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Translating the microbiome in health and disease

Guest Editor: Ramnik Xavier

New Content ItemGenome Medicine is pleased to present a special issue entitled 'Translating the microbiome in health and disease,' guest edited by Dr. Ramnik Xavier of the Broad Institute of MIT and Harvard. Research efforts exploring the human microbiome using large-scale metagenomics and multi-omics have rapidly expanded, facilitating characterization of microbiome composition, dynamics, variation, and function in health and disease. Such studies are increasing our understanding of the microbiome’s impact on the immune response and other physiological processes, and further enabling a shift from correlation to causation, with emerging insights into how this data can be utilized for diagnostic and therapeutic benefit. These efforts also highlight the need for the standardization of microbiome research protocols in order to accelerate progress through collaborative research. This special issue aims to capture recent insights into all aspects of the human microbiome in health and disease including standards for microbiome analyses in basic and clinical research, microbiome analysis tools and technologies, metagenomics and integrative multi-omics, antibiotics and the microbiome, microbial biochemistry and diet, translational interventions, and host-microbiome interactions. 


This collection of articles has not been sponsored and articles will undergo the journal’s standard peer-review process. The Guest Editor declares that they have no competing interests. Guest Editors serve an advisory role to guide the scope of the special issue and commissioned content; final editorial decisions lie with the Editor.

  1. Currently, over half of breast cancer cases are unrelated to known risk factors, highlighting the importance of discovering other cancer-promoting factors. Since crosstalk between gut microbes and host immunit...

    Authors: Alice Tzeng, Naseer Sangwan, Margaret Jia, Chin-Chih Liu, Karen S. Keslar, Erinn Downs-Kelly, Robert L. Fairchild, Zahraa Al-Hilli, Stephen R. Grobmyer and Charis Eng

    Citation: Genome Medicine 2021 13:60

    Content type: Research

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  2. Nursing home residents have increased rates of intestinal colonisation with multidrug-resistant organisms (MDROs). We assessed the colonisation and spread of MDROs among this population, determined clinical ri...

    Authors: Quinten R. Ducarmon, Elisabeth M. Terveer, Sam Nooij, Michelle N. Bloem, Karuna E. W. Vendrik, Monique A. A. Caljouw, Ingrid M. J. G. Sanders, Sofie M. van Dorp, Man C. Wong, Romy D. Zwittink and Ed J. Kuijper

    Citation: Genome Medicine 2021 13:54

    Content type: Research

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  3. Type 2 diabetes (T2D), a multifactorial disease influenced by host genetics and environmental factors, is the most common endocrine disease. Several studies have shown that the gut microbiota as a close-up env...

    Authors: Camila Alvarez-Silva, Alireza Kashani, Tue Haldor Hansen, Nishal Kumar Pinna, Ranjit Mohan Anjana, Anirban Dutta, Shruti Saxena, Julie Støy, Ulla Kampmann, Trine Nielsen, Torben Jørgensen, Visvanathan Gnanaprakash, Rameshkumar Gnanavadivel, Aswath Sukumaran, Coimbatore Subramanian Shanthi Rani, Kristine Færch…

    Citation: Genome Medicine 2021 13:37

    Content type: Research

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  4. Recent studies have indicated an association of gut microbiota and microbial metabolites with type 2 diabetes mellitus (T2D). However, large-scale investigation of the gut microbiota of “prediabetic” (PD) subj...

    Authors: Nishal Kumar Pinna, Ranjit Mohan Anjana, Shruti Saxena, Anirban Dutta, Visvanathan Gnanaprakash, Gnanavadivel Rameshkumar, Sukumaran Aswath, Srividhya Raghavan, Coimbatore Subramanian Shanthi Rani, Venkatesan Radha, Muthuswamy Balasubramanyam, Archana Pant, Trine Nielsen, Torben Jørgensen, Kristine Færch, Alireza Kashani…

    Citation: Genome Medicine 2021 13:36

    Content type: Research

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  5. Once antibiotic-resistant bacteria become established within the gut microbiota, they can cause infections in the host and be transmitted to other people and the environment. Currently, there are no effective ...

    Authors: Amy Langdon, Drew J. Schwartz, Christopher Bulow, Xiaoqing Sun, Tiffany Hink, Kimberly A. Reske, Courtney Jones, Carey-Ann D. Burnham, Erik R. Dubberke and Gautam Dantas

    Citation: Genome Medicine 2021 13:28

    Content type: Research

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  6. The incidence of colorectal cancer (CRC) is increasing in developing countries, yet limited research on the CRC- associated microbiota has been conducted in these areas, in part due to scarce resources, facili...

    Authors: Caroline Young, Henry M. Wood, Ramakrishnan Ayloor Seshadri, Pham Van Nang, Carlos Vaccaro, Luis Contreras Melendez, Mayilvahanan Bose, Mai Van Doi, Tamara Alejandra Piñero, Camilo Tapia Valladares, Julieta Arguero, Alba Fuentes Balaguer, Kelsey N. Thompson, Yan Yan, Curtis Huttenhower and Philip Quirke

    Citation: Genome Medicine 2021 13:27

    Content type: Research

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  7. Personalised dietary modulation of the gut microbiota may be key to disease management. Current investigations provide a broad understanding of the impact of diet on the composition and activity of the gut mic...

    Authors: Emily R. Leeming, Panayiotis Louca, Rachel Gibson, Cristina Menni, Tim D. Spector and Caroline I. Le Roy

    Citation: Genome Medicine 2021 13:10

    Content type: Review

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  8. The gut-liver axis plays a pivotal role in the pathogenesis of hepatocellular carcinoma (HCC). However, the correlations between the gut microbiome and the liver tumor transcriptome in patients with HCC and th...

    Authors: Hechen Huang, Zhigang Ren, Xingxing Gao, Xiaoyi Hu, Yuan Zhou, Jianwen Jiang, Haifeng Lu, Shengyong Yin, Junfang Ji, Lin Zhou and Shusen Zheng

    Citation: Genome Medicine 2020 12:102

    Content type: Research

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  9. Multiple studies suggest a key role for gut microbiota in IgE-mediated food allergy (FA) development, but to date, none has studied it in the persistent state.

    Authors: Michael R. Goldberg, Hadar Mor, Dafna Magid Neriya, Faiga Magzal, Efrat Muller, Michael Y. Appel, Liat Nachshon, Elhanan Borenstein, Snait Tamir, Yoram Louzoun, Ilan Youngster, Arnon Elizur and Omry Koren

    Citation: Genome Medicine 2020 12:92

    Content type: Research

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  10. During aging, there is a physiological decline, an increase of morbidity and mortality, and a natural change in the gut microbiome. In this study, we investigated the influence of the gut microbiome on differe...

    Authors: Dana Binyamin, Nir Werbner, Meital Nuriel-Ohayon, Atara Uzan, Hadar Mor, Atallah Abbas, Oren Ziv, Raffaele Teperino, Roee Gutman and Omry Koren

    Citation: Genome Medicine 2020 12:87

    Content type: Research

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  11. The human gut microbiome is a dynamic collection of bacteria, archaea, fungi, and viruses that performs essential functions for immune development, pathogen colonization resistance, and food metabolism. Pertur...

    Authors: Drew J. Schwartz, Amy E. Langdon and Gautam Dantas

    Citation: Genome Medicine 2020 12:82

    Content type: Review

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    The Correction to this article has been published in Genome Medicine 2021 13:26

  12. Although the microbiome is established as an important regulator of health and disease, the role of viruses that inhabit asymptomatic humans (collectively, the virome) is less defined. While we are still chara...

    Authors: Fatemeh Adiliaghdam and Kate L. Jeffrey

    Citation: Genome Medicine 2020 12:66

    Content type: Comment

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  13. There is increasing evidence that the intestinal microbiota plays a crucial role in the maturation of the immune system and the prevention of diseases during childhood. Early-life short-course antibiotic use m...

    Authors: Ceren Ozkul, Victoria E. Ruiz, Thomas Battaglia, Joseph Xu, Claire Roubaud-Baudron, Ken Cadwell, Guillermo I. Perez-Perez and Martin J. Blaser

    Citation: Genome Medicine 2020 12:65

    Content type: Research

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  14. Dietary glycans, widely used as food ingredients and not directly digested by humans, are of intense interest for their beneficial roles in human health through shaping the microbiome. Characterizing the consi...

    Authors: Richard Creswell, Jie Tan, Jonathan W. Leff, Brandon Brooks, Michael A. Mahowald, Ruth Thieroff-Ekerdt and Georg K. Gerber

    Citation: Genome Medicine 2020 12:59

    Content type: Research

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  15. Populations of closely related microbial strains can be simultaneously present in bacterial communities such as the human gut microbiome. We recently developed a de novo genome assembly approach that uses read...

    Authors: Soumaya Zlitni, Alex Bishara, Eli L. Moss, Ekaterina Tkachenko, Joyce B. Kang, Rebecca N. Culver, Tessa M. Andermann, Ziming Weng, Christina Wood, Christine Handy, Hanlee P. Ji, Serafim Batzoglou and Ami S. Bhatt

    Citation: Genome Medicine 2020 12:50

    Content type: Research

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  16. Cystic fibrosis is the most common autosomal recessive genetic disease in Caucasians. It is caused by mutations in the CFTR gene, leading to poor hydration of mucus and impairment of the respiratory, digestive, a...

    Authors: Gargi Dayama, Sambhawa Priya, David E. Niccum, Alexander Khoruts and Ran Blekhman

    Citation: Genome Medicine 2020 12:12

    Content type: Research

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