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Keles NA, Dogan S, Dogan A, Sudagidan M, Balci TN, Cetiner O, Kavruk M, Ozalp VC, Tuna BG. Long-term intermittent caloric restriction remodels the gut microbiota in mice genetically prone to breast cancer. Nutrition 2024; 126:112525. [PMID: 39168040 DOI: 10.1016/j.nut.2024.112525] [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: 12/25/2023] [Revised: 06/10/2024] [Accepted: 06/21/2024] [Indexed: 08/23/2024]
Abstract
OBJECTIVES Gut microbiota dysbiosis is among the risk factors for breast cancer development, together with genetic background and dietary habits. However, caloric restriction has been shown to remodel the gut microbiota and slow tumor growth. Here, we investigated whether the gut microbiota mediates the preventive effects of long-term chronic or intermittent caloric restriction on breast cancer predisposition. METHODS 10-week-old transgenic breast cancer-prone mice were randomly assigned to dietary groups (ad libitum, chronic caloric restriction, and intermittent caloric restriction groups) and fed up to week 81. Stool samples were collected at weeks 10 (baseline), 17 (young), 49 (adult), and 81 (old). 16S rRNA gene sequencing was performed to identify the gut microbiota profile of the different groups. In order to investigate the breast cancer gut microbiota profile within genetically predisposed individuals regardless of diet, mammary tumor-bearing mice and mammary tumor-free but genetically prone mice were selected from the ad libitum group (n = 6). RESULTS Intermittent caloric restriction increased the microbial diversity of adult mice and modified age-related compositional changes. A total of 13 genera were differentially abundant over time. Pathogenic Mycoplasma was enriched in the re-feeding period of the old intermittent caloric restriction group compared with baseline. Furthermore, mammary tumor-free mice showed shared gut microbiota characteristics with mammary tumor-bearing mice, suggesting an early link between genetic predisposition, gut microbiota, and breast cancer development. CONCLUSIONS Our study revealed the role of gut microbes in the preventive effects of caloric restriction against breast cancer development, implying the significance of diet and microbiome interplay.
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Affiliation(s)
- Nazim Arda Keles
- Department of Medical Biology, School of Medicine, Yeditepe University, Istanbul, Turkey
| | - Soner Dogan
- Department of Medical Biology, School of Medicine, Yeditepe University, Istanbul, Turkey
| | - Aysenur Dogan
- Department of Medical Biology, School of Medicine, Yeditepe University, Istanbul, Turkey
| | - Mert Sudagidan
- Department of Medical Biology, School of Medicine, Atilim University, Ankara, Turkey
| | - Tugce Nur Balci
- Department of Nutrition and Dietetics, School of Health Sciences, Atilim University, Ankara, Turkey
| | - Ozlem Cetiner
- Department of Nutrition and Dietetics, School of Health Sciences, Atilim University, Ankara, Turkey
| | - Murat Kavruk
- Department of Medical Biology, School of Medicine, Istanbul Aydin University, Istanbul, Turkey
| | - Veli Cengiz Ozalp
- Department of Medical Biology, School of Medicine, Atilim University, Ankara, Turkey
| | - Bilge Guvenc Tuna
- Department of Biophysics, School of Medicine, Yeditepe University, Istanbul, Turkey.
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Moreira MM, Carriço M, Capelas ML, Pimenta N, Santos T, Ganhão-Arranhado S, Mäkitie A, Ravasco P. The impact of pre-, pro- and synbiotics supplementation in colorectal cancer treatment: a systematic review. Front Oncol 2024; 14:1395966. [PMID: 38807764 PMCID: PMC11130488 DOI: 10.3389/fonc.2024.1395966] [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: 03/04/2024] [Accepted: 04/22/2024] [Indexed: 05/30/2024] Open
Abstract
Introduction The effectiveness of the supplementation of prebiotics, probiotics and synbiotics as a therapeutic approach in colorectal cancer (CRC) remains unclear. The aim of this systematic review is to critically examine the current scientific evidence on the impact of modulating the microbiota, through the use of prebiotics, probiotics and synbiotics, in patients diagnosed with CRC undergoing treatment, to determine the potential therapeutic use of this approach. Methods This systematic review was made according to the PRISMA 2020 guidelines. Inclusion criteria were randomized controlled trials (RCT) comparing the impact of pre-, pro-, or synbiotic supplementation with placebo or standard care in patients with CRC undergoing treatment. Exclusion criteria were non-human studies, non-RCTs, and studies in languages other than English or Portuguese. Six databases were consulted, namely, Cochrane Library, Pubmed, Scopus, Cinahl, MedicLatina and Web of Science until May of 2023. RAYYAN software was used to manage the search results and risk of bias was assessed according to the guidelines of the Cochrane Collaboration using the Rob 2.0 tool. Results Twenty-four RCTs met the inclusion criteria and were included in this review. Administration of pre-, pro-, or synbiotics improved surgical outcomes such as the incidence of infectious and non-infectious postoperative complications, return to normal gut function, hospital length of stay, and antibiotic usage. The supplementation of these microorganisms also alleviated some symptoms from chemotherapy and radiotherapy, mainly diarrhea. Evidence on the best approach in terms of types of strains, dosage and duration of intervention is still scarce. Conclusions Pre-, pro-, and synbiotics supplementation appears to be a beneficial therapeutic approach in CRC treatment to improve surgical outcomes and to alleviate side-effects such as treatment toxicity. More RCTs with larger sample sizes and less heterogeneity are needed to confirm these potential benefits and to determine the best strains, dosage, and duration of administration in each situation. Systematic review registration https://www.crd.york.ac.uk/prospero, identifier CRD42023413958.
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Affiliation(s)
- Mariana Melo Moreira
- Universidade Católica Portuguesa, Faculty of Health Sciences and Nursing (FCSE), Lisboa, Portugal
| | - Marta Carriço
- Champalimaud Foundation, Nutrition Service of Champalimaud Clinical Center, Lisbon, Portugal
| | - Manuel Luís Capelas
- Universidade Católica Portuguesa, Faculty of Health Sciences and Nursing (FCSE), Lisboa, Portugal
- Universidade Católica Portuguesa, Center for Interdisciplinary Research in Health (CIIS), Lisbon, Portugal
| | - Nuno Pimenta
- Universidade Católica Portuguesa, Center for Interdisciplinary Research in Health (CIIS), Lisbon, Portugal
- Polytechnic Institute of Santarém, Sport Sciences School of Rio Maior, Rio Maior, Portugal
- Sport Physical Activity and Health Research and Innovation Center (SPRINT), Santarém Polytechnic University, Rio Maior, Portugal
| | - Teresa Santos
- Universidade Católica Portuguesa, Center for Interdisciplinary Research in Health (CIIS), Lisbon, Portugal
- Faculdade de Ciências Sociais e Tecnologia, Universidade Europeia de Lisboa, Lisbon, Portugal
| | - Susana Ganhão-Arranhado
- Universidade Católica Portuguesa, Center for Interdisciplinary Research in Health (CIIS), Lisbon, Portugal
- Atlântica, Instituto Universitário, Barcarena, Portugal
- CINTESIS, Centre for Health Technology and Services Research, Porto, Portugal
| | - Antti Mäkitie
- Universidade Católica Portuguesa, Center for Interdisciplinary Research in Health (CIIS), Lisbon, Portugal
- Department of Otorhinolaryngology-Head and Neck Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Division of Ear, Nose and Throat Diseases, Department of Clinical Sciences, Intervention and Technology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Paula Ravasco
- Universidade Católica Portuguesa, Center for Interdisciplinary Research in Health (CIIS), Lisbon, Portugal
- Universidade Católica Portuguesa, Católica Medical School, Rio de Mouro, Portugal
- Center for Interdisciplinary Research Egas Moniz, Egas Moniz School of Health & Science, Almada, Portugal
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3
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Metsäniitty M, Hasnat S, Öhman C, Salo T, Eklund KK, Oscarsson J, Salem A. Extracellular vesicles from Aggregatibacter actinomycetemcomitans exhibit potential antitumorigenic effects in oral cancer: a comparative in vitro study. Arch Microbiol 2024; 206:244. [PMID: 38702412 PMCID: PMC11068833 DOI: 10.1007/s00203-024-03976-8] [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: 03/11/2024] [Accepted: 04/24/2024] [Indexed: 05/06/2024]
Abstract
Aggregatibacter actinomycetemcomitans is an opportunistic Gram-negative periodontopathogen strongly associated with periodontitis and infective endocarditis. Recent evidence suggests that periodontopathogens can influence the initiation and progression of oral squamous cell carcinoma (OSCC). Herein we aimed to investigate the effect of A. actinomycetemcomitans-derived extracellular vesicles (EVs) on OSCC cell behavior compared with EVs from periodontopathogens known to associate with carcinogenesis. EVs were isolated from: A. actinomycetemcomitans and its mutant strains lacking the cytolethal distending toxin (CDT) or lipopolysaccharide (LPS) O-antigen; Porphyromonas gingivalis; Fusobacterium nucleatum; and Parvimonas micra. The effect of EVs on primary and metastatic OSCC cells was assessed using cell proliferation, apoptosis, migration, invasion, and tubulogenesis assays. A. actinomycetemcomitans-derived EVs reduced the metastatic cancer cell proliferation, invasion, tubulogenesis, and increased apoptosis, mostly in CDT- and LPS O-antigen-dependent manner. EVs from F. nucleatum impaired the metastatic cancer cell proliferation and induced the apoptosis rates in all OSCC cell lines. EVs enhanced cancer cell migration regardless of bacterial species. In sum, this is the first study demonstrating the influence of A. actinomycetemcomitans-derived EVs on oral cancer in comparison with other periodontopathogens. Our findings revealed a potential antitumorigenic effect of these EVs on metastatic OSCC cells, which warrants further in vivo investigations.
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Affiliation(s)
- Marjut Metsäniitty
- Department of Oral and Maxillofacial Diseases, Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland
| | - Shrabon Hasnat
- Department of Oral and Maxillofacial Diseases, Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland
| | - Carina Öhman
- Oral Microbiology, Department of Odontology, Umeå University, Umeå, 90187, Sweden
| | - Tuula Salo
- Department of Oral and Maxillofacial Diseases, Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland
| | - Kari K Eklund
- Department of Rheumatology, University of Helsinki and Helsinki University Hospital, Helsinki, 00014, Finland
- Translational Immunology Research Program (TRIMM), Research Program Unit (RPU), Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland
| | - Jan Oscarsson
- Oral Microbiology, Department of Odontology, Umeå University, Umeå, 90187, Sweden
| | - Abdelhakim Salem
- Department of Oral and Maxillofacial Diseases, Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland.
- Translational Immunology Research Program (TRIMM), Research Program Unit (RPU), Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland.
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Rashad N, Eid Salem S, Meheissen MA, Refaat G, Mahmoud Sami H, Temerik A, Kordy N, Daniel MA, El-Kaffas M, Esam M, El Mansy H, Elkerm Y, Abdelaziz Elsaid A, Attia Ismail A, Saber Abdelhalim M, Moustafa Ahmad L, Akram Mahmoud M, El Desouky ED. Early-Onset Colorectal Cancer in Egypt: Pathological Characters, Patterns of Care, and Survival Compared to Average-Age Onset Colorectal Cancer: A Retrospective Multicenter Study. JCO Glob Oncol 2024; 10:e2300372. [PMID: 38547440 PMCID: PMC10994464 DOI: 10.1200/go.23.00372] [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: 09/30/2023] [Revised: 01/27/2024] [Accepted: 02/06/2024] [Indexed: 04/02/2024] Open
Abstract
PURPOSE Early-onset colorectal cancer (EOCRC) is a rising health problem. The incidence of EOCRC has increased over the past 2 decades all over the world. Reports from Egypt since the 1990s have reported a higher incidence among young populations with no identifiable risk factors. The aim of this study was to assess EOCRC in Egypt regarding incidence, characteristics, treatment pattern, and survival compared with average age onset and elderly patients. MATERIALS AND METHODS This was a retrospective, record-based, cohort study combining data from four different cancer centers in Egypt. We grouped patients according to age into three categories: the EOCRC group for patients age ≤45 years and the average age onset and elderly cancer group (for patients age ≥65 years). RESULTS The study included 1,310 patients with histopathologically proven colorectal cancer, representing four different geographical areas in Egypt. Patients with EOCRC represented 42.4% of the study population. Female patients were 50.6% among the EOCRC group and 52.5% among the average age group. Rectal tumors were significantly higher in EOCRC (54.7% v 40.6%; P < .001). There was no significant difference between both groups regarding the tumor stage at presentation, obstruction, or presence of metastases at presentation. Patients with EOCRC had a significantly higher rate of peritoneum/adnexa metastases than the average age ones (12.3% in EOCRC v 6.9% in the average age group; P < .001). No statistically significant differences between EOCRC and average age groups in both disease-free survival and overall survival were reported. CONCLUSION A comprehensive framework for the study of EOCRC is required in Egypt as well as a genomic analysis to identify possible underlying genetic alterations responsible for the high incidence of EOCRC.
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Affiliation(s)
- Noha Rashad
- Medical Oncology Department, Shefaa Al-Orman Oncology Hospital, Luxor, Egypt
- Clinical Oncology Department, Faculty of Medicine, Suez University, Suez, Egypt
| | - Salem Eid Salem
- Department of Medical Oncology, National Cancer Institute (NCI), Cairo University, Cairo, Egypt
| | - Mohamed A.M. Meheissen
- Clinical Oncology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
- Hope Cancer Center, Alexandria, Egypt
| | - Ghada Refaat
- Clinical Oncology and Nuclear Medicine Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Heba Mahmoud Sami
- Department of Medical Oncology, National Cancer Institute (NCI), Cairo University, Cairo, Egypt
| | - Abdelsalam Temerik
- Medical Oncology Department, Shefaa Al-Orman Oncology Hospital, Luxor, Egypt
| | - Nashwa Kordy
- Biostatistics, Epidemiology and Science Computing Department, Shefaa Al-Orman Oncology Hospital, Luxor, Egypt
| | - Mina A. Daniel
- Medical Oncology Department, Shefaa Al-Orman Oncology Hospital, Luxor, Egypt
| | - Mohamed El-Kaffas
- Medical Oncology Department, Shefaa Al-Orman Oncology Hospital, Luxor, Egypt
| | - Mohamed Esam
- Medical Oncology Department, Shefaa Al-Orman Oncology Hospital, Luxor, Egypt
| | - Hazem El Mansy
- Department of Cancer Management and Research, Medical Research Institute, University of Alexandria, Alexandria, Egypt
- Specialized Universal Network of Oncology (SUN), Alexandria, Egypt
| | - Yasser Elkerm
- Department of Cancer Management and Research, Medical Research Institute, University of Alexandria, Alexandria, Egypt
- Specialized Universal Network of Oncology (SUN), Alexandria, Egypt
| | - Amr Abdelaziz Elsaid
- Clinical Oncology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
- Specialized Universal Network of Oncology (SUN), Alexandria, Egypt
| | - Abdelsalam Attia Ismail
- Clinical Oncology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
- Specialized Universal Network of Oncology (SUN), Alexandria, Egypt
| | | | - Lamiaa Moustafa Ahmad
- Clinical Oncology and Nuclear Medicine Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Mai Akram Mahmoud
- Clinical Oncology and Nuclear Medicine Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Eman D. El Desouky
- Department of Biostatistics and Epidemiology, National Cancer Institute, Cairo University, Cairo, Egypt
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5
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Najjary S, Kros JM, Stricker BH, Ruiter R, Shuai Y, Kraaij R, Van Steen K, van der Spek P, Van Eijck CHJ, Ikram MA, Ahmad S. Association of blood cell-based inflammatory markers with gut microbiota and cancer incidence in the Rotterdam study. Cancer Med 2024; 13:e6860. [PMID: 38366800 PMCID: PMC10904974 DOI: 10.1002/cam4.6860] [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: 08/31/2023] [Revised: 11/29/2023] [Accepted: 12/12/2023] [Indexed: 02/18/2024] Open
Abstract
The immune response-gut microbiota interaction is implicated in various human diseases, including cancer. Identifying the link between the gut microbiota and systemic inflammatory markers and their association with cancer will be important for our understanding of cancer etiology. The current study was performed on 8090 participants from the population-based Rotterdam study. We found a significant association (false discovery rate [FDR] ≤0.05) between lymphocytes and three gut microbial taxa, namely the family Streptococcaceae, genus Streptococcus, and order Lactobacillales. In addition, we identified 95 gut microbial taxa that were associated with inflammatory markers (p < 0.05). Analyzing the cancer data, we observed a significant association between higher systemic immune-inflammation index (SII) levels at baseline (hazard ratio (HR): 1.65 [95% confidence interval (CI); 1.10-2.46, p ≤ 0.05]) and a higher count of lymphocytes (HR: 1.38 [95% CI: 1.15-1.65, p ≤ 0.05]) and granulocytes (HR: 1.69 [95% CI: 1.40-2.03, p ≤ 0.05]) with increased risk of lung cancer after adjusting for age, sex, body mass index (BMI), and study cohort. This association was lost for SII and lymphocytes after additional adjustment for smoking (SII = HR:1.46 [95% CI: 0.96-2.22, p = 0.07] and lymphocytes = HR: 1.19 [95% CI: 0.97-1.46, p = 0.08]). In the stratified analysis, higher count of lymphocyte and granulocytes at baseline were associated with an increased risk of lung cancer in smokers after adjusting for age, sex, BMI, and study cohort (HR: 1.33 [95% CI: 1.09-1.62, p ≤0.05] and HR: 1.57 [95% CI: 1.28-1.92, p ≤0.05], respectively). Our study revealed a positive association between gut microbiota, higher SII levels, and higher lymphocyte and granulocyte counts, with an increased risk of developing lung cancer.
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Affiliation(s)
- Shiva Najjary
- Department of Pathology and Clinical Bioinformatics, The Tumor Immuno‐Pathology LaboratoryErasmus University Medical CenterRotterdamthe Netherlands
| | - Johan M. Kros
- Department of Pathology and Clinical Bioinformatics, The Tumor Immuno‐Pathology LaboratoryErasmus University Medical CenterRotterdamthe Netherlands
| | - Bruno H. Stricker
- Department of EpidemiologyErasmus University Medical CenterRotterdamthe Netherlands
| | - Rikje Ruiter
- Department of EpidemiologyErasmus University Medical CenterRotterdamthe Netherlands
| | - Yu Shuai
- Department of EpidemiologyErasmus University Medical CenterRotterdamthe Netherlands
| | - Robert Kraaij
- Department of Internal MedicineErasmus University Medical CenterRotterdamthe Netherlands
| | - Kristel Van Steen
- Department of Human Genetics, Laboratory for Systems MedicineCenter for Human Genetics, KU LeuvenLeuvenBelgium
| | - Peter van der Spek
- Department of Pathology and Clinical Bioinformatics, The Tumor Immuno‐Pathology LaboratoryErasmus University Medical CenterRotterdamthe Netherlands
| | | | - M. Arfan Ikram
- Department of EpidemiologyErasmus University Medical CenterRotterdamthe Netherlands
| | - Shahzad Ahmad
- Department of EpidemiologyErasmus University Medical CenterRotterdamthe Netherlands
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6
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Zhao L, Cunningham CM, Andruska AM, Schimmel K, Ali MK, Kim D, Gu S, Chang JL, Spiekerkoetter E, Nicolls MR. Rat microbial biogeography and age-dependent lactic acid bacteria in healthy lungs. Lab Anim (NY) 2024; 53:43-55. [PMID: 38297075 PMCID: PMC10834367 DOI: 10.1038/s41684-023-01322-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: 11/24/2022] [Accepted: 12/21/2023] [Indexed: 02/02/2024]
Abstract
The laboratory rat emerges as a useful tool for studying the interaction between the host and its microbiome. To advance principles relevant to the human microbiome, we systematically investigated and defined the multitissue microbial biogeography of healthy Fischer 344 rats across their lifespan. Microbial community profiling data were extracted and integrated with host transcriptomic data from the Sequencing Quality Control consortium. Unsupervised machine learning, correlation, taxonomic diversity and abundance analyses were performed to determine and characterize the rat microbial biogeography and identify four intertissue microbial heterogeneity patterns (P1-P4). We found that the 11 body habitats harbored a greater diversity of microbes than previously suspected. Lactic acid bacteria (LAB) abundance progressively declined in lungs from breastfed newborn to adolescence/adult, and was below detectable levels in elderly rats. Bioinformatics analyses indicate that the abundance of LAB may be modulated by the lung-immune axis. The presence and levels of LAB in lungs were further evaluated by PCR in two validation datasets. The lung, testes, thymus, kidney, adrenal and muscle niches were found to have age-dependent alterations in microbial abundance. The 357 microbial signatures were positively correlated with host genes in cell proliferation (P1), DNA damage repair (P2) and DNA transcription (P3). Our study established a link between the metabolic properties of LAB with lung microbiota maturation and development. Breastfeeding and environmental exposure influence microbiome composition and host health and longevity. The inferred rat microbial biogeography and pattern-specific microbial signatures could be useful for microbiome therapeutic approaches to human health and life quality enhancement.
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Affiliation(s)
- Lan Zhao
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA.
- VA Palo Alto Health Care System, Palo Alto, CA, USA.
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA.
| | - Christine M Cunningham
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Adam M Andruska
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Katharina Schimmel
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Md Khadem Ali
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Dongeon Kim
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Shenbiao Gu
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Jason L Chang
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Edda Spiekerkoetter
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Mark R Nicolls
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA.
- VA Palo Alto Health Care System, Palo Alto, CA, USA.
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA.
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Li X, Wu D, Li Q, Gu J, Gao W, Zhu X, Yin W, Zhu R, Zhu L, Jiao N. Host-microbiota interactions contributing to the heterogeneous tumor microenvironment in colorectal cancer. Physiol Genomics 2024; 56:221-234. [PMID: 38073489 DOI: 10.1152/physiolgenomics.00103.2023] [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: 09/01/2023] [Revised: 11/15/2023] [Accepted: 12/01/2023] [Indexed: 01/23/2024] Open
Abstract
Colorectal cancer (CRC) exhibits pronounced heterogeneity and is categorized into four widely accepted consensus molecular subtypes (CMSs) with unique tumor microenvironments (TMEs). However, the intricate landscape of the microbiota and host-microbiota interactions within these TMEs remains elusive. Using RNA-sequencing data from The Cancer Genome Atlas, we analyzed the host transcriptomes and intratumoral microbiome profiles of CRC samples. Distinct host genes and microbial genera were identified among the CMSs. Immune microenvironments were evaluated using CIBERSORTx and ESTIMATE, and microbial coabundance patterns were assessed with FastSpar. Through LASSO penalized regression, we explored host-microbiota associations for each CMS. Our analysis revealed distinct host gene signatures within the CMSs, which encompassed ferroptosis-related genes and specific immune microenvironments. Moreover, we identified 293, 153, 66, and 109 intratumoral microbial genera with differential abundance, and host-microbiota associations contributed to distinct TMEs, characterized by 829, 1,270, 634, and 1,882 robust gene-microbe associations for each CMS in CMS1-CMS4, respectively. CMS1 featured inflammation-related HSF1 activation and gene interactions within the endothelin pathway and Flammeovirga. Integrin-related genes displayed positive correlations with Sutterella in CMS2, whereas CMS3 spotlighted microbial associations with biosynthetic and metabolic pathways. In CMS4, genes involved in collagen biosynthesis showed positive associations with Sutterella, contributing to disruptions in homeostasis. Notably, immune-rich subtypes exhibited pronounced ferroptosis dysregulation, potentially linked to tissue microbial colonization. This comprehensive investigation delineates the diverse landscapes of the TME within each CMS, incorporating host genes, intratumoral microbiota, and their complex interactions. These findings shed light on previously uncharted mechanisms underpinning CRC heterogeneity and suggest potential therapeutic targets.NEW & NOTEWORTHY This study determined the following: 1) providing a comprehensive landscape of consensus molecular subtype (CMS)-specific tumor microenvironments (TMEs); 2) constructing CMS-specific networks, including host genes, intratumoral microbiota, and enriched pathways, analyzing their associations to uncover unique patterns that demonstrate the intricate interplay within the TME; and 3) revealing a connection between immune-rich subtypes and ferroptosis activation, suggesting a potential regulatory role of the microbiota in ferroptosis dysregulation of the colorectal cancer TME.
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Affiliation(s)
- Xiaoyi Li
- Department of Nephrology, Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Dingfeng Wu
- Department of Nephrology, Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Qiuyu Li
- Department of Nephrology, Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Jinglan Gu
- Department of Nephrology, Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Wenxing Gao
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Xinyue Zhu
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Wenjing Yin
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Ruixin Zhu
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Lixin Zhu
- Department of Colorectal Surgery, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Na Jiao
- Department of Nephrology, Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
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8
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An HJ, Partha MA, Lee H, Lau BT, Pavlichin DS, Almeda A, Hooker AC, Shin G, Ji HP. Tumor-associated microbiome features of metastatic colorectal cancer and clinical implications. Front Oncol 2024; 13:1310054. [PMID: 38304032 PMCID: PMC10833227 DOI: 10.3389/fonc.2023.1310054] [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: 10/09/2023] [Accepted: 12/20/2023] [Indexed: 02/03/2024] Open
Abstract
Background Colon microbiome composition contributes to the pathogenesis of colorectal cancer (CRC) and prognosis. We analyzed 16S rRNA sequencing data from tumor samples of patients with metastatic CRC and determined the clinical implications. Materials and methods We enrolled 133 patients with metastatic CRC at St. Vincent Hospital in Korea. The V3-V4 regions of the 16S rRNA gene from the tumor DNA were amplified, sequenced on an Illumina MiSeq, and analyzed using the DADA2 package. Results After excluding samples that retained <5% of the total reads after merging, 120 samples were analyzed. The median age of patients was 63 years (range, 34-82 years), and 76 patients (63.3%) were male. The primary cancer sites were the right colon (27.5%), left colon (30.8%), and rectum (41.7%). All subjects received 5-fluouracil-based systemic chemotherapy. After removing genera with <1% of the total reads in each patient, 523 genera were identified. Rectal origin, high CEA level (≥10 ng/mL), and presence of lung metastasis showed higher richness. Survival analysis revealed that the presence of Prevotella (p = 0.052), Fusobacterium (p = 0.002), Selenomonas (p<0.001), Fretibacterium (p = 0.001), Porphyromonas (p = 0.007), Peptostreptococcus (p = 0.002), and Leptotrichia (p = 0.003) were associated with short overall survival (OS, <24 months), while the presence of Sphingomonas was associated with long OS (p = 0.070). From the multivariate analysis, the presence of Selenomonas (hazard ratio [HR], 6.35; 95% confidence interval [CI], 2.38-16.97; p<0.001) was associated with poor prognosis along with high CEA level. Conclusion Tumor microbiome features may be useful prognostic biomarkers for metastatic CRC.
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Affiliation(s)
- Ho Jung An
- Department of Medical Oncology, St. Vincent’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Mira A. Partha
- Department of Electrical Engineering, Stanford University, Palo Alto, CA, United States
| | - HoJoon Lee
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Billy T. Lau
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Dmitri S. Pavlichin
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Alison Almeda
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Anna C. Hooker
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Giwon Shin
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Hanlee P. Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, United States
- Department of Electrical Engineering, Stanford University, Palo Alto, CA, United States
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9
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Park PH, Keith K, Calendo G, Jelinek J, Madzo J, Gharaibeh RZ, Ghosh J, Sapienza C, Jobin C, Issa JPJ. Association between gut microbiota and CpG island methylator phenotype in colorectal cancer. Gut Microbes 2024; 16:2363012. [PMID: 38860458 PMCID: PMC11174071 DOI: 10.1080/19490976.2024.2363012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/29/2024] [Indexed: 06/12/2024] Open
Abstract
The intestinal microbiota is an important environmental factor implicated in CRC development. Intriguingly, modulation of DNA methylation by gut microbiota has been reported in preclinical models, although the relationship between tumor-infiltrating bacteria and CIMP status is currently unexplored. In this study, we investigated tumor-associated bacteria in 203 CRC tumor cases and validated the findings using The Cancer Genome Atlas datasets. We assessed the abundance of Bacteroides fragilis, Escherichia coli, Fusobacterium nucleatum, and Klebsiella pneumoniae through qPCR analysis and observed enrichment of all four bacterial species in CRC samples. Notably, except for E. coli, all exhibited significant enrichment in cases of CIMP. This enrichment was primarily driven by a subset of cases distinguished by high levels of these bacteria, which we labeled as "Superhigh". The bacterial Superhigh status showed a significant association with CIMP (odds ratio 3.1, p-value = 0.013) and with MLH1 methylation (odds ratio 4.2, p-value = 0.0025). In TCGA CRC cases (393 tumor and 45 adj. normal), bacterial taxa information was extracted from non-human whole exome sequencing reads, and the bacterial Superhigh status was similarly associated with CIMP (odds ratio 2.9, p < 0.001) and MLH1 methylation (odds ratio 3.5, p < 0.001). Finally, 16S ribosomal RNA gene sequencing revealed high enrichment of Bergeyella spp. C. concisus, and F. canifelinum in CIMP-Positive tumor cases. Our findings highlight that specific bacterial taxa may influence DNA methylation, particularly in CpG islands, and contribute to the development and progression of CIMP in colorectal cancer.
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Affiliation(s)
- Pyoung Hwa Park
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
| | - Kelsey Keith
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
| | - Gennaro Calendo
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
| | - Jaroslav Jelinek
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
- Biomedical Sciences, Cooper Medical School at Rowan University, Camden, NJ, USA
| | - Jozef Madzo
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
- Biomedical Sciences, Cooper Medical School at Rowan University, Camden, NJ, USA
| | - Raad Z. Gharaibeh
- Department of Medicine, University of Florida, Gainesville, FL, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Jayashri Ghosh
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Carmen Sapienza
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Jean-Pierre J. Issa
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
- Biomedical Sciences, Cooper Medical School at Rowan University, Camden, NJ, USA
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10
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Cai JA, Zhang YZ, Yu ED, Ding WQ, Li ZS, Zhong L, Cai QC. Association of cigarette smoking with risk of colorectal cancer subtypes classified by gut microbiota. Tob Induc Dis 2023; 21:99. [PMID: 37529669 PMCID: PMC10377954 DOI: 10.18332/tid/168515] [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: 11/05/2022] [Revised: 06/17/2023] [Accepted: 06/19/2023] [Indexed: 08/03/2023] Open
Abstract
INTRODUCTION Both cigarette smoking and gut microbiota play important roles in colorectal carcinogenesis. We explored whether the association between smoking and colorectal cancer (CRC) risk varies by gut microbial enterotypes and how smoking-related enterotypes promote colorectal carcinogenesis. METHODS A case-control study was conducted. Fecal microbiota was determined by 16S rDNA sequencing. The cases with CRC or adenoma were subclassified by gut microbiota enterotypes. Multivariate analyses were used to test associations between smoking and the odds of colorectal neoplasm subtypes. Mann-Whitney U tests were used to find differential genera, genes, and pathways between the subtypes. RESULTS Included in the study were 130 CRC patients (type I: n=77; type II: n=53), 120 adenoma patients (type I: n=66; type II: n=54), and 130 healthy participants. Smoking increased the odds for type II tumors significantly (all p for trend <0.05) but not for type I tumors. The associations of smoking with increased odds of colorectal neoplasm significantly differed by gut microbiota enterotypes (p<0.05 for heterogeneity). An increase in carcinogenic bacteria (genus Escherichia shigella) and a decrease in probiotics (family Lachnospiraceae and Ruminococcaceae) in type II tumors may drive disease progression by upregulating oncogenic signaling pathways and inflammatory/oxidative stress response pathways, as well as protein phospholipase D1/2, cytochrome C, and prostaglandin-endoperoxide synthase 2 expression. CONCLUSIONS Smoking was associated with a higher odds of type II colorectal neoplasms but not type I tumors, supporting a potential role for the gut microbiota in mediating the association between smoking and colorectal neoplasms.
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Affiliation(s)
- Jia-An Cai
- Department of Gastroenterology and Endoscopy, Huashan Hospital, Fudan University, Shanghai, China
| | - Yong-Zhen Zhang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- Department of Gastroenterology, 928 Hospital of PLA Joint Logistics Force, Haikou, China
| | - En-Da Yu
- Department of General Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Wei-Qun Ding
- Department of Gastroenterology and Endoscopy, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhao-Shen Li
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- National Clinical Research Center for Digestive Diseases, Shanghai, China
| | - Liang Zhong
- Department of Gastroenterology and Endoscopy, Huashan Hospital, Fudan University, Shanghai, China
| | - Quan-Cai Cai
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- National Clinical Research Center for Digestive Diseases, Shanghai, China
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11
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Katsaounou K, Yiannakou D, Nikolaou E, Brown C, Vogazianos P, Aristodimou A, Chi J, Costeas P, Agapiou A, Frangou E, Tsiaoussis G, Potamitis G, Antoniades A, Shammas C, Apidianakis Y. Fecal Microbiota and Associated Volatile Organic Compounds Distinguishing No-Adenoma from High-Risk Colon Adenoma Adults. Metabolites 2023; 13:819. [PMID: 37512526 PMCID: PMC10383435 DOI: 10.3390/metabo13070819] [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: 05/22/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Microbiota and the metabolites they produce within the large intestine interact with the host epithelia under the influence of a range of host-derived metabolic, immune, and homeostatic factors. This complex host-microbe interaction affects intestinal tumorigenesis, but established microbial or metabolite profiles predicting colorectal cancer (CRC) risk are missing. Here, we aimed to identify fecal bacteria, volatile organic compounds (VOC), and their associations that distinguish healthy (non-adenoma, NA) from CRC prone (high-risk adenoma, HRA) individuals. Analyzing fecal samples obtained from 117 participants ≥15 days past routine colonoscopy, we highlight the higher abundance of Proteobacteria and Parabacteroides distasonis, and the lower abundance of Lachnospiraceae species, Roseburia faecis, Blautia luti, Fusicatenibacter saccharivorans, Eubacterium rectale, and Phascolarctobacterium faecium in the samples of HRA individuals. Volatolomic analysis of samples from 28 participants revealed a higher concentration of five compounds in the feces of HRA individuals, isobutyric acid, methyl butyrate, methyl propionate, 2-hexanone, and 2-pentanone. We used binomial logistic regression modeling, revealing 68 and 96 fecal bacteria-VOC associations at the family and genus level, respectively, that distinguish NA from HRA endpoints. For example, isobutyric acid associations with Lachnospiraceae incertae sedis and Bacteroides genera exhibit positive and negative regression lines for NA and HRA endpoints, respectively. However, the same chemical associates with Coprococcus and Colinsella genera exhibit the reverse regression line trends. Thus, fecal microbiota and VOC profiles and their associations in NA versus HRA individuals indicate the significance of multiple levels of analysis towards the identification of testable CRC risk biomarkers.
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Affiliation(s)
- Kyriaki Katsaounou
- Department of Biological Sciences, University of Cyprus, Nicosia 2109, Cyprus
| | | | | | | | | | | | | | | | - Agapios Agapiou
- Department of Chemistry, University of Cyprus, Nicosia 2109, Cyprus
| | | | | | | | | | | | - Yiorgos Apidianakis
- Department of Biological Sciences, University of Cyprus, Nicosia 2109, Cyprus
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12
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Zhao L, Cunningham CM, Andruska AM, Schimmel K, Ali MK, Kim D, Gu S, Chang JL, Spiekerkoetter E, Nicolls MR. Rat microbial biogeography and age-dependent lactic acid bacteria in healthy lungs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.541527. [PMID: 37293045 PMCID: PMC10245737 DOI: 10.1101/2023.05.19.541527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The laboratory rat emerges as a useful tool for studying the interaction between the host and its microbiome. To advance principles relevant to the human microbiome, we systematically investigated and defined a multi-tissue full lifespan microbial biogeography for healthy Fischer 344 rats. Microbial community profiling data was extracted and integrated with host transcriptomic data from the Sequencing Quality Control (SEQC) consortium. Unsupervised machine learning, Spearman's correlation, taxonomic diversity, and abundance analyses were performed to determine and characterize the rat microbial biogeography and the identification of four inter-tissue microbial heterogeneity patterns (P1-P4). The 11 body habitats harbor a greater diversity of microbes than previously suspected. Lactic acid bacteria (LAB) abundances progressively declined in lungs from breastfeed newborn to adolescence/adult and was below detectable levels in elderly rats. LAB's presence and levels in lungs were further evaluated by PCR in the two validation datasets. The lung, testes, thymus, kidney, adrenal, and muscle niches were found to have age-dependent alterations in microbial abundance. P1 is dominated by lung samples. P2 contains the largest sample size and is enriched for environmental species. Liver and muscle samples were mostly classified into P3. Archaea species were exclusively enriched in P4. The 357 pattern-specific microbial signatures were positively correlated with host genes in cell migration and proliferation (P1), DNA damage repair and synaptic transmissions (P2), as well as DNA transcription and cell cycle in P3. Our study established a link between metabolic properties of LAB with lung microbiota maturation and development. Breastfeeding and environmental exposure influence microbiome composition and host health and longevity. The inferred rat microbial biogeography and pattern-specific microbial signatures would be useful for microbiome therapeutic approaches to human health and good quality of life.
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13
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Nearing JT, DeClercq V, Langille MGI. Investigating the oral microbiome in retrospective and prospective cases of prostate, colon, and breast cancer. NPJ Biofilms Microbiomes 2023; 9:23. [PMID: 37127667 PMCID: PMC10151362 DOI: 10.1038/s41522-023-00391-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 04/14/2023] [Indexed: 05/03/2023] Open
Abstract
The human microbiome has been proposed as a potentially useful biomarker for several cancers. To examine this, we made use of salivary samples from the Atlantic Partnership for Tomorrow's Health (PATH) project and Alberta's Tomorrow Project (ATP). Sample selection was divided into both a retrospective and prospective case control design examining prostate, breast, and colon cancer. In total 89 retrospective and 260 prospective cancer cases were matched to non-cancer controls and saliva samples were sequenced using 16S rRNA gene sequencing. We found no significant differences in alpha diversity. All beta diversity measures were insignificant except for unweighted UniFrac profiles in retrospective breast cancer cases and weighted UniFrac, Bray-Curtis and Robust Atchinson's distances in colon cancer after testing with age and sex adjusted MiRKAT models. Differential abundance (DA) analysis showed several taxa that were associated with previous cancer in all three groupings. Only one genus (Clostridia UCG-014) in breast cancer and one ASV (Fusobacterium periodonticum) in colon cancer was identified by more than one DA tool. In prospective cases three ASVs were associated with colon cancer, one ASV with breast cancer, and one ASV with prostate cancer. Random Forest classification showed low levels of signal in both study designs in breast and prostate cancer. Contrastingly, colon cancer did show signal in our retrospective analysis (AUC: 0.737) and in one of two prospective cohorts (AUC: 0.717). Our results indicate that it is unlikely that reliable microbial oral biomarkers for breast and prostate cancer exist.. However, further research into the oral microbiome and colon cancer could be fruitful.
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Affiliation(s)
- Jacob T Nearing
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada.
| | - Vanessa DeClercq
- Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Morgan G I Langille
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
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14
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Higashi DL, Krieger MC, Qin H, Zou Z, Palmer EA, Kreth J, Merritt J. Who is in the driver's seat? Parvimonas micra: An understudied pathobiont at the crossroads of dysbiotic disease and cancer. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023. [PMID: 36999244 DOI: 10.1111/1758-2229.13153] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/24/2023] [Indexed: 06/19/2023]
Abstract
Recent advances in our understanding of microbiome composition at sites of inflammatory dysbiosis have triggered a substantial interest in a variety of historically understudied bacteria, especially among fastidious obligate anaerobes. A plethora of new evidence suggests that these microbes play outsized roles in establishing synergistic polymicrobial infections at many different sites in the human body. Parvimonas micra is a prime example of such an organism. Despite being almost completely uncharacterized at the genetic level, it is one of the few species commonly detected in abundance at multiple mucosal sites experiencing either chronic or acute inflammatory diseases, and more recently, it has been proposed as a discriminating biomarker for multiple types of malignancies. In the absence of disease, P. micra is commonly found in low abundance, typically residing within the oral cavity and gastrointestinal tract. P. micra exhibits the typical features of an inflammophilic organism, meaning its growth actually benefits from active inflammation and inflammatory tissue destruction. In this mini-review, we will describe our current understanding of this underappreciated but ubiquitous pathobiont, specifically focusing upon the role of P. micra in polymicrobial inflammatory dysbiosis and cancer as well as the key emerging questions regarding its pathobiology. Through this timely work, we highlight Parvimonas micra as a significant driver of disease and discuss its unique position at the crossroads of dysbiosis and cancer.
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Affiliation(s)
- Dustin L Higashi
- Department of Restorative Dentistry, Oregon Health and Science University, Portland, Oregon, USA
| | - Madeline C Krieger
- Department of Restorative Dentistry, Oregon Health and Science University, Portland, Oregon, USA
| | - Hua Qin
- Department of Restorative Dentistry, Oregon Health and Science University, Portland, Oregon, USA
| | - Zhengzhong Zou
- Department of Restorative Dentistry, Oregon Health and Science University, Portland, Oregon, USA
| | - Elizabeth A Palmer
- Department of Pediatric Dentistry, Oregon Health and Science University, Portland, Oregon, USA
| | - Jens Kreth
- Department of Restorative Dentistry, Oregon Health and Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA
| | - Justin Merritt
- Department of Restorative Dentistry, Oregon Health and Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA
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15
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Zhao L, Luo JL, Ali MK, Spiekerkoetter E, Nicolls MR. The Human Respiratory Microbiome: Current Understandings and Future Directions. Am J Respir Cell Mol Biol 2023; 68:245-255. [PMID: 36476129 PMCID: PMC9989478 DOI: 10.1165/rcmb.2022-0208tr] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Microorganisms colonize the human body. The lungs and respiratory tract, previously believed to be sterile, harbor diverse microbial communities and the genomes of bacteria (bacteriome), viruses (virome), and fungi (mycobiome). Recent advances in amplicon and shotgun metagenomic sequencing technologies and data-analyzing methods have greatly aided the identification and characterization of microbial populations from airways. The respiratory microbiome has been shown to play roles in human health and disease and is an area of rapidly emerging interest in pulmonary medicine. In this review, we provide updated information in the field by focusing on four lung conditions, including asthma, chronic obstructive pulmonary disease, cystic fibrosis, and idiopathic pulmonary fibrosis. We evaluate gut, oral, and upper airway microbiomes and how they contribute to lower airway flora. The discussion is followed by a systematic review of the lower airway microbiome in health and disease. We conclude with promising research avenues and implications for evolving therapeutics.
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Affiliation(s)
- Lan Zhao
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, and.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, California.,VA Palo Alto Health Care System, Palo Alto, California; and
| | - Jun-Li Luo
- The Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, China
| | - Mohammed Khadem Ali
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, and.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, California
| | - Edda Spiekerkoetter
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, and.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, California
| | - Mark R Nicolls
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, and.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, California.,VA Palo Alto Health Care System, Palo Alto, California; and
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16
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Qi-Long-Tian capsule alleviates pulmonary fibrosis development by modulating inflammatory response and gut microbiota. Funct Integr Genomics 2023; 23:64. [PMID: 36810971 DOI: 10.1007/s10142-023-00988-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/24/2023]
Abstract
Pulmonary fibrosis (PF) is a chronic, progressive, and fibrotic interstitial lung disease with a high mortality rate. Qi-Long-Tian (QLT) capsule is an herbal formula with great potential for antifibrotic effects, consisting of San Qi (Notoginseng Radix et Rhizoma), Di Long [Pheretima aspergillum (E. Perrier)], and Hong Jingtian (Rhodiolae Crenulatae Radix et Rhizoma), and has been used in clinical practice for many years. To explore the relationship between the effects of Qi-Long-Tian capsule and gut microbiota of PF mice, pulmonary fibrosis model were established by tracheal drip injection of bleomycin. Thirty-six mice were randomly divided into 6 groups: control group (control), model group (model), QLT capsule low dose group (QL), QLT capsule medium dose group (QM), QLT capsule high dose group (QH), and pirfenidone group (PFD). After 21 days of treatment, after pulmonary function tests, the lung tissues, serums, and enterobacterial samples were collected for further analysis. HE staining and Masson's staining were used to detect changes as the main indicators of PF in each group, and the expression of hydroxyproline (HYP) related to collagen metabolism was detected by and alkaline hydrolysis method. qRT-PCR and ELISA were used to detect the mRNA and protein expressions of pro-inflammatory factors include interleukin 1β (IL-1β), interleukin 6 (IL-6), transforming growth factor β1 (TGF-β1), tumor necrosis factor α (TNF-α) in lung tissues and serums, and the inflammation-mediating factors include tight junction protein (ZO-1, Claudin, Occludin). ELISA was used to detect the protein expressions of secretory immunoglobulin A (sIgA), short-chain fatty acids (SCFAs), and lipopolysaccharide (LPS) in colonic tissues. 16sRNA gene sequencing was used to detect changes in the abundance and diversity of intestinal flora in the control, model, and QM groups, to search for differential genera, and analyze the correlation with inflammatory factors. QLT capsule effectively improved the status of pulmonary fibrosis and reduced HYP. In addition, QLT capsule significantly reduced the abnormal levels of pro-inflammatory factors, including IL-1β, IL-6, TNF-α, and TGF-β in lung tissue and serum, while improving the levels of pro-inflammatory related factors ZO-1, Claudin, Occludin, sIgA, SCFAs, and reducing LPS in the colon. The comparison between the alpha diversity and beta diversity in enterobacteria suggested that the composition of the gut flora in the control, model, and QLT capsule groups were different. QLT capsule significantly increased the relative abundance of Bacteroidia (which might limit the onset of inflammation) and decreased the relative abundance of Clostridia (which might promote inflammation). In addition, these two enterobacteria were closely associated with pro-inflammatory-related indicators and pro-inflammatory factors in PF. All these results suggest that QLT capsule intervenes in pulmonary fibrosis by regulating the differential genera of intestinal flora, increasing immunoglobulin secretion, repairing the intestinal mucosal barrier, reducing LPS entry into the blood, and decreasing inflammatory factor secretion in the serum, which in turn alleviates pulmonary inflammation. This study clarifies the therapeutic mechanism of QLT capsule in PF and provides a theoretical basis for it. It provides a theoretical basis for its further clinical application.
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17
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Lu Y, Li Z, Peng X. Regulatory effects of oral microbe on intestinal microbiota and the illness. Front Cell Infect Microbiol 2023; 13:1093967. [PMID: 36816583 PMCID: PMC9928999 DOI: 10.3389/fcimb.2023.1093967] [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: 11/09/2022] [Accepted: 01/16/2023] [Indexed: 02/04/2023] Open
Abstract
Over the past decade, the association between oral health, intestinal microbiota, and systemic diseases has been further validated. Some oral microbial species have been isolated from pathological intestine mucosa or feces and identified as biomarkers for intestinal diseases. A small proportion of oral microbiome passes through or colonizes the lower gastrointestinal tract, even in healthy individuals. Opportunistic pathogens from the oral cavity may expand and participate in the occurrence and progression of intestinal diseases when the anatomical barrier is disrupted. These disruptors interact with the intestinal microbiota, disturbing indigenous microorganisms, and mucosal barriers through direct colonization, blood circulation, or derived metabolite pathways. While interacting with the host's immune system, oral-derived pathogens stimulate inflammation responses and guide the transition of the intestinal microenvironment from a healthy state to a pre-disease state. Therefore, the oral-gut microbiome axis sheds light on new clinical therapy options, and gastrointestinal tract ecology balance necessitates simultaneous consideration of both oral and gut microbiomes. This review summarizes possible routes of oral microbes entering the intestine and the effects of certain oral bacteria on intestinal microbiota and the host's immune responses.
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18
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Dysbiotic microbiome variation in colorectal cancer patients is linked to lifestyles and metabolic diseases. BMC Microbiol 2023; 23:33. [PMID: 36709262 PMCID: PMC9883847 DOI: 10.1186/s12866-023-02771-7] [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] [Received: 09/07/2022] [Accepted: 01/12/2023] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Differences in the composition and diversity of the gut microbial communities among individuals are influenced by environmental factors. However, there is limited research on factors affecting microbiome variation in colorectal cancer patients, who display lower inter-individual variations than that of healthy individuals. In this study, we examined the association between modifiable factors and the microbiome variation in colorectal cancer patients. METHODS A total of 331 colorectal cancer patients who underwent resection surgery at the Department of Surgery, Seoul National University Hospital between October 2017 and August 2019 were included. Fecal samples from colorectal cancer patients were collected prior to the surgery. Variations in the gut microbiome among patients with different lifestyles and metabolic diseases were examined through the network analysis of inter-connected microbial abundance, the assessment of the Anna Karenina principle effect for microbial stochasticity, and the identification of the enriched bacteria using linear discrimination analysis effect size. Associations of dietary diversity with microbiome variation were investigated using the Procrustes analysis. RESULTS We found stronger network connectivity of microbial communities in non-smokers, non-drinkers, obese individuals, hypertensive subjects, and individuals without diabetes than in their counterparts. The Anna Karenina principle effect was found for history of smoking, alcohol consumption, and diabetes (with significantly greater intra-sample similarity index), whereas obesity and hypertension showed the anti-Anna Karenina principle effect (with significantly lower intra-sample similarity index). We found certain bacterial taxa to be significantly enriched in patients of different categories of lifestyles and metabolic diseases using linear discrimination analysis. Diversity of food and nutrient intake did not shape the microbial diversity between individuals (pProcrustes>0.05). CONCLUSIONS Our findings suggested an immune dysregulation and a reduced ability of the host and its microbiome in regulating the community composition. History of smoking, alcohol consumption, and diabetes were shown to affect partial individuals in shifting new microbial communities, whereas obesity and history of hypertension appeared to affect majority of individuals and shifted to drastic reductions in microbial compositions. Understanding the contribution of modifiable factors to microbial stochasticity may provide insights into how the microbiome regulates effects of these factors on the health outcomes of colorectal cancer patients.
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Kvakova M, Kamlarova A, Stofilova J, Benetinova V, Bertkova I. Probiotics and postbiotics in colorectal cancer: Prevention and complementary therapy. World J Gastroenterol 2022; 28:3370-3382. [PMID: 36158273 PMCID: PMC9346452 DOI: 10.3748/wjg.v28.i27.3370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/22/2022] [Accepted: 06/16/2022] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is a leading cause of human mortality worldwide. As conventional anticancer therapy not always being effective, there is growing interest in innovative “drug-free” cancer treatments or interventions that improve the efficacy of established therapy. CRC is associated with microbiome alterations, a process known as dysbiosis that involves depletion and/or enrichment of particular gut bacterial species and their metabolic functions. Supplementing patient treatment with traditional probiotics (with or without prebiotics), next-generation probiotics (NGP), or postbiotics represents a potentially effective and accessible complementary anticancer strategy by restoring gut microbiota composition and/or by signaling to the host. In this capacity, restoration of the gut microbiota in cancer patients can stabilize and enhance intestinal barrier function, as well as promote anticarcinogenic, anti-inflammatory, antimutagenic or other biologically important biochemical pathways that show high specificity towards tumor cells. Potential benefits of traditional probiotics, NGP, and postbiotics include modulating gut microbiota composition and function, as well as the host inflammatory response. Their application in CRC prevention is highlighted in this review, where we consider supportive in vitro, animal, and clinical studies. Based on emerging research, NGP and postbiotics hold promise in establishing innovative treatments for CRC by conferring physiological functions via the production of dominant natural products and metabolites that provide new host-microbiota signals to combat CRC. Although favorable results have been reported, further investigations focusing on strain and dose specificity are required to ensure the efficacy and safety of traditional probiotics, NGP, and postbiotics in CRC prevention and treatment.
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Affiliation(s)
- Monika Kvakova
- Center of Clinical and Preclinical Research MEDIPARK, Faculty of Medicine, P.J. Safarik University in Kosice, Kosice 04011, Slovakia
| | - Anna Kamlarova
- Center of Clinical and Preclinical Research MEDIPARK, Faculty of Medicine, P.J. Safarik University in Kosice, Kosice 04011, Slovakia
| | - Jana Stofilova
- Center of Clinical and Preclinical Research MEDIPARK, Faculty of Medicine, P.J. Safarik University in Kosice, Kosice 04011, Slovakia
| | - Veronika Benetinova
- Center of Clinical and Preclinical Research MEDIPARK, Faculty of Medicine, P.J. Safarik University in Kosice, Kosice 04011, Slovakia
| | - Izabela Bertkova
- Center of Clinical and Preclinical Research MEDIPARK, Faculty of Medicine, P.J. Safarik University in Kosice, Kosice 04011, Slovakia
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Wang Y, Li H. Gut microbiota modulation: a tool for the management of colorectal cancer. J Transl Med 2022; 20:178. [PMID: 35449107 PMCID: PMC9022293 DOI: 10.1186/s12967-022-03378-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/03/2022] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC) is the second cause of cancer death and the third most frequently diagnosed cancer. Besides the lifestyle, genetic and epigenetic alterations, and environmental factors, gut microbiota also plays a vital role in CRC development. The interruption of the commensal relationship between gut microbiota and the host could lead to an imbalance in the bacteria population, in which the pathogenic bacteria become the predominant population in the gut. Different therapeutic strategies have been developed to modify the gut immune system, prevent pathogen colonization, and alter the activity and composition of gut microbiota, such as prebiotics, probiotics, postbiotics, antibiotics, and fecal microbiota transplantation (FMT). Even though the employed strategies exhibit promising results, their translation into the clinic requires evaluating potential implications and risks, as well as assessment of their long-term effects. This study was set to review the gut microbiota imbalances and their relationship with CRC and their effects on CRC therapy, including chemotherapy and immunotherapy. More importantly, we reviewed the strategies that have been used to modulate gut microbiota, their impact on the treatment of CRC, and the challenges of each strategy.
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Affiliation(s)
- Yan Wang
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Hui Li
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
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Rockson SG, Zhou X, Zhao L, Hosseini DK, Jiang X, Sweatt AJ, Kim D, Tian W, Snyder MP, Nicolls MR. Exploring disease interrelationships in patients with lymphatic disorders: A single center retrospective experience. Clin Transl Med 2022; 12:e760. [PMID: 35452183 PMCID: PMC9028099 DOI: 10.1002/ctm2.760] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The lymphatic contribution to the circulation is of paramount importance in regulating fluid homeostasis, immune cell trafficking/activation and lipid metabolism. In comparison to the blood vasculature, the impact of the lymphatics has been underappreciated, both in health and disease, likely due to a less well-delineated anatomy and function. Emerging data suggest that lymphatic dysfunction can be pivotal in the initiation and development of a variety of diseases across broad organ systems. Understanding the clinical associations between lymphatic dysfunction and non-lymphatic morbidity provides valuable evidence for future investigations and may foster the discovery of novel biomarkers and therapies. METHODS We retrospectively analysed the electronic medical records of 724 patients referred to the Stanford Center for Lymphatic and Venous Disorders. Patients with an established lymphatic diagnosis were assigned to groups of secondary lymphoedema, lipoedema or primary lymphovascular disease. Individuals found to have no lymphatic disorder were served as the non-lymphatic controls. The prevalence of comorbid conditions was enumerated. Pairwise co-occurrence pattern analyses, validated by Jaccard similarity tests, was utilised to investigate disease-disease interrelationships. RESULTS Comorbidity analyses underscored the expected relationship between the presence of secondary lymphoedema and those diseases that damage the lymphatics. Cardiovascular conditions were common in all lymphatic subgroups. Additionally, statistically significant alteration of disease-disease interrelationships was noted in all three lymphatic categories when compared to the control population. CONCLUSIONS The presence or absence of a lymphatic disease significantly influences disease interrelationships in the study cohorts. As a physiologic substrate, the lymphatic circulation may be an underappreciated participant in disease pathogenesis. These relationships warrant further, prospective scrutiny and study.
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Affiliation(s)
- Stanley G Rockson
- Stanford Center for Lymphatic and Venous Disorders, Division of Cardiovascular Medicine, Stanford University, School of Medicine, Stanford, California, USA
| | - Xin Zhou
- Department of Genetics, Stanford University, School of Medicine, Stanford, California, USA
| | - Lan Zhao
- Veteran Affairs Palo Alto Health Care System, Palo Alto, California, USA.,Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, School of Medicine, Stanford, California, USA
| | - Davood K Hosseini
- Stanford Center for Lymphatic and Venous Disorders, Division of Cardiovascular Medicine, Stanford University, School of Medicine, Stanford, California, USA
| | - Xinguo Jiang
- Veteran Affairs Palo Alto Health Care System, Palo Alto, California, USA.,Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, School of Medicine, Stanford, California, USA
| | - Andrew J Sweatt
- Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, School of Medicine, Stanford, California, USA
| | - Dongeon Kim
- Veteran Affairs Palo Alto Health Care System, Palo Alto, California, USA.,Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, School of Medicine, Stanford, California, USA
| | - Wen Tian
- Veteran Affairs Palo Alto Health Care System, Palo Alto, California, USA.,Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, School of Medicine, Stanford, California, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, School of Medicine, Stanford, California, USA
| | - Mark R Nicolls
- Veteran Affairs Palo Alto Health Care System, Palo Alto, California, USA.,Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, School of Medicine, Stanford, California, USA
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Zhao L, Cho WC, Luo JL. Exploring the patient-microbiome interaction patterns for pan-cancer. Comput Struct Biotechnol J 2022; 20:3068-3079. [PMID: 35782745 PMCID: PMC9233187 DOI: 10.1016/j.csbj.2022.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 11/03/2022] Open
Abstract
Cancer subtype-specific sets of microbiomes, making pan-cancer heterogeneity at the microbial level. Approximately 60% of the untreated cancer patients have experienced microbial composition changes in their tumor tissues. Colorectal cancer (CRC) was largely composed of two subtypes (S4 and S6) driven by different microbial profiles. The identified seven pan-cancer subtypes with 424 subtype-specific microbial signatures will help us find new therapeutic targets and better treatment strategies for cancer patients.
Microbes play important roles in human health and disease. Immunocompromised cancer patients are more vulnerable to getting microbial infections. Regions of hypoxia and acidic tumor microenvironment shape the microbial community diversity and abundance. Each cancer has its own microbiome, making cancer-specific sets of microbiomes. High-throughput profiling technologies provide a culture-free approach for microbial profiling in tumor samples. Microbial compositional data was extracted and examined from the TCGA unmapped transcriptome data. Biclustering, correlation, and statistical analyses were performed to determine the seven patient-microbe interaction patterns. These two-dimensional patterns consist of a group of microbial species that show significant over-representation over the 7 pan-cancer subtypes (S1-S7), respectively. Approximately 60% of the untreated cancer patients have experienced tissue microbial composition and functional changes between subtypes and normal controls. Among these changes, subtype S5 had loss of microbial diversity as well as impaired immune functions. S1, S2, and S3 had been enriched with microbial signatures derived from the Gammaproteobacteria, Actinobacteria and Betaproteobacteria, respectively. Colorectal cancer (CRC) was largely composed of two subtypes, namely S4 and S6, driven by different microbial profiles. S4 patients had increased microbial load, and were enriched with CRC-related oncogenic pathways. S6 CRC together with other cancer patients, making up almost 40% of all cases were classified into the S6 subtype, which not only resembled the normal control’s microbiota but also retained their original “normal-like” functions. Lastly, the S7 was a rare and understudied subtype. Our study investigated the pan-cancer heterogeneity at the microbial level. The identified seven pan-cancer subtypes with 424 subtype-specific microbial signatures will help us find new therapeutic targets and better treatment strategies for cancer patients.
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