - Paolo Manghi
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - Dakota S Jones
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Ying Wu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Elsa F McMahon
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Soon-Nang Park
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Yun K Lim
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | | | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | | | - Ewa Sicinska
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Floyd E Dewhirst
- Forsyth Institute, Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Nicola Segata
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - Susan Bullman
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Christopher D Johnston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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17
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Hernández-Cabanyero C, Vonaesch P. Ectopic colonization by oral bacteria as an emerging theme in health and disease. FEMS Microbiol Rev 2024; 48:fuae012. [PMID: 38650052 PMCID: PMC11065354 DOI: 10.1093/femsre/fuae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/23/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024] Open
Abstract
The number of research papers published on the involvement of the oral microbiota in systemic diseases has grown exponentially over the last 4 years clearly demonstrating the growing interest in this field. Indeed, accumulating evidence highlights the central role of ectopic colonization by oral bacteria in numerous noncommunicable diseases including inflammatory bowel diseases (IBDs), undernutrition, preterm birth, neurological diseases, liver diseases, lung diseases, heart diseases, or colonic cancer. There is thus much interest in understanding the molecular mechanisms that lead to the colonization and maintenance of ectopic oral bacteria. The aim of this review is to summarize and conceptualize the current knowledge about ectopic colonization by oral bacteria, highlight wherever possible the underlying molecular mechanisms and describe its implication in health and disease. The focus lies on the newly discovered molecular mechanisms, showcasing shared pathophysiological mechanisms across different body sites and syndromes and highlighting open questions in the field regarding the pathway from oral microbiota dysbiosis to noncommunicable diseases.
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Affiliation(s)
- Carla Hernández-Cabanyero
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, UNIL-Sorge, 1015 Lausanne, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, UNIL-Sorge, 1015 Lausanne, Switzerland
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18
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Crowley C, Selvaraj A, Hariharan A, Healy CM, Moran GP. Fusobacterium nucleatum subsp. polymorphum recovered from malignant and potentially malignant oral disease exhibit heterogeneity in adhesion phenotypes and adhesin gene copy number, shaped by inter-subspecies horizontal gene transfer and recombination-derived mosaicism. Microb Genom 2024; 10:001217. [PMID: 38529905 PMCID: PMC10995627 DOI: 10.1099/mgen.0.001217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 02/29/2024] [Indexed: 03/27/2024] Open
Abstract
Fusobacterium nucleatum is an anaerobic commensal of the oral cavity associated with periodontitis and extra-oral diseases, including colorectal cancer. Previous studies have shown an increased relative abundance of this bacterium associated with oral dysplasia or within oral tumours. Using direct culture, we found that 75 % of Fusobacterium species isolated from malignant or potentially malignant oral mucosa were F. nucleatum subsp. polymorphum. Whole genome sequencing and pangenome analysis with Panaroo was carried out on 76 F. nucleatum subsp. polymorphum genomes. F. nucleatum subsp. polymorphum was shown to possesses a relatively small core genome of 1604 genes in a pangenome of 7363 genes. Phylogenetic analysis based on the core genome shows the isolates can be separated into three main clades with no obvious genotypic associations with disease. Isolates recovered from healthy and diseased sites in the same patient are generally highly related. A large repertoire of adhesins belonging to the type V secretion system (TVSS) could be identified with major variation in repertoire and copy number between strains. Analysis of intergenic recombination using fastGEAR showed that adhesin complement is shaped by horizontal gene transfer and recombination. Recombination events at TVSS adhesin genes were not only common between lineages of subspecies polymorphum, but also between different subspecies of F. nucleatum. Strains of subspecies polymorphum with low copy numbers of TVSS adhesin encoding genes tended to have the weakest adhesion to oral keratinocytes. This study highlights the genetic heterogeneity of F. nucleatum subsp. polymorphum and provides a new framework for defining virulence in this organism.
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Affiliation(s)
- Claire Crowley
- Division of Oral Biosciences, Dublin Dental University Hospital and School of Dental Science, Trinity College Dublin, Dublin, Ireland
| | - Ajith Selvaraj
- Division of Oral Biosciences, Dublin Dental University Hospital and School of Dental Science, Trinity College Dublin, Dublin, Ireland
| | - Arvind Hariharan
- Division of Oral Biosciences, Dublin Dental University Hospital and School of Dental Science, Trinity College Dublin, Dublin, Ireland
| | - Claire M. Healy
- Division of Oral and Maxillofacial Surgery, Oral Medicine and Oral Pathology, Dublin Dental University Hospital and School of Dental Science, Trinity College Dublin, Dublin, Ireland
| | - Gary P. Moran
- Division of Oral Biosciences, Dublin Dental University Hospital and School of Dental Science, Trinity College Dublin, Dublin, Ireland
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Xu J, Yu L, Ye S, Ye Z, Yang L, Xu X. Oral microbiota-host interaction: the chief culprit of alveolar bone resorption. Front Immunol 2024; 15:1254516. [PMID: 38455060 PMCID: PMC10918469 DOI: 10.3389/fimmu.2024.1254516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 02/02/2024] [Indexed: 03/09/2024] Open
Abstract
There exists a bidirectional relationship between oral health and general well-being, with an imbalance in oral symbiotic flora posing a threat to overall human health. Disruptions in the commensal flora can lead to oral diseases, while systemic illnesses can also impact the oral cavity, resulting in the development of oral diseases and disorders. Porphyromonas gingivalis and Fusobacterium nucleatum, known as pathogenic bacteria associated with periodontitis, play a crucial role in linking periodontitis to accompanying systemic diseases. In periodontal tissues, these bacteria, along with their virulence factors, can excessively activate the host immune system through local diffusion, lymphatic circulation, and blood transmission. This immune response disruption contributes to an imbalance in osteoimmune mechanisms, alveolar bone resorption, and potential systemic inflammation. To restore local homeostasis, a deeper understanding of microbiota-host interactions and the immune network phenotype in local tissues is imperative. Defining the immune network phenotype in periodontal tissues offers a promising avenue for investigating the complex characteristics of oral plaque biofilms and exploring the potential relationship between periodontitis and associated systemic diseases. This review aims to provide an overview of the mechanisms underlying Porphyromonas gingivalis- and Fusobacterium nucleatum-induced alveolar bone resorption, as well as the immunophenotypes observed in host periodontal tissues during pathological conditions.
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Affiliation(s)
- Jingyu Xu
- Department of Orthodontics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Ling Yu
- Department of Orthodontics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Surong Ye
- Department of Orthodontics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Zitong Ye
- Department of Orthodontics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Luyi Yang
- Department of Orthodontics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Xiaoxi Xu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
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20
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Zhou P, G. C. B, Stolte F, Wu C. Use of CRISPR interference for efficient and rapid gene inactivation in Fusobacterium nucleatum. Appl Environ Microbiol 2024; 90:e0166523. [PMID: 38185820 PMCID: PMC10880640 DOI: 10.1128/aem.01665-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
Gene inactivation by creating in-frame deletion mutations in Fusobacterium nucleatum is time consuming, and most fusobacterial strains are genetically intractable. Addressing these problems, we introduced a riboswitch-based inducible CRISPR interference (CRISPRi) system. This system employs the nuclease-inactive Streptococcus pyogenes Cas9 protein (dCas9), specifically guided to the gene of interest by a constantly expressed single-guide RNA (sgRNA). Mechanistically, this dCas9-sgRNA complex serves as an insurmountable roadblock for RNA polymerase, thus repressing the target gene transcription. Leveraging this system, we first examined two non-essential genes, ftsX and radD, which are pivotal for fusobacterial cytokinesis and coaggregation. Upon adding the inducer, theophylline, ftsX suppression caused filamentous cell formation akin to chromosomal ftsX deletion, while targeting radD significantly reduced RadD protein levels, abolishing RadD-mediated coaggregation. The system was then extended to probe essential genes bamA and ftsZ, which are vital for outer membrane biogenesis and cell division. Impressively, bamA suppression disrupted membrane integrity and bacterial separation, stalling growth, while ftsZ targeting yielded elongated cells in broth with compromised agar growth. Further studies on F. nucleatum clinical strain CTI-2 and Fusobacterium periodonticum revealed reduced indole synthesis when targeting tnaA. Moreover, silencing clpB in F. periodonticum decreased ClpB, increasing thermal sensitivity. In summary, our CRISPRi system streamlines gene inactivation across various fusobacterial strains.IMPORTANCEHow can we effectively investigate the gene functions in Fusobacterium nucleatum, given the dual challenges of gene inactivation and the inherent genetic resistance of many strains? Traditional methods have been cumbersome and often inadequate. Addressing this, our work introduces a novel inducible CRISPR interference (CRISPRi) system in which dCas9 expression is controlled at the translation level by a theophylline-responsive riboswitch unit, and single-guide RNA expression is driven by the robust, constitutive rpsJ promoter. This approach simplifies gene inactivation in the model organism (ATCC 23726) and extends its application to previously considered genetically intractable strains like CTI-2 and Fusobacterium periodonticum. With CRISPRi's potential, it is a pivotal tool for in-depth genetic studies into fusobacterial pathogenesis, potentially unlocking targeted therapeutic strategies.
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Affiliation(s)
- Peng Zhou
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
| | - Bibek G. C.
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
| | - Flynn Stolte
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
| | - Chenggang Wu
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
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21
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Jones J, Shi Q, Nath RR, Brito IL. Keystone pathobionts associated with colorectal cancer promote oncogenic reprograming. PLoS One 2024; 19:e0297897. [PMID: 38363784 PMCID: PMC10871517 DOI: 10.1371/journal.pone.0297897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 01/12/2024] [Indexed: 02/18/2024] Open
Abstract
Fusobacterium nucleatum (Fn) and enterotoxigenic Bacteroides fragilis (ETBF) are two pathobionts consistently enriched in the gut microbiomes of patients with colorectal cancer (CRC) compared to healthy counterparts and frequently observed for their direct association within tumors. Although several molecular mechanisms have been identified that directly link these organisms to features of CRC in specific cell types, their specific effects on the epithelium and local immune compartment are not well-understood. To fill this gap, we leveraged single-cell RNA sequencing (scRNA-seq) on wildtype mice and mouse model of CRC. We find that Fn and ETBF exacerbate cancer-like transcriptional phenotypes in transit-amplifying and mature enterocytes in a mouse model of CRC. We also observed increased T cells in the pathobiont-exposed mice, but these pathobiont-specific differences observed in wildtype mice were abrogated in the mouse model of CRC. Although there are similarities in the responses provoked by each organism, we find pathobiont-specific effects in Myc-signaling and fatty acid metabolism. These findings support a role for Fn and ETBF in potentiating tumorigenesis via the induction of a cancer stem cell-like transit-amplifying and enterocyte population and the disruption of CTL cytotoxic function.
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Affiliation(s)
- Josh Jones
- Meinig School for Biomedical Engineering, Cornell University, Ithaca, NY, United States of America
| | - Qiaojuan Shi
- Meinig School for Biomedical Engineering, Cornell University, Ithaca, NY, United States of America
| | - Rahul R. Nath
- Meinig School for Biomedical Engineering, Cornell University, Ithaca, NY, United States of America
| | - Ilana L. Brito
- Meinig School for Biomedical Engineering, Cornell University, Ithaca, NY, United States of America
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22
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El Tekle G, Andreeva N, Garrett WS. The Role of the Microbiome in the Etiopathogenesis of Colon Cancer. Annu Rev Physiol 2024; 86:453-478. [PMID: 38345904 DOI: 10.1146/annurev-physiol-042022-025619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Studies in preclinical models support that the gut microbiota play a critical role in the development and progression of colorectal cancer (CRC). Specific microbial species and their corresponding virulence factors or associated small molecules can contribute to CRC development and progression either via direct effects on the neoplastic transformation of epithelial cells or through interactions with the host immune system. Induction of DNA damage, activation of Wnt/β-catenin and NF-κB proinflammatory pathways, and alteration of the nutrient's availability and the metabolic activity of cancer cells are the main mechanisms by which the microbiota contribute to CRC. Within the tumor microenvironment, the gut microbiota alter the recruitment, activation, and function of various immune cells, such as T cells, macrophages, and dendritic cells. Additionally, the microbiota shape the function and composition of cancer-associated fibroblasts and extracellular matrix components, fashioning an immunosuppressive and pro-tumorigenic niche for CRC. Understanding the complex interplay between gut microbiota and tumorigenesis can provide therapeutic opportunities for the prevention and treatment of CRC.
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Affiliation(s)
- Geniver El Tekle
- Department of Immunology and Infectious Diseases and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA;
- The Harvard Chan Microbiome in Public Health Center, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
| | - Natalia Andreeva
- Department of Immunology and Infectious Diseases and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA;
- The Harvard Chan Microbiome in Public Health Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Wendy S Garrett
- Department of Immunology and Infectious Diseases and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA;
- The Harvard Chan Microbiome in Public Health Center, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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23
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Wang B, Deng J, Donati V, Merali N, Frampton AE, Giovannetti E, Deng D. The Roles and Interactions of Porphyromonas gingivalis and Fusobacterium nucleatum in Oral and Gastrointestinal Carcinogenesis: A Narrative Review. Pathogens 2024; 13:93. [PMID: 38276166 PMCID: PMC10820765 DOI: 10.3390/pathogens13010093] [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: 12/03/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
Epidemiological studies have spotlighted the intricate relationship between individual oral bacteria and tumor occurrence. Porphyromonas gingivalis and Fusobacteria nucleatum, which are known periodontal pathogens, have emerged as extensively studied participants with potential pathogenic abilities in carcinogenesis. However, the complex dynamics arising from interactions between these two pathogens were less addressed. This narrative review aims to summarize the current knowledge on the prevalence and mechanism implications of P. gingivalis and F. nucleatum in the carcinogenesis of oral squamous cell carcinoma (OSCC), colorectal cancer (CRC), and pancreatic ductal adenocarcinoma (PDAC). In particular, it explores the clinical and experimental evidence on the interplay between P. gingivalis and F. nucleatum in affecting oral and gastrointestinal carcinogenesis. P. gingivalis and F. nucleatum, which are recognized as keystone or bridging bacteria, were identified in multiple clinical studies simultaneously. The prevalence of both bacteria species correlated with cancer development progression, emphasizing the potential impact of the collaboration. Regrettably, there was insufficient experimental evidence to demonstrate the synergistic function. We further propose a hypothesis to elucidate the underlying mechanisms, offering a promising avenue for future research in this dynamic and evolving field.
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Affiliation(s)
- Bing Wang
- Department of Medical Oncology, Amsterdam University Medical Center, Cancer Center Amsterdam, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (B.W.); (J.D.); (V.D.); (E.G.)
| | - Juan Deng
- Department of Medical Oncology, Amsterdam University Medical Center, Cancer Center Amsterdam, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (B.W.); (J.D.); (V.D.); (E.G.)
| | - Valentina Donati
- Department of Medical Oncology, Amsterdam University Medical Center, Cancer Center Amsterdam, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (B.W.); (J.D.); (V.D.); (E.G.)
- Unit of Pathological Anatomy 2, Azienda Ospedaliero-Universitaria Pisana, 56100 Pisa, Italy
| | - Nabeel Merali
- Minimal Access Therapy Training Unit (MATTU), Royal Surrey County Hospital, NHS Foundation Trust, Egerton Road, Guildford GU2 7XX, UK; (N.M.); (A.E.F.)
- Department of Hepato-Pancreato-Biliary (HPB) Surgery, Royal Surrey County Hospital, NHS Foundation Trust, Egerton Road, Guildford GU2 7XX, UK
- Section of Oncology, Department of Clinical and Experimental Medicine, Faculty of Health Medical Science, University of Surrey, Guilford GU2 7WG, UK
| | - Adam E. Frampton
- Minimal Access Therapy Training Unit (MATTU), Royal Surrey County Hospital, NHS Foundation Trust, Egerton Road, Guildford GU2 7XX, UK; (N.M.); (A.E.F.)
- Department of Hepato-Pancreato-Biliary (HPB) Surgery, Royal Surrey County Hospital, NHS Foundation Trust, Egerton Road, Guildford GU2 7XX, UK
- Section of Oncology, Department of Clinical and Experimental Medicine, Faculty of Health Medical Science, University of Surrey, Guilford GU2 7WG, UK
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam University Medical Center, Cancer Center Amsterdam, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (B.W.); (J.D.); (V.D.); (E.G.)
- Fondazione Pisana per la Scienza, 56100 Pisa, Italy
| | - Dongmei Deng
- Department of Prevention Dentistry, Academic Center for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universitreit Amsterdam, 1081 LA Amsterdam, The Netherlands
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24
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Britton TA, Wu C, Chen YW, Franklin D, Chen Y, Camacho MI, Luong TT, Das A, Ton-That H. The respiratory enzyme complex Rnf is vital for metabolic adaptation and virulence in Fusobacterium nucleatum. mBio 2024; 15:e0175123. [PMID: 38059640 PMCID: PMC10790702 DOI: 10.1128/mbio.01751-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/20/2023] [Indexed: 12/08/2023] Open
Abstract
IMPORTANCE This paper illuminates the significant question of how the oral commensal Fusobacterium nucleatum adapts to the metabolically changing environments of several extra-oral sites such as placenta and colon to promote various diseases as an opportunistic pathogen. We demonstrate here that the highly conserved Rhodobacter nitrogen-fixation complex, commonly known as Rnf complex, is key to fusobacterial metabolic adaptation and virulence. Genetic disruption of this Rnf complex causes global defects in polymicrobial interaction, biofilm formation, cell growth and morphology, hydrogen sulfide production, and ATP synthesis. Targeted metabolomic profiling demonstrates that the loss of this respiratory enzyme significantly diminishes catabolism of numerous amino acids, which negatively impacts fusobacterial virulence as tested in a preterm birth model in mice.
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Affiliation(s)
- Timmie A. Britton
- Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Chenggang Wu
- Department of Microbiology & Molecular Genetics, University of Texas McGovern Medical School, Houston, Texas, USA
| | - Yi-Wei Chen
- Division of Oral & Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, California, USA
| | - Dana Franklin
- Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Yimin Chen
- Division of Oral & Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, California, USA
| | - Martha I. Camacho
- Division of Oral & Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, California, USA
| | - Truc T. Luong
- Division of Oral & Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, California, USA
| | - Asis Das
- Department of Medicine, Neag Comprehensive Cancer Center, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Hung Ton-That
- Molecular Biology Institute, University of California, Los Angeles, California, USA
- Division of Oral & Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, California, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, California, USA
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25
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Kvich L, Fritz BG, Zschach H, Terkelsen T, Raskov H, Høst-Rasmussen K, Jakobsen MR, Gheorghe AG, Gögenur I, Bjarnsholt T. Biofilms and core pathogens shape the tumor microenvironment and immune phenotype in colorectal cancer. Gut Microbes 2024; 16:2350156. [PMID: 38726597 PMCID: PMC11093030 DOI: 10.1080/19490976.2024.2350156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
Extensive research has explored the role of gut microbiota in colorectal cancer (CRC). Nonetheless, metatranscriptomic studies investigating the in situ functional implications of host-microbe interactions in CRC are scarce. Therefore, we characterized the influence of CRC core pathogens and biofilms on the tumor microenvironment (TME) in 40 CRC, paired normal, and healthy tissue biopsies using fluorescence in situ hybridization (FISH) and dual-RNA sequencing. FISH revealed that Fusobacterium spp. was associated with increased bacterial biomass and inflammatory response in CRC samples. Dual-RNA sequencing demonstrated increased expression of pro-inflammatory cytokines, defensins, matrix-metalloproteases, and immunomodulatory factors in CRC samples with high bacterial activity. In addition, bacterial activity correlated with the infiltration of several immune cell subtypes, including M2 macrophages and regulatory T-cells in CRC samples. Specifically, Bacteroides fragilis and Fusobacterium nucleatum correlated with the infiltration of neutrophils and CD4+ T-cells, respectively. The collective bacterial activity/biomass appeared to exert a more significant influence on the TME than core pathogens, underscoring the intricate interplay between gut microbiota and CRC. These results emphasize how biofilms and core pathogens shape the immune phenotype and TME in CRC while highlighting the need to extend the bacterial scope beyond CRC pathogens to advance our understanding and identify treatment targets.
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Affiliation(s)
- Lasse Kvich
- Center for Surgical Science, Department of Surgery, Zealand University Hospital, Region Zealand, Denmark
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Blaine Gabriel Fritz
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Henrike Zschach
- Center for Health Data Science, University of Copenhagen, Copenhagen, Denmark
| | - Thilde Terkelsen
- Center for Health Data Science, University of Copenhagen, Copenhagen, Denmark
| | - Hans Raskov
- Center for Surgical Science, Department of Surgery, Zealand University Hospital, Region Zealand, Denmark
| | - Kathrine Høst-Rasmussen
- Center for Surgical Science, Department of Surgery, Zealand University Hospital, Region Zealand, Denmark
| | - Morten Ragn Jakobsen
- Center for Surgical Science, Department of Surgery, Zealand University Hospital, Region Zealand, Denmark
| | - Alexandra Gabriella Gheorghe
- Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ismail Gögenur
- Center for Surgical Science, Department of Surgery, Zealand University Hospital, Region Zealand, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
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26
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Kotzur R, Kahlon S, Isaacson B, Gamliel M, Charpak-Amikam Y, Lieberman J, Bachrach G, Goldman-Wohl D, Yagel S, Beharier O, Mandelboim O. Pregnancy trained decidual NK cells protect pregnancies from harmful Fusobacterium nucleatum infection. PLoS Pathog 2024; 20:e1011923. [PMID: 38215172 PMCID: PMC10826933 DOI: 10.1371/journal.ppat.1011923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/30/2024] [Accepted: 12/22/2023] [Indexed: 01/14/2024] Open
Abstract
Natural killer cells (NKs) found during pregnancy at the maternal-fetal interface named decidual (d)NKs, show signs of education following first pregnancy, resulting in better placentation and fetus-growth, hence termed pregnancy trained dNKs (PTdNKs). Here we show that PTdNKs provide increased protection of the fetus from Fusobacterium nucleatum (FN) infection. We demonstrate that PTdNKs secrete elevated amounts of the bacteriocidal protein granulysin (GNLY) upon incubation with FN compared to dNKs derived from first pregnancies, which leads to increased killing of FN. Furthermore, we showed mechanistically that the GNLY secretion is mediated through the interaction of the FN's Fap2 protein with Gal-GalNAc present on PTdNKs. Finally, we show in vivo, using GNLY-tg mice that enhanced protection of the fetuses from FN infection is observed, as compared to wild type and that this enhance protection is NK cell dependent. Altogether, we show a new function for PTdNKs as protectors of the fetus from bacterial infection.
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Affiliation(s)
- Rebecca Kotzur
- The Lautenberg Center for General and Tumor Immunology, Institute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Shira Kahlon
- The Lautenberg Center for General and Tumor Immunology, Institute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Batya Isaacson
- The Lautenberg Center for General and Tumor Immunology, Institute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Moriya Gamliel
- The Lautenberg Center for General and Tumor Immunology, Institute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Yoav Charpak-Amikam
- The Lautenberg Center for General and Tumor Immunology, Institute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children’ Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gilad Bachrach
- The Institute of Dental Sciences, The Hebrew University-Hadassah School of Dental Medicine, Jerusalem, Israel
| | - Debra Goldman-Wohl
- Department of Obstetrics and Gynecology, Hadassah-University Hospital, Mt. Scopus, Jerusalem, Israel
| | - Simcha Yagel
- Department of Obstetrics and Gynecology, Hadassah-University Hospital, Mt. Scopus, Jerusalem, Israel
| | - Ofer Beharier
- Department of Obstetrics and Gynecology, Hadassah-University Hospital, Mt. Scopus, Jerusalem, Israel
| | - Ofer Mandelboim
- The Lautenberg Center for General and Tumor Immunology, Institute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Jerusalem, Israel
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27
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Constantin M, Chifiriuc MC, Mihaescu G, Vrancianu CO, Dobre EG, Cristian RE, Bleotu C, Bertesteanu SV, Grigore R, Serban B, Cirstoiu C. Implications of oral dysbiosis and HPV infection in head and neck cancer: from molecular and cellular mechanisms to early diagnosis and therapy. Front Oncol 2023; 13:1273516. [PMID: 38179168 PMCID: PMC10765588 DOI: 10.3389/fonc.2023.1273516] [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: 08/06/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Head and neck cancer (HNC) is the sixth most common type of cancer, with more than half a million new cases annually. This review focuses on the role of oral dysbiosis and HPV infection in HNCs, presenting the involved taxons, molecular effectors and pathways, as well as the HPV-associated particularities of genetic and epigenetic changes and of the tumor microenvironment occurred in different stages of tumor development. Oral dysbiosis is associated with the evolution of HNCs, through multiple mechanisms such as inflammation, genotoxins release, modulation of the innate and acquired immune response, carcinogens and anticarcinogens production, generation of oxidative stress, induction of mutations. Thus, novel microbiome-derived biomarkers and interventions could significantly contribute to achieving the desideratum of personalized management of oncologic patients, regarding both early diagnosis and treatment. The results reported by different studies are not always congruent regarding the variations in the abundance of different taxons in HNCs. However, there is a consistent reporting of a higher abundance of Gram-negative species such as Fusobacterium, Leptotrichia, Treponema, Porphyromonas gingivalis, Prevotella, Bacteroidetes, Haemophilus, Veillonella, Pseudomonas, Enterobacterales, which are probably responsible of chronic inflammation and modulation of tumor microenvironment. Candida albicans is the dominant fungi found in oral carcinoma being also associated with shorter survival rate. Specific microbial signatures (e.g., F. nucleatum, Bacteroidetes and Peptostreptococcus) have been associated with later stages and larger tumor, suggesting their potential to be used as biomarkers for tumor stratification and prognosis. On the other hand, increased abundance of Corynebacterium, Kingella, Abiotrophia is associated with a reduced risk of HNC. Microbiome could also provide biomarkers for differentiating between oropharyngeal and hypopharyngeal cancers as well as between HPV-positive and HPV-negative tumors. Ongoing clinical trials aim to validate non-invasive tests for microbiome-derived biomarkers detection in oral and throat cancers, especially within high-risk populations. Oro-pharyngeal dysbiosis could also impact the HNCs therapy and associated side-effects of radiotherapy, chemotherapy, and immunotherapy. HPV-positive tumors harbor fewer mutations, as well as different DNA methylation pattern and tumor microenvironment. Therefore, elucidation of the molecular mechanisms by which oral microbiota and HPV infection influence the HNC initiation and progression, screening for HPV infection and vaccination against HPV, adopting a good oral hygiene, and preventing oral dysbiosis are important tools for advancing in the battle with this public health global challenge.
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Affiliation(s)
- Marian Constantin
- Department of Microbiology, Institute of Biology of Romanian Academy, Bucharest, Romania
- The Research Institute of the University of Bucharest, ICUB, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- The Research Institute of the University of Bucharest, ICUB, Bucharest, Romania
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Department of Life, Medical and Agricultural Sciences, Biological Sciences Section, Romanian Academy, Bucharest, Romania
| | - Grigore Mihaescu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Corneliu Ovidiu Vrancianu
- The Research Institute of the University of Bucharest, ICUB, Bucharest, Romania
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- DANUBIUS Department, National Institute of Research and Development for Biological Sciences, Bucharest, Romania
| | - Elena-Georgiana Dobre
- The Research Institute of the University of Bucharest, ICUB, Bucharest, Romania
- Immunology Department, “Victor Babes” National Institute of Pathology, Bucharest, Romania
| | - Roxana-Elena Cristian
- The Research Institute of the University of Bucharest, ICUB, Bucharest, Romania
- DANUBIUS Department, National Institute of Research and Development for Biological Sciences, Bucharest, Romania
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Coralia Bleotu
- The Research Institute of the University of Bucharest, ICUB, Bucharest, Romania
- Cellular and Molecular Pathology Department, Ştefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Serban Vifor Bertesteanu
- Coltea Clinical Hospital, ENT, Head & Neck Surgery Department, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Raluca Grigore
- Coltea Clinical Hospital, ENT, Head & Neck Surgery Department, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Bogdan Serban
- University Emergency Hospital, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Catalin Cirstoiu
- University Emergency Hospital, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
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28
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Bista PK, Pillai D, Narayanan SK. Characterization of Three New Outer Membrane Adhesion Proteins in Fusobacterium necrophorum. Microorganisms 2023; 11:2968. [PMID: 38138112 PMCID: PMC10745669 DOI: 10.3390/microorganisms11122968] [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: 09/29/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Fusobacterium necrophorum, an anaerobic Gram-negative pathogen, causes necrotic cattle infections, impacting livestock health and the US feedlot industry. Antibiotic administration is the mainstay for treating F. necrophorum infections, although resistance hampers their effectiveness. Vaccination, especially targeting outer membrane proteins (OMPs) due to their antigenic properties and host specificity, offers an alternative to antibiotics. This study identified high-binding-affinity adhesion proteins from F. necrophorum using binding and pull-down assays with bovine adrenal gland endothelial cells (EJG). Four OMP candidates (17.5 kDa/OmpH, 22.7 kDa/OmpA, 66.3 kDa/cell surface protein (CSP), and a previously characterized 43 kDa OMP) were expressed as recombinant proteins and purified. Rabbit polyclonal antibodies to recombinant OMPs were generated, and their ability to inhibit bacterial binding in vitro was assessed. The results show that treatment with individual polyclonal antibodies against 43 kDa significantly inhibited bacterial adhesion, while other antibodies were less potent. However, combinations of two or more antibodies showed a more prominent inhibitory effect on host-cell adhesion. Thus, our findings suggest that the identified OMPs are involved in fusobacterial attachment to host cells and may have the potential to be leveraged in combination for vaccine development. Future in vivo studies are needed to validate their roles and test the feasibility of an OMP-based subunit vaccine against fusobacterial infections.
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Affiliation(s)
- Prabha K. Bista
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA; (P.K.B.); (D.P.)
| | - Deepti Pillai
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA; (P.K.B.); (D.P.)
- Indiana Animal Disease and Diagnostic Laboratory, Purdue University, West Lafayette, IN 47907, USA
| | - Sanjeev K. Narayanan
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA; (P.K.B.); (D.P.)
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29
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Agarwal K, Choudhury B, Robinson LS, Morrill SR, Bouchibiti Y, Chilin-Fuentes D, Rosenthal SB, Fisch KM, Peipert JF, Lebrilla CB, Allsworth JE, Lewis AL, Lewis WG. Resident microbes shape the vaginal epithelial glycan landscape. Sci Transl Med 2023; 15:eabp9599. [PMID: 38019934 PMCID: PMC11419735 DOI: 10.1126/scitranslmed.abp9599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 11/01/2023] [Indexed: 12/01/2023]
Abstract
Epithelial cells are covered in carbohydrates (glycans). This glycan coat or "glycocalyx" interfaces directly with microbes, providing a protective barrier against potential pathogens. Bacterial vaginosis (BV) is a condition associated with adverse health outcomes in which bacteria reside in direct proximity to the vaginal epithelium. Some of these bacteria, including Gardnerella, produce glycosyl hydrolase enzymes. However, glycans of the human vaginal epithelial surface have not been studied in detail. Here, we elucidate key characteristics of the "normal" vaginal epithelial glycan landscape and analyze the impact of resident microbes on the surface glycocalyx. In human BV, glycocalyx staining was visibly diminished in electron micrographs compared to controls. Biochemical and mass spectrometric analysis showed that, compared to normal vaginal epithelial cells, BV cells were depleted of sialylated N- and O-glycans, with underlying galactose residues exposed on the surface. Treatment of primary epithelial cells from BV-negative women with recombinant Gardnerella sialidases generated BV-like glycan phenotypes. Exposure of cultured VK2 vaginal epithelial cells to recombinant Gardnerella sialidase led to desialylation of glycans and induction of pathways regulating cell death, differentiation, and inflammatory responses. These data provide evidence that vaginal epithelial cells exhibit an altered glycan landscape in BV and suggest that BV-associated glycosidic enzymes may lead to changes in epithelial gene transcription that promote cell turnover and regulate responses toward the resident microbiome.
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Affiliation(s)
- Kavita Agarwal
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, United States of America
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego (UCSD), La Jolla, CA 92093, United States of America
- Glycobiology Research and Training Center, UCSD, La Jolla, CA 92093, United States of America
| | - Biswa Choudhury
- Glycobiology Research and Training Center, UCSD, La Jolla, CA 92093, United States of America
| | - Lloyd S. Robinson
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Sydney R. Morrill
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, United States of America
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego (UCSD), La Jolla, CA 92093, United States of America
- Glycobiology Research and Training Center, UCSD, La Jolla, CA 92093, United States of America
| | - Yasmine Bouchibiti
- Department of Chemistry, University of California, Davis, Davis, CA 95616, United States of America
- Department of Food Science and Technology, University of California, Davis, Davis, CA 95616, United States of America
| | - Daisy Chilin-Fuentes
- Center for Computational Biology & Bioinformatics, UCSD, La Jolla, CA 92093, United States of America
| | - Sara B. Rosenthal
- Center for Computational Biology & Bioinformatics, UCSD, La Jolla, CA 92093, United States of America
| | - Kathleen M. Fisch
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego (UCSD), La Jolla, CA 92093, United States of America
- Center for Computational Biology & Bioinformatics, UCSD, La Jolla, CA 92093, United States of America
| | - Jeffrey F. Peipert
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN 46202, United States of America
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, Davis, CA 95616, United States of America
- Department of Food Science and Technology, University of California, Davis, Davis, CA 95616, United States of America
| | - Jenifer E. Allsworth
- Department of Biomedical and Health Informatics, University of Missouri, Kansas City School of Medicine, Kansas City, MO 64110, United States of America
| | - Amanda L. Lewis
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, United States of America
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego (UCSD), La Jolla, CA 92093, United States of America
- Glycobiology Research and Training Center, UCSD, La Jolla, CA 92093, United States of America
| | - Warren G. Lewis
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, United States of America
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego (UCSD), La Jolla, CA 92093, United States of America
- Glycobiology Research and Training Center, UCSD, La Jolla, CA 92093, United States of America
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Tortora SC, Agurto MG, Martello LA. The oral-gut-circulatory axis: from homeostasis to colon cancer. Front Cell Infect Microbiol 2023; 13:1289452. [PMID: 38029267 PMCID: PMC10663299 DOI: 10.3389/fcimb.2023.1289452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
The human microbiota is widely recognized as providing crucial health benefits to its host, specifically by modulating immune homeostasis. Microbial imbalance, known as dysbiosis, is linked to several conditions in the body. The oral cavity and gut host the two largest microbial communities playing a major role in microbial-associated diseases. While the oral-gut axis has been previously explored, our review uniquely highlights the significance of incorporating the circulatory system into this axis. The interaction between immune cells, inflammatory factors, circulating bacteria, and microbial metabolites influences the homeostasis of both the oral and gut microbiota in a bidirectional manner. In this comprehensive review, we aim to describe the bacterial components of the oral-gut-circulatory axis in both health and disease, with a specific focus on colon cancer.
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Affiliation(s)
- Sofia C. Tortora
- Department of Medicine and Division of Gastroenterology & Hepatology, SUNY Downstate Health Sciences University, Brooklyn, NY, United States
| | - Maria Gonzalez Agurto
- Departamento de Rehabilitación Craneofacial Integral, Universidad de Los Andes, Santiago, Chile
| | - Laura A. Martello
- Department of Medicine and Division of Gastroenterology & Hepatology, SUNY Downstate Health Sciences University, Brooklyn, NY, United States
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Merritt J, Kreth J. Illuminating the oral microbiome and its host interactions: tools and approaches for molecular microbiology studies. FEMS Microbiol Rev 2023; 47:fuac050. [PMID: 36549660 PMCID: PMC10719069 DOI: 10.1093/femsre/fuac050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Advancements in DNA sequencing technologies within the last decade have stimulated an unprecedented interest in the human microbiome, largely due the broad diversity of human diseases found to correlate with microbiome dysbiosis. As a direct consequence of these studies, a vast number of understudied and uncharacterized microbes have been identified as potential drivers of mucosal health and disease. The looming challenge in the field is to transition these observations into defined molecular mechanistic studies of symbiosis and dysbiosis. In order to meet this challenge, many of these newly identified microbes will need to be adapted for use in experimental models. Consequently, this review presents a comprehensive overview of the molecular microbiology tools and techniques that have played crucial roles in genetic studies of the bacteria found within the human oral microbiota. Here, we will use specific examples from the oral microbiome literature to illustrate the biology supporting these techniques, why they are needed in the field, and how such technologies have been implemented. It is hoped that this information can serve as a useful reference guide to help catalyze molecular microbiology studies of the many new understudied and uncharacterized species identified at different mucosal sites in the body.
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Affiliation(s)
- Justin Merritt
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, OR, United States
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, United States
| | - Jens Kreth
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, OR, United States
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, United States
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Zhou P, G C B, Stolte F, Wu C. Use of CRISPR interference for efficient and rapid gene inactivation in Fusobacterium nucleatum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558491. [PMID: 37781593 PMCID: PMC10541141 DOI: 10.1101/2023.09.19.558491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Gene inactivation via creating in-frame deletion mutations in Fusobacterium nucleatum is time-consuming, and most fusobacterial strains are genetically intractable. Addressing these problems, we introduced a riboswitch-based inducible CRISPRi system. This system employs the nuclease-inactive Streptococcus pyogenes Cas9 protein (dCas9), specifically guided to the gene of interest by a constantly expressed single guide RNA (sgRNA). Mechanistically, this dCas9-sgRNA complex serves as an insurmountable roadblock for RNA polymerase, thus repressing the target gene transcription. Leveraging this system, we first examined two non-essential genes, ftsX, and radD , pivotal for fusobacterial cytokinesis and coaggregation. Upon adding the inducer, theophylline, ftsX suppression caused filamentous cell formation akin to chromosomal ftsX deletion, while targeting radD significantly reduced RadD protein levels, abolishing coaggregation. The system was then extended to probe essential genes bamA and ftsZ , vital for outer membrane biogenesis and cell division. Impressively, bamA suppression disrupted membrane integrity and bacterial separation, stalling growth, while ftsZ- targeting yielded elongated cells in broth with compromised agar growth. Further studies on F. nucleatum clinical strain CTI-2 and Fusobacterium periodonticum revealed reduced indole synthesis when targeting tnaA . Moreover, silencing clpB in F. periodonticum decreased ClpB, increasing thermal sensitivity. In summary, our CRISPRi system streamlines gene inactivation across various fusobacterial strains. IMPORTANCE How can we effectively investigate the gene functions in Fusobacterium nucleatum , given the dual challenges of gene inactivation and the inherent genetic resistance of many strains? Traditional methods have been cumbersome and often inadequate. Addressing this, our work introduces a novel inducible CRISPRi system in which dCas9 expression is controlled at the translation level by a theophylline-responsive riboswitch unit, and sgRNA expression is driven by the robust, constitutive rpsJ promoter. This approach simplifies gene inactivation in the model organism (ATCC 23726) and extends its application to previously considered resistant strains like CTI-2 and Fusobacterium periodontium . With CRISPRi's potential, it is a pivotal tool for in-depth genetic studies into fusobacterial pathogenesis, potentially unlocking targeted therapeutic strategies.
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Abstract
Cancer cells originate from a series of acquired genetic mutations that can drive their uncontrolled cell proliferation and immune evasion. Environmental factors, including the microorganisms that colonize the human body, can shift the metabolism, growth pattern and function of neoplastic cells and shape the tumour microenvironment. Dysbiosis of the gut microbiome is now recognized as a hallmark of cancer by the scientific community. However, only a few microorganisms have been identified that directly initiate tumorigenesis or skew the immune system to generate a tumour-permissive milieu. Over the past two decades, research on the human microbiome and its functionalities within and across individuals has revealed microbiota-focused strategies for health and disease. Here, we review the evolving understanding of the mechanisms by which the microbiota acts in cancer initiation, promotion and progression. We explore the roles of bacteria in gastrointestinal tract malignancies and cancers of the lung, breast and prostate. Finally, we discuss the promises and limitations of targeting or harnessing bacteria in personalized cancer prevention, diagnostics and treatment.
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Affiliation(s)
- Geniver El Tekle
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- The Harvard T. H. Chan Microbiome in Public Health Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wendy S Garrett
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- The Harvard T. H. Chan Microbiome in Public Health Center, Boston, MA, USA.
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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Feng Q, Zakaria S, Morrison D, Tram K, Gu J, Salena BJ, Li Y. A Fluorogenic DNAzyme for A Thermally Stable Protein Biomarker from Fusobacterium nucleatum, a Human Bacterial Pathogen. Angew Chem Int Ed Engl 2023; 62:e202306272. [PMID: 37404195 DOI: 10.1002/anie.202306272] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/06/2023]
Abstract
Fusobacterium nucleatum has been correlated to many poor human conditions including oral infections, adverse pregnancies and cancer, and thus molecular tools capable of detecting this human pathogen can be used to develop diagnostic tests for them. Using a new selection method targeting thermally stable proteins without a counter-selection step, we derived an fluorogenic RNA-cleaving DNAzyme, named RFD-FN1, that can be activated by a thermally stable protein target that is unique to F. nucleatum subspecies. High thermal stability of protein targets is a very desirable attribute for DNAzyme-based biosensing directly with biological samples because nucleases found inherently in these samples can be heat-inactivated. We further demonstrate that RFD-FN1 can function as a fluorescent sensor in both human saliva and human stool samples. The discovery of RFD-FN1 paired with a highly thermal stable protein target presents opportunities for developing simpler diagnostic tests for this important pathogen.
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Affiliation(s)
- Qian Feng
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
| | - Sandy Zakaria
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
| | - Devon Morrison
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
| | - Kha Tram
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
| | - Jim Gu
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
| | - Bruno J Salena
- Department of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
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Smith TJ, Sundarraman D, Melancon E, Desban L, Parthasarathy R, Guillemin K. A mucin-regulated adhesin determines the spatial organization and inflammatory character of a bacterial symbiont in the vertebrate gut. Cell Host Microbe 2023; 31:1371-1385.e6. [PMID: 37516109 PMCID: PMC10492631 DOI: 10.1016/j.chom.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 05/11/2023] [Accepted: 07/06/2023] [Indexed: 07/31/2023]
Abstract
In a healthy gut, microbes are often aggregated with host mucus, yet the molecular basis for this organization and its impact on intestinal health are unclear. Mucus is a viscous physical barrier separating resident microbes from epithelia, but it also provides glycan cues that regulate microbial behaviors. Here, we describe a mucin-sensing pathway in an Aeromonas symbiont of zebrafish, Aer01. In response to the mucin-associated glycan N-acetylglucosamine, a sensor kinase regulates the expression of an aggregation-promoting adhesin we named MbpA. Upon MbpA disruption, Aer01 colonizes to normal levels but is largely planktonic and more pro-inflammatory. Increasing cell surface MbpA rescues these traits. MbpA-like adhesins are common in human-associated bacteria, and the expression of an Akkermansia muciniphila MbpA-like adhesin in MbpA-deficient Aer01 restores lumenal aggregation and reverses its pro-inflammatory character. Our work demonstrates how resident bacteria use mucin glycans to modulate behaviors congruent with host health.
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Affiliation(s)
- T Jarrod Smith
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
| | - Deepika Sundarraman
- Department of Physics and Materials Science Institute, University of Oregon, Eugene, OR, USA
| | - Ellie Melancon
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Laura Desban
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Raghuveer Parthasarathy
- Department of Physics and Materials Science Institute, University of Oregon, Eugene, OR, USA
| | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA; Institute of Neuroscience, University of Oregon, Eugene, OR, USA; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON, Canada.
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Huang H, Zhong W, Wang X, Yang Y, Wu T, Chen R, Liu Y, He F, Li J. The role of gastric microecological dysbiosis in gastric carcinogenesis. Front Microbiol 2023; 14:1218395. [PMID: 37583514 PMCID: PMC10423824 DOI: 10.3389/fmicb.2023.1218395] [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: 05/07/2023] [Accepted: 07/10/2023] [Indexed: 08/17/2023] Open
Abstract
Gastric cancer (GC) is the leading cause of cancer-related death worldwide, and reducing its mortality has become an urgent public health issue. Gastric microecological dysbiosis (including bacteria, fungi, viruses, acid suppressants, antibiotics, and surgery) can lead to gastric immune dysfunction or result in a decrease in dominant bacteria and an increase in the number and virulence of pathogenic microorganisms, which in turn promotes development of GC. This review analyzes the relationship between gastric microecological dysbiosis and GC, elucidates dynamic alterations of the microbiota in Correa's cascade, and identifies certain specific microorganisms as potential biomarkers of GC to aid in early screening and diagnosis. In addition, this paper presents the potential of gastric microbiota transplantation as a therapeutic target for gastric cancer, providing a new direction for future research in this field.
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Affiliation(s)
- Hui Huang
- Chengdu Medical College, Chengdu, Sichuan, China
| | - Wei Zhong
- Chengdu Medical College, Chengdu, Sichuan, China
| | | | - Ying Yang
- Chengdu Medical College, Chengdu, Sichuan, China
| | - Tianmu Wu
- Chengdu Medical College, Chengdu, Sichuan, China
| | - Runyang Chen
- Chengdu Medical College, Chengdu, Sichuan, China
| | - Yanling Liu
- Chengdu Medical College, Chengdu, Sichuan, China
| | - Feng He
- Chengdu Medical College, Chengdu, Sichuan, China
- Department of Gastroenterology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Jun Li
- Chengdu Medical College, Chengdu, Sichuan, China
- Department of Gastroenterology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
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37
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Britton TA, Wu C, Chen YW, Franklin D, Chen Y, Camacho MI, Luong TT, Das A, Ton-That H. The respiratory enzyme complex Rnf is vital for metabolic adaptation and virulence in Fusobacterium nucleatum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544113. [PMID: 37398403 PMCID: PMC10312631 DOI: 10.1101/2023.06.13.544113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
A prominent oral commensal and opportunistic pathogen, Fusobacterium nucleatum can traverse to extra-oral sites such as placenta and colon, promoting adverse pregnancy outcomes and colorectal cancer, respectively. How this anaerobe sustains many metabolically changing environments enabling its virulence potential remains unclear. Informed by our genome-wide transposon mutagenesis, we report here that the highly conserved Rnf complex, encoded by the rnfCDGEAB gene cluster, is key to fusobacterial metabolic adaptation and virulence. Genetic disruption of the Rnf complex via non-polar, in-frame deletion of rnfC (Δ rnfC ) abrogates polymicrobial interaction (or coaggregation) associated with adhesin RadD and biofilm formation. The defect in coaggregation is not due to reduced cell surface of RadD, but rather an increased level of extracellular lysine, which binds RadD and inhibits coaggregation. Indeed, removal of extracellular lysine via washing Δ rnfC cells restores coaggregation, while addition of lysine inhibits this process. These phenotypes mirror that of a mutant (Δ kamAΔ ) that fails to metabolize extracellular lysine. Strikingly, the Δ rnfC mutant is defective in ATP production, cell growth, cell morphology, and expression of the enzyme MegL that produces hydrogen sulfide from cysteine. Targeted metabolic profiling demonstrated that catabolism of many amino acids, including histidine and lysine, is altered in Δ rnfC cells, thereby reducing production of ATP and metabolites including H2S and butyrate. Most importantly, we show that the Δ rnfC mutant is severely attenuated in a mouse model of preterm birth. The indispensable function of Rnf complex in fusobacterial pathogenesis via modulation of bacterial metabolism makes it an attractive target for developing therapeutic intervention.
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Ma X, Sun T, Zhou J, Zhi M, Shen S, Wang Y, Gu X, Li Z, Gao H, Wang P, Feng Q. Pangenomic Study of Fusobacterium nucleatum Reveals the Distribution of Pathogenic Genes and Functional Clusters at the Subspecies and Strain Levels. Microbiol Spectr 2023; 11:e0518422. [PMID: 37042769 PMCID: PMC10269558 DOI: 10.1128/spectrum.05184-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/26/2023] [Indexed: 04/13/2023] Open
Abstract
Fusobacterium nucleatum is a prevalent periodontal pathogen and is associated with many systemic diseases. Our knowledge of the genomic characteristics and pathogenic effectors of different F. nucleatum strains is limited. In this study, we completed the whole genome assembly of the 4 F. nucleatum strains and carried out a comprehensive pangenomic study of 30 strains with their complete genome sequences. Phylogenetic analysis revealed that the F. nucleatum strains are mainly divided into 4 subspecies, while 1 of the sequenced strains was classified into a new subspecies. Gene composition analysis revealed that a total of 517 "core/soft-core genes" with housekeeping functions widely distributed in almost all the strains. Each subspecies had a unique gene cluster shared by strains within the subspecies. Analysis of the virulence factors revealed that many virulence factors were widely distributed across all the strains, with some present in multiple copies. Some virulence genes showed no consistent occurrence rule at the subspecies level and were specifically distributed in certain strains. The genomic islands mainly revealed strain-specific characteristics instead of subspecies level consistency, while CRISPR types and secondary metabolite biosynthetic gene clusters were identically distributed in F. nucleatum strains from the same subspecies. The variation in amino acid sites in the adhesion protein FadA did not affect the monomer and dimer 3D structures, but it may affect the binding surface and the stability of binding to host receptors. This study provides a basis for the pathogenic study of F. nucleatum at the subspecies and strain levels. IMPORTANCE We used F. nucleatum as an example to analyze the genomic characteristics of oral pathogens at the species, subspecies, and strain levels and elucidate the similarities and differences in functional genes and virulence factors among different subspecies/strains of the same oral pathogen. We believe that the unique biological characteristics of each subspecies/strain can be attributed to the differences in functional gene clusters or the presence/absence of certain virulence genes. This study showed that F. nucleatum strains from the same subspecies had similar functional gene compositions, CRISPR types, and secondary metabolite biosynthetic gene clusters, while pathogenic genes, such as virulence genes, antibiotic resistance genes, and GIs, had more strain level specificity. The findings of this study suggest that, for microbial pathogenicity studies, we should carefully consider the subspecies/strains being used, as different strains may vary greatly.
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Affiliation(s)
- Xiaomei Ma
- Department of Human Microbiome & Implantology & Orthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, China
| | - Tianyong Sun
- Department of Human Microbiome & Implantology & Orthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, China
| | - Jiannan Zhou
- Department of Human Microbiome & Implantology & Orthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, China
- The State Key Laboratory Breeding Base of Basic Sciences of Stomatology, Key Laboratory of Oral Biomedicine, Ministry of Education (Hubei-MOST KLOS & KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Mengfan Zhi
- Department of Human Microbiome & Implantology & Orthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, China
| | - Song Shen
- Department of Human Microbiome & Implantology & Orthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, China
| | - Yushang Wang
- Department of Human Microbiome & Implantology & Orthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, China
| | - Xiufeng Gu
- Department of Human Microbiome & Implantology & Orthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, China
| | - Zixuan Li
- Department of Human Microbiome & Implantology & Orthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, China
| | - Haiting Gao
- Department of Human Microbiome & Implantology & Orthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, China
| | - Pingping Wang
- Department of Human Microbiome & Implantology & Orthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, China
| | - Qiang Feng
- Department of Human Microbiome & Implantology & Orthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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Jones J, Shi Q, Nath RR, Brito IL. Keystone pathobionts associated with colorectal cancer promote oncogenic reprograming. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535410. [PMID: 37066368 PMCID: PMC10103987 DOI: 10.1101/2023.04.03.535410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Fusobacterium nucleatum (Fn) and enterotoxigenic Bacteroides fragilis (ETBF) are two pathobionts consistently enriched in the gut microbiomes of patients with colorectal cancer (CRC) compared to healthy counterparts and frequently observed for their direct association within tumors. Although several molecular mechanisms have been identified that directly link these organisms to features of CRC in specific cell types, their specific effects on the epithelium and local immune compartment are not well-understood. To fill this gap, we leveraged single-cell RNA sequencing (scRNA-seq) on wildtype mice and mouse model of CRC. We find that Fn and ETBF exacerbate cancer-like transcriptional phenotypes in transit-amplifying and mature enterocytes in a mouse model of CRC. We also observed increased T cells in the pathobiont-exposed mice, but these pathobiont-specific differences observed in wildtype mice were abrogated in the mouse model of CRC. Although there are similarities in the responses provoked by each organism, we find pathobiont-specific effects in Myc-signaling and fatty acid metabolism. These findings support a role for Fn and ETBF in potentiating tumorigenesis via the induction of a cancer stem cell-like transit-amplifying and enterocyte population and the disruption of CTL cytotoxic function.
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Affiliation(s)
- Josh Jones
- Meinig School for Biomedical Engineering, Cornell University, Ithaca, NY
| | - Qiaojuan Shi
- Meinig School for Biomedical Engineering, Cornell University, Ithaca, NY
| | - Rahul R. Nath
- Meinig School for Biomedical Engineering, Cornell University, Ithaca, NY
| | - Ilana L. Brito
- Meinig School for Biomedical Engineering, Cornell University, Ithaca, NY
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Growth Conditions Influence Lactobacillus Cell-Free Supernatant Impact on Viability, Biofilm Formation, and Co-Aggregation of the Oral Periodontopathogens Fusobacterium nucleatum and Porphyromonas gingivalis. Biomedicines 2023; 11:biomedicines11030859. [PMID: 36979838 PMCID: PMC10045872 DOI: 10.3390/biomedicines11030859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
Fusobacterium nucleatum and Porphyromonas gingivalis human periodontopathogens play a leading part in oral squamous cell carcinoma through cell proliferation, invasion, and persistent inflammation promotion and maintenance. To explore how the activity of Lactobacillus-derived cell-free supernatants (CFSs) can be influenced by growth medium components, CFSs were produced both in the standard MRS and the novel animal-derivative-free “Terreno Industriale Lattobacilli” (TIL) media, and in vitro screened for the containment of F. nucleatum and P. gingivalis both single and co-cultured and also for the interference on their co-aggregation. The viability assay demonstrated that the Limosilactobacillus reuteri LRE11 and Ligilactobacillus salivarius LS03 MRS-produced CFSs were significantly more effective against single and co-cultured pathogens. All the other CFSs significantly improved their efficacy when produced in TIL. Both MRS- and TIL-produced CFSs significantly inhibited the single and co-cultured pathogen biofilm formation. Only Levilactobacillus brevis LBR01 CFS in MRS specifically reduced F. nucleatum and P. gingivalis co-aggregation, while viable LBR01, LS03, and LRE11 in MRS significantly co-aggregated with the pathogens, but only LS03 cultivated in TIL improved this effect. This work paves the way to better consider environmental growth conditions when screening for probiotic and postbiotic efficacy as crucial to pathogen aggregation, adhesion to the host’s niches, and exclusion.
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Motamedi H, Ari MM, Shahlaei M, Moradi S, Farhadikia P, Alvandi A, Abiri R. Designing multi-epitope vaccine against important colorectal cancer (CRC) associated pathogens based on immunoinformatics approach. BMC Bioinformatics 2023; 24:65. [PMID: 36829112 PMCID: PMC9951438 DOI: 10.1186/s12859-023-05197-0] [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: 10/10/2022] [Accepted: 02/20/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND It seems that several members of intestinal gut microbiota like Streptococcus bovis, Bacteroides fragilis, Helicobacter pylori, Fusobacterium nucleatum, Enterococcus faecalis, Escherichia coli, Peptostreptococcus anaerobius may be considered as the causative agents of Colorectal Cancer (CRC). The present study used bioinformatics and immunoinformatics approaches to design a potential epitope-based multi-epitope vaccine to prevent CRC with optimal population coverage. METHODS In this study, ten amino acid sequences of CRC-related pathogens were retrieved from the NCBI database. Three ABCpred, BCPREDS and LBtope online servers were considered for B cells prediction and the IEDB server for T cells (CD4+ and CD8+) prediction. Then, validation, allergenicity, toxicity and physicochemical analysis of all sequences were performed using web servers. A total of three linkers, AAY, GPGPG, and KK were used to bind CTL, HTL and BCL epitopes, respectively. In addition, the final construct was subjected to disulfide engineering, molecular docking, immune simulation and codon adaptation to design an effective vaccine production strategy. RESULTS A total of 19 sequences of different lengths for linear B-cell epitopes, 19 and 18 sequences were considered as epitopes of CD4+ T and CD8+ cells, respectively. The predicted epitopes were joined by appropriate linkers because they play an important role in producing an extended conformation and protein folding. The final multi-epitope construct and Toll-like receptor 4 (TLR4) were evaluated by molecular docking, which revealed stable and strong binding interactions. Immunity simulation of the vaccine showed significantly high levels of immunoglobulins, helper T cells, cytotoxic T cells and INF-γ. CONCLUSION Finally, the results showed that the designed multi-epitope vaccine could serve as an excellent prophylactic candidate against CRC-associated pathogens, but in vitro and animal studies are needed to justify our findings for its use as a possible preventive measure.
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Affiliation(s)
- Hamid Motamedi
- grid.412112.50000 0001 2012 5829Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran ,grid.412112.50000 0001 2012 5829Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Marzie Mahdizade Ari
- grid.411746.10000 0004 4911 7066Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran ,grid.411746.10000 0004 4911 7066Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Mohsen Shahlaei
- grid.412112.50000 0001 2012 5829Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sajad Moradi
- grid.412112.50000 0001 2012 5829Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Parisa Farhadikia
- grid.412112.50000 0001 2012 5829Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amirhoushang Alvandi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran. .,Medical Technology Research Center, Health Technology Institute,, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Ramin Abiri
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran. .,Fertility and Infertility Research Center, Health Technology Institute,, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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Cell Surface Fibroblast Activation Protein-2 (Fap2) of Fusobacterium nucleatum as a Vaccine Candidate for Therapeutic Intervention of Human Colorectal Cancer: An Immunoinformatics Approach. Vaccines (Basel) 2023; 11:vaccines11030525. [PMID: 36992108 DOI: 10.3390/vaccines11030525] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/18/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers and is the second-highest in cancer-related deaths worldwide. The changes in gut homeostasis and microbial dysbiosis lead to the initiation of the tumorigenesis process. Several pathogenic gram-negative bacteria including Fusobacterium nucleatum are the principal contributors to the induction and pathogenesis of CRC. Thus, inhibiting the growth and survival of these pathogens can be a useful intervention strategy. Fibroblast activation protein-2 (Fap2) is an essential membrane protein of F. nucleatum that promotes the adherence of the bacterium to the colon cells, recruitment of immune cells, and induction of tumorigenesis. The present study depicts the design of an in silico vaccine candidate comprising the B-cell and T-cell epitopes of Fap2 for improving cell-mediated and humoral immune responses against CRC. Notably, this vaccine participates in significant protein–protein interactions with human Toll-like receptors, especially with TLR6 reveals, which is most likely to be correlated with its efficacy in eliciting potential immune responses. The immunogenic trait of the designed vaccine was verified by immune simulation approach. The cDNA of the vaccine construct was cloned in silico within the expression vector pET30ax for protein expression. Collectively, the proposed vaccine construct may serve as a promising therapeutic in intervening F. nucleatum-induced human CRC.
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Louis-Jean SF, Agrawal N, Bisht S. Fusobacterium nucleatum Pyogenic Liver Abscess and the Role of Bacterial Virulence and Gut Microbiota Dysbiosis. Cureus 2023; 15:e34548. [PMID: 36879688 PMCID: PMC9985409 DOI: 10.7759/cureus.34548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2023] [Indexed: 02/05/2023] Open
Abstract
In the United States, pyogenic liver abscesses are often due to monomicrobial infection and are rarely documented to be a consequence of Fusobacterium infection, a common cause of Lemierre's syndrome. Recent advances in gut microbial studies have identified Fusobacterium as a commensal gut flora that becomes pathogenic in the setting of dysbiosis resulting from colorectal diseases, such as diverticulitis. While the bacteria's tropism for the liver remains to be elucidated, the virulence pattern of Fusobacterium and the portal venous drainage system have allowed us to understand the bacterium's propensity for causing right hepatic abscesses. In this case report, we detail an immunocompetent man with a history of sigmoid diverticulitis who developed a right hepatic abscess due to Fusobacterium nucleatum, while delineating a review of the literature on the virulent properties of the bacterium and the impact of gut microbiota dysbiosis in its pathogenicity. A descriptive analysis was also performed to identify the characteristics of patients who are at risk in hopes of further improving the clinical diagnostic schema for this condition.
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Affiliation(s)
| | - Nirav Agrawal
- Internal Medicine, Anne Arundel Medical Center, Annapolis, USA
| | - Sushrit Bisht
- Internal Medicine, Anne Arundel Medical Center, Annapolis, USA
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Yu X, Shi Y, Yuan R, Chen Z, Dong Q, Han L, Wang L, Zhou J. Microbial dysbiosis in oral squamous cell carcinoma: A systematic review and meta-analysis. Heliyon 2023; 9:e13198. [PMID: 36793959 PMCID: PMC9922960 DOI: 10.1016/j.heliyon.2023.e13198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 01/15/2023] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
Objective The aim of this study was to summarize previously published data and assess the alterations in the composition of the oral microbiome in OSCC using a systematic review and meta-analysis. Design Electronic databases were systematically searched for studies on the oral microbiome in OSCC published before December 2021. Qualitative assessments of compositional variations at the phylum level were performed. The meta-analysis on abundance changes of bacteria genera was performed via a random-effects model. Results A total of 18 studies involving 1056 participants were included. They consisted of two categories of studies: 1) case-control studies (n = 9); 2) nine studies that compared the oral microbiome between cancerous tissues and paired paracancerous tissues. At the phylum level, enrichment of Fusobacteria but depletion in Actinobacteria and Firmicutes in the oral microbiome was demonstrated in both categories of studies. At the genus level, Fusobacterium showed an increased abundance in OSCC patients (SMD = 0.65, 95% CI: 0.43-0.87, Z = 5.809, P = 0.000) and in cancerous tissues (SMD = 0.54, 95% CI: 0.36-0.72, Z = 5.785, P = 0.000). The abundance of Streptococcus was decreased in OSCC (SMD = -0.46, 95% CI: -0.88-0.04, Z = -2.146, P = 0.032) and in cancerous tissues (SMD = -0.45, 95% CI: -0.78-0.13, Z = -2.726, P = 0.006). Conclusions Disturbances in the interactions between enriched Fusobacterium and depleted Streptococcus may participate in or prompt the occurrence and development of OSCC and could be potential biomarkers for detection of OSCC.
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Affiliation(s)
- Xiaoyun Yu
- Graduate School of Dalian Medical University, Dalian, 116044, China
- Department of Stomatology, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266071, China
| | - Yongmei Shi
- Department of Outpatient, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266071, China
| | - Rongtao Yuan
- Department of Stomatology, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266071, China
| | - Zhenggang Chen
- Department of Stomatology, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266071, China
| | - Quanjiang Dong
- Central Laboratories and Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266071, China
| | - Linzi Han
- Graduate School of Dalian Medical University, Dalian, 116044, China
- Department of Stomatology, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266071, China
| | - Lili Wang
- Central Laboratories and Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266071, China
| | - Jianhua Zhou
- Department of Stomatology, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266071, China
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Morrison AG, Sarkar S, Umar S, Lee STM, Thomas SM. The Contribution of the Human Oral Microbiome to Oral Disease: A Review. Microorganisms 2023; 11:318. [PMID: 36838283 PMCID: PMC9962706 DOI: 10.3390/microorganisms11020318] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023] Open
Abstract
The oral microbiome is an emerging field that has been a topic of discussion since the development of next generation sequencing and the implementation of the human microbiome project. This article reviews the current literature surrounding the oral microbiome, briefly highlighting most recent methods of microbiome characterization including cutting edge omics, databases for the microbiome, and areas with current gaps in knowledge. This article also describes reports on microorganisms contained in the oral microbiome which include viruses, archaea, fungi, and bacteria, and provides an in-depth analysis of their significant roles in tissue homeostasis. Finally, we detail key bacteria involved in oral disease, including oral cancer, and the current research surrounding their role in stimulation of inflammatory cytokines, the role of gingival crevicular fluid in periodontal disease, the creation of a network of interactions between microorganisms, the influence of the planktonic microbiome and cospecies biofilms, and the implications of antibiotic resistance. This paper provides a comprehensive literature analysis while also identifying gaps in knowledge to enable future studies to be conducted.
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Affiliation(s)
- Austin Gregory Morrison
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Soumyadev Sarkar
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Shahid Umar
- Department of General Surgery, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Sonny T. M. Lee
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
- 1717 Claflin Road, 136 Ackert Hall, Manhattan, KS 66506, USA
| | - Sufi Mary Thomas
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Departments of Otolaryngology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Departments of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- 3901 Rainbow Blvd., 4031 Wahl Hall East, MS 3040, Kansas City, KS 66160, USA
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Yamaguchi-Kuroda Y, Kikuchi Y, Kokubu E, Ishihara K. Porphyromonas gingivalis diffusible signaling molecules enhance Fusobacterium nucleatum biofilm formation via gene expression modulation. J Oral Microbiol 2023; 15:2165001. [PMID: 36687169 PMCID: PMC9848294 DOI: 10.1080/20002297.2023.2165001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Background Periodontitis is caused by a dysbiotic shift in the dental plaque microbiome. Fusobacterium nucleatum is involved in the colonization of Porphyromonas gingivalis, which plays a key role in dysbiosis, via coaggregation and synergy with this microorganism. Aim We investigated the effect of diffusible signaling molecules from P. gingivalis ATCC 33277 on F. nucleatum TDC 100 to elucidate the synergistic mechanisms involved in dysbiosis. Methods The two species were cocultured separated with an 0.4-µm membrane in tryptic soy broth, and F. nucleatum gene expression profiles in coculture with P. gingivalis were compared with those in monoculture. Results RNA sequencing revealed 139 genes differentially expressed between the coculture and monoculture. The expression of 52 genes was upregulated, including the coaggregation ligand-coding gene. Eighty-seven genes were downregulated. Gene Ontology analysis indicated enrichment for the glycogen synthesis pathway and a decrease in de novo synthesis of purine and pyrimidine. Conclusion These results indicate that diffusible signaling molecules from P. gingivalis induce metabolic changes in F. nucleatum, including an increase in polysaccharide synthesis and reduction in de novo synthesis of purine and pyrimidine. The metabolic changes may accelerate biofilm formation by F. nucleatum with P. gingivalis. Further, the alterations may represent potential therapeutic targets for preventing dysbiosis.
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Affiliation(s)
- Yukiko Yamaguchi-Kuroda
- Department of Endodontics, Tokyo Dental College, 2-9-18 Kanda-Misakicho, Tokyo 101-0061, Chiyoda-ku, Japan
| | - Yuichiro Kikuchi
- Department of Microbiology, Tokyo Dental College, 2-1-14 Kanda-Misakicho, Tokyo 101-0061, Chiyoda-ku, Japan
| | - Eitoyo Kokubu
- Department of Microbiology, Tokyo Dental College, 2-1-14 Kanda-Misakicho, Tokyo 101-0061, Chiyoda-ku, Japan
| | - Kazuyuki Ishihara
- Department of Microbiology, Tokyo Dental College, 2-1-14 Kanda-Misakicho, Tokyo 101-0061, Chiyoda-ku, Japan,CONTACT Kazuyuki Ishihara Department of Microbiology, Tokyo Dental College, 2-1-14 Kanda-Misakicho, Chiyoda-ku, Tokyo101-0061, Japan
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Fan Z, Tang P, Li C, Yang Q, Xu Y, Su C, Li L. Fusobacterium nucleatum and its associated systemic diseases: epidemiologic studies and possible mechanisms. J Oral Microbiol 2023; 15:2145729. [PMID: 36407281 PMCID: PMC9673791 DOI: 10.1080/20002297.2022.2145729] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background Fusobacterium nucleatum (F. nucleatum) is an anaerobic oral commensal and the major coaggregation bridge organism linking early and late colonisers. In recent years, a large number of studies suggest that F. nucleatum is closely related to the development of various systemic diseases, such as cardiovascular diseases, adverse pregnancy outcomes, inflammatory bowel diseases, cancer, Alzheimer's disease, respiratory infection, rheumatoid arthritis, etc. Objective To review the effect of F. nucleatum on systemic diseases and its possible pathogenesis and to open new avenues for prevention and treatment of F. nucleatum-associated systemic diseases. Design The research included every article published up to July 2022 featuring the keywords 'Systemic diseases' OR 'Atherosclerotic cardiovascular diseases' OR 'Atherosclerosis' OR 'Adverse pregnancy outcomes' OR 'Inflammatory bowel disease' OR 'Ulcerative colitis' OR 'Crohn’s disease' OR 'Cancers' OR 'Oral squamous cell carcinomas' OR 'Gastrointestinal cancers' OR 'Colorectal cancer' OR 'Breast cancer' OR 'Genitourinary cancers' OR 'Alzheimer’s disease ' OR 'Rheumatoid arthritis' OR 'Respiratory diseases' AND 'Fusobacterium nucleatum' OR 'Periodontal pathogen' OR 'Oral microbiota' OR 'Porphyromonas gingivalis' and was conducted in the major medical databases. Results F. nucleatum can induce immune response and inflammation in the body through direct or indirect pathways, and thus affect the occurrence and development of systemic diseases. Only by continuing to investigate the pathogenic lifestyles of F. nucleatum will we discover the divergent pathways that may be leveraged for diagnostic, preventive and therapeutic purposes.
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Affiliation(s)
- Zixin Fan
- Department of Periodontics, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Shanghai road 1, Nanjing, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Pengzhou Tang
- Department of Periodontics, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Shanghai road 1, Nanjing, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Cheng Li
- Department of Periodontics, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Shanghai road 1, Nanjing, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Qi Yang
- Department of Periodontics, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Shanghai road 1, Nanjing, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yan Xu
- Department of Periodontics, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Shanghai road 1, Nanjing, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chuan Su
- State KeyLaboratory of Reproductive Medicine, Jiangsu Key Laboratory of Pathogen Biology, Department of Pathogen Biology and Immunology, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lu Li
- Department of Periodontics, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Shanghai road 1, Nanjing, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
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关 志, 徐 天, 沈 松, 李 晓, 冯 强. [Pathways and Mechanisms of Periodontitis Contributing to Adverse Pregnancy Outcomes]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2023; 54:39-48. [PMID: 36647641 PMCID: PMC10409026 DOI: 10.12182/20230160501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Indexed: 01/18/2023]
Abstract
Periodontitis is a chronic oral inflammatory disease with a high incidence in the global population. Periodontal pathogens can colonize and infect multiple human tissues and organs through blood transmission, which is an important risk factor of many systemic diseases. Recently, the correlation between periodontitis and adverse pregnancy outcomes (APOs) has attracted growing research interest. Herein, we systematically reviewed the research progress in the relationship between periodontitis and APOs and summarized reported findings on the pathways and mechanisms by which periodontitis contributes to APOs. We also clarified that intrauterine infection caused by oral pathogens transmitted through blood is an important pathway by which periodontitis interferes with pregnancy. In addition, further research focused on the discovery of more APOs-related oral pathogenic bacteria and their virulence factors, analysis of the interaction between pathogenic bacteria and placental tissue, and pathogenic pathways of oral bacterial invasion of the fetus will promote thorough analysis of the specific molecular mechanism of how periodontitis affects APOs. Furthermore, the validation of the results of human population-based studies through animal/cell experiments and the translation into effective intervention strategies are of great clinical significance to the prevention and control of the occurrence and development of APOs.
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Affiliation(s)
- 志炜 关
- 山东大学齐鲁医学院口腔医学院·口腔医院 人体微生态实验室 山东省口腔组织再生重点实验室 山东省口腔生物材料与组织再生工程实验室 山东省口腔疾病临床医学研究中心 (济南 250012)Department of Human Microbiome, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, Shandong Key Laboratory of Oral Tissue Regeneration, Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, and Shandong Provincial Clinical Research Center for Oral Diseases, Jinan 250012, China
- 齐鲁师范学院生命科学学院 (济南 250200)School of Life Science, Qilu Normal University, Jinan 250200, China
| | - 天琪 徐
- 山东大学齐鲁医学院口腔医学院·口腔医院 人体微生态实验室 山东省口腔组织再生重点实验室 山东省口腔生物材料与组织再生工程实验室 山东省口腔疾病临床医学研究中心 (济南 250012)Department of Human Microbiome, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, Shandong Key Laboratory of Oral Tissue Regeneration, Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, and Shandong Provincial Clinical Research Center for Oral Diseases, Jinan 250012, China
| | - 松 沈
- 山东大学齐鲁医学院口腔医学院·口腔医院 人体微生态实验室 山东省口腔组织再生重点实验室 山东省口腔生物材料与组织再生工程实验室 山东省口腔疾病临床医学研究中心 (济南 250012)Department of Human Microbiome, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, Shandong Key Laboratory of Oral Tissue Regeneration, Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, and Shandong Provincial Clinical Research Center for Oral Diseases, Jinan 250012, China
| | - 晓 李
- 山东大学齐鲁医学院口腔医学院·口腔医院 人体微生态实验室 山东省口腔组织再生重点实验室 山东省口腔生物材料与组织再生工程实验室 山东省口腔疾病临床医学研究中心 (济南 250012)Department of Human Microbiome, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, Shandong Key Laboratory of Oral Tissue Regeneration, Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, and Shandong Provincial Clinical Research Center for Oral Diseases, Jinan 250012, China
| | - 强 冯
- 山东大学齐鲁医学院口腔医学院·口腔医院 人体微生态实验室 山东省口腔组织再生重点实验室 山东省口腔生物材料与组织再生工程实验室 山东省口腔疾病临床医学研究中心 (济南 250012)Department of Human Microbiome, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, Shandong Key Laboratory of Oral Tissue Regeneration, Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, and Shandong Provincial Clinical Research Center for Oral Diseases, Jinan 250012, China
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Kudra A, Muszyński D, Sobocki BK, Atzeni A, Carbone L, Kaźmierczak-Siedlecka K, Połom K, Kalinowski L. Insights into oral microbiome and colorectal cancer - on the way of searching new perspectives. Front Cell Infect Microbiol 2023; 13:1159822. [PMID: 37124035 PMCID: PMC10130407 DOI: 10.3389/fcimb.2023.1159822] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/28/2023] [Indexed: 05/02/2023] Open
Abstract
Microbiome is a keystone polymicrobial community that coexist with human body in a beneficial relationship. These microorganisms enable the human body to maintain homeostasis and take part in mechanisms of defense against infection and in the absorption of nutrients. Even though microbiome is involved in physiologic processes that are beneficial to host health, it may also cause serious detrimental issues. Additionally, it has been proven that bacteria can migrate to other human body compartments and colonize them even although significant structural differences with the area of origin exist. Such migrations have been clearly observed when the causes of genesis and progression of colorectal cancer (CRC) have been investigated. It has been demonstrated that the oral microbiome is capable of penetrating into the large intestine and cause impairments leading to dysbiosis and stimulation of cancerogenic processes. The main actors of such events seem to be oral pathogenic bacteria belonging to the red and orange complex (regarding classification of bacteria in the context of periodontal diseases), such as Porphyromonas gingivalis and Fusobacterium nucleatum respectively, which are characterized by significant amount of cancerogenic virulence factors. Further examination of oral microbiome and its impact on CRC may be crucial on early detection of this disease and would allow its use as a precise non-invasive biomarker.
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Affiliation(s)
- Anna Kudra
- Scientific Circle of Studies Regarding Personalized Medicine Associated with Department of Medical Laboratory Diagnostics, Medical University of Gdansk, Gdansk, Poland
| | - Damian Muszyński
- Scientific Circle of Studies Regarding Personalized Medicine Associated with Department of Medical Laboratory Diagnostics, Medical University of Gdansk, Gdansk, Poland
| | - Bartosz Kamil Sobocki
- Scientific Circle of Oncology and Radiotherapy, Medical University of Gdansk, Gdansk, Poland
| | - Alessandro Atzeni
- Institut d’Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Unitat de Nutrició, Reus, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain
| | - Ludovico Carbone
- Department of Medicine Surgery and Neuroscience, University of Siena, Siena, Italy
| | - Karolina Kaźmierczak-Siedlecka
- Department of Medical Laboratory Diagnostics – Fahrenheit Biobank BBMRI.pl, Medical University of Gdansk, Gdansk, Poland
- *Correspondence: Karolina Kaźmierczak-Siedlecka,
| | - Karol Połom
- Department of Surgical Oncology, Medical University of Gdansk, Gdansk, Poland
| | - Leszek Kalinowski
- Department of Medical Laboratory Diagnostics – Fahrenheit Biobank BBMRI.pl, Medical University of Gdansk, Gdansk, Poland
- BioTechMed Centre, Department of Mechanics of Materials and Structures, University of Technology, Gdansk, Poland
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Enhanced Fusobacterium nucleatum Genetics Using Host DNA Methyltransferases To Bypass Restriction-Modification Systems. J Bacteriol 2022; 204:e0027922. [PMID: 36326270 PMCID: PMC9764991 DOI: 10.1128/jb.00279-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial restriction-modification (R-M) systems are a first-line immune defense against foreign DNA from viruses and other bacteria. While R-M systems are critical in maintaining genome integrity, R-M nucleases unfortunately present significant barriers to targeted genetic modification. Bacteria of the genus Fusobacterium are oral, Gram-negative, anaerobic, opportunistic pathogens that are implicated in the progression and severity of multiple cancers and tissue infections, yet our understanding of their direct roles in disease have been severely hindered by their genetic recalcitrance. Here, we demonstrate a path to overcome these barriers in Fusobacterium by using native DNA methylation as a host mimicry strategy to bypass R-M system cleavage of transformed plasmid DNA. We report the identification, characterization, and successful use of Fusobacterium nucleatum type II and III DNA methyltransferase (MTase) enzymes to produce a multifold increase in gene knockout efficiency in the strain Fusobacterium nucleatum subsp. nucleatum 23726, as well as the first system for efficient gene knockouts and complementations in F. nucleatum subsp. nucleatum 25586. We show plasmid protection can be accomplished in vitro with purified enzymes, as well as in vivo in an Escherichia coli host that constitutively expresses F. nucleatum subsp. nucleatum MTase enzymes. In summary, this proof-of-concept study characterizes specific MTases that are critical for bypassing R-M systems and has enhanced our understanding of enzyme combinations that could be used to genetically modify clinical isolates of Fusobacterium that have thus far been inaccessible to molecular characterization. IMPORTANCE Fusobacterium nucleatum is an oral opportunistic pathogen associated with diseases that include cancer and preterm birth. Our understanding of how this bacterium modulates human disease has been hindered by a lack of genetic systems. Here, we show that F. nucleatum DNA methyltransferase-modified plasmid DNA overcomes the transformation barrier and has allowed the development of a genetic system in a previously inaccessible strain. We present a strategy that could potentially be expanded to enable the genetic modification of highly recalcitrant strains, thereby fostering investigational studies to uncover novel host-pathogen interactions in Fusobacterium.
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