Literature DB >> 32647386

Gut microbiome, big data and machine learning to promote precision medicine for cancer.

Giovanni Cammarota1, Gianluca Ianiro2, Anna Ahern3, Carmine Carbone4, Andriy Temko5,6, Marcus J Claesson3, Antonio Gasbarrini2, Giampaolo Tortora4.   

Abstract

The gut microbiome has been implicated in cancer in several ways, as specific microbial signatures are known to promote cancer development and influence safety, tolerability and efficacy of therapies. The 'omics' technologies used for microbiome analysis continuously evolve and, although much of the research is still at an early stage, large-scale datasets of ever increasing size and complexity are being produced. However, there are varying levels of difficulty in realizing the full potential of these new tools, which limit our ability to critically analyse much of the available data. In this Perspective, we provide a brief overview on the role of gut microbiome in cancer and focus on the need, role and limitations of a machine learning-driven approach to analyse large amounts of complex health-care information in the era of big data. We also discuss the potential application of microbiome-based big data aimed at promoting precision medicine in cancer.

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Mesh:

Year:  2020        PMID: 32647386     DOI: 10.1038/s41575-020-0327-3

Source DB:  PubMed          Journal:  Nat Rev Gastroenterol Hepatol        ISSN: 1759-5045            Impact factor:   46.802


  200 in total

1.  Do pregnancy-related changes in the microbiome stimulate innate immunity?

Authors:  Sergey R Konstantinov; C Janneke van der Woude; Maikel P Peppelenbosch
Journal:  Trends Mol Med       Date:  2013-07-08       Impact factor: 11.951

Review 2.  Gut dysbiosis, leaky gut, and intestinal epithelial proliferation in neurological disorders: towards the development of a new therapeutic using amino acids, prebiotics, probiotics, and postbiotics.

Authors:  Mia Maguire; Greg Maguire
Journal:  Rev Neurosci       Date:  2019-01-28       Impact factor: 4.353

3.  Persistent microbiome alterations modulate the rate of post-dieting weight regain.

Authors:  Christoph A Thaiss; Shlomik Itav; Daphna Rothschild; Mariska T Meijer; Maayan Levy; Claudia Moresi; Lenka Dohnalová; Sofia Braverman; Shachar Rozin; Sergey Malitsky; Mally Dori-Bachash; Yael Kuperman; Inbal Biton; Arieh Gertler; Alon Harmelin; Hagit Shapiro; Zamir Halpern; Asaph Aharoni; Eran Segal; Eran Elinav
Journal:  Nature       Date:  2016-11-24       Impact factor: 49.962

4.  Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk.

Authors:  W H Wilson Tang; Zeneng Wang; Bruce S Levison; Robert A Koeth; Earl B Britt; Xiaoming Fu; Yuping Wu; Stanley L Hazen
Journal:  N Engl J Med       Date:  2013-04-25       Impact factor: 91.245

5.  ClickGene: an open cloud-based platform for big pan-cancer data genome-wide association study, visualization and exploration.

Authors:  Jia-Hao Bi; Yi-Fan Tong; Zhe-Wei Qiu; Xing-Feng Yang; John Minna; Adi F Gazdar; Kai Song
Journal:  BioData Min       Date:  2019-06-26       Impact factor: 2.522

6.  Modulation of cytokine patterns and microbiome during pregnancy in IBD.

Authors:  Janine van der Giessen; Dana Binyamin; Omry Koren; Gwenny Manel Fuhler; Anna Belogolovski; Sigal Frishman; Kinneret Tenenbaum-Gavish; Eran Hadar; Yoram Louzoun; Maikel Petrus Peppelenbosch; Christien Janneke van der Woude
Journal:  Gut       Date:  2019-06-05       Impact factor: 23.059

7.  Impact of Fecal Microbiota Transplantation on Obesity and Metabolic Syndrome-A Systematic Review.

Authors:  Zhengxiao Zhang; Valentin Mocanu; Chenxi Cai; Jerry Dang; Linda Slater; Edward C Deehan; Jens Walter; Karen L Madsen
Journal:  Nutrients       Date:  2019-09-25       Impact factor: 5.717

8.  Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.

Authors:  Eva G Alvarez; Adrian Baez-Ortega; Jorge Zamora; Fran Supek; Bernardo Rodriguez-Martin; Jonas Demeulemeester; Martin Santamarina; Young Seok Ju; Javier Temes; Daniel Garcia-Souto; Harald Detering; Yilong Li; Jorge Rodriguez-Castro; Ana Dueso-Barroso; Alicia L Bruzos; Stefan C Dentro; Miguel G Blanco; Gianmarco Contino; Daniel Ardeljan; Marta Tojo; Nicola D Roberts; Sonia Zumalave; Paul A W Edwards; Joachim Weischenfeldt; Montserrat Puiggròs; Zechen Chong; Ken Chen; Eunjung Alice Lee; Jeremiah A Wala; Keiran Raine; Adam Butler; Sebastian M Waszak; Fabio C P Navarro; Steven E Schumacher; Jean Monlong; Francesco Maura; Niccolo Bolli; Guillaume Bourque; Mark Gerstein; Peter J Park; David C Wedge; Rameen Beroukhim; David Torrents; Jan O Korbel; Inigo Martincorena; Rebecca C Fitzgerald; Peter Van Loo; Haig H Kazazian; Kathleen H Burns; Peter J Campbell; Jose M C Tubio
Journal:  Nat Genet       Date:  2020-02-05       Impact factor: 38.330

Review 9.  Inflammatory Bowel Disease: A Potential Result from the Collusion between Gut Microbiota and Mucosal Immune System.

Authors:  Bei Yue; Xiaoping Luo; Zhilun Yu; Sridhar Mani; Zhengtao Wang; Wei Dou
Journal:  Microorganisms       Date:  2019-10-11

Review 10.  The gut microbiota and host health: a new clinical frontier.

Authors:  Julian R Marchesi; David H Adams; Francesca Fava; Gerben D A Hermes; Gideon M Hirschfield; Georgina Hold; Mohammed Nabil Quraishi; James Kinross; Hauke Smidt; Kieran M Tuohy; Linda V Thomas; Erwin G Zoetendal; Ailsa Hart
Journal:  Gut       Date:  2015-09-02       Impact factor: 23.059

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  42 in total

Review 1.  Omics in gut microbiome analysis.

Authors:  Tae Woong Whon; Na-Ri Shin; Joon Yong Kim; Seong Woon Roh
Journal:  J Microbiol       Date:  2021-02-23       Impact factor: 3.422

Review 2.  Microbial source tracking using metagenomics and other new technologies.

Authors:  Shahbaz Raza; Jungman Kim; Michael J Sadowsky; Tatsuya Unno
Journal:  J Microbiol       Date:  2021-02-10       Impact factor: 3.422

3.  Nature-inspired metaheuristics model for gene selection and classification of biomedical microarray data.

Authors:  Rabia Musheer Aziz
Journal:  Med Biol Eng Comput       Date:  2022-04-11       Impact factor: 2.602

4.  Machine-learning algorithms for asthma, COPD, and lung cancer risk assessment using circulating microbial extracellular vesicle data and their application to assess dietary effects.

Authors:  Andrea McDowell; Juwon Kang; Jinho Yang; Jihee Jung; Yeon-Mok Oh; Sung-Min Kym; Tae-Seop Shin; Tae-Bum Kim; Young-Koo Jee; Yoon-Keun Kim
Journal:  Exp Mol Med       Date:  2022-09-30       Impact factor: 12.153

Review 5.  Precision medicine journey through omics approach.

Authors:  Mandana Hasanzad; Negar Sarhangi; Sima Ehsani Chimeh; Nayereh Ayati; Monireh Afzali; Fatemeh Khatami; Shekoufeh Nikfar; Hamid Reza Aghaei Meybodi
Journal:  J Diabetes Metab Disord       Date:  2021-11-24

6.  Large-Scale, High-Throughput Phenotyping of the Postharvest Storage Performance of 'Rustenburg' Navel Oranges and the Development of Shelf-Life Prediction Models.

Authors:  Abiola Owoyemi; Ron Porat; Amnon Lichter; Adi Doron-Faigenboim; Omri Jovani; Noam Koenigstein; Yael Salzer
Journal:  Foods       Date:  2022-06-22

7.  Artificial Intelligence and Precision Medicine: A Perspective.

Authors:  Jacek Lorkowski; Oliwia Kolaszyńska; Mieczysław Pokorski
Journal:  Adv Exp Med Biol       Date:  2022       Impact factor: 2.622

Review 8.  Approaching precision medicine by tailoring the microbiota.

Authors:  Gaeun Ryu; Hyojin Kim; Ara Koh
Journal:  Mamm Genome       Date:  2021-03-01       Impact factor: 2.957

Review 9.  Towards multi-label classification: Next step of machine learning for microbiome research.

Authors:  Shunyao Wu; Yuzhu Chen; Zhiruo Li; Jian Li; Fengyang Zhao; Xiaoquan Su
Journal:  Comput Struct Biotechnol J       Date:  2021-04-28       Impact factor: 7.271

Review 10.  Exploring the Oral Microbiome in Rheumatic Diseases, State of Art and Future Prospective in Personalized Medicine with an AI Approach.

Authors:  Silvia Bellando-Randone; Edda Russo; Vincenzo Venerito; Marco Matucci-Cerinic; Florenzo Iannone; Sabina Tangaro; Amedeo Amedei
Journal:  J Pers Med       Date:  2021-06-30
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