Biology subjects

Hale, V. L.

Publications and source records attributed to Hale, V. L..

At least 19 recordsLinked to original sources

bioRxiv2026

AI-guided discovery of antimicrobial peptides for urinary tract infections leveraging a new catalogue of the human urinary microbiome

Urinary tract infections (UTIs) are common infections that pose a critical burden on healthcare and society. Despite growing recognition that the human urinary tract harbors its own microbiome, its composition, functional potential, and alterations in UTI remain limited. Here, we leveraged the publicly available whole-metagenome shotgun sequencing data from 450 urinary microbiome samples collected in four independent cohorts together with genome assembly and metagenomic binning to construct an extensive human urinary microbiome catalog consisting of [~]1.3 million non-redundant microbial genes and 705 non-redundant metagenome-assembled genomes (nrMAGs). We found that microbiomes from patients with UTI carry significantly more genes linked to antibiotic resistance and virulence vs controls. There was an enrichment of multiple Escherichia strains in patients with UTI from two independent case-control cohorts. UTIs are becoming multidrug-resistant, and we used machine learning models to identify potential antimicrobial peptides (AMPs) in 705 nrMAGs. Furthermore, we experimentally demonstrated that two of these AMPs exhibited strong inhibitory activity against uropathogenic Escherichia coli strains. Our study provides a valuable resource for studying the human urinary microbiome and suggests urinary microbiome-derived AMPs represent a source of new therapeutics for UTIs.

microbiology↗

bioRxiv2025

Environment and weight class linked to skin microbiome structure of juvenile Eastern hellbenders (Cryptobranchus alleganiensis alleganiensis) in human care

Amphibian skin is integral to promoting normal physiological processes in the body and promotes both innate and adaptive immunity against pathogens. The amphibian skin microbiota is comprised of a complex assemblage of microbes and is shaped by internal host characteristics and external influences. Skin disease is a significant source of morbidity and mortality in amphibians, and increasing research has shown that the amphibian skin microbiota is an important component in host health. The Eastern hellbender (Cryptobranchus alleganiensis alleganiensis) is a giant salamander declining in many parts of its range, and captive-rearing programs are important to hellbender recovery efforts. Survival rates of juvenile hellbenders in captive-rearing programs are highly variable, and mortality rates are overall poorly understood. Deceased juvenile hellbenders often present with low body condition and skin abnormalities. To investigate potential links between the skin microbiota and body condition, we collected skin swab samples from 116 juvenile hellbenders and water samples from two holding tanks in a captive-rearing program. We used 16s rRNA gene sequencing to characterize the skin and water microbiota and observed significant differences in the skin microbiota by weight class and tank. The skin microbiota of hellbenders that were housed in tanks in close proximity were generally more similar than those housed physically distant. A single taxa, Parcubacteria, was differentially abundant by weight class only and observed in higher abundance in low weight hellbenders. These results suggest a true association between this taxa and Low weight hellbenders. Additional research is needed to investigate how husbandry factors and potential pathogenic organisms, such as Parcubacteria, impact the skin microbiota of hellbenders and ultimately morbidity and mortality in the species.

microbiology↗

bioRxiv2025

Nuclear Disruption as a Mechanism of the Chemotherapeutic Drug Paclitaxel in Interphase

Regulation of Lamin A/C levels and distribution is crucial for nuclear integrity and mechanotransduction via the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex. Dysregulation of Lamin A/C correlates with poor cancer prognosis, and its levels determine sensitivity to the microtubule-stabilising drug paclitaxel. Paclitaxel is well-known for disrupting mitosis, yet it also reduces tumour size in slow-dividing tumours, indicating an additional, poorly characterised interphase mechanism. Here, we reveal that paclitaxel induces nuclear aberrations in interphase through SUN2-dependent Lamin A/C disruption. Using advanced optical imaging and electron cryo-tomography, we show the formation of aberrant microtubule-vimentin bundles during paclitaxel treatment, which coincides with nuclear deformation and altered Lamin A/C protein levels and organisation at the nuclear envelope. SUN2 is required for Lamin A/C reduction in paclitaxel and is in turn regulated by polyubiquitination. Furthermore, Lamin A/C expression levels determine not only cell survival during treatment but also recovery after drug removal. Our findings support a model in which paclitaxel acts through both defective mitosis and interphase nuclear-cytoskeletal disruption, providing additional mechanistic insights into a widely used anticancer drug.

cell biology↗

bioRxiv2024

Are you my mother?: When host genetics and gut microbiota tell different phylogenetic stories in the Africanized honey bee hybrid (Apis mellifera scutellata x sspp.)

Africanized honey bees (Apis mellifera scutellata x sspp.) originated in Brazil through the crossbreeding of African (A. mellifera scutellata) and European (A. mellifera sspp.) honey bee subspecies. African genes came to dominate in these hybrid honey bees over time. Gut microbiota co-evolve with their hosts and generally reflect host phylogeny. To examine if this was true in Africanized honey bee hybrids, we compared the gut microbiota (16S rRNA) of 3 honey bee subspecies: African, European, and Africanized honey bees. Publicly available sequencing data from five honey bee studies were downloaded from NCBI. European bee samples (n=42) came from United Kingdom, Switzerland, and United States. African bee samples (n=82) came from Kenya. Africanized bee samples (n=10) came from Brazil. Unexpectedly, Africanized honey bee gut microbiota was far more similar to European bees than to African bees despite the closer host genetic relationship between African and Africanized bees. All three subspecies shared similar relative abundances of core taxa. We posit that the similarity in gut microbiota between Africanized and European honey bees arose from the nature of the crossbreeding, and the social / environmental transmission of gut microbiota within hives. Namely, African queens took over European hives. However, the hybrid offspring acquired their gut microbiota from European nurse bees and European hive materials, resulting in the stable transmission of European gut microbiota across generations. Our results provide an intriguing insight into the potential ecological, social, and environmental factors that shape the gut microbiota of the Africanized honey bee hybrid. ImportanceAfricanized honey bee hybrids originated in Brazil through the crossbreeding of African and European honey bee subspecies. In this study, we examined the gut microbiota of all 3 honey bee subspecies (African, European, Africanized). A few core microbiota were shared across all subspecies. Interestingly, while African honey bee genes dominated in the Africanized honey bee hybrids, their gut microbial composition was most similar to European bees. This is likely related to the way these bees were crossbred - with African queens taking over European hives, while gut microbial inoculation of hybrids came from European nurse bees and European hive matierals. Gut microbiota are critical to honey bee health, and studying the gut microbiota of closely related honey bee subspecies helps understand the factors that influence gut microbial composition. This is important for our broader understanding of honey bee health, conservation, and evolution.

microbiology↗

bioRxiv2023

Simian Immunodeficiency Virus and Storage Buffer: Field-friendly preservation methods for RNA viral detection in primate feces

Wild non-human primates carry many types of RNA viruses, including simian immunodeficiency virus (SIV), simian foamy virus, simian T-cell leukemia virus, and hepatitis C virus. These viruses can also infect humans via zoonotic transmission through handling and consumption of primate bushmeat. Characterizing viral prevalence and shedding in natural hosts is critical to understand infection and transmission risks within and between primate species. Here, we sought to identify a robust "field-friendly" method (i.e., without freezing or refrigeration) for preserving viral RNA, specifically SIV, in primate fecal samples. Fecal samples were collected from a mantled guereza colobus (Colobus guereza) housed at the Columbus Zoo and Aquarium. Samples were homogenized and inoculated with three concentrations (low, medium, high) of inactivated SIV virus and preserved in four different storage buffers (DNA/RNA Shield, RNAlater, 95% Ethanol, and Viral Transport Medium). SIV viral RNA was then extracted from samples at four time points (1 week, 4 weeks, 8 weeks, and 12 weeks) to determine the efficacy of each buffer for preserving SIV RNA. Quantitative RT-PCR was used for detection and quantification of viral RNA. At all concentrations, DNA/RNA Shield yielded the highest average SIV virion concentrations. We then successfully validated this approach using fecal samples from known SIV-positive and SIV-negative sooty mangabeys (Cercocebus atys) housed at Emory National Primate Research Center. Our results indicate that DNA/RNA shield is an optimal "field-friendly" buffer for preserving SIV RNA in fecal samples over time, and may also be effective for preserving other RNA viruses in feces. ImportanceHuman immunodeficiency virus (HIV) was introduced into human populations through zoonotic transmission of SIV from African primates, leading to a global epidemic and ongoing worldwide public health issue. SIV occurs naturally in over 40 primate species in sub-Saharan Africa and these viruses have crossed species barriers on multiple occasions, leading to the spread of HIV-1 and HIV-2. Quantifying RNA viruses in wild primate populations can be challenging as invasive sampling is often not feasible, and many field stations lack ready access to a freezer for storing biological samples. This study compares SIV RNA preservation and recovery across multiple storage buffers to identify a robust field-friendly option for RNA viral detection in noninvasively collected feces. Our results will inform future fieldwork and facilitate improved approaches to characterizing prevalence, shedding, and transmission of RNA viruses like SIV in natural hosts including wild-living nonhuman primates.

microbiology↗

bioRxiv2023

All about urine: Longitudinal examination of urine pH, specific gravity, proteins, culture, and resistance profiles in healthy dogs

BackgroundUrine is routinely evaluated in dogs to assess health. Reference ranges for many urine properties are well established, but the scope of variation in these properties over time within heathy dogs is not well characterized. ObjectivesLongitudinally characterize urine properties in healthy dogs over 3 months. AnimalsFourteen healthy client-owned dogs. MethodsDogs were evaluated for health; then, mid-stream free catch urine was collected from each dog at 12 timepoints: Mornings / afternoons of Days 1, 2, 3; end of Weeks 4, 5, 6, 7 and Months 2 and 3. Urine pH, urine specific gravity (USG), protein, cultures, and antimicrobial resistance profiles were evaluated at each timepoint. ResultsUrine pH varied significantly within and between dogs over time (Friedmans test: within p = 0.031; between p < 0.005). However, USG, protein, and bacterial richness of urine were consistent within dogs over time, and only varied significantly between dogs (Kruskal-Wallis: between all p < 0.005). Antimicrobial resistant isolates were identified in 13 out of 14 dogs with 71% (34 of 48) of the isolates demonstrating resistance to amoxicillin. Conclusions and clinical importance1) Urine pH should be assessed at multiple timepoints via pH meter prior to making clinical decisions. 2) Mid-stream free catch urine from multiple healthy dogs yielded high concentrations of bacteria in culture (>105 CFU/mL) and should not be considered the only indicator of urinary tract infection. 3) Bacterial isolates demonstrated widespread resistance to amoxicillin / oxacillin underscoring the need for antimicrobial stewardship.

zoology↗

bioRxiv2022

Surveillance for SARS-CoV-2 in Ohio's wildlife, companion, and agricultural animals

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in humans in late 2019 and spread rapidly to become a global pandemic. A zoonotic spillover event from animal to human was identified as the presumed origin. Subsequently, reports began emerging regarding spillback events resulting in SARS-CoV-2 infections in multiple animal species. These events highlighted critical links between animal and human health while also raising concerns about the development of new reservoir hosts and potential viral mutations that could alter virulence and transmission or evade immune responses. Characterizing susceptibility, prevalence, and transmission between animal species became a priority to help protect animal and human health. In this study, we coalesced a large team of investigators and community partners to surveil for SARS-CoV-2 in domestic and free-ranging animals around Ohio between May 2020 and August 2021. We focused on species with known or predicted susceptibility to SARS-CoV-2 infection, highly congregated or medically compromised animals (e.g. shelters, barns, veterinary hospitals), and animals that had frequent contact with humans (e.g. pets, agricultural animals, zoo animals, or animals in wildlife hospitals). This included free-ranging deer (n=76), mink (n=57), multiple species of bats (n=65), and other wildlife in addition to domestic cats (n=275) and pigs (n= 184). In total, we tested 800 animals (34 species) via rRT-PCR for SARS-CoV-2 RNA. SARS-CoV-2 viral RNA was not detected in any of the tested animals despite a major peak in human SARS-CoV-2 cases that occurred in Ohio subsequent to the peak of animal samplings. Importantly, due to lack of validated tests for animals, we did not test for SARS-CoV-2 antibodies in this study, which limited our ability to assess exposure. While the results of this study were negative, the surveillance effort was critical and remains key to understanding, predicting, and preventing re-emergence of SARS-CoV-2 in humans or animals.

microbiology↗

bioRxiv2022

Zinc and laboratory emerge date impact honey bee gut microbiota and survival

Honey bees (Apis mellifera) may be exposed to a wide variety of chemicals in the environment, including pesticides, antibiotics, and metals. Zinc, for example, is commonly included in fertilizers, pesticides, and feed additives, and is found in agricultural runoff. Honey bees can be exposed to zinc directly or indirectly by consuming zinc-contaminated nectar and pollen. However, there is a paucity of studies addressing the putative effects of zinc on honey bees health. In this study, we tested the effects of zinc on honey bee survivorship and gut microbiota. To evaluate survivorship, we exposed bees to six concentrations of zinc (0, 50, 100, 250, 500, or 1000 mg/L) and assessed survival daily for 10 days. To evaluate effects of zinc on gut microbiota, we exposed bees to 5 or 100 mg/L zinc. Bees were sampled before (day 0) and after zinc exposure (days 3, 6, and 9). Abdominal contents underwent DNA extraction and 16S rRNA sequencing (V3-V4) on an Illumina MiSeq. Sequences were filtered and processed through QIIME2 and DADA2. Zinc treatment had minimal effects on bacterial DNA concentrations and absolute cell counts while emerge date (the date a bee emerged from the brood comb) had a significant effect with decreased bacterial concentrations and cell counts observed at later emerge dates. Survival was only minimally impacted (>89% survival) at zinc concentrations up to 100 mg/L. Zinc had limited effects on overall gut microbial composition, diversity, and taxonomic abundances, with the greatest differences noted in the bee group exposed to the higher concentration of zinc (100 mg/L). In this group, several beneficial taxa (Lactobacillus, Rhizobiaceae, Gilliamella) were found at reduced abundances, while Paenibacillus, a potentially pathogenic taxa, was found at increased abundances. This suggests that zinc exposure, even at relatively low levels, may negatively impact honey bee health, even if survivorship is not dramatically impacted. Notably, emerge date effects were also observed in microbial composition. These results demonstrate the need to include assessments of honey bee gut microbiota in addition to other metrics of honey bee health and survivorship when evaluating the potential effects of agrochemicals on honey bees

ecology↗

bioRxiv2022

Divisome core complex in bacterial cell division revealed by cryo-EM

Cell division, or cytokinesis is a fundamental process of life and, in most bacteria, is driven by peptidoglycan synthesis at the septum1. It is catalysed by the divisome, a multi-protein complex with more than 20 components that spans the cell envelope in bacteria harbouring a cell wall2. Central to the divisome is the peptidoglycan-synthesising protein complex FtsWI, with the transglycosylase (TG) FtsW polymerising glycan strands from its substrate Lipid II3,4, and the transpeptidase (TP) FtsI crosslinking peptide stems, thus forming a covalent mesh between glycan strands5,6 (Fig. 1a). Septal peptidoglycan synthesis occurs after activation of the divisome glycosyltransferase-transpeptidase pair FtsWI3, in particular through an interaction with the heterotrimer FtsQBL7. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/517367v1_fig1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@1242fe6org.highwire.dtl.DTLVardef@c4d2c2org.highwire.dtl.DTLVardef@1e8eb0forg.highwire.dtl.DTLVardef@a02fff_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1:C_FLOATNO Biochemical and structural characterisation of the core divisome complex FtsWIQBL from P. aeruginosa. a) Septal peptidoglycan synthesis by FtsWIQBL during Gram-negative bacterial cell division. The transglycosylase FtsW (red), and transpeptidase FtsI (blue) bind the non-enzymatic subcomplex FtsQBL (green, violet and yellow, respectively). The complex contains 14 transmembrane helices - ten from FtsW and one each from FtsIQLB. The transglycosylase FtsW catalyses the polymerisation of GlcNAc-MurNAc disaccharides from Lipid II. The transpeptidase FtsI crosslinks the peptides from the nascent chain to adjacent peptides in the peptidoglycan layer between residues three and four. OM: outer membrane, IM: inner membrane, GlcNAc: N-acetylglucosamine, MurNAc: N-acetylmuramic acid, CC: coiled coil, TM: transmembrane. b) SDS-PAGE of the co-purified PaFtsWIQBL complex after size-exclusion chromatography. c) Western blot showing glycan strand ladders synthesised by divisome core complexes from Lipid II, demonstrating transglycosylase activity. The negative control does not contain any FtsWIQBL (lane 1). WT P. aeruginosa and E. coli FtsWIQBL complexes (lanes 2 and 4) are active transglycosylases, while the P. aeruginosa putative active site mutant FtsWD275AIQBL (lane 3) is inactive. d) Three representative 2D classes of our PaFtsWIQBL cryo-EM data. e) Left panel: side-view of the PaFtsWIQBL cryo-EM density at an overall resolution of 3.7 [A]. Protein colours are the same as those in a). Residual density from the detergent micelle is visible around the transmembrane domain in grey. Right panel: model of PaFtsWIQBL, rotated by 120{degrees} with respect to the density on the left-hand side. The putative FtsW active site residue D275 is indicated, as is the FtsI active site residue S294. The FtsW loop 219-233 and FtsI loop 45-50 are shown as a dotted line as they were too flexible to build. FtsQ and FtsQ were not resolved and are not shown. f) Top view of the periplasmic domain, showing interactions between FtsI, FtsL, FtsB and FtsQ. C_FIG Here, we present the cryo-EM structure of the catalytic divisome core complex FtsWIQBL from Pseudomonas aeruginosa at 3.7 [A] resolution. The structure reveals the intricate details of the periplasmic interfaces within FtsWIQBL, including the positioning of FtsI by the coiled coil of FtsBL, as well as a transmembrane domain containing FtsWIBL but not FtsQ. With our structure we are able to provide molecular mechanisms of a multitude of known mutations that interfere with divisome activation and regulation. Finally, we reveal a large conformational switch between presumably inactive and active states of the FtsWI core enzymes. Our work is foundational for further structural, biochemical and genetic studies elucidating the molecular mechanisms of bacterial cell division. Since the divisome peptidoglycan synthase is essential for cell division in most bacteria, and is absent in eukaryotic cells entirely, it is a key target of important antibiotics and antibiotic development8, and we suggest that our structure will help to accelerate these efforts.

molecular biology↗

bioRxiv2022

Antibacterial effects of propolis and brood comb extracts on the causative agent of European Foulbrood (Melissococcus plutonius) in honey bees (Apis mellifera)

Among a long list of parasites and pathogens that threaten the European honey bee (Apis mellifera), European Foulbrood (EFB) has become an urgent apiary disease, as epidemic outbreaks are becoming increasingly common. EFB is a bacterial disease of larval honey bees, caused by a gram-positive, anaerobic bacterium, Melissococcus plutonius. The most effective current treatment for EFB, oxytetracycline hydrochloride, can disrupt the bee microbiome, cause bee mortality and residues may persist in honey harvested for human consumption. In this study, we explore the efficacy of more sustainable bee-derived solutions, including propolis, honey comb and brood comb ethanol extracts. Using a series of dilutions of these extracts, we determined the minimum inhibitory concertation (MIC) of each bee-derived product on M. plutonius, as well as two model bacterial species, Staphylococcus saprophyticus (gram-positive) and Escherichia coli (gram-negative). Overall, we found that propolis extract was most effective at inhibiting growth of gram-positive bacteria, and that M. plutonious was also susceptible to honey comb (MIC = 16.00 mg/mL) and brood comb (MIC = 45.33 mg/mL) extracts, but at much higher concentrations than that of propolis (MIC = 1.14 mg/mL).

microbiology↗

bioRxiv2021

Urine and Fecal Microbiota in a Canine Model of Bladder Cancer

IntroductionUrothelial carcinoma (UC) is the tenth most diagnosed cancer in humans worldwide. Dogs are a robust model for invasive UC as tumor development and progression is similar in humans and dogs. Recent studies on urine microbiota in humans revealed alterations in microbial diversity and composition in individuals with UC; however, the potential role of microbiota in UC has yet to be elucidated. Dogs could be valuable models for this research, but microbial alterations in dogs with UC have not been evaluated. ObjectiveThe objective of this this pilot study was to compare the urine and fecal microbiota of dogs with UC (n = 7) and age-, sex-, and breed-matched healthy controls (n = 7). MethodsDNA was extracted from mid-stream free-catch urine and fecal samples using Qiagen Bacteremia and PowerFecal kits, respectively. 16S rRNA gene sequencing was performed followed by sequence processing and analyses (QIIME 2 and R). ResultsCanine urine and fecal samples were dominated by taxa similar to those found in humans. Significantly decreased microbial diversity (Kruskal-Wallis: Shannon, p = 0.048) and altered bacterial composition were observed in the urine but not feces of dogs with UC (PERMANOVA: Unweighted UniFrac, p = 0.011). The relative abundances of Fusobacterium was also increased, although not significantly, in the urine and feces of dogs with UC. ConclusionThis study characterizes urine and fecal microbiota in dogs with UC, and it provides a foundation for future work exploring host-microbe dynamics in UC carcinogenesis, prognosis, and treatment.

cancer biology↗

bioRxiv2021

SARS-CoV-2 infection in free-ranging white-tailed deer (Odocoileus virginianus)

Human-to-animal spillover of SARS-CoV-2 virus has occurred in a wide range of animals, but thus far, the establishment of a new natural animal reservoir has not been detected. Here, we detected SARS-CoV-2 virus using rRT-PCR in 129 out of 360 (35.8%) free-ranging white-tailed deer (Odocoileus virginianus) from northeast Ohio (USA) sampled between January-March 2021. Deer in 6 locations were infected with at least 3 lineages of SARS-CoV-2 (B.1.2, B.1.596, B.1.582). The B.1.2 viruses, dominant in Ohio at the time, spilled over multiple times into deer populations in different locations. Deer-to-deer transmission may have occurred in three locations. The establishment of a natural reservoir of SARS-CoV-2 in white-tailed deer could facilitate divergent evolutionary trajectories and future spillback to humans, further complicating long-term COVID-19 control strategies. One-Sentence SummaryA significant proportion of SARS-CoV-2 infection in free-ranging US white-tailed deer reveals a potential new reservoir.

molecular biology↗

bioRxiv2021

Gut microbiota and age shape susceptibility to clostridial enteritis in lorikeets under human care

BackgroundEnteritis is a common cause of morbidity and mortality in lorikeets that can be challenging to diagnose and treat. In this study, we examine gut microbiota in two lorikeet flocks with enteritis (Columbus Zoo and Aquarium - CZA; Denver Zoo - DZ). Since 2012, the CZA flock has experienced repeated outbreaks of enteritis despite extensive diet, husbandry, and clinical modifications. In 2018, both CZA and DZ observed a spike in enteritis. Recent research has revealed that the gut microbiota can influence susceptibility to enteropathogens. We hypothesized that a dysbiosis, or alteration in the gut microbial community, was making some lorikeets more susceptible to enteritis, and our goal was to characterize this dysbiosis and determine the features that predicted susceptibility. ResultsWe employed 16S rRNA sequencing to characterize the cloacal microbiota in lorikeets (CZA n = 67, DZ n = 24) over time. We compared the microbiota of healthy lorikeets, to lorikeets with enteritis, and lorikeets susceptible to enteritis, with "susceptible" being defined as healthy birds that subsequently developed enteritis. Based on sequencing data, culture, and toxin gene detection in intestinal contents, we identified Clostridium perfringens type A (CZA and DZ) and C. colinum (CZA only) at increased relative abundances in birds with enteritis. Histopathology and immunohistochemistry further identified the presence of gram-positive bacilli and C. perfringens, respectively, in the necrotizing intestinal lesions. Finally, using Random Forests and LASSO models, we identified several features (young age and the presence of Rhodococcus fascians and Pseudomonas umsongensis) associated with susceptibility to clostridial enteritis. ConclusionsWe identified C. perfringens type A and C. colinum associated with lorikeet necrohemorrhagic enteritis at CZA and DZ. Susceptibility testing of isolates lead to an updated clinical treatment plan which ultimately resolved the outbreaks at both institutions. This work provides a foundation for understanding gut microbiota features that are permissive to clostridial colonization and host factors (e.g. age, prior infection) that shape responses to infection.

microbiology↗

bioRxiv2021

Tetracycline exposure alters key gut microbiota in Africanized honey bees (Apis mellifera scutellata x spp.)

Honey bees play a critical role in ecosystem health, biodiversity maintenance, and crop yield. Antimicrobials, such as tetracyclines, are used widely used across agriculture, medicine, and in bee keeping, and bees can be directly or indirectly exposed to tetracycline residues in the environment. In European honey bees, tetracycline exposure has been linked with shifts in the gut microbiota that negatively impact bee health. However, the effects of antimicrobials on Africanized honey bee gut microbiota have not been examined. The aim of this study was to investigate the effects of tetracycline exposure on the gut microbial community of Africanized honey bees (Apis mellifera scutellata x spp), which are important pollinators in South, Central, and North America. Bees (n=1,000) were collected from hives in Areia-PB, Northeastern Brazil, placed into plastic chambers and kept under controlled temperature and humidity conditions. The control group (CON) was fed daily with syrup (10g) consisting of a 1:1 solution of demerara sugar and water, plus a solid protein diet (10g) composed of 60% soy extract and 40% sugar syrup. The tetracycline group (TET) was fed identically but with the addition of tetracycline hydrochloride (450 {micro}g/g) to the sugar syrup. Bees were sampled from each group before (day 0), and after tetracycline exposure (days 3, 6 and 9). Abdominal contents dissected out of each bee underwent DNA extraction and 16S rRNA sequencing (V3-V4) on an Illumina MiSeq. Sequences were filtered and processed through QIIME2 and DADA2. Microbial community composition and diversity and differentially abundant taxa were evaluated by treatment and time. Bee gut microbial composition (Jaccard) and diversity (Shannon) differed significantly and increasingly over time and between CON and TET groups. Tetracycline exposure was associated with decreased relative abundances of Bombella and Fructobacillus, along with decreases in key core microbiota such as Snodgrassella, Gilliamella, Rhizobiaceae, and Apibacter. These microbes are critical for nutrient metabolism and pathogen defense, and decreased abundances of these microbes could negatively affect bee health. Considering the global ecological and economic importance of honey bees as pollinators, it is critical to understand the effects of agrochemicals including antimicrobials on honey bees.

ecology↗

bioRxiv2021

Evaluating Extraction Methods to Study Canine Urine Microbiota

The urinary microbiota is the collection of microbes present in urine that play a role in host health. Studies of urine microbiota have traditionally relied upon culturing methods aimed at identifying pathogens. However, recent culture-free sequencing studies of the urine microbiota have determined that a diverse array of microbes are present in health and disease. To study these microbes and their potential role in diseases like bladder cancer or interstitial cystitis, consistent extraction and detection of microbial DNA from urine is critical. However, urine is a low biomass substrate, requiring sensitive methods to capture DNA and making the risk of contamination high. To address this challenge, we collected urine samples from ten healthy dogs and extracted DNA from each sample using five different commercially available extraction methods. Extraction methods were compared based on total and bacterial DNA concentrations and microbial community composition and diversity assessed through 16S rRNA gene sequencing. Significant differences in the urinary microbiota were observed by dog and sex but not extraction method. The Bacteremia kit yielded the highest total DNA concentrations (Kruskal-Wallis, p = 0.165, not significant) and the highest bacterial DNA concentrations (Kruskal-Wallis, p = 0.044). Bacteremia also extracted bacterial DNA from the greatest number of samples. Taken together, these results suggest that the Bacteremia kit is an effective option for studying the urine microbiota. This work lays the foundation to study the urine microbiome in a wide range of urogenital diseases in dogs and other species. HighlightsO_LICanine urine microbiota differed by sex and dog but not extraction method. C_LIO_LIQiagen Bacteremia kit yielded the highest bacterial DNA concentrations from urine. C_LIO_LIThe Bacteremia kit extracted bacterial DNA from the greatest number of samples. C_LIO_LIAbsolute abundance of Sphingomonas species increased in female dog urine. C_LIO_LIPasteurellaceae bacterium canine oral taxon 272 increased in male dog urine. C_LI

microbiology↗

bioRxiv2021

Alterations in gut microbiota linked to provenance, sex, and chronic wasting disease in white-tailed deer (Odocoileus virginianus)

Chronic wasting disease (CWD) is a fatal, contagious, neurodegenerative prion disease affecting both free-ranging and captive cervid species. CWD is spread via direct or indirect contact or oral ingestion of prions. In the gastrointestinal tract, prions enter the body through microfold cells (M-cells), and the abundance of these cells can be influenced by the gut microbiota. To explore potential links between the gut microbiota and CWD, we collected fecal samples from farmed and free-ranging white-tailed deer (Odocoileus virginianus) around the Midwest. Farmed deer orignated from farms that were depopulated due to CWD. Free-ranging deer were sampled during annual deer harvests. All farmed deer were tested for CWD via ELISA and IHC, and we used 16S rRNA gene sequencing to characterize the gut microbiota. We report significant differences in gut microbiota by provenance (Farm 1, Farm 2, Free-ranging), sex, and CWD status. CWD-positive deer from Farm 1 and 2 had increased abundances of Akkermansia, Lachnospireacea UCG-010, and RF39 taxa. Overall, differences by provenance and sex appear to be driven by diet, while differences by CWD status may be linked to CWD pathogenesis.

microbiology↗

bioRxiv2020

Unique maternal immune and functional microbial profiles during prenatal stress

Maternal stress during pregnancy is widespread and stress-induced fetal neuroinflammation is thought to derive from a disruption in intrauterine immune homeostasis, though the exact origins are incompletely defined. We aimed to identify divergent immune and microbial metagenome profiles of stressed gestating mice that may underlie detrimental inflammatory signaling at the maternal-fetal interface. In response to stress, maternal glucocorticoid circuit activation corresponded with diminished spleen mass and IL-1{beta} production, reflecting systemic immunosuppression. At the maternal-fetal interface, density of placental mononuclear leukocytes decreased with stress. Yet maternal whole blood leukocyte analysis indicated monocytosis and classical M1 phenotypic shifts. Genome-resolved microbial metagenomic analyses revealed reductions in genes, microbial strains, and metabolic pathways in stressed dams that are primarily associated with pro-inflammatory function. Overall, these data indicate that stress disrupts maternal immunological and microbial regulation during pregnancy, characterized by concurrent anti- and pro-inflammatory signatures, which may displace immune equilibrium at the maternal-fetal interface.

immunology↗

bioRxiv2019

Bactofilins form non-polar filaments that bind to membranes directly

Bactofilins are small beta-helical proteins that form cytoskeletal filaments in a range of bacteria. Bactofilins have diverse functions: filaments in Caulobacter crescentus are involved in cell stalk formation whereas Myxococcus xanthus filaments aid chromosome segregation and motility. The precise molecular architecture of bactofilin filaments has remained unclear. Here we revealed by sequence analyses and electron microscopy that in addition to wide distribution across bacteria and archaea, bactofilins are also present in a few eukaryotic cells such as oomycetes. The sole bactofilin from Thermus thermophilus was demonstrated to form constitutive filaments and cryo-EM analysis revealed that protofilaments formed through end-to-end association of the beta-helical domains. Using a nanobody against Thermus bactofilin we determined the near-atomic filament structure, showing that the filaments are non-polar, with subunits arranged head-to-head and tail-to-tail. A polymerisation-impaired mutant F105R, that disrupts one of the two protofilament interfaces, enabled crystallisation. The crystal structure also revealed non-polar protofilaments, and the dominance of the beta-stacking interface that formed despite the inhibiting mutation. To confirm the generality of the lack of polarity, we performed co-evolutionary analysis of a large set of sequences. Finally, using Thermus bactofilin, we determined that the N-terminal disordered tail of the protein is responsible for direct binding to lipid membranes both on liposomes and by electron cryotomography in E. coli cells. The tail is conserved, suggesting that membrane binding is likely a general feature of these very common but only recently discovered filaments of the prokaryotic cytoskeleton.

biochemistry↗