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Zhang Y, Xing H, Bolotnikov G, Krämer M, Gotzmann N, Knippschild U, Kissmann AK, Rosenau F. Enriched Aptamer Libraries in Fluorescence-Based Assays for Rikenella microfusus-Specific Gut Microbiome Analyses. Microorganisms 2023; 11:2266. [PMID: 37764110 PMCID: PMC10535755 DOI: 10.3390/microorganisms11092266] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/29/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Rikenella microfusus is an essential intestinal probiotic with great potential. The latest research shows that imbalance in the intestinal flora are related to the occurrence of various diseases, such as intestinal diseases, immune diseases, and metabolic diseases. Rikenella may be a target or biomarker for some diseases, providing a new possibility for preventing and treating these diseases by monitoring and optimizing the abundance of Rikenella in the intestine. However, the current monitoring methods have disadvantages, such as long detection times, complicated operations, and high costs, which seriously limit the possibility of clinical application of microbiome-based treatment options. Therefore, the intention of this study was to evolve an enriched aptamer library to be used for specific labeling of R. microfusus, allowing rapid and low-cost detection methods and, ultimately the construction of aptamer-based biosensors. In this study, we used Rikenella as the target bacterium for an in vitro whole Cell-SELEX (Systematic Evolution of Ligands by EXponential Enrichment) to evolve and enrich specific DNA oligonucleotide aptamers. Five other prominent anaerobic gut bacteria were included in this process for counterselection and served as control cells. The aptamer library R.m-R13 was evolved with high specificity and strong affinity (Kd = 9.597 nM after 13 rounds of selection). With this enriched aptamer library, R. microfusus could efficiently be discriminated from the control bacteria in complex mixtures using different analysis techniques, including fluorescence microscopy or fluorometric suspension assays, and even in human stool samples. These preliminary results open new avenues toward the development of aptamer-based microbiome bio-sensing applications for fast and reliable monitoring of R. microfusus.
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Affiliation(s)
- Yiting Zhang
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
| | - Hu Xing
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
| | - Grigory Bolotnikov
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
| | - Markus Krämer
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
| | - Nina Gotzmann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
| | - Uwe Knippschild
- Department of General and Visceral Surgery, Surgery Center, Ulm University, Albert-Einstein-Allee 23, 89081 Ulm, Germany;
| | - Ann-Kathrin Kissmann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
- Max-Planck-Institute for Polymer Research Mainz, Ackermannweg 10, 55128 Mainz, Germany
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
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Nanayakkara AK, Boucher HW, Fowler VG, Jezek A, Outterson K, Greenberg DE. Antibiotic resistance in the patient with cancer: Escalating challenges and paths forward. CA Cancer J Clin 2021; 71:488-504. [PMID: 34546590 DOI: 10.3322/caac.21697] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/23/2021] [Accepted: 08/12/2021] [Indexed: 12/13/2022] Open
Abstract
Infection is the second leading cause of death in patients with cancer. Loss of efficacy in antibiotics due to antibiotic resistance in bacteria is an urgent threat against the continuing success of cancer therapy. In this review, the authors focus on recent updates on the impact of antibiotic resistance in the cancer setting, particularly on the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.). This review highlights the health and financial impact of antibiotic resistance in patients with cancer. Furthermore, the authors recommend measures to control the emergence of antibiotic resistance, highlighting the risk factors associated with cancer care. A lack of data in the etiology of infections, specifically in oncology patients in United States, is identified as a concern, and the authors advocate for a centralized and specialized surveillance system for patients with cancer to predict and prevent the emergence of antibiotic resistance. Finding better ways to predict, prevent, and treat antibiotic-resistant infections will have a major positive impact on the care of those with cancer.
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Affiliation(s)
- Amila K Nanayakkara
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, University of Texas Southwestern, Dallas, Texas
| | - Helen W Boucher
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, Massachusetts
| | - Vance G Fowler
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Amanda Jezek
- Infectious Diseases Society of America, Arlington, Virginia
| | - Kevin Outterson
- CARB-X, Boston, Massachusetts
- Boston University School of Law, Boston, Massachusetts
| | - David E Greenberg
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, University of Texas Southwestern, Dallas, Texas
- Department of Microbiology, University of Texas Southwestern, Dallas, Texas
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Tian M, Zhang S, Tseng Y, Shen X, Dong L, Xue R. Gut Microbiota and Immune Checkpoint Inhibitors-Based Immunotherapy. Anticancer Agents Med Chem 2021; 22:1244-1256. [PMID: 34229597 DOI: 10.2174/1871520621666210706110713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/15/2021] [Accepted: 04/12/2021] [Indexed: 11/22/2022]
Abstract
Application of immune checkpoint inhibitors (ICIs) is a major breakthrough in the field of cancer therapy, which has displayed tremendous potential in various types of malignancies. However, their response rates range widely in different cancer types and a significant number of patients experience immune-related adverse effects (irAEs) induced by these drugs, limiting the proportion of patients who can truly benefit from ICIs. Gut microbiota has gained increasing attention due to its emerging role in regulating the immune system. In recent years, numerous studies have shown that gut microbiota can modulate antitumor response, as well as decrease the risk of colitis due to ICIs in patients receiving immunotherapy. The present review analyzed recent progress of relevant basic and clinical studies in this area and explored new perspectives to enhance the efficacy of ICIs and alleviate associated irAEs via manipulation of the gut microbiota.
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Affiliation(s)
- Mingming Tian
- Department of Gastroenterology and Hepatology, Shanghai Institute of Liver Diseases, Zhongshan Hospital of Fudan University, Shanghai, 200032, China
| | - Si Zhang
- Key Laboratory of Glycoconjugate Research Ministry of Public Health, Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yujen Tseng
- Department of Digestive diseases, Huashan Hospital, Fudan University, Shanghai, 200032, China
| | - Xizhong Shen
- Department of Gastroenterology and Hepatology, Shanghai Institute of Liver Diseases, Zhongshan Hospital of Fudan University, Shanghai, 200032, China
| | - Ling Dong
- Department of Gastroenterology and Hepatology, Shanghai Institute of Liver Diseases, Zhongshan Hospital of Fudan University, Shanghai, 200032, China
| | - Ruyi Xue
- Department of Gastroenterology and Hepatology, Shanghai Institute of Liver Diseases, Zhongshan Hospital of Fudan University, Shanghai, 200032, China
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Hasan RA, Koh AY, Zia A. The gut microbiome and thromboembolism. Thromb Res 2020; 189:77-87. [PMID: 32192995 DOI: 10.1016/j.thromres.2020.03.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 01/09/2020] [Accepted: 03/05/2020] [Indexed: 02/06/2023]
Abstract
The gut microbiome plays a critical role in various inflammatory conditions, and its modulation is a potential treatment option for these conditions. The role of the gut microbiome in the pathogenesis of thromboembolism has not been fully elucidated. In this review, we summarize the evidence linking the gut microbiome to the pathogenesis of arterial and venous thrombosis. In a human host, potentially pathogenic bacteria are normal residents of the human gut microbiome, but significantly outnumbered by commensal anaerobic bacteria. Several disease states with an increased risk of venous thromboembolism (VTE) are associated with an imbalance in the gut microbiome characterized by a decrease in commensal anaerobic bacteria and an increase in the abundance of pathogenic bacteria of which the most common is the gram-negative Enterobacteriaceae (ENTERO) family. Bacterial lipopolysaccharides (LPS), the glycolipids found on the outer membrane of gram-negative bacteria, is one of the links between the microbiome and hypercoagulability. LPS binds to toll-like receptors to activate endothelial cells and platelets, leading to activation of the coagulation cascade. Bacteria in the microbiome can also metabolite compounds in the diet to produce important metabolites like trimethylamine-N-oxide (TMAO). TMAO causes platelet hyperreactivity, promotes thrombus formation and is associated with cardiovascular disease. Modulating the gut microbiome to target LPS and TMAO levels may be an innovative approach for decreasing the risk of thrombosis.
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Affiliation(s)
- Rida Abid Hasan
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Andrew Y Koh
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America; Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America; Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Ayesha Zia
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America.
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Abstract
PURPOSE OF REVIEW The present review aims to describe the relationship between nutrition and the gut microbiome in critical illness. RECENT FINDINGS Critical illness disrupts not only cells of human origin but also the intestinal microbiome, with a decrease in bacterial diversity and transformation into a pathobiome. Under basal conditions, nutrition profoundly alters microbial composition with significant salutatory effects on human health. In critical illness, enteral nutrition is recommended and has theoretical (but not proven) advantages towards improved inner microbial health and diminution of bacterial translocation. Dietary supplements such as probiotics and fiber have been shown to improve microbial derangements in health. However, their impact on the microbiome in critical illness is unclear and although they may have some beneficial effects on patient-centric outcomes, they do not alter mortality. The precise mechanisms of how nutrition and dietary supplements modulate the gut microbiome remain to be determined. SUMMARY Nutrition and supplements such as probiotics appear to play a significant role in modulating the microbiome in health, yet the relationship in critical illness is unclear. Further investigation is required to determine the mechanistic determinants of the impact of nutrition on the microbiome in critical illness and the potential clinical implications of this.
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Chong PP, Koh AY. The gut microbiota in transplant patients. Blood Rev 2019; 39:100614. [PMID: 31492463 DOI: 10.1016/j.blre.2019.100614] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/22/2019] [Accepted: 08/27/2019] [Indexed: 02/09/2023]
Abstract
Solid organ transplant (SOT) and hematopoietic stem cell transplant (HSCT) recipients are at increased risk for developing infections due to underlying immunosuppression. Antibiotic use, and in HSCT recipients, the use of preparative regimens prior to transplantation can deplete gut commensal bacteria, resulting in intestinal dysbiosis. Emerging evidence in transplant patients, particularly HSCT, suggest that disturbances in gut microbiota populations are associated with a number of adverse outcomes. Here, we review the outcomes of HSCT and SOT recipients with gut microbiota imbalance or dysbiosis, explore the nascent field of gut microbiome therapeutic approaches including fecal microbiota transplantation and the use of precision probiotics in HSCT and SOT recipients.
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Affiliation(s)
- Pearlie P Chong
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Andrew Y Koh
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Frankel AE, Deshmukh S, Reddy A, Lightcap J, Hayes M, McClellan S, Singh S, Rabideau B, Glover TG, Roberts B, Koh AY. Cancer Immune Checkpoint Inhibitor Therapy and the Gut Microbiota. Integr Cancer Ther 2019; 18:1534735419846379. [PMID: 31014119 PMCID: PMC6482659 DOI: 10.1177/1534735419846379] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 12/18/2022] Open
Abstract
The past decade has seen tremendous advances in both our understanding of cancer immunosuppressive microenvironments and colonic bacteria facilitated by immune checkpoint inhibitor antibodies and next generation sequencing, respectively. Because an important role of the host immune system is to communicate with and regulate the gut microbial community, it should not come as a surprise that the behavior of one is coupled to the other. In this review, we will attempt to dissect some of the studies demonstrating cancer immunotherapy modulation by specific gut microbes and discuss possible molecular mechanisms for this effect.
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Affiliation(s)
- Arthur E. Frankel
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, USA
| | - Sachin Deshmukh
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, USA
| | - Amit Reddy
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, USA
| | - John Lightcap
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, USA
| | - Maureen Hayes
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, USA
| | - Steven McClellan
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, USA
| | - Seema Singh
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, USA
| | | | | | | | - Andrew Y. Koh
- University of Texas Southwestern Medical Center, Dallas, TX, USA
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