Biology subjects

Brown, T. L.

Publications and source records attributed to Brown, T. L..

7 recordsLinked to original sources

bioRxiv2026

The effects of bacteriophage cocktail treatment on healthy gut microbiota: an in vitro human colon model study

The human gut microbiome is a complex community that plays an important role in health, where perturbations can result in dysbiosis and disease. Bacteriophages (phages) can provide treatment for bacterial gastrointestinal disease, and commercial preparations such as the Intesti bacteriophage cocktail can be taken orally to target bacterial pathogens. However, interactions between these phages and the native gut microbiota are understudied. To investigate the impact of phage treatment, we used simulated gut models seeded with healthy donor microbiota from three individuals, sequenced the DNA, and analysed the bacterial and viral portion from samples obtained over time. Each donor had a unique bacterial composition which diverged with time. When comparing phage treated to control samples, we observed that Escherichia coli abundance accounted for the largest portion of bacterial community variance and was more associated with the controls. The lower abundance in phage treated samples may have resulted from the lytic action of phages from the cocktail. Additionally, our analyses of the viral portion revealed a phage bloom exclusive to phage treated samples. A highly abundant phage in this bloom was matched with the Intesti bacteriophage cocktail, showed similarity to Enterobacteria phage phi92, and provided evidence of productive infection within the model. While we did observe fluctuations in relative abundance of additional viral sequences in the presence of the phage cocktail, these changes were often transient. Furthermore, we detected only slight differences to typical members of the virome, and low numbers of active prophages. Our experiments suggest that the phage cocktail had minimal interruption to the native gut microbiota within the model. Impact statementBacteriophages are increasingly investigated and tested for their efficacy in treating infections and are a key component in fight against antimicrobial resistant bacterial infections. Because of their specificity, it has become almost a dogma to state that they do not alter the gut microbiome. We have now tested this in an in vitro study using a commercially available cocktail and real human faecal microbiota. We show minimal effects on the composition of the healthy microbiota with an individual-specific effect on Escherichia coli caused by productive infection of one phage in the cocktail.

microbiology↗

bioRxiv2025

Systemic administration of a reported extracellular vesicle inhibitor, dimethyl amiloride, induces preterm birth and fetal growth restriction in pregnant mice.

Successful pregnancy is dependent on extensive coordination between maternal, placental, and fetal units. Alterations in maternal-placental signaling or abnormal placental development can lead to a wide variety of pregnancy complications. This commonly includes preterm birth and fetal growth restriction, which are associated with a high rate of maternal and fetal morbidity and mortality. Maternal-placental signaling is in part mediated by the release of extracellular vesicles. These lipid-bilayer nanoparticles are secreted by various cell types and act as key regulators of both normal and pathogenic cell-cell communication. In a healthy pregnancy, maternal plasma extracellular vesicle concentrations increase as gestation progresses. However, in the pregnancy-associated disorder, preeclampsia, excessive extracellular vesicle secretion occurs and may be involved in the pathogenesis of the condition. Thus, there is a critical need - as a first step - to understand if modifying extracellular vesicle concentration, specifically during pregnancy can attenuate or exacerbate gestational pathogenesis. In this study, we evaluated the effects of administering a reported extracellular vesicle inhibitor, dimethyl amiloride, on maternal extracellular vesicle concentrations in healthy pregnant mice and assessed maternal and fetal outcomes. Maternal administration of dimethyl amiloride resulted in a significant decrease in maternal weight as well as fetal growth and substantially increased the rate of preterm birth. In contrast to previous reports in non-pregnant animals, we found that dimethyl amiloride did not significantly reduce maternal extracellular vesicle concentrations in pregnant mice. Our data demonstrate that systemic administration of dimethyl amiloride drastically impacts the mother and fetus during gestation and caution is suggested against its use during pregnancy.

developmental biology↗

bioRxiv2025

Intersecting Transcriptomic Landscapes of Hypertension and Kidney Function in African American Women

BackgroundHypertension is a major risk factor for chronic kidney disease (CKD) and disproportionately affects African American women, contributing to disparities in kidney health outcomes. The biological mechanisms connecting hypertension to reduced kidney function, particularly in understudied populations, remain poorly understood. This study leverages transcriptomic analyses to uncover shared molecular signatures associated with hypertension and kidney function, focusing on female-specific profiles. MethodsThe study analyzed whole-blood mRNA sequencing data from a cohort of 344 African American women, divided equally into discovery (n = 172) and validation (n = 172) datasets, along with 147 African American men. Differential expression (DE) analyses were performed to identify mRNAs associated with hypertension and kidney function (measured as eGFR). Female-specific findings were determined by comparing results between females and males. Pathway enrichment analyses were subsequently conducted to link the identified mRNAs to key biological mechanisms. ResultsComparative analyses revealed unique transcriptomic profiles in females, underscoring the role of sex-specific factors in disease progression. DE analyses identified 95 female-specific genes associated with both hypertension and eGFR. Subsequent pathway enrichment analysis with the 95 genes revealed key pathways related to fibrosis, inflammation, lipid metabolism, and endothelial dysfunction. The list of 95 includes TGF-{beta}1 and PNPLA2 implicated in fibrotic and metabolic dysregulation, and immune system players such as IL32 and TNFSF12 that amplify inflammation and kidney injury. ConclusionsThis study provides novel insights into the transcriptomic mechanisms underlying hypertension and kidney function in African American women. The findings emphasize the importance of addressing sex-specific and population-specific molecular mechanisms to inform precision medicine approaches and reduce health disparities hypertension-related impaired kidney function. Future research should prioritize experimental validation and longitudinal studies to further elucidate these pathways.

genomics↗

bioRxiv2025

Diverse Defence Systems and Prophages in Human-Associated Bifidobacterium Species Reveal "Arms Race" Dynamics

Bacteria of the genus Bifidobacterium are pivotal for human health, especially in early life, where they dominate the gut microbiome in healthy infants. Bacteriophages, viruses of bacteria, are drivers of gut bacterial composition in the human gut and could affect bifidobacterial abundance. Here, we use a bioinformatics approach to explore the direct interactions occurring between human-associated Bifidobacterium spp. and prophages, as evidenced by their genomes. A total of 1,086 bifidobacterial genomes were analysed in this study, revealing complex systems to prevent viral invasion. Despite their characteristically small genomes, Bifidobacterium strains harboured more than double the number of defence systems as most bacteria. In total, 34 defence system types and 56 subtypes were detected, including several different CRISPR-Cas systems with spacers that targeted almost three-quarters of bifidobacteria-derived prophages. We identified at least one prophage which met our stringent quality control measures in [~]63% of strains, with phages exhibiting high genomic diversity and evidence of historical recombination. Additionally, prophages were found to encode various anti-defence systems, such as anti-CRISPR genes and restriction modification resistance mechanisms. In summary, our investigation reveals "arms race" dynamics drive genomic diversity in both bifidobacteria and their phages. ImportanceMembers of the Bifidobacterium genus are widely acknowledged as being highly important for human health, particularly in infants. To date, there have been a limited number of large-scale studies that have investigated the presence of prophages and anti-viral defence systems of Bifidobacterium strains from multiple human-associated species. Here, we have uncovered a complex set of anti-phage strategies encoded by Bifidobacterium strains. In addition, we have also identified a highly diverse phage mobilome present within the genomes of bifidobacteria across the genus, which also encode several unique systems for overcoming bacterial defences. Elucidating these co-evolutionary dynamics between phages and bifidobacteria may provide valuable insight into developing high-throughput methods for identifying next-generation probiotic or live biotherapeutic candidates, which may then be applied for the prevention and treatment of various diseases in humans.

microbiology↗

bioRxiv2023

A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses

Bacteriophages (phages) within the Przondovirus genus are T7-like podoviruses belonging to the Studiervirinae subfamily, within the Autographiviridae family and have a highly conserved genome organisation. The genome size of these phages ranges from 37 kb to 42 kb, encode 50-60 genes and are characterised by the presence of direct terminal repeats (DTRs) flanking the linear chromosome. These DTRs are often deleted during short-read-only and hybrid assemblies. Moreover, long-read-only assemblies are often littered with sequencing and/or assembly errors and require additional curation. Here, we present the isolation and characterisation of ten novel przondoviruses targeting Klebsiella spp. We describe HYPPA - a HYbrid and Poly-polish Phage Assembly workflow, which utilises long-read assemblies in combination with short-read sequencing to resolve phage DTRs and correcting errors, negating the need for laborious primer walking and Sanger sequencing validation. Our data demonstrate the importance of careful curation of phage assemblies before publication, and prior to using them for comparative genomics. IMPACT STATEMENTThe current workflows employed for phage genome assembly are often error-prone and can lead to many incomplete phage genomes being deposited within databases. This can create challenges when performing comparative genomics, and may also lead to incorrect taxonomic assignment. To overcome these challenges we proposed HYPPA, a workflow that can produce complete and high-quality phage genomes without the need for laborious lab-based validation. DATA SUMMARYPhage raw reads are available from the National Centre for Biotechnology Information Sequence Read Archive (NCBI-SRA) under the BioProject number PRJNA914245. Phage annotated genomes have been deposited at GenBank under the accessions OQ579023-OQ579032 (Table 1). Bacterial WGS data for clinical preterm infant samples have been deposited at GenBank under BioProject accession PRJNA471164 (Table S1). Bacterial raw reads for food samples are available from NCBI-SRA with individual accessions (SAMN33593347-SAMN33593351), and can be found under the BioProject number PRJNA941224 (Table S1). Strain-specific details for bacteria and publicly-available phages used in these analyses, along with accessions for the latter can be found in Table S1 and Table S6, respectively. The CL1-CL8 clinical Klebsiella strains (Table S1) were under a Materials Transfer Agreement, for which sequencing data and strain information is not available. O_TBL View this table: org.highwire.dtl.DTLVardef@8cae53org.highwire.dtl.DTLVardef@8e512org.highwire.dtl.DTLVardef@1f71a67org.highwire.dtl.DTLVardef@1e6947dorg.highwire.dtl.DTLVardef@11ebc58_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONPrzondoviruses within the collection to date and data relating to the closest database relative. C_TABLECAPTION C_TBL

microbiology↗

bioRxiv2022

Dermal appendage-dependent patterning of zebrafish atoh1a+ Merkel cells

Touch system function requires precise interactions between specialized skin cells and somatosensory axons, as exemplified by the vertebrate mechanosensory Merkel cell-neurite complex. Development and patterning of Merkel cells and associated neurites during skin organogenesis remains poorly understood, partly due to the in utero development of mammalian embryos. Here, we discover Merkel cells in the zebrafish epidermis and identify Atonal homolog 1a (Atoh1a) as a marker of zebrafish Merkel cells. We show that zebrafish Merkel cells derive from basal keratinocytes, express neurosecretory and mechanosensory machinery, extend actin-rich microvilli, and complex with somatosensory axons, all hallmarks of mammalian Merkel cells. Merkel cells populate all major adult skin compartments, with region-specific densities and distribution patterns. In vivo photoconversion reveals that Merkel cells undergo steady loss and replenishment during skin homeostasis. Merkel cells develop concomitant with dermal appendages along the trunk, and preventing dermal appendage formation reduces Merkel cell density by affecting both cell differentiation and maintenance. By contrast, altering dermal appendage morphology changes the distribution, but not density, of Merkel cells. Overall, our studies provide insights into touch system maturation during skin organogenesis and establish zebrafish as an experimentally accessible in vivo model for the study of Merkel cell biology.

developmental biology↗

bioRxiv2022

mTORC2 loss in oligodendrocyte progenitor cells results in regional hypomyelination in the central nervous system

In the central nervous system (CNS), oligodendrocyte progenitor cells (OPCs) differentiate into mature oligodendrocytes to generate myelin, which is essential for normal nervous system function. OPC differentiation is driven by signaling pathways such as mTOR (Mechanistic Target of Rapamycin), which functions in two distinct complexes: mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2), containing Raptor or Rictor respectively. In the current studies, mTORC2 signaling was selectively deleted from OPCs in PDGFR-Cre X Rictorfl/fl mice. This study examined developmental myelination in male and female mice, comparing the impact of mTORC2 deletion in the corpus callosum and spinal cord. In both corpus callosum and spinal cord, Rictor loss in OPCs resulted in early reduction in myelin RNAs and some myelin proteins. However, these deficits rapidly recovered in spinal cord, where normal myelin abundance and thickness was noted at post-natal day 21 and 1.5 months. By contrast, the losses in corpus callosum resulted in severe hypomyelination, and increased unmyelinated axons. The current studies focus on uniquely altered signaling pathways following mTORC2 loss in developing oligodendrocytes. A major mTORC2 substrate is phospho-Akt-S473, which was significantly reduced throughout development in both corpus callosum and spinal cord at all ages measured, yet this had little impact in spinal cord. Loss of mTORC2 signaling resulted in decreased expression of actin regulators such as gelsolin in corpus callosum, but only minimal loss in spinal cord. The current study establishes a regionally-specific role for mTORC2 signaling in OPCs, particularly in the corpus callosum. Significance StatementmTORC1 and mTORC2 signaling have differential impact on myelination in the central nervous system. Numerous studies identify a role for mTORC1, but deletion of Rictor (mTORC2 signaling) in late-stage oligodendrocytes had little impact on myelination in the CNS. However, the current studies establish that deletion of mTORC2 signaling from oligodendrocyte progenitor cells results in reduced myelination of brain axons. These studies also establish a regional impact of mTORC2, with little change in spinal cord in these conditional Rictor deletion mice. Importantly, in both, brain and spinal cord, mTORC2 downstream signaling targets were impacted by Rictor deletion. Yet, these signaling changes had little impact on myelination in spinal cord, while they resulted in long term alterations in myelination in brain.

developmental biology↗