Biology subjects

Embree, J.

Publications and source records attributed to Embree, J..

4 recordsLinked to original sources

bioRxiv2026

Butyrivibrio azoria sp. nov., a novel cellulolytic microorganism isolated from the rumen of a Holstein dairy cow

This study describes the characteristics of NATIVEDY162T (= JL13D10T = NRRL B-68525T) a novel bacterium isolated from the rumen of a healthy Holstein dairy cow. NATIVEDY162T was discovered to be an obligately anaerobic, slightly curved, rod that stains Gram-negative, and presents as singlets or short chains. Tests confirmed it is indole-, catalase-, oxidase-negative, and it is not motile. NATIVEDY162T indicated a growth preference within the pH range of 6.5-7.5 with optimal growth at pH 7.0. Carbon panel assays found NATIVEDY162T can utilize D-glucose, L-rhamnose, esculin/ferric citrate, D-lactose, and D-trehalose, whereas weak growth was observed on D-xylose and D-cellobiose. It was also capable of degrading starch and digesting both soluble and insoluble forms of cellulose, with genomic analysis providing further support by revealing a diverse array of carbohydrate-active enzymes (CAZymes) targeting starch and plant structural components like pectin and cellulose. Fermentation of glucose by NATIVEDY162T resulted in the major fermentation products lactate and butyrate. Phylogenetic analysis of the 16S rRNA gene positioned NATIVEDY162T in close relation to other Butyrivibrio species. Genome comparisons using BLAST ANI identified its closest relative as Butyrivibrio proteoclasticus (75.7% identity); however, the similarity did not meet the 95% threshold for species identification. Phylogenetic, genomic, and chemotaxonomic findings highlight differences between NATIVEDY162T and other Butyrivibrio species, indicating it is a novel species. NATIVEDY162T was isolated from a lactating Holstein dairy cow located in Californias San Joaquin Valley, a region rich in Portuguese influence from Azorean migrants who played a key role in the development of the California dairy industry, producing most of the states milk by the mid-20th century. Given this historical context, we propose the name Butyrivibrio azoria type strain NATIVEDY162T in honor of the significant contributions of Azorean and Portuguese dairy farmers in the region.

microbiology↗

bioRxiv2026

Ruminococcus hollandia sp. nov. and Ruminococcus vasco sp. nov., two novel starch-degrading Ruminococcus isolated from the rumen of Holstein dairy cattle

This study investigated the genomic and biochemical characteristics of two amylolytic microbial strains, NATIVEDY160T (= JE7B6T = NRRL B-68523T) and NATIVEDY161T (= JL13D9T, = NRRL B-68524T) isolated from the rumen of healthy Holstein dairy cattle. Both strains are obligately anaerobic, non-motile, Gram positive, catalase-negative, and oxidase-negative. Morphologically, NATIVEDY160T grows in long coccoid chains while NATIVEDY161T grows in short chains or pairs. NATIVEDY160T can catabolize amygdalin, esculin/ferric citrate, and starch, compared to NATIVEDY161T which utilizes amygdalin, arbutin, esculin/ferric citrate, glycogen, and D-maltose as determined by API 50 CH carbon panels. Starch degradation ability was verified for both strains, but neither showed cellulolytic activity as confirmed by starch agar and Congo red agar assays, respectively. HPLC analysis revealed that lactate was the primary end product of both strains carbohydrate fermentation, while strain NATIVEDY161T also produced small amounts of acetate. 16S rRNA sequences from both strains cluster with the Oscillospiraceae (formerly Ruminococcaceae) lineage Ruminococcus species, but average nucleotide identity of either strain compared to closely related Ruminococcus members was under the species threshold (95%). Genomic, phylogenetic, and phenotypic interrogation support NATIVEDY160T and NATIVEDY161T as novel species. Each strain was isolated from the rumen of dairy cows located within the central valley of southern California, which has a rich history of Dutch and Basque dairy farm ownership and is still the case today in the region. In recognition of the contributions and heritage of the central and southern California dairy industry, the names Ruminococcus hollandia and Ruminococcus vasco are proposed with NATIVEDY160T and NATIVEDY161T as their respective type strains.

microbiology↗

bioRxiv2025

Fast Hyperspectral and Super-Resolved Mapping of Lipid Membrane Polarity with Single-Molecule Sensitivity

Cell membranes display nanoscale heterogeneity in lipid composition and organization that regulates vital biological processes yet remains challenging to resolve with conventional imaging. We introduce spectral phasor single molecule localization microscopy (SP-SMLM), a hyperspectral and super-resolution method that combines wavefront-like optical filtering with single molecule imaging for simultaneous spatial and spectral analysis. A lab-built three-channel imager with sine/cosine filters encodes emission spectra of single molecules into the phasor space, enabling high-throughput, high-SNR mapping of membrane polarity at sub-50 nm spatial and 15-sec temporal resolutions. Through simulation, we validate that the phasor angle correlates with the spectral mean for single dye molecules. When applied to Nile Red-stained COS-7 cells, SP-SMLM revealed organelle-specific polarity differences and dynamic remodeling of lipid composition within live cells. The methods hyperspectral capability, rapid acquisition, and compatibility with 2D/3D imaging platforms position SP-SMLM as a powerful tool for studying membrane heterogeneity and dynamics in live cells.

biophysics↗

bioRxiv2025

High Throughput Hyperspectral and Multiplexed Super-Resolution Fluorescence Imaging by SP-STORM

Simultaneous determination of spatial location and spectral color of single molecules at large molecular density with high throughput was achieved by combining single molecule photoswitching and in-hardware transformation based spectral phasor analysis. The method, named spectral phasor enabled stochastic optical reconstruction microscopy (SP-STORM), achieved simultaneous super-resolution imaging of five subcellular structures with minimum crosstalk for the first time. The high throughput feature of SP-STORM enables these subcellular structures to be readily resolved in about one minute, which is more than a magnitude faster than other multiplexing single molecule localization microscopy techniques. The concept of SP-STORM is also compatible with and can be readily applicable to other super-resolution microscopy.

biophysics↗