Article
Nutrition & Dietetics
Teresa Vezza, Jose Garrido-Mesa, Patricia Diez-Echave, Laura Hidalgo-Garcia, Antonio J. Ruiz-Malagon, Federico Garcia, Manuel Sanchez, Marta Toral, Miguel Romero, Juan Duarte, Enrique Guillamon, Alberto Banos, Rocio Moron, Julio Galvez, Alba Rodriguez-Nogales, Maria Elena Rodriguez-Cabezas
Summary: The study found that propyl propane thiosulfonate (PTSO) helps reduce weight gain, improve plasma markers, and attenuate obesity-associated inflammation, improving gut barrier integrity.
Article
Microbiology
Patricia Q. Tran, Samantha C. Bachand, C. Jacob, Kristopher Kieft, Elizabeth A. McDaniel, Katherine D. McMahon, Karthik Anantharaman
Summary: This study investigates the ecological significance of cysteine degradation in producing hydrogen sulfide (H2S), a toxic compound found in freshwater lakes. The researchers identified bacterial strains from a lake that can produce H2S in the presence of oxygen, highlighting the importance of this process in natural ecosystems.
Article
Agriculture, Multidisciplinary
Alicia Moreno-Ortega, Giuseppe Di Pede, Gema Pereira-Caro, Luca Calani, Pedro Mena, Daniele Del Rio, Jose Manuel Moreno-Rojas
Summary: This study examines the effect of in vitro colonic fermentation on fresh and black garlic and its impact on the transformation of bioactive compounds. The results show that both fresh and black garlic experience a decrease in phenolic content during fermentation, while black garlic also experiences a significant decrease in organosulfur compounds. Several specific compounds, such as 4-hydroxybenzoic acid, S-allylcysteine, and methionine sulfoxide, were found to have the highest concentrations after fermentation. These compounds may contribute to the health benefits associated with the consumption of garlic.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Cell Biology
Wellinton M. do Nascimento, Aline Machiavelli, Luiz G. E. Ferreira, Luisa Cruz Silveira, Suwellen S. D. de Azevedo, Gonzalo Bello, Daniel P. Smith, Melissa P. Mezzari, Joseph F. Petrosino, Rubens Tadeu Delgado Duarte, Carlos R. Zarate-Blades, Aguinaldo R. Pinto
Summary: The study investigated the gut microbiota profile of antiretroviral therapy-naive HIV-1 patients and healthy donors, revealing that different infection routes and HIV subtypes may be associated with variations in gut microbiota composition.
Review
Immunology
Peng Zhang, Shangwen Pan, Shiying Yuan, You Shang, Huaqing Shu
Summary: Sepsis is a potentially lethal organ impairment triggered by an inadequate host reaction to infection (Sepsis-3). Viral sepsis is a potentially deadly organ impairment state caused by the host's inappropriate reaction to a viral infection. This study focuses on the alterations in glucose metabolism during viral sepsis and their impact on viral infection, aiming to explore new potential therapeutic targets for viral sepsis.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Review
Virology
Xiangyang Yao, Zhenzhen Xu, Chen Duan, Yangjun Zhang, Xiaoliang Wu, Huahui Wu, Kai Liu, Xiongmin Mao, Bo Li, Yang Gao, Hua Xu, Xinghuan Wang
Summary: This study systematically reviews the relationship between HPV-associated viruses and bladder cancer, aiming to elucidate the role of these viruses in the onset and progression of the disease. It also assesses potential strategies for treating virus-induced bladder cancer and introduces the rapid development of oncolytic viruses as a novel treatment option.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Multidisciplinary Sciences
Yosuke Yamada, Xueying Zhang, Mary E. T. Henderson, Hiroyuki Sagayama, Herman Pontzer, Daiki Watanabe, Tsukasa Yoshida, Misaka Kimura, Philip N. Ainslie, Lene F. Andersen, Liam J. Anderson, Lenore Arab, Issad Baddou, Kweku Bedu-Addo, Ellen E. Blaak, Stephane Blanc, Alberto G. Bonomi, Carlijn V. C. Bouten, Pascal Bovet, Maciej S. Buchowski, Nancy F. Butte, Stefan G. Camps, Graeme L. Close, Jamie A. Cooper, Richard Cooper, Sai Krupa Das, Lara R. Dugas, Simon Eaton, Ulf Ekelund, Sonja Entringer, Terrence Forrester, Barry W. Fudge, Annelies H. Goris, Michael Gurven, Lewis G. Halsey, Catherine Hambly, Asmaa El Hamdouchi, Marije B. Hoos, Sumei Hu, Noorjehan Joonas, Annemiek M. Joosen, Peter Katzmarzyk, Kitty P. Kempen, William E. Kraus, Wantanee Kriengsinyos, Robert F. Kushner, Estelle V. Lambert, William R. Leonard, Nader Lessan, Corby K. Martin, Anine C. Medin, Erwin P. Meijer, James C. Morehen, James P. Morton, Marian L. Neuhouser, Theresa A. Nicklas, Robert M. Ojiambo, Kirsi H. Pietilainen, Yannis P. Pitsiladis, Jacob Plange-Rhule, Guy Plasqui, Ross L. Prentice, Roberto A. Rabinovich, Susan B. Racette, David A. Raichlen, Eric Ravussin, Leanne M. Redman, John J. Reilly, Rebecca M. Reynolds, Susan B. Roberts, Albertine J. Schuit, Luis B. Sardinha, Analiza M. Silva, Anders M. Sjodin, Eric Stice, Samuel S. Urlacher, Giulio Valenti, Ludo M. Van Etten, Edgar A. Van Mil, Jonathan C. K. Wells, George Wilson, Brian M. Wood, Jack A. Yanovski, Alexia J. Murphy-Alford, Cornelia U. Loechl, Amy H. Luke, Jennifer Rood, Klaas R. Westerterp, William W. Wong, Motohiko Miyachi, Dale A. Schoeller, John R. Speakman
Summary: This study investigated the determinants of human water turnover in different age groups and countries. The results show that age, body size and composition, physical activity, socioeconomic status, and environmental characteristics are closely related to water turnover. People living in countries with a low human development index have higher water turnover. Predictive equations for human water turnover in relation to anthropometric, economic, and environmental factors are provided based on the extensive dataset.
Article
Multidisciplinary Sciences
Isreal Moreno, Irene Rodriguez-Sanchez, Xenia Schafer, Joshua Munger
Summary: HCMV infection induces the expression of a tissue atypical neuronal glycolytic enzyme, activating glycolysis and UDP-sugar metabolism, increasing the accumulation of glycosyl building blocks, and enabling the expression of an essential viral glycoprotein and the production of infectious virions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
David K. Liscombe, Yusuke Kamiyoshihara, Jeremie Ghironzi, Christine J. Kempthorne, Kevin Hooton, Blandine Bulot, Vassili Kanellis, James McNulty, Nghi B. Lam, Louis Felix Nadeau, Michael Pautler, Denise M. Tieman, Harry J. Klee, Charles Goulet
Summary: Tomato produces a wide range of volatile chemicals during fruit ripening, including nitrogen-containing compounds whose biosynthetic pathways are not well understood. Research has shown that cysteine provides the nitrogen atom for all nitrogenous volatiles in tomato fruit.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Engineering, Environmental
Mengyang Zhang, Nihal Altan-Bonnet, Yun Shen, Danmeng Shuai
Summary: Waterborne human pathogenic viruses can transmit in populations through interactions with microbial communities, enhancing their infectivity and persistence while resisting disinfection. Overlooking these interactions may underestimate the environmental and public health risks of the viruses.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Francesca Cialdai, Austin M. Brown, Cory W. Baumann, Debora Angeloni, Sarah Baatout, Alexandra Benchoua, Juergen Bereiter-Hahn, Daniele Bottai, Judith-Irina Buchheim, Marco Calvaruso, Eugenie Carnero-Diaz, Sara Castiglioni, Duccio Cavalieri, Gabriele Ceccarelli, Alexander Chouker, Gianni Ciofani, Giuseppe Coppola, Gabriella Cusella, Andrea Degl'Innocenti, Jean-Francois Desaphy, Jean-Pol Frippiat, Michael Gelinsky, Giada Genchi, Maria Grano, Daniela Grimm, Alain Guignandon, Christiane Hahn, Jason Hatton, Raul Herranz, Christine E. Hellweg, Carlo Saverio Iorio, Thodoris Karapantsios, Jack van Loon, Matteo Lulli, Jeanette Maier, Jos Malda, Emina Mamaca, Lucia Morbidelli, Angelique van Ombergen, Andreas Osterman, Aleksandr Ovsianikov, Francesco Pampaloni, Elizabeth Pavezlorie, Veronica Pereda-Campos, Cyrille Przybyla, Christopher Puhl, Petra Rettberg, Chiara Risaliti, Angela Maria Rizzo, Kate Robson-Brown, Leonardo Rossi, Giorgio Russo, Alessandra Salvetti, Daniela Santucci, Matthias Sperl, Felice Strollo, Kevin Tabury, Sara Tavella, Christiane Thielemann, Ronnie Willaert, Nathaniel J. Szewczyk, Monica Monici
Summary: This white paper presents the indications and recommendations of the SciSpacE Science Community on filling the gaps of knowledge regarding the effects of gravity alterations on animal and human systems at a cellular and tissue level. Despite previous studies, a comprehensive integrated model of the changes occurring at different system and functional levels is still lacking, making it difficult to predict the long-term consequences of human adaptation to the space environment and implement effective medical support plans.
Review
Biochemistry & Molecular Biology
Bozena Bukowska, Katarzyna Mokra, Jaromir Michalowicz
Summary: Benzo[a]pyrene (B[a]P) is a representative polycyclic aromatic hydrocarbon (PAH) that is commonly found in the environment and human surroundings. It has been shown to have toxic effects on DNA, reproduction, neurology, and development. The metabolism of B[a]P is mediated by cytochrome P450 (CYP P450) and its polymorphism determines the sensitivity to B[a]P. Additionally, B[a]P may facilitate the replication of viruses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Xiaoyu Li, Lan Xu
Summary: The study found an inverted U-shaped relationship between the Environment Degradation Index (EDI) and the Human Development Index (HDI), recommending the government to accelerate human development to surpass the turning point of this relationship as soon as possible.
Article
Environmental Sciences
Antonio Cascajosa-Lira, Remedios Guzman-Guillen, Alberto Banos Arjona, Maria Arantzazu Aguinaga-Casanas, Nahum Ayala-Soldado, M. Rosario Moyano-Salvago, Ana Molina, Angeles Jos, Ana M. Camean, Silvia Pichardo
Summary: The organosulfur compound PTSO from Allium cepa has potential applications in the agrifood industry. In vivo study on mice showed that exposure to PTSO did not cause significant reproductive toxicity, confirming its safety for agrifood applications.
ENVIRONMENTAL RESEARCH
(2023)
Article
Environmental Sciences
Zhao Jie Chen, Yun Lv, Xiao Yan Zhai, Hong Yang
Summary: The study found that MTR significantly affects the growth and toxicological responses in rice, with identified transcriptional components responsible for MTR degradation. Exposure to environmentally realistic MTR concentrations upregulated numerous genes in roots and shoots, involving MTR-degradative enzymes and resistance to environmental stress. HRLC-Q-TOF-MS/MS was used to characterize MTR metabolites, unveiling the detailed degradative mechanisms and pathways of MTR.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Review
Biochemistry & Molecular Biology
Phil Huss, Jackie Chen, Srivatsan Raman
Summary: Bacteriophage research is crucial to modern biology. New technologies can help understand the relationship between sequence and function in phages, leading to advancements in basic science and engineering goals.
TRENDS IN BIOCHEMICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Benjamin D. Lee, Uri Neri, Simon Roux, Yuri I. Wolf, Antonio Pedro Camargo, Mart Krupovic, Peter Simmonds, Nikos Kyrpides, Uri Gophna, Valerian V. Dolja, Eugene V. Koonin
Summary: We developed a computational pipeline to identify viroid-like cccRNAs and found a 5-fold increase in the number of identified elements compared to previous studies. The presence of viroid-like cccRNAs in diverse transcriptomes and ecosystems suggests that their host range is broader than currently known.
Article
Biochemistry & Molecular Biology
Yu-Yu Cheng, Zhichao Zhou, James M. Papadopoulos, Jason D. Zuke, Tanya G. Falbel, Karthik Anantharaman, Briana M. Burton, Ophelia S. Venturelli
Summary: The factors influencing HGT via natural transformation in microbial communities, including extracellular DNA release, plasmid properties, donor stress responses and lysis rates, as well as interspecies interactions, have been investigated in a microbial co-culture. It has been found that plasmid release and HGT efficiency are enhanced in the co-culture compared to monocultures, with the key determining factor being the donor's ability to induce SOS response and release plasmids in high concentrations. Notably, HGT efficiency is independent of the viability state of the donor cells.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Antonio Pedro Camargo, Stephen Nayfach, I-Min A. Chen, Krishnaveni Palaniappan, Anna Ratner, Ken Chu, Stephan J. Ritter, T. B. K. Reddy, Supratim Mukherjee, Frederik Schulz, Lee Call, Russell Y. Neches, Tanja Woyke, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Nikos C. Kyrpides, Simon Roux
Summary: Viruses play critical roles in all microbiomes and their genomic diversity and impacts on biological processes are extensively explored through metagenomics. IMG/VR is a platform providing access to a large collection of viral sequences along with functional annotation and metadata. The latest version, IMG/VR v4, contains over 15 million virus genomes and genome fragments.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
I-Min A. Chen, Ken Chu, Krishnaveni Palaniappan, Anna Ratner, Jinghua Huang, Marcel Huntemann, Patrick Hajek, Stephan J. Ritter, Cody Webb, Dongying Wu, Neha J. Varghese, T. B. K. Reddy, Supratim Mukherjee, Galina Ovchinnikova, Matt Nolan, Rekha Seshadri, Simon Roux, Axel Visel, Tanja Woyke, Emiley A. Eloe-Fadrosh, Nikos C. Kyrpides, Natalia N. Ivanova
Summary: The Integrated Microbial Genomes & Microbiomes system (IMG/M) at the Department of Energy Joint Genome Institute (JGI) provides support for comparative analysis of various genomes, metagenomes, and metatranscriptomes. It includes datasets from JGI, as well as imported datasets from public sources and user-submitted datasets. In recent years, efforts have been made to improve annotation pipeline, upgrade reference database versions, and add new analysis functionalities.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Till L. V. Bornemann, Sarah P. Esser, Tom L. Stach, Tim Burg, Alexander J. Probst
Summary: uBin is a GUI-based standalone software for bin refinement, which improves the quality of bacterial and archaeal genomes from metagenomes by using GC content, coverage, and taxonomy. It has shown success in improving 78.9% of bins by reducing contamination when applied to the public CAMI dataset. It can also be used as a standalone binner for metagenomes from the International Space Station, revealing the active proliferation of microbes in Earth's lower orbit. uBin is easy to install and can be used for binning, communicating metagenomic results, and education purposes. The software and its helper scripts are open source and available online.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Ecology
Zhichao Zhou, Patricia Q. Tran, Alyssa M. Adams, Kristopher Kieft, John A. Breier, Caroline S. Fortunato, Cody S. Sheik, Julie A. Huber, Meng Li, Gregory J. Dick, Karthik Anantharaman
Summary: In globally distributed deep-sea hydrothermal vent plumes, microbiomes are influenced by the redox energy landscapes created by the mixing of hydrothermal vent fluids and seawater. The core microbiome of plumes is defined by sulfur metabolism and drives metabolic connectivity in the microbial community. The impacts of plume biogeochemistry on the oceans and the links between biogeography, evolution, and metabolic connectivity are poorly understood.
Article
Virology
Victoria Turzynski, Lea Griesdorn, Cristina Moraru, Andre R. Soares, Sophie A. A. Simon, Tom L. L. Stach, Janina Rahlff, Sarah P. P. Esser, Alexander J. J. Probst
Summary: The spatial and temporal distribution of lytic viruses in deep groundwater has not been explored yet. In this study, we investigate viral infections of Altivir_1_MSI in biofilms dominated by the uncultivated host Candidatus Altiarchaeum hamiconexum sampled from deep anoxic groundwater over a four-year period. By using virus-targeted direct-geneFISH (virusFISH), we observe a significant and steady increase in virus infections from 2019 to 2022. Our findings also reveal different stages of viral infections in biofilms for single sampling events, demonstrating the progression of infection in deep groundwater. The stable virus-host interaction observed in these samples suggests that the uncultivated virus-host system described here could serve as a suitable model for studying deep biosphere virus-host interactions in future research endeavors.
Article
Biochemistry & Molecular Biology
Simon E. Roux, Antonio Pedro Camargo, Felipe H. Coutinho, Shareef M. Dabdoub, Bas E. Dutilh, Stephen Nayfach, Andrew Tritt
Summary: The extraordinary diversity of viruses infecting bacteria and archaea can be studied through metagenomics. However, metagenome-derived viral sequences lack key information about host association. We introduce iPHoP, a framework that integrates multiple methods to predict host taxonomy for a range of uncultivated viruses, while maintaining a low false discovery rate. Using a large dataset from the IMG/VR database, iPHoP shows promise in providing extensive host prediction for uncultivated viruses.
Article
Microbiology
Patricia Q. Tran, Samantha C. Bachand, C. Jacob, Kristopher Kieft, Elizabeth A. McDaniel, Katherine D. McMahon, Karthik Anantharaman
Summary: This study investigates the ecological significance of cysteine degradation in producing hydrogen sulfide (H2S), a toxic compound found in freshwater lakes. The researchers identified bacterial strains from a lake that can produce H2S in the presence of oxygen, highlighting the importance of this process in natural ecosystems.
Editorial Material
Ecology
Simon Roux, Jennifer R. Brum
Article
Biochemistry & Molecular Biology
Antonio Pedro Camargo, Lee Call, Simon Roux, Stephen Nayfach, Marcel Huntemann, Krishnaveni Palaniappan, Anna Ratner, Ken Chu, Supratim Mukherjeep, T. B. K. Reddy, I-Min A. Chen, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Tanja Woyke, David A. Baltrus, Salvador Castaneda-Barba, Fernando de la Cruz, Barbara E. Funnell, James P. J. Hall, Aindrila Mukhopadhyay, Eduardo P. C. Rocha, Thibault Stalder, Eva Top, Nikos C. Kyrpides
Summary: This study introduces the IMG/PR database, which collects a large number of plasmid sequences from various microbiome samples and provides rich metadata and multiple browsing methods.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Janina Rahlff, Sarah P. Esser, Julia Plewka, Mara Elena Heinrichs, Andre Soares, Claudio Scarchilli, Paolo Grigioni, Heike Wex, Helge-Ansgar Giebel, Alexander J. Probst
Summary: Marine viruses can be dispersed into the atmosphere through the air-sea interface and detected in rainwater. Virus enrichment in the surface microlayer and sea foams, as well as higher G/C base content in viruses from rain and aerosols, were observed. These findings support the transmission of viruses along the water cycle.
NATURE COMMUNICATIONS
(2023)
Article
Ecology
Dinesh Kumar Kuppa Baskaran, Shreyansh Umale, Zhichao Zhou, Karthik Raman, Karthik Anantharaman
Summary: Deep-sea hydrothermal vents are abundant and have important roles in ocean biogeochemistry. By studying microbial communities in the Guaymas Basin hydrothermal system, we identified key species and their interactions. Metabolic models were used to infer metabolic exchanges and horizontal gene transfer events within the community. Our findings highlight the importance of microbial interactions in driving community structure and organization in hydrothermal plume microbiomes.
ISME COMMUNICATIONS
(2023)
Article
Ecology
Janina Rahlff, Matthias Wietz, Helge-Ansgar Giebel, Oliver Bayfield, Emelie Nilsson, Kristofer Bergstrom, Kristopher Kieft, Karthik Anantharaman, Mariana Ribas-Ribas, Hannah D. Schweitzer, Oliver Wurl, Matthias Hoetzinger, Alfred Antson, Karin Holmfeldt
Summary: This study characterizes viruses and bacteria in a brackish slick surface microlayer (SML), comparing them to non-slick SML and subsurface water. The slick SML contains higher abundances of virus-like particles, prokaryotic cells, and dissolved organic carbon. The community of viral operational taxonomic units (vOTUs) in slick SML is distinct and shows specific metabolic profiles of bacteria. The study also isolates previously unknown lytic phages that contribute to biogeochemical cycling in coastal ecosystems.
ISME COMMUNICATIONS
(2023)