R. Knight

Medication Use is Associated with Distinct Microbial Features in Anxiety and Depression

This study links medication use to distinct gut microbial features in anxiety and depression, showing antidepressants have a larger effect on microbiota than diagnoses.

Comparative metabolomics and microbiome analysis of Ethanol vs. OMNImet/gene GUT fecal stabilization

This study compares the stability of fecal metabolome and microbiome using 95% ethanol and commercial kits under different storage conditions, finding comparable results to flash freezing.

Jumbo phages are active against extensively-drug-resistant eyedrop-associated Pseudomonas aeruginosa infections.

The paper identifies jumbo and non-jumbo phages effective against XDR Pseudomonas aeruginosa isolates causing eyedrop-associated infections.

Variability and Bias in Microbiome Metagenomic Sequencing: an Interlaboratory Study Comparing Experimental Protocols

This study evaluates how different laboratory methods affect microbiome metagenomic sequencing results through an interlaboratory comparison of 44 labs analyzing shared reference samples.

Evidence for microbially-mediated tradeoffs between growth and defense throughout coral evolution

This study shows that microbial symbionts, particularly Endozoicomonas, influence coral growth and disease susceptibility across 425 million years of evolution.

Integrated multi-cohort analysis of the Parkinson's disease gut metagenome

This study analyzes the gut microbiome in Parkinson's disease across multiple cohorts, identifying consistent taxonomic and functional changes associated with the disease.

Effects of Variation in Urine Sample Storage Conditions on 16S Urogenital Microbiome Analyses

This study evaluates how urine sample storage conditions affect 16S rRNA gene sequencing results, finding that AssayAssure reduces microbial bias at colder temperatures but not significantly compared to no preservative.

Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades

This study examines the impact of wastewater treatment upgrades on the microbiome of an urban river system over seven years, finding that seasonality, not the upgrades, dominated microbial community dynamics.

A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice

A prebiotic diet reduces motor deficits and microglial activation in α-synuclein overexpressing mice by altering gut microbiota and microglial states.

A comparison of six DNA extraction protocols for 16S, ITS, and shotgun metagenomic sequencing of microbial communities

The paper compares six DNA extraction protocols for 16S, ITS, and shotgun metagenomic sequencing, finding the MagMAX Microbiome kit performs best across multiple criteria.

Fish microbiomes 101: disentangling the rules governing marine fish mucosal microbiomes across 101 species

The paper analyzes microbiomes of 101 marine fish species to identify factors influencing microbial diversity and distribution across body sites and environments.

Multi-omic analysis along the gut-brain axis points to a functional architecture of autism

The paper identifies a functional architecture of autism along the gut-brain axis using multi-omic data, revealing microbial and metabolic profiles linked to autism symptoms.

Bacterial metatranscriptomes in wastewater can differentiate virally infected human populations

The paper shows that bacterial metatranscriptomes in wastewater can distinguish SARS-CoV-2 infected from uninfected human populations without directly detecting viral transcripts.

Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence

This study compares RT-qPCR signal intensity and persistence of heat-inactivated and infectious SARS-CoV-2 on different surfaces, showing similar decay patterns and enabling simplified environmental monitoring protocols.

Peripheral Neuronal Activation Shapes the Microbiome and Alters Gut Physiology

This study activates specific gut neurons in mice to show they influence microbiome structure and gut physiology, including bile acids and fecal output, without brain signals.

Probiotic bacteria and bile acid profile are modulated by prebiotic diet and associate with facilitated diurnal clock/sleep realignment after chronic disruption of rhythms

This study shows that a prebiotic diet increases beneficial gut bacteria and bile acids, helping rats realign sleep and circadian rhythms after chronic disruption.

A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities

The paper compares DNA/RNA extraction protocols for microbial community sequencing, finding one protocol equivalent or better than a standard DNA-only method for RNA-based organisms.

A scale-free, fully connected global transition network underlies known microbiome diversity

The paper constructs a global microbiome transition network showing microbiomes are closely connected despite habitat differences, with a scale-free structure and a roadmap of dispersal.

Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity

This study shows that commensal bacteria modify heparan sulfate, reducing SARS-CoV-2 spike protein binding and that this bacterial presence decreases with age, increasing COVID-19 susceptibility.

Microbial ecology of Atlantic salmon, Salmo salar, hatcheries: impacts of the built environment on fish mucosal microbiota

This study examines how the microbiota of water and tank biofilms in Atlantic salmon hatcheries influences fish mucosal microbiota across gill, skin, and digesta sites.

Microbe-metabolite associations linked to the rebounding murine gut microbiome post-colonization with vancomycin resistant Enterococcus faecium

This study investigates how the gut microbiome changes in mice after colonization with vancomycin-resistant Enterococcus faecium, identifying metabolite associations linked to bacterial shifts.

Characterizing the response of Acinetobacter baumannii ATCC 17978 to azithromycin in multiple in vitro growth conditions

This study examines how MDR A. baumannii responds to azithromycin in different growth conditions using multiple analytical techniques.

Profiling the effect of nafcillin on HA-MRSA D592 using bacteriological and physiological media

This study investigates how nafcillin affects HA-MRSA D592 in different media types, revealing media-dependent antibiotic activity through multi-dimensional analysis.

Expanding magnetic organelle biogenesis in the domain Bacteria

This study expands the known diversity of magnetosome biogenesis in bacteria by analyzing new genomes and revealing an early evolutionary origin of magnetic nanoparticle formation.

Early-life gut dysbiosis linked to mass mortality in ostriches

The paper links early-life gut dysbiosis in ostriches to mass mortality by showing distinct microbial composition in deceased individuals compared to controls and the early presence of pathobionts.

The urinary tract microbiome in older women exhibits host genetics and environmental influences

This study identifies host genetic and environmental factors influencing the urinary microbiome in older women using twin data and metagenomic analysis.

Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules

This study uses deep metagenomics to analyze the oral microbiome in children with and without dental caries, identifying novel taxa and host-microbe interactions.

Temporal, environmental, and biological drivers of the mucosal microbiome in a wild marine fish, Scomber japonicus

This study examines how environmental and biological factors shape the mucosal microbiome of wild marine fish over time, identifying key drivers like temperature and fish age.

The Molecular and Microbial Microenvironments in Chronically Diseased Lungs

The paper generates 3D maps of microbiomes and metabolomes in cystic fibrosis lungs, revealing personalized and regiospecific chemical environments and microbial interactions.

Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids

The paper identifies novel conjugated bile acids produced by the microbiome in mice and humans using mass spectrometry and a murine 3D model.