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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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Adekoya AE, Kargbo HA, Ibberson CB. Defining microbial community functions in chronic human infection with metatranscriptomics. mSystems 2023; 8:e0059323. [PMID: 37823640 PMCID: PMC10734476 DOI: 10.1128/msystems.00593-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/31/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE The microbial diversity in polymicrobial infections (PMIs) allows for community members to establish interactions with one another, which can result in enhanced disease outcomes such as increased antibiotic tolerance and chronicity. Chronic PMIs result in large burdens on health systems, as they affect a significant proportion of the population and are expensive and difficult to treat. However, investigations into physiology of microbial communities in actual human infection sites are lacking. Here, we highlight that the predominant functions in chronic PMIs differ, and anaerobes, often described as bystanders, may be significant in the progression of chronic infections. Determining the community structure and functions in PMIs is a critical step toward understanding the molecular mechanisms that increase the virulence potential of the microbial community in these environments.
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Affiliation(s)
- Aanuoluwa E. Adekoya
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Hoody A. Kargbo
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Carolyn B. Ibberson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
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Agidigbi TS, Kwon HK, Knight JR, Zhao D, Lee FY, Oh I. Transcriptomic identification of genes expressed in invasive S. aureus diabetic foot ulcer infection. Front Cell Infect Microbiol 2023; 13:1198115. [PMID: 37434783 PMCID: PMC10332306 DOI: 10.3389/fcimb.2023.1198115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/25/2023] [Indexed: 07/13/2023] Open
Abstract
Introduction Infection in diabetic foot ulcers (DFUs) is one of the major complications associated with patients with diabetes. Staphylococcus aureus is the most common offending pathogen in patients with infected DFU. Previous studies have suggested the application of species-specific antibodies against S. aureus for diagnosis and monitoring treatment response. Early and accurate identification of the main pathogen is critical for management of DFU infection. Understanding the host immune response against species-specific infection may facilitate diagnosis and may suggest potential intervention options to promote healing infected DFUs. We sought to investigate evolving host transcriptome associated with surgical treatment of S. aureus- infected DFU. Methods This study compared the transcriptome profile of 21 patients with S. aureus- infected DFU who underwent initial foot salvage therapy with irrigation and debridement followed by intravenous antibiotic therapy. Blood samples were collected at the recruitment (0 weeks) and 8 weeks after therapy to isolate peripheral blood mononuclear cells (PBMCs). We analyzed the PBMC expression of transcriptomes at two different time points (0 versus 8 weeks). Subjects were further divided into two groups at 8 weeks: healed (n = 17, 80.95%) versus non-healed (n = 4, 19.05%) based on the wound healing status. DESeq2 differential gene analysis was performed. Results and discussion An increased expression of IGHG1, IGHG2, IGHG3, IGLV3-21, and IGLV6-57 was noted during active infection at 0 weeks compared with that at 8 weeks. Lysine- and arginine-rich histones (HIST1H2AJ, HIST1H2AL, HIST1H2BM, HIST1H3B, and HIST1H3G) were upregulated at the initial phase of active infection at 0 weeks. CD177 and RRM2 were also upregulated at the initial phase of active infection (0 weeks) compared with that at 8 weeks of follow-up. Genes of heat shock protein members (HSPA1A, HSPE1, and HSP90B1) were high in not healed patients compared with that in healed patients 8 weeks after therapy. The outcome of our study suggests that the identification of genes evolution based on a transcriptomic profiling could be a useful tool for diagnosing infection and assessing severity and host immune response to therapies.
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Affiliation(s)
- Taiwo Samuel Agidigbi
- Department of Orthopedics and Rehabilitation, Yale School of Medicine, New Haven, CT, United States
| | - Hyuk-Kwon Kwon
- Department of Orthopedics and Rehabilitation, Yale School of Medicine, New Haven, CT, United States
- Division of Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - James R. Knight
- Yale Center for Genome Analysis, Department of Genetics, Yale School of Medicine, New Haven, CT, United States
| | - Dejian Zhao
- Yale Center for Genome Analysis, Department of Genetics, Yale School of Medicine, New Haven, CT, United States
| | - Francis Y. Lee
- Department of Orthopedics and Rehabilitation, Yale School of Medicine, New Haven, CT, United States
| | - Irvin Oh
- Department of Orthopedics and Rehabilitation, Yale School of Medicine, New Haven, CT, United States
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Adekoya AE, Kargbo HA, Ibberson CB. Defining Microbial Community Functions in Chronic Human Infection with Metatranscriptomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543868. [PMID: 37333206 PMCID: PMC10274682 DOI: 10.1101/2023.06.06.543868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Chronic polymicrobial infections (cPMIs) harbor complex bacterial communities with diverse metabolic capacities, leading to competitive and cooperative interactions. Although the microbes present in cPMIs have been established through culture-dependent and-independent methods, the key functions that drive different cPMIs and the metabolic activities of these complex communities remain unknown. To address this knowledge gap, we analyzed 102 published metatranscriptomes collected from cystic fibrosis sputum (CF) and chronic wound infections (CW) to identify key bacterial members and functions in cPMIs. Community composition analysis identified a high prevalence of pathogens, particularly Staphylococcus and Pseudomonas, and anaerobic members of the microbiota, including Porphyromonas, Anaerococcus, and Prevotella. Functional profiling with HUMANn3 and SAMSA2 revealed that while functions involved in bacterial competition, oxidative stress response, and virulence were conserved across both chronic infection types, >40% of the functions were differentially expressed (padj < 0.05, fold-change >2). Higher expression of antibiotic resistance and biofilm functions were observed in CF, while tissue destructive enzymes and oxidative stress response functions were highly expressed in CW samples. Of note, strict anaerobes had negative correlations with traditional pathogens in both CW (P = -0.43) and CF (P = -0.27) samples and they significantly contributed to the expression of these functions. Additionally, we show microbial communities have unique expression patterns and distinct organisms fulfill the expression of key functions in each site, indicating the infection environment strongly influences bacterial physiology and that community structure influences function. Collectively, our findings indicate that community composition and function should guide treatment strategies for cPMIs.
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Affiliation(s)
- Aanuoluwa E. Adekoya
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019
| | - Hoody A. Kargbo
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019
| | - Carolyn B. Ibberson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019
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Meng H, Peng Y, Li P, Su J, Jiang Y, Fu X. Global trends in research of high-throughput sequencing technology associated with chronic wounds from 2002 to 2022: A bibliometric and visualized study. Front Surg 2023; 10:1089203. [PMID: 36911623 PMCID: PMC9992981 DOI: 10.3389/fsurg.2023.1089203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/06/2023] [Indexed: 02/24/2023] Open
Abstract
Background Chronic wounds are a complex medical problem. With the difficulty of skin healing, the microbial ecology of chronic wounds is an essential factor affecting wound healing. High-throughput sequencing (HTS) technology is a vital method to reveal the microbiome diversity and population structure of chronic wounds. Objective The aim of this paper was to delineate the scientific output characteristics, research trends, hotspots and frontiers of HTS technologies related to chronic wounds globally over the past 20 years. Methods We searched the Web of Science Core Collection (WoSCC) database for articles published between 2002 and 2022 and their full record information. The Bibliometrix software package was used to analyze bibliometric indicators and VOSviewer visualization analysis results. Results Ultimately, a total of 449 original articles were reviewed, and the results showed that the number of annual publications (Nps) about HTS associated with chronic wounds has steadily increased over the last 20 years. The United States and China produce the most articles and have the highest H-index, while the United States and England have the largest number of citations (Nc) in this field. The University of California, Wound Repair and Regeneration and National Institutes of Health Nih United States were the most published institutions, journals and fund resources, respectively. The global research could be divided into 3 clusters as follows: microbial infection of chronic wounds, the healing process of wounds and microscopic processes, skin repair mechanism stimulated by antimicrobial peptides and oxidative stress. In recent years, "wound healing", "infections", "expression", "inflammation", "chronic wounds", "identification" and "bacteria" "angiogenesis", "biofilms" and "diabetes" were the most frequently used keywords. In addition, research on "prevalence", "gene expression", "inflammation" and "infection" has recently become a hotspot. Conclusions This paper compares the research hotspots and directions in this field globally from the perspectives of countries, institutions and authors, analyzes the trend of international cooperation, and reveals the future development direction of the field and research hotspots of great scientific research value. Through this paper, we can further explore the value of HTS technology in chronic wounds to better solve the problem of chronic wounds.
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Affiliation(s)
- Hao Meng
- Research Center for Wound Repair and Tissue Regeneration, Medical Innovation Research Department, The PLA General Hospital, Beijing, China
| | - Yu Peng
- Research Center for Wound Repair and Tissue Regeneration, Medical Innovation Research Department, The PLA General Hospital, Beijing, China.,School of Medicine, Nankai University, Tianjin, China
| | - Pinxue Li
- School of Medicine, Nankai University, Tianjin, China
| | - Jianlong Su
- Research Center for Wound Repair and Tissue Regeneration, Medical Innovation Research Department, The PLA General Hospital, Beijing, China
| | - Yufeng Jiang
- Research Center for Wound Repair and Tissue Regeneration, Medical Innovation Research Department, The PLA General Hospital, Beijing, China
| | - Xiaobing Fu
- Research Center for Wound Repair and Tissue Regeneration, Medical Innovation Research Department, The PLA General Hospital, Beijing, China.,School of Medicine, Nankai University, Tianjin, China
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Lichtenberg M, Kvich L, Larsen SLB, Jakobsen TH, Bjarnsholt T. Inoculum Concentration Influences Pseudomonas aeruginosa Phenotype and Biofilm Architecture. Microbiol Spectr 2022; 10:e0313122. [PMID: 36354337 PMCID: PMC9769529 DOI: 10.1128/spectrum.03131-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/21/2022] [Indexed: 11/12/2022] Open
Abstract
In infections, bacterial cells are often found as relatively small multicellular aggregates characterized by a heterogeneous distribution of phenotype, genotype, and growth rates depending on their surrounding microenvironment. Many laboratory models fail to mimic these characteristics, and experiments are often initiated from planktonic bacteria given optimal conditions for rapid growth without concerns about the microenvironmental characteristics during biofilm maturation. Therefore, we investigated how the initial bacterial concentration (henceforth termed the inoculum) influences the microenvironment during initial growth and how this affects the sizes and distribution of developed aggregates in an embedded biofilm model-the alginate bead biofilm model. Following 24 h of incubation, the viable biomass was independent of starting inoculum but with a radically different microenvironment which led to differences in metabolic activity depending on the inoculum. The inoculum also affected the number of cells surviving treatment with the antibiotic tobramycin, where the highest inoculum showed higher survival rates than the lowest inoculum. The change in antibiotic tolerance was correlated with cell-specific RNA content and O2 consumption rates, suggesting a direct role of metabolic activity. Thus, the starting number of bacteria results in different phenotypic trajectories governed by different microenvironmental characteristics, and we demonstrate some of the possible implications of such physiological gradients on the outcome of in vitro experiments. IMPORTANCE Biofilm aggregates grown in the alginate bead biofilm model bear resemblance to features of in vivo biofilms. Here, we show that changing the initial concentration of bacteria in the biofilm model leads to widely different behavior of the bacteria following an incubation period. This difference is influenced by the local conditions experienced by the bacteria during growth, which impact their response to antibiotic treatment. Our study provides a framework for manipulating aggregate sizes in in vitro biofilm models. It underlines the importance of how experiments are initiated, which can profoundly impact the outcomes and interpretation of microbiological experiments.
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Affiliation(s)
- Mads Lichtenberg
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Lasse Kvich
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Sara Louise Borregaard Larsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Tim Holm Jakobsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
- Department of Clinical Microbiology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
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