Article
Biochemistry & Molecular Biology
Jia Li, Song Li, Hua Su, Minjie Yu, Jiahui Xu, Zhenzhen Yi
Summary: Ciliate species within the class Armophorea, widely distributed in anaerobic environments, have attracted interest for researchers exploring the evolution and adaptation of eukaryotes to extreme habitats. However, the phylogenetic relationships within the class, particularly the order Armophorida and family Metopidae, remain uncertain. This study sequenced the transcriptomes and SSU rDNA of five armophorean species and conducted comprehensive phylogenomic analyses, revealing the closest relationship between Armophorea, Muranotrichea, and Parablepharismea. The findings suggest that the order Armophorida may belong to Armophorea or represent a new class within APM. Additionally, the family Metopidae is nonmonophyletic and requires further classification based on molecular and morphological evidence.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Veterinary Sciences
Vikash K. Singh, Victor Neira, Barbara Brito, Naomi Ariyama, Matt Sturos, Sunil K. Mor
Summary: Bovine rotavirus A (boRVA) strains are common causes of diarrhea in calves and can reassort with human rotaviruses. This study detected the genetic material of boRVA in fecal samples from calves with diarrhea and identified a novel boRVA genotype closely related to human rotavirus strains from the USA.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Microbiology
Pilar Vesga, Eva Augustiny, Christoph Keel, Monika Maurhofer, Jordan Vacheron
Summary: Strains of Pseudomonas protegens and Pseudomonas chlororaphis have the ability to control soilborne plant pathogens and kill pest insects by producing virulence factors. The study found that P. protegens strains were more homogeneous in phylogeny, biocontrol, and insecticidal capabilities, while P. chlororaphis strains were more heterogeneous. Analysis of closely related P. chlororaphis isolates revealed variations in genes encoding insecticidal factors, which may explain the reduced insecticidal activity in certain strains.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Microbiology
Isabel Hennig-Pauka, Christoph Sudendey, Sven Kleinschmidt, Werner Ruppitsch, Igor Loncaric, Joachim Spergser
Summary: A new mycoplasma species, Mycolplasma sp. 1654_15, was isolated from conjunctival swabs of affected pigs in three unrelated swine farms in Germany. It may cause conjunctivitis as it potentially uses myo-inositol as an alternative energy source on the conjunctival surface, leading to robust colonization by outcompeting other bacteria. This novel species shows significant differences from M. hyorhinis, suggesting a specialized role in causing local eye disease in pigs.
Article
Biodiversity Conservation
Kathryn C. Grabenstein, Ken A. Otter, Theresa M. Burg, Scott A. Taylor
Summary: Human habitat disturbances are positively correlated with hybridization between black-capped and mountain chickadees, with more hybrids found in disturbed habitats. The offspring of these birds have mixed genetic ancestries.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Evolutionary Biology
Jimmy H. Saw, Tanai Cardona, Gustavo Montejano
Summary: This study presents the complete genome sequence of a new species of the cyanobacterial genus Gloeobacter, named Gloeobacter morelensis, isolated from a waterfall cave in Mexico. The genome shows a low similarity with existing Gloeobacter species and possesses unique genes not found in other species. Additionally, the discovery of a highly divergent psbA gene encoding an atypical D1 core subunit of Photosystem II suggests a complex evolutionary relationship within this genus.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Christen L. Grettenberger
Summary: Photosynthetic Cyanobacteria and their order Gloeobacterales play a crucial role in oxygenic photosynthesis and hold clues to the evolutionary history of this process. However, the limited number of genomes and taxa available from Gloeobacterales poses challenges for studying their evolution. New methods are needed to search for these evolutionarily important taxa for a better understanding of the origin and evolution of oxygenic photosynthesis.
Article
Microbiology
Flavia Dematheis, Mathias C. Walter, Daniel Lang, Markus Antwerpen, Holger C. Scholz, Marie-Theres Pfalzgraf, Enrico Mantel, Christin Hinz, Roman Wolfel, Sabine Zange
Summary: In this study, MALDI-TOF mass spectrometry was used to differentiate closely related species of Brucella. The results showed that both unsupervised and optimized supervised machine learning models achieved excellent predictive performances.
Article
Biodiversity Conservation
Robin Pouteau, Mark van Kleunen, Dominique Strasberg
Summary: Alien species are a major contributor to extinction risk, and preventing the introduction of high-impact aliens is essential in mitigating the current biodiversity crisis. However, invasive species risk assessments often overlook the differences between potential invaders and native species they might threaten. In this study, we investigated whether the extinction risk of native plants can be predicted by their phylogenetic distance from alien species. Our findings show that natives facing threats from closely related alien species have a significantly higher risk of extinction, especially on oceanic islands. These findings highlight the importance of considering phylogenetic distance and the presence of related native species in risk assessments and management strategies for alien species.
BIOLOGICAL CONSERVATION
(2023)
Article
Veterinary Sciences
Bernat Perez de Val, Claudia Perea, Josep Estruch, Carlos Solano-Manrique, Carles Riera, Albert Sanz, Enric Vidal, Roser Velarde
Summary: This is the first reported case of TB caused by M. caprae in a fox in the Iberian Peninsula. WGS and SNP analysis, along with spatial-temporal investigations, associated this case with recent M. caprae outbreaks in cattle and goat herds of the area.
BMC VETERINARY RESEARCH
(2022)
Article
Microbiology
Yang Liu, Tao Pei, Shuoxing Yi, Juan Du, Xianjiao Zhang, Xiaoqin Deng, Qing Yao, Ming-Rong Deng, Honghui Zhu
Summary: Investigating the gyrB gene can address the limitations of 16S rRNA gene sequencing and whole-genome sequencing in identifying members of Myxococcus, Corallococcus, and Pyxidicoccus. The gyrB gene is a powerful molecular marker for the taxonomy and phylogeny of bacteria within these closely related genera, allowing for accurate differentiation of isolates at the species level.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Evolutionary Biology
Jimmy H. Saw, Tanai Cardona, Gustavo Montejano
Summary: This study presented a new Gloeobacter species, Gloeobacter morelensis, isolated from a waterfall cave in Mexico, with a complete genome significantly different from existing Gloeobacter species, especially in the psbA gene. The psbA gene in G. morelensis and two other Gloeobacter genomes showed evidence of concerted evolution, suggesting a common ancestor among cyanobacteria.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Virology
Rachel E. Loney, Veronique A. Delesalle, Brianne E. Chaudry, Megan Czerpak, Alexandra A. Guffey, Leo Goubet-McCall, Michael McCarty, Madison S. Strine, Natalie T. Tanke, Albert C. Vill, Greg P. Krukonis
Summary: This study revealed high genetic similarity between seven Bacillus subtilis phages isolated from desert soil in the southwest United States, forming a novel subcluster. Interestingly, the tail fiber and lysin genes of these phages appear to have been acquired from different origins and have slightly different functions. The findings suggest that these phages are adapting to hosts with different cell walls, as supported by host range assays.
Article
Plant Sciences
Scott A. A. Ford, Rory J. J. Craig, Rob W. W. Ness
Summary: We present a new method for efficiently sampling Chlamydomonas reinhardtii and closely related species using colony PCR-based screen and novel primer sets designed for specific detection. We collected 130 soil samples from various habitats in Ontario, Canada, and identified 33 candidate algae, which were analyzed using rbcL plastid gene sequencing, 18S rRNA gene sequencing, and YPT4 nuclear marker sequencing. Phylogenetic and haplotype network analyses revealed seven novel isolates of C. reinhardtii and one closely related species. The molecular screen was validated by demonstrating the ability of the seven new C. reinhardtii strains to freely interbreed with previously collected field isolates.
JOURNAL OF PHYCOLOGY
(2023)
Article
Virology
Julia Anabell Braeuer, Jens Andre Hammerl, Sabrin El-Mustapha, Julius Fuhrmann, Andrea Barac, Stefan Hertwig
Summary: Telomere phages are a small group of temperate phages that replicate as linear plasmids and have a specific host specificity. Their unique characteristics make them important in research.
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
Veterinary Sciences
Monica Aleman, Shara. A. Sheldon, Guillaume Jospin, David Coil, Meri Stratton-Phelps, Jonathan Eisen
Summary: This study aimed to investigate the difference in cecal microbiota between horses with TMHS and a control group. The results showed that the cecal microbiota of horses with TMHS was similar to the control group in terms of diversity, but Methanocorpusculum spp. had a higher abundance in horses with TMHS.
VETERINARY MEDICINE AND SCIENCE
(2022)
Article
Ecology
Elizabeth G. Wilbanks, Hugo Dore, Meredith H. Ashby, Cheryl Heiner, Richard J. Roberts, Jonathan A. Eisen
Summary: The plasticity of bacterial and archaeal genomes makes it challenging to recover complete genomes from metagenomes. In this study, the researchers used strain-specific patterns of DNA methylation to successfully resolve complex bacterial genomes from metagenomic data. They recovered the largest and most complex circularized bacterial genome ever recovered from a metagenome and identified instances of horizontal gene transfer, phage infection, and strain-level structural variation.
Article
Multidisciplinary Sciences
Rogelio Zuniga-Montanez, David A. Coil, Jonathan A. Eisen, Randi Pechacek, Roque G. Guerrero, Minji Kim, Karen Shapiro, Heather N. Bischel
Summary: Testing surfaces in school classrooms for the presence of SARS-CoV-2 can provide important public-health information. A study conducted in schools in California found that swab samples from high-efficiency particulate air (HEPA) filters were more sensitive in detecting the virus compared to floor samples. The positive samples detected likely contained RNA from previous infections or were transported into the classrooms through contaminated objects.
Review
Immunology
Kara T. T. Kleber, Khurshid R. R. Iranpur, Lauren M. M. Perry, Sylvia M. M. Cruz, Aryana M. M. Razmara, William T. N. Culp, Michael S. S. Kent, Jonathan A. A. Eisen, Robert B. B. Rebhun, Robert J. J. Canter
Summary: The microbiome plays an important role in tumor immunology and immunotherapy, including immune surveillance and response to immune checkpoint inhibitors. Studies using fecal microbial transplantation have shown that modulation of the gut microbiome can affect response to checkpoint immunotherapies. Canine cancer models, which closely resemble human cancers, provide valuable insights for studying microbiota-host immune and metabolic interactions and testing interventions for modifying gut microbiomes.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Geochemistry & Geophysics
Jessica A. Watkins, John P. Grotzinger, Nathan T. Stein, Steven G. Banham, Sanjeev Gupta, David M. Rubin, Kathryn Stack Morgan, Kenneth S. Edgett, Jens Frydenvang, Kirsten L. Siebach, Michael P. Lamb, Dawn Y. Sumner, Kevin W. Lewis
Summary: Sedimentary rocks on Mars provide a record of the planet's ancient climate, and their stratal geometries and sedimentary structures reveal changes between subaqueous and eolian depositional environments. By studying the sedimentary sequence on the flanks of Aeolis Mons in Gale crater, researchers have identified a dynamic evolution of deposition and erosion, suggesting a transition from a wet to dry climate and providing important insights into the geological history and habitability of Mars.
JOURNAL OF GEOPHYSICAL RESEARCH-PLANETS
(2022)
Article
Geochemistry & Geophysics
S. Gwizd, C. Fedo, J. Grotzinger, S. Banham, F. Rivera-Hernandez, K. M. Stack, K. Siebach, M. Thorpe, L. Thompson, C. O'Connell-Cooper, N. Stein, L. Edgar, S. Gupta, D. Rubin, D. Sumner, A. R. Vasavada
Summary: This study utilizes instruments from the Curiosity rover to reconstruct the paleoenvironment and composition of a specific interval of stratigraphy in Gale crater, Mars. The findings indicate the presence of a lake and sand dunes in this area.
JOURNAL OF GEOPHYSICAL RESEARCH-PLANETS
(2022)
Article
Biology
Friederike Clever, Jade M. Sourisse, Richard F. Preziosi, Jonathan A. Eisen, E. Catalina Rodriguez Guerra, Jarrod J. Scott, Laetitia G. E. Wilkins, Andrew H. Altieri, W. Owen McMillan, Matthieu Leray
Summary: Environmental degradation can affect key mutualistic relationships in ecological communities. A study found significant differences in the gut microbiome composition of a coral-feeding butterflyfish across Caribbean reefs with varying live coral cover. The fish gut microbiomes were more variable and had changes in the abundance of stress-associated taxa in degraded reefs. The findings suggest that severe coral degradation can impact the essential interactions between fish and their microbiomes.
COMMUNICATIONS BIOLOGY
(2022)
Article
Microbiology
David A. Coil, Randi Pechacek, Mo Kaze, Rogelio Zuniga-Montanez, Roque G. Guerrero, Jonathan A. Eisen, Karen Shapiro, Heather N. Bischel
Summary: Environmental monitoring of SARS-CoV-2 has become increasingly important in infectious disease research and public health surveillance. Monitoring virus in wastewater can provide early warning signals and information on infection trends in communities. Surface and air filter monitoring is less common and its effectiveness is debated. A study found SARS-CoV-2 RNA on surfaces in a dorm room for up to 8 months after a COVID-19-positive individual had left. This highlights the need to address relic RNA in environmental monitoring.
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
Geosciences, Multidisciplinary
Elizabeth J. Trower, James R. Gutoski, Virginia T. Wala, Tyler J. Mackey, Carl Simpson
Summary: This study reports the occurrence of ikaite, a carbonate mineral that forms in cold sedimentary environments, in the Beck Spring Dolomite, a carbonate succession deposited between approximately 780 and 730 Ma. These findings suggest that global climate was cool for tens of millions of years before the onset of Snowball Earth glaciation, in conflict with previous interpretations of pre-glacial carbonates.
GEOPHYSICAL RESEARCH LETTERS
(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)
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)
