Article
Microbiology
Michelle A. A. Hauer, Corinna Breusing, Elizabeth Trembath-Reichert, Julie A. A. Huber, Roxanne A. A. Beinart
Summary: This study compared the genomes of free-living and host-associated symbionts of the deep-sea snail Alviniconcha hessleri and found that they have the same population structure but significant differences in gene content, suggesting that geographic isolation and adaptation to local habitat conditions are important determinants of symbiont population structure and intra-host composition.
Article
Multidisciplinary Sciences
Corinna Breusing, Maximilian Genetti, Shelbi L. Russell, Russell B. Corbett-Detig, Roxanne A. Beinart
Summary: Symbiont specificity plays a crucial role in nutritional symbiosis between invertebrate animals and chemosynthetic bacteria at deep-sea hydrothermal vents. It affects habitat distribution, genetic structuring, and ecological adaptation of host populations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Geochemistry & Geophysics
John W. Jamieson, Christopher Galley, Natalie McNeil, Dennis Sanchez Mora
Summary: Hydrothermal episodicity, a common characteristic of high-temperature seafloor hydrothermal systems, is often studied through analysis of age distribution of rock samples. However, simulation results suggest that large time gaps between dated samples do not indicate episodic venting, and the lack of geochronological evidence for episodicity suggests continuous hydrothermal fluid circulation.
EARTH AND PLANETARY SCIENCE LETTERS
(2023)
Article
Geochemistry & Geophysics
Karmina A. Aquino, Gretchen L. Fruh-Green, Joerg Rickli, Stefano M. Bernasconi, Susan Q. Lang, Marvin D. Lilley, David A. Butterfield
Summary: Serpentinization-influenced hydrothermal systems, such as the Lost City Hydrothermal Field, have the potential for the origin of life. However, microbial habitability in these systems may be limited due to high pH, elevated temperatures, and low carbon concentrations. The fluid chemistry and isotope data from the LCHF indicate that all fluids are derived from a single endmember produced in the hotter, deeper subsurface without microbial activity. The spatial variability among the vents is influenced by biotic and abiotic processes along different flow paths.
GEOCHIMICA ET COSMOCHIMICA ACTA
(2022)
Article
Microbiology
Elaina Thomas, Rika E. Anderson, Viola Li, L. Jenni Rogan, Julie A. Huber
Summary: Deep-sea hydrothermal vents harbor diverse and active viral assemblages that are largely localized to specific vent sites with narrow host ranges. The impact of viral infection is likely to be highly constrained and specific to certain taxa in these unique habitats.
Article
Environmental Sciences
Elin A. Thomas, Aoife Molloy, Nova B. Hanson, Monika Boehm, Mary Seddon, Julia D. Sigwart
Summary: The study shows that 62% of molluscs endemic to hydrothermal vents are under threat, with some species fully protected while others facing threats from deep-sea mining. The relative threat index highlights greater risks at vent fields in the Indian Ocean, while vent sites within established marine protected areas have a higher proportion of species assessed as Least Concern.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Biotechnology & Applied Microbiology
Sabrina Flutsch, Fabian Wiestner, Lisa Butticaz, Dominik Moor, Kai N. Stolting
Summary: In this study, a quantitative NGS-based method was developed to accurately measure Vibrio sp. at the limit of quantification through DNA standards and digital PCR. The method represents an advancement in quantitative genomics and supports the development of statistical approaches for measurement uncertainties in NGS. It provides a useful tool for future metagenomic studies aiming to quantify microbial DNA in an absolute manner.
Article
Chemistry, Medicinal
Yujian Wang, Jian Zhang, Yuanyuan Sun, Li Sun
Summary: Crus1, a type of antimicrobial peptide from deep-sea shrimp, effectively kills Gram-positive bacteria by inducing membrane leakage and structure damage in a pH, temperature, and disulfide linkage-dependent manner. Serine substitution of cysteine residues in the WAP domain does not affect bacterial binding capacity but completely abolishes the bactericidal activity of rCrus1.
Article
Geochemistry & Geophysics
Nicholas J. Tosca, Benjamin M. Tutolo
Summary: Precambrian iron formation provides insights into the formation of ancient marine environments. Traditional models suggest that Fe(III)-oxide formation is the result of chemical or biological oxidation of soluble Fe2+. However, new evidence shows that Fe(III)-oxides may have been derived from the oxidation of Fe(II)-silicate mineral greenalite. By studying the interactions between ancient hydrothermal vent fluids and anoxic seawater, it is suggested that the mixing of these fluids may have been a principal mechanism for the formation of Archean iron formation.
GEOCHIMICA ET COSMOCHIMICA ACTA
(2023)
Article
Biochemical Research Methods
Yafei Chang, Qilian Fan, Jialin Hou, Yu Zhang, Jing Li
Summary: Investigations on metaproteomics of deep-sea hydrothermal vent microbiota can be challenging, but with the right analysis strategy and database, protein identification rates and information richness can significantly increase, providing us with a deeper understanding of microbial lifestyles and metabolic capabilities in extreme environments.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Microbiology
Zhichao Zhou, Emily St. John, Karthik Anantharaman, Anna-Louise Reysenbach
Summary: This study explores the genomic diversity in 42 metagenomes from deep-sea hydrothermal vents and documents their potential implications in biogeochemical cycles. The findings reveal a significant expansion of microbial genomic diversity associated with hydrothermal vent deposits and highlight the metabolic adaptation of taxonomic guilds.
Article
Veterinary Sciences
Lin Zheng, Ling-Wei Zhu, Jie Jing, Jia-yao Guan, Ge-Jin Lu, Lin-Hong Xie, Xue Ji, Dong Chu, Yang Sun, Ping Chen, Xue-Jun Guo
Summary: Migratory birds are recognized as potential carriers of Vibrio strains, with varying genetic divergence in both Vibrio cholerae and Vibrio metschnikovii isolated from migratory bird samples. While V. cholerae strains isolated from birds are unlikely to be pandemic-inducing, a V. metschnikovii isolate containing a complete T6SS system was identified for the first time, providing new insights into the diversity of Vibrio isolates from migratory birds.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Environmental Sciences
J. Marticorena, M. Matabos, E. Ramirez-Llodra, C. Cathalot, A. Laes-Huon, R. Leroux, S. Hourdez, J. -P. Donval, J. Sarrazin
Summary: This study implemented a novel experimental approach to assess the recovery potential of vent communities along the slow-spreading northern Mid-Atlantic Ridge. Within 2 years after inducing a small-scale disturbance, most taxonomic richness had recovered, but there was only partial recovery of faunal densities and a major change in faunal composition. The results suggest a potential role of mobile predators in early-colonisation stages.
MARINE ENVIRONMENTAL RESEARCH
(2021)
Article
Environmental Sciences
Jennifer M. Polinski, Mattie Rodrigue, Jason D. Meyer, Matthew J. Harke
Summary: This study focuses on hydrothermal vent plume waters above the Moytirra hydrothermal vent field and examines the biodiversity and metabolic activities of the microbial communities in the plume. The results reveal a rich diversity of microorganisms and suggest the importance of sulfur compounds as an energy source in these waters. The study also highlights the decreasing metabolic functions and quiescent stages of bacterial communities with distance from the vent source.
FRONTIERS IN MARINE SCIENCE
(2023)
Review
Geochemistry & Geophysics
Carmen Rizzo, Erika Arcadi, Rosario Calogero, Valentina Sciutteri, Pierpaolo Consoli, Valentina Esposito, Simonepietro Canese, Franco Andaloro, Teresa Romeo
Summary: Marine hydrothermal systems are extreme environments that strongly impact living organisms. They are of ecological and biotechnological importance, serving as natural laboratories for studying the effects of global environmental changes and as sources of isolated microbes for biotechnological purposes.
Article
Biotechnology & Applied Microbiology
Imen Nouioui, Sung-Min Ha, Inwoo Baek, Jongsik Chun, Michael Goodfellow
Summary: This study identified a new species within the genus Nocardia, called Nocardia alni sp. nov, through a genome-based taxonomic analysis. The strain ncl2(T) showed unique characteristics and was closely related to Nocardia nova, Nocardia jiangxiensis, Nocardia miyuensis, and Nocardia vaccinii. The genomes of N. alni and N. vaccinii strains contained multiple biosynthetic gene clusters, suggesting the potential synthesis of novel specialized products, particularly antibiotics.
Article
Multidisciplinary Sciences
Candice A. Price, Guillaume Jospin, Kristy Brownell, Jonathan A. Eisen, Barbara Laraia, Elissa S. Epel
Summary: The prevalence of overweight and obesity is highest among Black women in the U.S., leading to a higher prevalence of type 2 diabetes compared to White women. Black women tend to have greater insulin resistance compared to White women, but the underlying mechanisms are not fully understood. The gut microbiome may play a role in obesity, insulin resistance, and cardiometabolic disease. This study found differences in gut microbiome profiles between Black and White women, suggesting that the gut microbiome may contribute to health disparities in Black women.
Article
Biochemistry & Molecular Biology
Dongwook Kim, Cameron L. M. Gilchrist, Jongsik Chun, Martin Steinegger
Summary: Phylogenomics studies the evolutionary relationship of organisms using their genomic information. The UFCG database and pipeline provide a tool for genome-wide phylogenetic analysis of fungi.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Connie A. Rojas, Kay E. Holekamp, Mariette Viladomat Jasso, Valeria Souza, Jonathan A. Eisen, Kevin R. Theis
Summary: This study investigated the variability and function of gut microbiome in wild spotted hyenas over a 23-year period and found that the composition and function of the microbiome are influenced by host factors such as age and diet. The study also discovered novel genomic diversity in the hyena gut microbiome.
Article
Microbiology
William A. Norfolk, Erin K. Lipp
Summary: This study demonstrates and evaluates the effectiveness of pVSV102 plasmid as a tool for tagging Vibrio and related species. The results show that pVSV102 is a stable GFP plasmid that can be used to tag a broad range of vibrios and enable easy differentiation within complex mixtures of cells.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biotechnology & Applied Microbiology
William A. Norfolk, Carolina Melendez-Declet, Erin K. Lipp
Summary: The mucus membrane is the front line of defense against pathogens in corals. Understanding disease transmission in corals is complicated, but most of the established transmission pathways are associated with damage rather than evasion of immune defenses. However, this study suggests that ingestion may be an important pathway for the transmission of coral pathogens that bypasses the mucus membrane.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Marina Estella De Leon, Harriet S. Wilson, Guillaume Jospin, Jonathan A. Eisen
Summary: We isolated and characterized six violacein-producing bacterial strains and three non-violacein-producing close relatives from aquatic environments or moist food materials in northern California, USA. Through various analyses including phenotypic characterization, genome sequencing, and taxonomic and phylogenetic analyses, we were able to assign putative identifications to the nine isolates, which belong to different genera. We also discussed the usefulness of different metrics for taxonomic assignment in these groups.
MICROBIAL GENOMICS
(2023)
Correction
Microbiology
Jihyeon Kim, Seong-In Na, Dongwook Kim, Jongsik Chun
JOURNAL OF MICROBIOLOGY
(2023)
Article
Microbiology
Seong-In Na, Michael James Bailey, Mauricio Chalita, Jae Hyoung Cho, Jongsik Chun
Summary: In the post-genomic era, phylogenomics is widely used to discover evolutionary relationships between microorganisms. This study established an up-to-date archaeal core gene set (UACG) for inferring archaeal phylogenomic trees. The UACG tool was found to be consistent with the orthoANIu dendrogram, in contrast to the 16S rRNA gene phylogeny which showed discrepancies. The UACG software tool is available at https://www.ezbiocloud.net/tools/uacg.
JOURNAL OF MICROBIOLOGY
(2023)
Correction
Microbiology
Dongwook Kim, Sein Park, Jongsik Chun
JOURNAL OF MICROBIOLOGY
(2023)
Article
Microbiology
Kyle D. Brumfield, Moiz Usmani, Sanneri Santiago, Komalpreet Singh, Mayank Gangwar, Nur A. Hasan, Michael Netherland Jr, Katherine Deliz, Christine Angelini, Norman L. Beatty, Anwar Huq, Antarpreet S. Jutla, Rita R. Colwell
Summary: Changing climatic conditions influence the growth of pathogenic Vibrio spp., leading to an increased incidence of vibriosis. Genetic analysis, environmental data, and remote sensing provide valuable information for proactive detection and characterization of environmental pathogens, particularly vibrios.
Article
Infectious Diseases
Bradd J. Haley, Seon Woo Kim, Serajus Salaheen, Ernest Hovingh, Jo Ann S. Van Kessel
Summary: The gastrointestinal tracts of dairy calves and cows are reservoirs of antimicrobial-resistant bacteria. Young calves harbor a greater abundance of resistant bacteria than older cows, but the factors driving this high abundance are unknown. This study aimed to characterize multidrug-resistant (MDR) and antimicrobial-susceptible Escherichia coli strains isolated from different stages of dairy cows and identify accessory genes associated with MDR to discover genetic targets for mitigating antimicrobial resistance on dairy farms.
Article
Veterinary Sciences
Connie A. Rojas, Zhandra Entrolezo, Jessica K. Jarett, Guillaume Jospin, Dawn D. Kingsbury, Alex Martin, Jonathan A. Eisen, Holly H. Ganz
Summary: The study investigates the effects of fecal microbiota transplants (FMTs) on the intestinal microbial communities of domestic cats. 46 cats experiencing chronic digestive issues were given FMTs. Analysis shows changes in the composition of the fecal microbiome in all cats. The study highlights the importance of clinical signs and diet on microbiome responses to FMTs.
VETERINARY SCIENCES
(2023)
Article
Multidisciplinary Sciences
Connie A. Rojas, Stanley L. Marks, Eva Borras, Hira Lesea, Mitchell M. McCartney, David A. Coil, Cristina E. Davis, Jonathan A. Eisen
Summary: This study found that the anal gland microbiome in domestic cats is dominated by several bacterial genera and varies with host age and obesity. The microbiome is modestly correlated with the metabolites found in the anal gland secretions. The research also identified certain bacterial species that could play a role in the production of volatile compounds and scent in mammalian anal glands.
SCIENTIFIC REPORTS
(2023)
Meeting Abstract
Oncology
Lauren M. Perry, Sylvia M. Cruz, Morgan A. Darrow, Louis B. Jones, Ugur N. Basmaci, Nikhil Joshi, Matthew L. Settles, Blythe P. Durbin-Johnson, Arta Monjazeb, Janai Carr-Ascher, Steven Thorpe, Sean Judge, William J. Murphy, Jonathan Eisen, Robert J. Canter
ANNALS OF SURGICAL ONCOLOGY
(2022)