Editorial Material
Neurosciences
Ryan R. Richardson, Devon C. Crawford, John Ngai, Andrea C. Beckel-Mitchener
Summary: Leveraging the diversity and inclusion of the scientific workforce can foster innovation and problem-solving, the NIH BRAIN Initiative is taking steps to promote the best science.
Review
Biotechnology & Applied Microbiology
Kristin Bornstein, Gary Gryan, E. Sally Chang, Aron Marchler-Bauer, Valerie A. Schneider
Summary: Comparative genomics involves comparing genetic information to understand the evolution, structure, and function of genes, proteins, and non-coding regions. This analysis can aid in understanding biological relationships, gene structure and function, and disease and drug targets. Despite challenges, new tools and approaches are needed to meet research needs.
Article
Anesthesiology
Meredith C. B. Adams, Robert W. Hurley, Andrew Siddons, Umit Topaloglu, Laura D. Wandner
Summary: The NIH HEAL Initiative aims to maximize the value of federal investment in pain and opioid-use disorder research by making data FAIR. This involves standardizing the use of CDE for clinical research across a pain and opioid use disorder clinical trials network. The alignment of the network allows for the incorporation of newer data standards, supporting robust secondary data analyses and potential for insurance coverage determinations.
Editorial Material
Neurosciences
Daniel M. Ramos, William C. Skarnes, Andrew B. Singleton, Mark R. Cookson, Michael E. Ward
Summary: iNDI is the largest iPSC genome engineering project, aiming to model over 100 mutations associated with Alzheimer's disease and related dementias. The resulting cell lines and phenotypic datasets will be widely shared with the research community.
News Item
Multidisciplinary Sciences
Mitch Leslie
Summary: This article introduces a major effort by an agency to explore the importance of accumulating mutations in somatic cells.
Article
Microbiology
Florencia Velez-Cortes, Harris Wang
Summary: Bacterially secreted proteins are crucial for the functioning of bacterial cells and communities. In this study, a computational pipeline was used to predict and analyze the bacterial metasecretome of the human gut, revealing the presence of diverse families of secreted carbohydrate-active enzymes and their distribution across taxonomic groups. By mapping secreted proteins to metagenomic data from endoscopic sampling of the human gastrointestinal tract, specific regions were identified where resident microbes secrete glycosidases. The comprehensive analysis of the metasecretome provides valuable insights for microbiome research and understanding the impact of gut bacteria on human health.
Letter
Microbiology
Tim van den Bossche, Magnus O. Arntzen, Dorte Becher, Dirk Benndorf, Vincent G. H. Eijsink, Celine Henry, Pratik D. Jagtap, Nico Jehmlich, Catherine Juste, Benoit J. Kunath, Bart Mesuere, Thilo Muth, Phillip B. Pope, Jana Seifert, Alessandro Tanca, Sergio Uzzau, Paul Wilmes, Robert L. Hettich, Jean Armengaud
Summary: Metaproteomics is a crucial approach for understanding microbiome function through genomic and metabolic connections. The international metaproteomics community has launched the Metaproteomics Initiative to promote dissemination of fundamentals, advancements, and applications, while also serving as a central information hub and meeting place for collaboration in microbiome research.
Editorial Material
Multidisciplinary Sciences
Ruth Ley
Summary: The survey of humanity's 'second genome' is crucial and needs to be more comprehensive.
Article
Ecology
Weizhong Li, Karen E. Nelson
Summary: Recent studies suggest that many species of human gut microbiota acquired in early childhood can persist into senior adulthood, with some species showing a higher likelihood of being shared between twins, indicating a potential genetic component in microbiota transmission.
Editorial Material
Microbiology
Aleksandar D. Kostic
Summary: This commentary reflects on the author's research journey in the human microbiome field and provides an overview of the field's progress.
CELL HOST & MICROBE
(2022)
Review
Physiology
Benchen Rao, Tong Ren, Xuemei Wang, Haiyu Wang, Yawen Zou, Ying Sun, Shanshuo Liu, Zhigang Ren, Zujiang Yu
Summary: The human microbiome is closely related to cholangiocarcinoma, with specific alterations observed in the microbiome of CCA patients. Studies have explored the impact of Helicobacter pylori on CCA and the potential mechanisms by which human microbial dysbiosis promotes the progression of CCA.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Gastroenterology & Hepatology
Colleen R. Kelly, Eugene F. Yen, Ari M. Grinspan, Stacy A. Kahn, Ashish Atreja, James D. Lewis, Thomas A. Moore, David T. Rubin, Alison M. Kim, Sonya Serra, Yanina Nersesova, Lydia Fredell, Dea Hunsicker, Daniel McDonald, Rob Knight, Jessica R. Allegretti, Joel Pekow, Imad Absah, Ronald Hsu, Jennifer Vincent, Sahil Khanna, Lyn Tangen, Carl Crawford, Mark C. Mattar, Lea Ann Chen, Monika Fischer, Razvan Arsenescu, Paul Feuerstadt, Jonathan Goldstein, David Kerman, Adam C. Ehrlich, Gary D. Wu, Loren Laine
Summary: This study demonstrated the high effectiveness and good safety profile of FMT for CDI. Assessment of new conditions at long-term follow-up will be important for determining the full safety profile of FMT as this registry grows.
Article
Green & Sustainable Science & Technology
Tanya O'Garra, Sangeeta Mangubhai, Arundhati Jagadish, Margaret Tabunakawai-Vakalalabure, Alifereti Tawake, Hugh Govan, Morena Mills
Summary: Understanding the mechanisms and impacts of community-based initiatives in environmental management is crucial, but such evaluations are rare. This study presents a national-scale evaluation of a locally managed marine areas network in Fiji, showing that it improves participation, knowledge, management, and financial support. However, these mechanisms do not lead to significant social outcomes or perceived ecological health improvement.
NATURE SUSTAINABILITY
(2023)
Article
Multidisciplinary Sciences
Robert H. George Markowitz, Abigail Leavitt LaBella, Mingjian Shi, Antonis Rokas, John A. Capra, Jane F. Ferguson, Jonathan D. Mosley, Seth R. Bordenstein
Summary: This study analyzed the effects of genetic variations related to the gut microbiome on clinical traits and discovered associations with neurological, metabolic, digestive, and circulatory diseases. The study also found correlations between specific genetic variants and the abundance of specific microbial strains. These findings highlight the triad relationship between the human genome, microbiome, and disease, and suggest the potential for precision diagnostics and therapeutics based on genetic influences on the microbiome.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Agustin Enrique Ure, Camilla Lagheden, Laila Sara Arroyo Muhr
Summary: HPV negative and HPV positive cervical cancers show no significant difference in the metatranscriptome of bacteria and viruses, except for the presence of alpha-papillomaviruses.
SCIENTIFIC REPORTS
(2022)
Review
Physiology
Jack J. Scala, Ariel B. Ganz, Michael P. Snyder
Summary: By utilizing multi-modal biomarkers and advanced technologies, precision medicine has the potential to revolutionize psychiatric care by providing better diagnostics and treatment decisions. The emerging field of precision psychiatry aims to develop diagnostic tests, monitor treatment efficacy, and reduce ineffective treatments in order to mitigate challenges in mental health care. This narrative-style review summarizes the breakthroughs and challenges in applying precision medicine to mental health.
Article
Microbiology
Lepeng Zhou, Wen Qiu, Jie Wang, Aihua Zhao, Chuhui Zhou, Tao Sun, Ziyu Xiong, Peihua Cao, Wei Shen, Jingfen Chen, Xiaolu Lai, Liu-hong Zhao, Yue Wu, Meng Li, Feng Qiu, Yanhong Yu, Zhenjiang Zech Xu, Hongwei Zhou, Wei Jia, Yan Liao, Ravi Retnakaran, Daniel Krewski, Shi Wu Wen, Jose C. Clemente, Tianlu Chen, Ri-hua Xie, Yan He
Summary: The microbiomes of cesarean-born infants differ from vaginally delivered infants and are associated with increased disease risks. Vaginal microbiota transfer (VMT) to newborns may reverse C-section-related micro biome disturbances. In this study, VMT was found to be safe and had positive effects on infant neurodevelopment, gut microbiota maturation, and fecal metabolites.
CELL HOST & MICROBE
(2023)
Review
Immunology
Kenneth C. P. Cheung, Jiao Ma, Rodrigo Azevedo Loiola, Xingxuan Chen, Wei Jia
Summary: Bile acid-activated receptors have important roles in regulating microbiota-host immunity and may influence the development of metabolic disorders. This perspective provides a summary of regulatory pathways and mechanisms of these receptors, their impact on immune system, cell proliferation, and signaling in inflammatory diseases. It also discusses new therapeutic approaches and clinical projects on bile acids for disease treatment.
EUROPEAN JOURNAL OF IMMUNOLOGY
(2023)
Editorial Material
Biochemistry & Molecular Biology
Mahdi Moqri, Michael Snyder
Summary: A multiorgan model has been developed to understand the aging network among different organs and predict the risks of chronic diseases and mortality.
Review
Gastroenterology & Hepatology
Matthias Zilbauer, Kylie James, Mandeep Kaur, Sebastian Pott, Zhixin Li, Albert Burger, Jay L. Thiagarajah, Joseph Burclaff, Frode L. Jahnsen, Francesca Perrone, Alexander D. Ross, Gianluca Matteoli, Nathalie Stakenborg, Tomohisa Sujino, Andreas Moor, Raquel Bartolome-Casado, Espen S. Baekkevold, Ran S. Zhou, Bingqing Xie, Ken T. Lau, Shahida Din, Scott T. Magness, Qiuming Yao, Semir Beyaz, Mark Arends, Alexandre Denadai-Souza, Lori A. Coburn, Jellert T. Gaublomme, Richard Baldock, Irene Papatheodorou, Jose Ordovas-Montanes, Guy Boeckxstaens, Anna Hupalowska, Sarah A. Teichmann, Aviv Regev, Ramnik J. Xavier, Alison Simmons, Michael P. Snyder, Keith T. Wilson
Summary: The number of single-cell profiling studies in the human gastrointestinal tract has significantly increased, presenting an opportunity to generate the first Human Gut Cell Atlas (HGCA). However, there are still major challenges that need to be addressed, including the need for structured and coordinated efforts globally. This Roadmap provides a comprehensive direction and overview of the challenges, as well as recommendations for future studies and the integration of the healthy gut atlas with diseases and gut organoids.
NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY
(2023)
Article
Toxicology
Anitha Vijay, Nina R. Boyle, Supriya M. Kumar, Gary H. Perdew, Shanthi Srinivasan, Andrew D. Patterson
Summary: This study investigates the effects of a persistent organic pollutant on the enteric nervous system, finding that it leads to delayed intestinal motility and neuronal damage, thereby affecting gastrointestinal function.
TOXICOLOGICAL SCIENCES
(2023)
Article
Multidisciplinary Sciences
Lulu Sun, Yi Zhang, Jie Cai, Bipin Rimal, Edson R. Rocha, James P. Coleman, Chenran Zhang, Robert G. Nichols, Yuhong Luo, Bora Kim, Yaozong Chen, Kristopher W. Krausz, Curtis C. Harris, Andrew D. Patterson, Zhipeng Zhang, Shogo Takahashi, Frank J. Gonzalez
Summary: Bile salt hydrolase (BSH) in Bacteroides is associated with the development of colorectal cancer (CRC) by activating the beta-catenin/CCL28 pathway and promoting the generation of immunosuppressive T-reg cells. Inhibition of BSH activity could slow down CRC progression and serve as a potential target for CRC prevention and treatment.
NATURE COMMUNICATIONS
(2023)
Review
Computer Science, Artificial Intelligence
Lauren M. Sanders, Ryan T. Scott, Jason H. Yang, Amina Ann Qutub, Hector Garcia Martin, Daniel C. Berrios, Jaden J. A. Hastings, Jon Rask, Graham Mackintosh, Adrienne L. Hoarfrost, Stuart Chalk, John Kalantari, Kia Khezeli, Erik L. Antonsen, Joel Babdor, Richard Barker, Sergio E. Baranzini, Afshin Beheshti, Guillermo M. Delgado-Aparicio, Benjamin S. Glicksberg, Casey S. Greene, Melissa Haendel, Arif A. Hamid, Philip Heller, Daniel Jamieson, Katelyn J. Jarvis, Svetlana V. Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Christopher E. Mason, Mona Matar, George I. Mias, Jack Miller, Jerry G. Myers Jr, Charlotte Nelson, Jonathan Oribello, Seung-min Park, Patricia Parsons-Wingerter, R. K. Prabhu, Robert J. Reynolds, Amanda Saravia-Butler, Suchi Saria, Aenor Sawyer, Nitin Kumar Singh, Michael Snyder, Frank Soboczenski, Karthik Soman, Corey A. Theriot, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Marinka Zitnik, Sylvain V. Costes
Summary: Deep space exploration missions require new technologies to support astronaut health systems and independent biological monitoring and research systems. A NASA workshop explores how artificial intelligence advances can address these challenges and discusses the intersection between artificial intelligence and space biology.
NATURE MACHINE INTELLIGENCE
(2023)
Review
Computer Science, Artificial Intelligence
Ryan T. Scott, Lauren M. Sanders, Erik L. Antonsen, Jaden J. A. Hastings, Seung-min Park, Graham Mackintosh, Robert J. Reynolds, Adrienne L. Hoarfrost, Aenor Sawyer, Casey S. Greene, Benjamin S. Glicksberg, Corey A. Theriot, Daniel C. Berrios, Jack Miller, Joel Babdor, Richard Barker, Sergio E. Baranzini, Afshin Beheshti, Stuart Chalk, Guillermo M. Delgado-Aparicio, Melissa Haendel, Arif A. Hamid, Philip Heller, Daniel Jamieson, Katelyn J. Jarvis, John Kalantari, Kia Khezeli, Svetlana V. Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Hector Garcia Martin, Christopher E. Mason, Mona Matar, George I. Mias, Jerry G. Myers Jr, Charlotte Nelson, Jonathan Oribello, Patricia Parsons-Wingerter, R. K. Prabhu, Amina Ann Qutub, Jon Rask, Amanda Saravia-Butler, Suchi Saria, Nitin Kumar Singh, Michael Snyder, Frank Soboczenski, Karthik Soman, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Jason H. Yang, Marinka Zitnik, Sylvain V. Costes
Summary: Deep-space exploration requires new technologies for astronaut health systems and autonomous biomonitoring. This article discusses the vision for precision space health based on the findings from a NASA workshop on artificial intelligence and machine learning.
NATURE MACHINE INTELLIGENCE
(2023)
Review
Biology
Xue Yang, Ying Wang, Valentina Rovella, Eleonora Candi, Wei Jia, Francesca Bernassola, Pierluigi Bove, Mauro Piacentini, Manuel Scimeca, Giuseppe Sica, Giuseppe Tisone, Alessandro Mauriello, Lixin Wei, Gerry Melino, Yufang Shi
Summary: Natural ageing of organisms and age-related diseases are mainly caused by stem cell ageing and inflammaging. Mesenchymal stem cells (MSCs) have high immune-regulating capacity and are potential candidates for immune-related disease treatment. However, MSC application is not satisfactory for some patients, especially the elderly, possibly due to changes in MSCs with ageing, including reduced cell population and differentiation ability, decreased migratory and homing capacity, and defective immunosuppression. It is important to explore the relationship between inflammaging and aged MSCs in order to prevent age-related diseases and improve the therapeutic effects of MSCs. This review discusses the changes in naturally ageing MSCs mainly from an inflammation perspective and proposes ideas for rejuvenating aged MSCs in future treatments.
Article
Immunology
Summer Mengelkoch, Sophia Miryam Schuessler-Fiorenza Rose, Ziv Lautman, Jenna C. Alley, Lydia G. Roos, Benjamin Ehlert, Daniel P. Moriarity, Samuel Lancaster, Michael P. Snyder, George M. Slavich
Summary: The field of psychoneuroimmunology (PNI) has grown in importance and relevance over the past 40 years. However, most PNI studies are limited to a small number of analytes. To advance this field, adopting a multi-omics approach can provide a more comprehensive understanding of biological functions and their relationship to clinical and behavioral outcomes. This article provides an overview of multi-omics research and its potential applications in PNI.
BRAIN BEHAVIOR AND IMMUNITY
(2023)
Article
Biochemistry & Molecular Biology
Mahdi Moqri, Chiara Herzog, Jamie Justice, Daniel W. Belsky, Albert Higgins-Chen, Alexey Moskalev, Georg Fuellen, Alan A. Cohen, Ivan Bautmans, Martin Widschwendter, Jingzhong Ding, Alexander Fleming, Joan Mannick, Jing-Dong Jackie Han, Alex Zhavoronkov, Nir Barzilai, Matt Kaeberlein, Steven Cummings, Brian K. Kennedy, Luigi Ferrucci, Steve Horvath, Eric Verdin, Andrea B. Maier, Michael P. Snyder, Vittorio Sebastiano, Vadim N. Gladyshev
Summary: This study discusses the terminology, characterization, and potential clinical applications of biomarkers of aging, and proposes a framework for their further development and validation. The framework sets the stage for the development of valid biomarkers of aging and their utilization in clinical trials and practice.
Correction
Multidisciplinary Sciences
Waihay J. Wong, Connor Emdin, Alexander G. Bick, Seyedeh M. Zekavat, Abhishek Niroula, James Pirruccello, Laura Dichtel, Gabriel Griffin, Md Mesbah E. Uddin, Christopher Gibson, Veronica T. Kovalcik, Amy Lin, Marie McConkey, Amelie Vromman, Rob Sellar, Peter Kim, Mridul Agrawal, Joshua Weinstock, Michelle Long, Bing Yu, Rajarshi Banerjee, Rowan Nicholls, Andrea Dennis, Matt Kelly, Po-Ru Loh, Steve McCarroll, Eric Boerwinkle, Ramachandran Vasan, Siddhartha Jaiswal, Andrew Johnson, Raymond Chung, Kathleen Corey, Daniel Levy, Christie Ballantyne, Benjamin Ebert, Pradeep Natarajan
Article
Food Science & Technology
Xiaoling Chen, Andrew D. Patterson, Gary H. Perdew, Iain A. Murray, Joshua J. Kellogg
Summary: A novel AHR modulator, 2-amino-4-methyl-benzothiazole, was predicted, identified, and characterized in white button mushrooms using a molecular networking approach. Cell-based assays showed that this compound has agonistic activity and upregulates CYP1A1 expression. These findings demonstrate the potential of molecular networking in identifying novel receptor modulators from natural products.
JOURNAL OF FUNCTIONAL FOODS
(2023)
Article
Biology
Yashvardhan Jain, Leah L. L. Godwin, Yingnan Ju, Naveksha Sood, Ellen M. M. Quardokus, Andreas Bueckle, Teri Longacre, Aaron Horning, Yiing Lin, Edward D. D. Esplin, John W. W. Hickey, Michael P. P. Snyder, Nathan Heath Patterson, Jeffrey M. M. Spraggins, Katy Borner
Summary: The Human BioMolecular Atlas Program (HuBMAP) aims to create a Human Reference Atlas (HRA) for the healthy adult body at the cellular level. To achieve this, accurate and efficient machine-learning algorithms are needed for the segmentation of functional tissue units (FTUs). A Kaggle competition was organized to develop such algorithms and the winning algorithm, Tom, outperformed others in an expanded study. Tom has been implemented in the HuBMAP infrastructure for large-scale kidney FTU segmentation, showcasing the value of Kaggle competitions in advancing research.
COMMUNICATIONS BIOLOGY
(2023)
