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Shen K, Din AU, Sinha B, Zhou Y, Qian F, Shen B. Translational informatics for human microbiota: data resources, models and applications. Brief Bioinform 2023; 24:7152256. [PMID: 37141135 DOI: 10.1093/bib/bbad168] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
With the rapid development of human intestinal microbiology and diverse microbiome-related studies and investigations, a large amount of data have been generated and accumulated. Meanwhile, different computational and bioinformatics models have been developed for pattern recognition and knowledge discovery using these data. Given the heterogeneity of these resources and models, we aimed to provide a landscape of the data resources, a comparison of the computational models and a summary of the translational informatics applied to microbiota data. We first review the existing databases, knowledge bases, knowledge graphs and standardizations of microbiome data. Then, the high-throughput sequencing techniques for the microbiome and the informatics tools for their analyses are compared. Finally, translational informatics for the microbiome, including biomarker discovery, personalized treatment and smart healthcare for complex diseases, are discussed.
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Affiliation(s)
- Ke Shen
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Ahmad Ud Din
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Baivab Sinha
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Yi Zhou
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Fuliang Qian
- Center for Systems Biology, Suzhou Medical College of Soochow University, Suzhou 215123, China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Suzhou 215123, China
| | - Bairong Shen
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
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Maślak E, Miśta W, Złoch M, Błońska D, Pomastowski P, Monedeiro F, Buszewski B, Mrochem-Kwarciak J, Bojarska K, Gabryś D. A New Approach to Imaging and Rapid Microbiome Identification for Prostate Cancer Patients Undergoing Radiotherapy. Biomedicines 2022; 10:biomedicines10081806. [PMID: 36009352 PMCID: PMC9405325 DOI: 10.3390/biomedicines10081806] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/18/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
(1) Background: Little is known about the impact of urinary microflora, in particular, its effects on side effects after radiotherapy. The use of mass spectrometry identification method (MALDI) may bring a new look at the issue of the composition and significance of the urinary microbiome. This study aimed to use the mass spectrometry identification method (MALDI) to identify the microbiome of urine samples collected from 50 irradiated prostate cancer patients. (2) Methods: Blood and urine samples were collected before gold marker implantation, at the start and last day of radiotherapy, 1, 4 months after. Patients do not always collect the urine from the midstream; therefore, samples were collected from the first void and midstream in 12 patients for MALDI analysis; in the remaining 38 patients—from the midstream void for MALDI and biochemical analysis. (3) Results: Microorganisms were present in 140/181 urine samples. We found 33 different species 3G(−) and 30G(+). The most frequently isolated strains were: Staphylococcus haemolyticus, Staphylococcus epidermidis, Staphylococcus hominis, Enterococcus faecalis, and Micrococcus luteus. When comparing the type of urine samples, bacteria were more common in samples from the first-void urine than from the midstream one. The absence of bacteria was found in 12.2% of samples from the first-void urine and in 24.7% from the midstream. There was no difference in the total incidence of species between streams (p = 0.85). Before fiducial implantation, the total number of detected bacterial species was significantly higher in comparison to the end of radiotherapy (p = 0.038), indicating that the administered therapy resulted in depleting the local microbiome. One month after radiotherapy, an increase in the number of isolated bacteria was observed. The number of bacterial species in urine did not correlate with blood parameters. The presence of leukocytes (p = 0.013) and proteins (p = 0.004) in urine was related to a greater variety of bacteria found in urine specimens. (4) Conclusions: We obtained a similar spectrum of bacteria from the initial and middle urine streams. We also showed that there is a change in bacteria species affected by the treatment of prostate cancer patients, with both antibiotics before gold fiducial implantation and radiotherapy.
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Affiliation(s)
- Ewelina Maślak
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (M.Z.); (D.B.); (P.P.); (F.M.); (B.B.)
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7 Str., 87-100 Toruń, Poland
| | - Wioletta Miśta
- Radiotherapy Department, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15 Str., 44-102 Gliwice, Poland;
| | - Michał Złoch
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (M.Z.); (D.B.); (P.P.); (F.M.); (B.B.)
| | - Dominika Błońska
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (M.Z.); (D.B.); (P.P.); (F.M.); (B.B.)
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7 Str., 87-100 Toruń, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (M.Z.); (D.B.); (P.P.); (F.M.); (B.B.)
| | - Fernanda Monedeiro
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (M.Z.); (D.B.); (P.P.); (F.M.); (B.B.)
| | - Bogusław Buszewski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (M.Z.); (D.B.); (P.P.); (F.M.); (B.B.)
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7 Str., 87-100 Toruń, Poland
| | - Jolanta Mrochem-Kwarciak
- Analytics and Clinical Biochemistry Department, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15 Str., 44-102 Gliwice, Poland; (J.M.-K.); (K.B.)
| | - Katarzyna Bojarska
- Analytics and Clinical Biochemistry Department, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15 Str., 44-102 Gliwice, Poland; (J.M.-K.); (K.B.)
| | - Dorota Gabryś
- Radiotherapy Department, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15 Str., 44-102 Gliwice, Poland;
- Correspondence: ; Tel.: +48-32-278-80-51
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Lorenzo AJ. Vesicoureteral Reflux, Renal Scars, and Urinary Tract Infections in Children: A New Way to Think About an Old Problem. Eur Urol 2021; 81:155-156. [PMID: 34635343 DOI: 10.1016/j.eururo.2021.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 09/22/2021] [Indexed: 11/17/2022]
Affiliation(s)
- Armando J Lorenzo
- Department of Surgery, University of Toronto, Division of Urology, Hospital for Sick Children, Toronto, Canada.
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Zhou H, Suo J, Zhu J. [Therapeutic Relevance of Human Microbiota and Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2019; 22:464-469. [PMID: 31315786 PMCID: PMC6712272 DOI: 10.3779/j.issn.1009-3419.2019.07.09] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
人体菌群与人类健康状态密切相关,如人体菌群的失调可能导致糖尿病、胃肠道疾病、肥胖等疾病的发生。人体内微生物与约20%的恶性肿瘤有关,肺癌(lung cancer, LC)是目前最为常见的恶性肿瘤之一,我国男性LC发病率及死亡率高居所有恶性肿瘤之首。近来研究表明,人体菌群可能通过代谢、炎症或免疫等途径影响着LC的发生,同时影响LC对放化疗、基因治疗、免疫治疗等治疗方法的疗效,如免疫治疗,是用于治疗LC的一种极有前景的手段,但不同患者从中获益不一,包含以肺癌细胞株的实验表明肠道微生物群可通过与宿主免疫系统的相互作用调节对免疫治疗的反应。但针对肺癌患者,肠道菌群是否仍能对免疫治疗进行调节仍存在争议。本文就人体菌群与LC的治疗相关性的近来研究进展进行综述。
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Affiliation(s)
- Huijie Zhou
- Department of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jiaojiao Suo
- Department of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jiang Zhu
- Department of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
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Massari F, Mollica V, Di Nunno V, Gatto L, Santoni M, Scarpelli M, Cimadamore A, Lopez-Beltran A, Cheng L, Battelli N, Montironi R, Brandi G. The Human Microbiota and Prostate Cancer: Friend or Foe? Cancers (Basel) 2019; 11:E459. [PMID: 30935126 PMCID: PMC6521295 DOI: 10.3390/cancers11040459] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/21/2019] [Accepted: 03/26/2019] [Indexed: 02/06/2023] Open
Abstract
The human microbiome is gaining increasing attention in the medical community, as knowledge on its role not only in health but also in disease development and response to therapies is expanding. Furthermore, the connection between the microbiota and cancer, especially the link between the gut microbiota and gastrointestinal tumors, is becoming clearer. The interaction between the microbiota and the response to chemotherapies and, more recently, to immunotherapy has been widely studied, and a connection between a peculiar type of microbiota and a better response to these therapies and a different incidence in toxicities has been hypothesized. As knowledge on the gut microbiota increases, interest in the residing microbial population in other systems of our body is also increasing. Consequently, the urinary microbiota is under evaluation for its possible implications in genitourinary diseases, including cancer. Prostate cancer is the most common cancer in the male population; thus, research regarding its etiology and possible factors correlated to disease progression or the response to specific therapies is thriving. This review has the purpose to recollect the current knowledge on the relationship between the human microbiota and prostate cancer.
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Affiliation(s)
- Francesco Massari
- Division of Oncology, S. Orsola-Malpighi Hospital, 40138 Bologna, Italy.
| | - Veronica Mollica
- Division of Oncology, S. Orsola-Malpighi Hospital, 40138 Bologna, Italy.
| | - Vincenzo Di Nunno
- Division of Oncology, S. Orsola-Malpighi Hospital, 40138 Bologna, Italy.
| | - Lidia Gatto
- Division of Oncology, S. Orsola-Malpighi Hospital, 40138 Bologna, Italy.
| | | | - Marina Scarpelli
- Section of Pathological Anatomy, Polytechnic University of the Marche Region, School of Medicine, United Hospitals, 60126 Ancona, Italy.
| | - Alessia Cimadamore
- Section of Pathological Anatomy, Polytechnic University of the Marche Region, School of Medicine, United Hospitals, 60126 Ancona, Italy.
| | | | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | | | - Rodolfo Montironi
- Section of Pathological Anatomy, Polytechnic University of the Marche Region, School of Medicine, United Hospitals, 60126 Ancona, Italy.
| | - Giovanni Brandi
- Oncology Unit, Department of Experimental, Diagnostic and Specialty Medicine, Sant'Orsola-Malpighi Hospital, University of Bologna, 40138 Bologna, Italy.
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