Daniel R. Utter
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View article: Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities
Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities Open
Dense microbial communities, like the gut and soil microbiomes, are dynamic societies. Bacteria can navigate these environments by deploying proteins that alter foreign cells’ behavior, such as interbacterial effectors. Current models sugg…
View article: Author response: Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities
Author response: Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities Open
View article: Carbon monoxide oxidation expands the known metabolic capacity in anaerobic methanotrophic consortia
Carbon monoxide oxidation expands the known metabolic capacity in anaerobic methanotrophic consortia Open
Efficient energy metabolism is essential for microorganisms living on the thermodynamic edge. Consortia of anaerobic methane-oxidizing archaea (ANME-2) and sulphate-reducing bacteria (SRB) represent globally relevant syntrophic association…
View article: Identification of key steps in the evolution of anaerobic methanotrophy in <i>Candidatus</i> Methanovorans (ANME-3) archaea
Identification of key steps in the evolution of anaerobic methanotrophy in <i>Candidatus</i> Methanovorans (ANME-3) archaea Open
Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recently evolved b…
View article: CABO-16S—a Combined Archaea, Bacteria, Organelle 16S rRNA database framework for amplicon analysis of prokaryotes and eukaryotes in environmental samples
CABO-16S—a Combined Archaea, Bacteria, Organelle 16S rRNA database framework for amplicon analysis of prokaryotes and eukaryotes in environmental samples Open
Identification of both prokaryotic and eukaryotic microorganisms in environmental samples is currently challenged by the need for additional sequencing to obtain separate 16S and 18S ribosomal RNA (rRNA) amplicons or the constraints impose…
View article: Array of metabolic pathways in a kleptoplastidic foraminiferan protist supports chemoautotrophy in dark, euxinic seafloor sediments
Array of metabolic pathways in a kleptoplastidic foraminiferan protist supports chemoautotrophy in dark, euxinic seafloor sediments Open
Investigations of the metabolic capabilities of anaerobic protists advances our understanding of the evolution of eukaryotic life on Earth and for uncovering analogous extraterrestrial complex microbial life. Certain species of foraminifer…
View article: CABO-16S – A Combined Archaea, Bacteria, Organelle 16S database for amplicon analysis of prokaryotes and eukaryotes in environmental samples
CABO-16S – A Combined Archaea, Bacteria, Organelle 16S database for amplicon analysis of prokaryotes and eukaryotes in environmental samples Open
Identification of both prokaryotic and eukaryotic microorganisms in environmental samples is currently challenged by either the burden of additional sequencing required to obtain both 16S and 18S rRNA sequences or the introduction of multi…
View article: Thermotogota diversity and distribution patterns revealed in <i>Auka</i> and <i>JaichMaa ‘ja ‘ag</i> hydrothermal vent fields in the Pescadero Basin, Gulf of California
Thermotogota diversity and distribution patterns revealed in <i>Auka</i> and <i>JaichMaa ‘ja ‘ag</i> hydrothermal vent fields in the Pescadero Basin, Gulf of California Open
Discovering new deep hydrothermal vent systems is one of the biggest challenges in ocean exploration. They are a unique window to elucidate the physical, geochemical, and biological processes that occur on the seafloor and are involved in …
View article: Author response: Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities
Author response: Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities Open
Dense microbial communities, like the gut and soil microbiomes, are dynamic societies. Bacteria can navigate these environments by deploying proteins that alter foreign cells' behavior, such as interbacterial effectors. Current models sugg…
View article: Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities
Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities Open
Dense microbial communities, like the gut and soil microbiomes, are dynamic societies. Bacteria can navigate these environments by deploying proteins that alter foreign cells’ behavior, such as interbacterial effectors. Current models sugg…
View article: Persistent enrichment of multidrug-resistant Klebsiella in oral and nasal communities during long-term starvation
Persistent enrichment of multidrug-resistant Klebsiella in oral and nasal communities during long-term starvation Open
Background The human oral and nasal cavities can act as reservoirs for opportunistic pathogens capable of causing acute infection. These microbes asymptomatically colonize the human oral and nasal cavities which facilitates transmission wi…
View article: Convergence and horizontal gene transfer drive the evolution of anaerobic methanotrophy in archaea
Convergence and horizontal gene transfer drive the evolution of anaerobic methanotrophy in archaea Open
1 Abstract Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recentl…
View article: DeepSee: Multidimensional Visualizations of Seabed Ecosystems
DeepSee: Multidimensional Visualizations of Seabed Ecosystems Open
Scientists studying deep ocean microbial ecosystems use limited numbers of sediment samples collected from the seafloor to characterize important life-sustaining biogeochemical cycles in the environment. Yet conducting fieldwork to sample …
View article: The Life Methanic: Microbial Activity in the Deep Ocean Methanosphere of the Southern California Borderland
The Life Methanic: Microbial Activity in the Deep Ocean Methanosphere of the Southern California Borderland Open
The deep ocean methanosphere is defined by the microbial communities that cycle methane, the animals that directly consume or form symbioses with methane-consuming microbes, and the transitional animal communities that gain energy indirect…
View article: Persistent enrichment of multidrug resistant<i>Klebsiella</i>in oral and nasal communities during long-term starvation
Persistent enrichment of multidrug resistant<i>Klebsiella</i>in oral and nasal communities during long-term starvation Open
The human oral and nasal cavities can act as reservoirs for opportunistic pathogens capable of causing acute infection. These microbes asymptomatically colonize the human oral and nasal cavities which facilitates transmission within human …
View article: Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities
Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities Open
Dense microbial communities, like the gut and soil microbiomes, are dynamic societies. Bacteria can navigate these environments by deploying proteins (effectors) that alter foreign cells’ behavior. Immunity proteins preferentially protect …
View article: Reviewer #2 (Public Review): Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities
Reviewer #2 (Public Review): Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities Open
Dense microbial communities, like the gut and soil microbiomes, are dynamic societies. Bacteria can navigate these environments by deploying proteins (effectors) that alter foreign cells' behavior. Immunity proteins preferentially protect …
View article: Reviewer #1 (Public Review): Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities
Reviewer #1 (Public Review): Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities Open
Dense microbial communities, like the gut and soil microbiomes, are dynamic societies. Bacteria can navigate these environments by deploying proteins (effectors) that alter foreign cells' behavior. Immunity proteins preferentially protect …
View article: Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities
Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities Open
Dense microbial communities, like the gut and soil microbiomes, are dynamic societies. Bacteria can navigate these environments by deploying proteins that alter foreign cells’ behavior, such as interbacterial effectors. Current models sugg…
View article: Author Response: Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities
Author Response: Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities Open
Dense microbial communities, like the gut and soil microbiomes, are dynamic societies. Bacteria can navigate these environments by deploying proteins (effectors) that alter foreign cells' behavior. Immunity proteins preferentially protect …
View article: Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities
Non-cognate immunity proteins provide broader defenses against interbacterial effectors in microbial communities Open
Dense microbial communities, like the gut and soil microbiomes, are dynamic societies. Bacteria can navigate these environments by deploying proteins that alter foreign cells’ behavior, such as interbacterial effectors. Current models sugg…
View article: Gifts hidden in shadowy genome islands
Gifts hidden in shadowy genome islands Open
View article: Two canonically aerobic foraminifera express distinct peroxisomal and mitochondrial metabolisms
Two canonically aerobic foraminifera express distinct peroxisomal and mitochondrial metabolisms Open
Certain benthic foraminifera thrive in marine sediments with low or undetectable oxygen. Potential survival avenues used by these supposedly aerobic protists include fermentation and anaerobic respiration, although details on their adaptiv…
View article: Genome-Centric Dynamics Shape the Diversity of Oral Bacterial Populations
Genome-Centric Dynamics Shape the Diversity of Oral Bacterial Populations Open
The oral microbiome represents a microbial community of critical relevance to human health. Recent studies have documented the diversity and dynamics of different bacteria to reveal a rich, stable ecosystem characterized by strain-level dy…
View article: Exploitation of a Bacterium-Encoded Lytic Transglycosylase by a Human Oral Lytic Phage To Facilitate Infection
Exploitation of a Bacterium-Encoded Lytic Transglycosylase by a Human Oral Lytic Phage To Facilitate Infection Open
The evidence for the presence of a diverse and abundant phage population in the host-associated oral microbiome came largely from metagenomic analysis or the observation of virus-like particles within saliva/plaque samples, while the isola…
View article: Draft Genome Sequences of Nine “ <i>Candidatus</i> Nanosynbacter sp. HMT-352” Strains Cultured from the Human Oral Cavity
Draft Genome Sequences of Nine “ <i>Candidatus</i> Nanosynbacter sp. HMT-352” Strains Cultured from the Human Oral Cavity Open
Here, we report draft genome sequences for nine strains of “ Candidatus Nanosynbacter sp. HMT-352.” These strains and their sequences were used to interrogate strain-level variations in host range, gene content, and growth dynamics among t…
View article: Two canonically aerobic foraminifera express distinct peroxisomal and mitochondrial metabolisms
Two canonically aerobic foraminifera express distinct peroxisomal and mitochondrial metabolisms Open
Certain benthic foraminifera are known to thrive in marine sediments with low oxygen or even without detectable oxygen. Potential survival avenues used by these supposedly aerobic protists include fermentation and anaerobic respiration, al…
View article: Strain-Level Variation and Diverse Host Bacterial Responses in Episymbiotic Saccharibacteria
Strain-Level Variation and Diverse Host Bacterial Responses in Episymbiotic Saccharibacteria Open
Candidate phylum radiation (CPR) bacteria comprise a poorly understood phylum that is estimated to encompass ∼26% of all diversity of domain bacteria. Among CPR bacteria, the Saccharibacteria lineage (TM7) is of particular interest, as it …
View article: Acquisition of the arginine deiminase system benefits epiparasitic Saccharibacteria and their host bacteria in a mammalian niche environment
Acquisition of the arginine deiminase system benefits epiparasitic Saccharibacteria and their host bacteria in a mammalian niche environment Open
Significance The Candidate Phyla Radiation (CPR) is a large monophyletic lineage with poorly understood biology. Saccharibacteria are ultrasmall parasitic CPR bacteria with highly reduced genomes that have made the transition from an envir…
View article: SBB_Data_Repository
SBB_Data_Repository Open
Assemblies, annotations, and abundance mapping of (meta)transcriptome data from laboratory treatments of benthic foraminifera obtained from Santa Barbara Basin, Nonionella stella and Bolivina argentea.