Article
Microbiology
Juan J. Roda-Garcia, Jose M. Haro-Moreno, Francisco Rodriguez-Valera, Salvador Almagro-Moreno, Mario Lopez-Perez
Summary: The SAR86 clade of bacteria shows genome reduction and relies on co-occurring microbes for survival in the marine environment, as evidenced by the streamlined genomes, reduced biosynthesis of essential molecules, and decreased ability to sense and respond to environmental factors.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Marine & Freshwater Biology
Anetta Ameryk, Janina Kownacka, Mariusz Zalewski, Kasia Piwosz
Summary: The Vistula Lagoon is a semi-closed basin in the southern coast of the Baltic Sea with a unique environment for both freshwater and marine bacteria. Salinity strongly influenced the abundance of marine bacterial groups (SAR11 clade I/II) with a distinct seasonal pattern, while freshwater bacterial groups (SAR11 clade IIIb, Limnohabitans, Burkholderiales) were more associated with other environmental factors like temperature and nutrients. The results suggest that the Vistula Lagoon is not ideal for marine bacteria, but freshwater bacteria are able to establish niches within this ecosystem.
ESTUARINE COASTAL AND SHELF SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
S. A. Lee, H. H. Stein
Summary: The objective of this study was to investigate the effects of dietary calcium concentration on the apparent ileal digestibility of amino acids in pigs, and to explore the interactions between calcium, phosphorus, and amino acids. The results showed that the digestibility of amino acids was affected by the dietary calcium concentration, with a linear increase in calcium digestibility and a quadratic decrease in phosphorus digestibility within a certain range of calcium levels.
ANIMAL FEED SCIENCE AND TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Chang Shu, Qinglan Sun, Guomei Fan, Kesheng Peng, Zhengfei Yu, Yingfeng Luo, Shenghan Gao, Juncai Ma, Tao Deng, Songnian Hu, Linhuan Wu
Summary: The VarEPS-Influ database is a risk assessment system for influenza virus variations that comprehensively evaluates various aspects of mutations, including physical and chemical properties, structural features, receptor affinity, antibody binding capacity, etc., and considers factors such as time and spatial distribution and host species distribution. It accurately evaluates and predicts the risk of influenza virus variations.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Environmental Sciences
Anwesha Ghosh, Punyasloke Bhadury
Summary: Tannic acid, a secondary compound in mangrove litterfall, influences DOC and DON pools in adjacent estuaries. Laboratory experiments show that tannic acid affects bacterioplankton community structure, particularly the abundance of Proteobacteria. The breakdown of tannic acid could impact marine nitrogen and carbon cycling in estuaries.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Green & Sustainable Science & Technology
Bifei Mao, Guanghao Li, Mingmei Wang, Xiangyuan Deng, Kun Gao, Bingcong Zhang
Summary: Nitrogen starvation and excess phosphorus regulation during algae cultivation can modify the biochemical composition of algal biomass and subsequently improve butanol production from LEA.
Article
Environmental Sciences
Guozhu Ye, Xu Zhang, Xinyu Liu, Xu Liao, Han Zhang, Changzhou Yan, Yi Lin, Qiansheng Huang
Summary: The study found that exposure to polystyrene microplastics significantly altered the metabolism of marine medaka livers, leading to changes in various metabolic pathways and levels of specific metabolites. The effects of different sizes of microplastics (10-mu m and 200-mu m) on hepatic metabolism were observed, with differences in the impact on carbohydrate, amino acid, and lipid metabolism. Overall, the results provide new insights into the ecotoxicology of microplastics in aquatic organisms.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Cell Biology
Nathaniel L. Hepowit, Eric Blalock, Sangderk Lee, Kimberly M. Bretland, Jason A. MacGurn, Robert C. Dickson
Summary: As the elderly population increases, chronic diseases associated with aging are becoming a challenge for healthcare systems worldwide. Nutrient restriction has been shown to slow down aging and improve health, but it is difficult for most people to practice. Therefore, alternative pharmacological strategies are being explored, such as myriocin, which has been found to increase lifespan in yeast by impairing sphingolipid synthesis and lowering amino acid levels. This study investigates the cellular response to myriocin and reveals a new role for ubiquitin in promoting longevity.
Article
Biochemistry & Molecular Biology
Xiangqi Hao, Yanchao Li, Xiangyu Xiao, Bo Chen, Pei Zhou, Shoujun Li
Summary: Canine parvovirus (CPV-2) is a significant pathogen in dogs. Despite the development of vaccines, CPV-2 continues to circulate in the dog population. CPV-2c is replacing CPV-2a as the dominant variant in Asia, South America, North America, and Africa, with evidence of spillover.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Ecology
Hyewon Heather Kim, Jeff S. Bowman, Ya-Wei Luo, Hugh W. Ducklow, Oscar M. Schofield, Deborah K. Steinberg, Scott C. Doney
Summary: This study investigates the association between bacterial traits and ecosystem functions using a bacteria-oriented ecosystem model. The results show that both taxonomic and physiological traits of bacteria reflect the variability in bacterial carbon demand, net primary production, and particle sinking flux. Numerical experiments suggest a potential shift from low nucleic acid bacteria to high nucleic acid bacteria-dominated communities in the coastal WAP under perturbed climate conditions.
Article
Microbiology
Siaw Shi Boon, Chichao Xia, Maggie Haitian Wang, Ka Lai Yip, Ho Yin Luk, Sile Li, Rita W. Y. Ng, Christopher K. C. Lai, Paul Kay Sheung Chan, Zigui Chen
Summary: The study revealed a significant increase in the number of SARS-CoV-2 S protein variants since October 2020, with key amino acids under positive selection. Using computational approaches, the impact of amino acid variations on viral infectivity and antigenicity was predicted. Potential amino acid mutations that could favor SARS-CoV-2 virulence were also forecasted.
Article
Biochemistry & Molecular Biology
Keyue Wu, Yiyang Li, Yuqi Lin, Baojun Xu, Jiajia Yang, Li Mo, Riming Huang, Xiaoyong Zhang
Summary: This study isolated and characterized a sulfated exopolysaccharide, AVP141-A, from the broth of marine-derived fungus. AVP141-A exhibited potential as an immune activator by significantly enhancing the activity of inflammation factors and activating specific signaling pathways in macrophages. These findings suggest that AVP141-A has the potential for further development as a marine fungal-derived therapeutic compound.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Applied
Shuai Zhuang, Xiaochang Liu, Yan Li, Longteng Zhang, Hui Hong, Jun Liu, Yongkang Luo
Summary: The study revealed the deamination and decarboxylation activities of spoilage microbiota in chill-stored grass carp fillets. It was found that different taste amino acids were affected differently by microbial deamination activities. Additionally, putrescine in fish fillets was mainly produced through microbial decarboxylation activity of ornithine, and spoilage microbiota showed active glucose utilization during the late period of storage.
Article
Multidisciplinary Sciences
Xuan Shao, Guangming Cao, Dunjin Chen, Juan Liu, Bolan Yu, Ming Liu, Yu-Xia Li, Bin Cao, Yoel Sadovsky, Yan-Ling Wang
Summary: The syncytiotrophoblast adapts to nutrient stress by inducing macropinocytosis through repression of mTOR signaling, supporting fetal survival and growth under nutrient deprivation. Placentas derived from fetal growth restriction patients show reduced mTOR signaling, increased syncytialization, and enhanced macropinocytosis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Food Science & Technology
Ling Lin, Jiao Zhang, Lin He, Lanlan Li, Yuxin Song, Wenjun Xiao, Zhihua Gong
Summary: This study found that LTA can regulate protein metabolism in high-protein diets, mitigating kidney and liver damage and improving serum biochemical indices.
MOLECULAR NUTRITION & FOOD RESEARCH
(2023)
Article
Microbiology
Xingqin Lin, Jesse McNichol, Xiao Chu, Yang Qian, Haiwei Luo
Summary: This study reveals that marine intertidal sediments serve as important habitats for denitrifying bacteria, with different ecotypes showing distinct denitrification abilities and growth patterns under varying oxygen concentrations and carbon sources. The evidence suggests the presence of cryptic niches in coastal intertidal sediments that support divergent evolution of denitrifying bacteria.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Ecology
Robert M. Bowers, Stephen Nayfach, Frederik Schulz, Sean P. Jungbluth, Ilona A. Ruhl, Andriy Sheremet, Janey Lee, Danielle Goudeau, Emiley A. Eloe-Fadrosh, Ramunas Stepanauskas, Rex R. Malmstrom, Nikos C. Kyrpides, Peter F. Dunfield, Tanja Woyke
Summary: Advancements in single-cell genomics have enabled rapid and affordable sequencing of microbial communities, providing a comprehensive snapshot of community composition and function. This approach also allows for the direct linkage of mobile elements to hosts and analysis of population heterogeneity among dominant community members.
Article
Multidisciplinary Sciences
Clara Martinez-Perez, Chris Greening, Sean K. Bay, Rachael J. Lappan, Zihao Zhao, Daniele De Corte, Christina Hulbe, Christian Ohneiser, Craig Stevens, Blair Thomson, Ramunas Stepanauskas, Jose M. Gonzalez, Ramiro Logares, Gerhard J. Herndl, Sergio E. Morales, Federico Baltar
Summary: Using a multi-omics approach, this study provides insights into the microbial communities beneath the Ross Ice Shelf in coastal Antarctica. The findings reveal a taxonomically distinct microbial community adapted to a highly oligotrophic marine environment, with aerobic lithoautotrophic archaea and bacteria driving the production of new organic carbon, and aerobic organoheterotrophic bacteria capable of degrading complex organic carbon substrates.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Timothy D'Angelo, Jacqueline Goordial, Nicole J. Poulton, Lauren Seyler, Julie A. Huber, Ramunas Stepanauskas, Beth N. Orcutt
Summary: The application of redox-sensitive fluorescent molecules for flow cytometric sorting of cells allows for single cell genomic sequencing from low biomass crustal fluid, providing a powerful tool for studying microbial biospheres in low biomass systems or sites with limited sample volumes available for analysis.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Ecology
Zhuoyu Chen, Xiaojun Wang, Yu Song, Qinglu Zeng, Yao Zhang, Haiwei Luo
Summary: The authors found that the effective population size of Prochlorococcus is smaller than that of many free-living bacteria, indicating the important role of drift in their evolution. Despite sharing characteristics with endosymbiotic bacteria, Prochlorococcus have a different evolutionary mechanism, where genetic drift plays a key role.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Svetlana Lyalina, Ramunas Stepanauskas, Frank Wu, Shomyseh Sanjabi, Katherine S. Pollard
Summary: By using flow cytometry and low-coverage sequencing, we captured and identified the genomes of the mouse gut microbiome, significantly enriching the gene catalog and phylogenetic breadth of this community. We also discovered previously invisible microbial functional pathways.
Article
Multidisciplinary Sciences
Marianne Acker, Shane L. Hogle, Paul M. Berube, Thomas Hackl, Allison Coe, Ramunas Stepanauskas, Sallie W. Chisholm, Daniel J. Repeta
Summary: This study reveals that a small fraction of microbial producers in the ocean sustain the presence of phosphonates and allocate a significant portion of their phosphorus quota for phosphonate production. The phosphonates may be associated with cell-surface glycoproteins, mediating ecological interactions between the cell and its surrounding environment.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Cell Biology
Brayon J. Fremin, Ami S. Bhatt, Nikos C. Kyrpides
Summary: This study used a large-scale comparative genomics approach to discover that small genes are more prevalent in phage genomes than in host prokaryotic genomes. These small genes may have important functions, such as encoding anti-CRISPR proteins and antimicrobial proteins.
Article
Biochemistry & Molecular Biology
Uri Neri, Yuri I. Wolf, Simon Roux, Antonio Pedro Camargo, Benjami Lee, Darius Kazlauskas, I. Min Chen, Natalia Ivanova, Lisa Zeigler Allen, David Paez-Espino, Donald A. Bryant, Devaki Bhaya, Mart Krupovic, Valerian V. Dolja, Nikos C. Kyrpides, Eugene Koonin, Uri Gophna
Summary: High-throughput RNA sequencing allows us to explore the diversity of RNA viruses on Earth. By analyzing diverse metatranscriptomes and RNA-dependent RNA polymerases, we discovered a 5-fold increase in the known diversity of RNA viruses, as well as new protein domains and virus-host interactions. Additionally, we identified two new bacteriophage phyla and potential new classes and orders.
Article
Biochemistry & Molecular Biology
Thomas Hackl, Raphael Laurenceau, Markus J. Ankenbrand, Christina Bliem, Zev Cariani, Elaina Thomas, Keven D. Dooley, Aldo A. Arellano, Shane L. Hogle, Paul Berube, Gabriel E. Leventhal, Elaine Luo, John M. Eppley, Ahmed A. Zayed, John Beaulaurier, Ramunas Stepanauskas, Matthew B. Sullivan, Edward F. DeLong, Steven J. Biller, Sallie W. Chisholm
Summary: Horizontal gene transfer plays a crucial role in microbial evolution, and the newly discovered tycheposons, a family of DNA transposons, are found to be key drivers of genomic remodeling. Tycheposons are widely distributed in the marine environment and are dispersed through vesicles and phage particles. Similar elements are also found in microbes co-existing with Prochlorococcus, suggesting a common mechanism for microbial diversification in the vast oligotrophic oceans.
Article
Multidisciplinary Sciences
Jacob H. Munson-McGee, Melody R. Lindsay, Eva Sintes, Julia M. Brown, Timothy D'Angelo, Joe Brown, Laura C. Lubelczyk, Paxton Tomko, David Emerson, Beth N. Orcutt, Nicole J. Poulton, Gerhard J. Herndl, Ramunas Stepanauskas
Summary: The respiration rates of marine microbes vary significantly among different prokaryoplankton genera. Minority members of prokaryoplankton perform the majority of respiration, while the most prevalent lineages have extremely low respiration rates. Proteorhodopsin-based phototrophy is likely an important source of energy for prokaryoplankton, indicating a need to reevaluate the mechanistic understanding of the global carbon cycle.
Article
Ecology
Timothy D'Angelo, Jacqueline Goordial, Melody R. Lindsay, Julia McGonigle, Anne Booker, Duane Moser, Ramunas Stepanauskus, Beth N. Orcutt
Summary: The phyla Nitrospirota and Nitrospinota have received significant research attention due to their unique nitrogen metabolisms. These phyla are common inhabitants of marine and terrestrial subsurface environments and have diverse physiologies. Basal clades primarily inhabit these subsurface environments and have smaller, more densely coded genomes compared to later-branching clades. Both phyla share many traits inferred to be present in their respective common ancestors. Later-branching groups have genome expansions that include gene clusters performing unique nitrogen metabolisms. Modern subsurface environments represent a genomic repository for ancestral metabolic traits.
Article
Ecology
Anne E. Booker, Timothy D'Angelo, Annabelle Adams-Beyea, Julia M. Brown, Olivia Nigro, Michael S. Rappe, Ramunas Stepanauskas, Beth N. Orcutt
Summary: Through single cell genomics and metagenomics, we have revealed the life strategies of two uncultivated Aminicenantia bacteria lineages from the basaltic subseafloor oceanic crust. Both lineages scavenge organic carbon and have genetic potential to catabolize amino acids and fatty acids. Seawater recharge and necromass may serve as important carbon sources for microorganisms in this environment. Both lineages generate ATP through various mechanisms including substrate-level phosphorylation and electron transport. Genomic comparisons suggest extracellular electron transfer to iron or sulfur oxides. One lineage has small genomes and retains characteristics of early evolved life. Overall, Aminicenantia are well adapted to oceanic crust environments by utilizing simple organic molecules and extracellular electron transport.
Article
Multidisciplinary Sciences
Julia Anstett, Alvaro M. Plominsky, Edward F. DeLong, Alyse Kiesser, Klaus Juergens, Connor Morgan-Lang, Ramunas Stepanauskas, Frank J. Stewart, Osvaldo Ulloa, Tanja Woyke, Rex Malmstrom, Steven J. Hallam
Summary: Oxygen-deficient marine waters known as OMZs or AMZs are common oceanographic features that host microorganisms adapted to low oxygen conditions. The metabolic interactions of these microorganisms drive biogeochemical cycles and impact nitrogen loss and trace gas production and consumption. With the expansion and intensification of oxygen-deficient waters due to global warming, studying microbial communities in these areas is important for understanding the effects of climate change on marine ecosystem functions and services.
Article
Microbiology
Cale O. Seymour, Marike Palmer, Eric D. Becraft, Ramunas Stepanauskas, Ariel D. Friel, Frederik Schulz, Tanja Woyke, Emiley Eloe-Fadrosh, Dengxun Lai, Jian-Yu Jiao, Zheng-Shuang Hua, Lan Liu, Zheng-Han Lian, Wen-Jun Li, Maria Chuvochina, Brianna K. Finley, Benjamin J. Koch, Egbert Schwartz, Paul Dijkstra, Duane P. Moser, Bruce A. Hungate, Brian P. Hedlund
Summary: The candidate bacterial phylum Omnitrophota is poorly studied. By analyzing genomes and data from the Earth Microbiome Project, researchers found that Omnitrophota are ultra-small cells mainly found in water, sediments, and soils. These bacteria have reduced genomes but retain key metabolic pathways and symbiotic gene clusters, indicating a host-associated lifestyle. Additionally, stable-isotope probing identified certain Omnitrophota families as potential obligate bacterial predators. Overall, most Omnitrophota inhabit various ecosystems as predators or parasites.
NATURE MICROBIOLOGY
(2023)