Biology subjects

Franks, A. E.

Publications and source records attributed to Franks, A. E..

9 recordsLinked to original sources

bioRxiv2026

Identification of novel enolase negative Segatella copri subspecies supports notion of Segatella copri speciation via alternative phosphoenolpyruvate synthesis pathways

BackgroundSegatella copri is characterised as a prominent glycolytic plant-based fiber utiliser within the human gut. My recent work has introduced a new interpretation of the positive impacts of plant-based polysaccharides on S. copri, as a significant negative relationship between S. copri and Blautia spp. was identified. The high rate of electron donor consumption by Blautia spp. indicated that competition for the electron donors, formate, ferredoxin and fumarate, could be the route of the negative relationship but would also explain the positive relationship with plant-based polysaccharides, as they are products of fiber fermentation intestinally. MethodsForty two genomes of S. copri were annotated via Prokka to identify alternative PEP pathways. Phylogenetics allowed effectively classification of the S. copri isolates into species and subspecies clusters. The sequence homology of nucleotides and proteins were analysed against the control, S. copri DSM 18205, to determine the level of conservation in the alternative phosphoenolpyruvate synthesis pathways. ResultsEnolase (eno) was not identified in the S. copri strains; JCM 13468, LKV-178-WT-2C, RHA03, RHA01 and RHA02, and the whole genome phylogenetic grouping of these strains, has proposed the existence of an eno(-) subspecies of S. copri. This work furthered this idea by identifying alternative PEP pathways from formate, ferredoxin and fumarate, which were the most conserved in the eno(-) S. copri genomes. ConclusionThis work has provided rationale to why enolase may not be present within the eno(-) S. copri isolates and have shown that these alternative PEP synthesis pathways could negate the requirement of enolase in cells and may be factor in evolution of S. copri metabolism.

evolutionary biology↗

bioRxiv2026

Chorismate and isochorismate turnover reveal hidden dynamics of aromatic metabolism in Arabidopsis

The shikimate pathway provides precursors for phenolic metabolites in plant primary and secondary metabolism. Carbon flux measurements in intact Arabidopsis leaves using a novel isotopologue MS/MS methodology revealed unexpected dynamics between chorismate and isochorismate pools. 13CO2 labeling kinetics point to chloroplast-derived shikimate as a major bifurcation point, with approximately one third diverted away from the chloroplast. In contrast, the small pool of chorismate was almost exclusively chloroplast-localized and turned over rapidly, reaching more than 70% labeling within minutes. Isochorismate, a precursor to salicylic acid (SA) in the Brassicales, was present at 50-fold molar excess over chorismate but labeled much more slowly and appeared primarily extra-chloroplastic. Total isochorismate declined by 90% in the Arabidopsis enhanced disease susceptibility mutant, which lacks the isochorismate exporter. Non-aqueous fractionation further supported a primarily chloroplast-localized chorismate pool but extra-plastidic isochorismate. Populus trichocarpa and Nicotiana benthamiana leaves contained chorismate but only trace isochorismate, consistent with their use of the benzoyl-CoA route to SA. Carbon commitment calculations indicated that one third of the total chorismate pool in Arabidopsis leaves is diverted to isochorismate. Global leaf calculations based on elemental analysis-isotope ratio mass spectrometry and targeted isotope recovery indicate that only 0.03% of total assimilated carbon (5.27 pmol{middle dot}mg-1 D.W.{middle dot}min-1) enters the shikimate pathway in photosynthetically active mesophyll. For comparison [~]0.05% (7.75 pmol{middle dot}mg-1 D.W.{middle dot}min-1) enters the 2-C-methyl-D-erythritol 4-phosphate pathway, which provides precursors for photosynthetic pigments and electron carriers. The compartmentalization and turnover dynamics of shikimate, chorismate, and isochorismate suggest continuous demand for aromatic precursors in mesophyll tissue is comparable to demand for MEP-pathway derived pigments.

plant biology↗

bioRxiv2025

Efficacy of a bacteriophage cocktail targeting pathogenic bacteria associated with gastrointestinal dysfunction

The use of bacteriophage viruses that infect and kill bacteria is increasingly explored as an alternative to antibiotics for treatment of infections caused by opportunistic pathogens. Examples of opportunistic pathogens that disrupt the intestinal barrier and contribute to microbial imbalance in the gastrointestinal tract include Klebsiella pneumoniae, Pseudomonas aeruginosa and Serratia marcescens. This study evaluated the in vitro effectiveness of a bacteriophage cocktail composed of three host-specific phages: Lilla1 targeting Klebsiella pneumoniae, PAE1 targeting Pseudomonas aeruginosa and Smarc1 targeting Serratia marcescens. Bacterial growth was monitored by measuring optical density at 600 nm, and phage replication was quantified by plaque-forming unit assays. Each phage exhibited strong host specificity and produced significant reduction of growth of the corresponding bacterium while increasing in concentration during incubation. When applied as a cocktail, these three phages produced stronger and more sustained suppression of bacterial growth than single-phage treatments, both in individual cultures and in mixed cultures containing all three pathogens. In mixed cultures, continuous inhibition of bacterial growth persisted throughout a 24-hour incubation, and concentrations of Lilla1, PAE1 and Smarc1 increased significantly, indicating active replication and enhanced efficacy in combination. In single bacterial growth assays, bacterial populations that were initially suppressed showed regrowth after extended incubation. Regrowth manifested as a renewed increase in optical density several hours after initial decline and is consistent with selection of phage-resistant subpopulations, potentially arising from modification of surface receptors, phase variation or activation of adaptive defence systems. The observed biphasic response highlights the need for measures to limit microbial resistance to phage treatment, including expanded phage cocktails, adjusted dosing strategies and combined phage-antibiotic regimens. The results demonstrate that a three-phage cocktail can simultaneously inhibit multiple bacterial pathogens associated with gastrointestinal dysfunction and provide a basis for further in vivo evaluation and therapeutic development.

microbiology↗

bioRxiv2025

Bioengineered visible polymeric mesh to enhance urogynaecological health

Pelvic floor disorders, including pelvic organ prolapse and stress urinary incontinence, are prevalent health concerns, affecting approximately 50% of females over their lifetime, with about 75% of women over 65 years of age being impacted. Traditional surgical interventions, such as transvaginal mesh implants, have led to numerous complications, resulting in their prohibition in several countries. This study introduces an innovative composite mesh designed to mitigate these issues by combining polymethylmethacrylate and thermoplastic polyurethane, further enhanced with iodine-doped carbon nanoparticles to enable visibility via medical imaging. The mesh is coated with 2-methacryloyloxyethyl phosphorylcholine polymer to prevent protein adsorption and promote tissue regeneration. In vitro studies showed high cell viability and low protein adsorption, indicating excellent biocompatibility. Implantation of mesh (with or without iodine) in mice revealed no adverse effects on overall animal health. Mouse spleen weight (an indicator of inflammation) was similar between groups; however, levels of some cytokines (i.e., IL-10, IL-17A and GM-CSF) were elevated following implantation of iodinated mesh in mice suggesting that further refinement of the composite mesh is required. Analysis of the fecal microbiome, which is correlated with physiological states, showed that sham and iodinated mesh implant groups maintained consistent microbial profiles with stable diversity (richness and evenness) measures over time. In contrast, the non-iodinated mesh group exhibited decreased species richness post mesh implantation, likely due to a distinct starting microbiome composition prior to implantation. This research is envisaged to contribute to a safer and more effective solution for treating pelvic floor disorders, providing non-invasive post-implantation monitoring and enhanced mechanical compatibility of surgical mesh with native tissue. Our findings demonstrate that this composite mesh possesses mechanical properties that closely mimic human tissue, ensuring biocompatibility, strength, and flexibility without stimulating significant inflammatory or foreign body responses.

bioengineering↗

bioRxiv2022

The autism-associated Neuroligin-3 R451C mutation alters mucus density and the spatial distribution of bacteria in the mouse gastrointestinal tract

The intestinal mucus layer protects the host from invading pathogens and is essential for maintaining a healthy mucosal microbial community. Alterations in the mucus layer and composition of mucus-residing microbiota in people diagnosed with Autism Spectrum Disorder (ASD; autism) may contribute to dysbiosis and gastrointestinal (GI) dysfunction. Although microbial dysbiosis based on sequencing data is frequently reported in autism, spatial profiling of microbes adjacent to the mucosa is needed to identify changes in bacterial subtypes in close contact with host tissues. Here, we analysed the spatial distribution of the MUC-2 protein using immunofluorescence as well as total bacteria, Bacteroidetes, Firmicutes phyla and Akkermansia muciniphila (A. muciniphila) using fluorescent in situ hybridization in mice expressing the autism-associated R451C mutation in the Neuroligin-3 (Nlgn3) gene. We show that the Nlgn3 R451C mutation increases mucus density adjacent to the distal ileal epithelium in mice. The relative density of total bacteria, Firmicutes and A. muciniphila was increased whereas the density of Bacteroidetes was decreased closer to the epithelium in Nlgn3R451C mice. In summary, this study suggests that increased mucus density could contribute to mucosal microbial dysbiosis in ASD.

neuroscience↗

bioRxiv2022

Caecal dysfunction in the NL3R451C mouse model of autism

The mouse caecum is a pouch-like structure that is anatomically similar to the human appendix and is hypothesised to serve as a reservoir for commensal bacteria. The gastrointestinal tract is also home to the largest immunological organ of the body and the enteric nervous system (ENS), which regulates gut motility and secretion. The caecum is therefore an ideal location to study neuro-immune-microbe interactions in gut-brain communication. Individuals with Autism Spectrum Disorder (ASD; autism) frequently present with gastrointestinal symptoms in addition to core diagnostic behavioural features, implying a gut-brain link. More broadly, changes in gut-brain connectivity are now thought to play a critical role in a range of neurodevelopmental disorders. Here, we employed a mouse model of autism expressing a missense mutation in the neuroligin-3 post-synaptic protein that affects brain and enteric neuronal activity (NL3R451C mice). We previously observed abnormal caecal ENS architecture and immune cell morphology in the caecal patch in this model, however it is unknown if caecal function is altered in NL3R451C mice. Using a tri-cannulation approach to record motility patterns in the mouse caecum, we identified novel caecal motor complexes in ex vivo preparations. Caecal permeability and neurally-evoked secretion levels were also studied. Key immune populations including gut macrophages and dendritic cells within the caecal patch were stained using immunofluorescence to investigate shifts in immune activity. Caecal motility patterns in NL3R451C mice differed from wildtype littermates. Specifically, caecal motor complexes occurred at a higher frequency and for a shorter duration in NL3R451C mice than in wildtype littermates. In NL3R451C mice, neurally-evoked caecal secretion was reduced in response to the nicotinic acetylcholine receptor agonist (DMPP), but permeability was unchanged. Increased numbers of caecal patches were observed in NL3R451C mice compared to wildtype, with no alterations in morphology of selected immune populations. Future research is warranted to better understand caecal function and how neuro-immune interactions in the caecum affect health and influence GI function in neurodevelopmental disorders via the gut-brain axis.

neuroscience↗

bioRxiv2022

Quantitative analysis of neuroligin-3 expression in the enteric nervous system of the Neuroligin-3R451C mouse model of autism

Mutations in the Neuroligin-3 (Nlgn3) gene are implicated in autism spectrum disorder (ASD) and gastrointestinal (GI) dysfunction but its cellular expression in the GI tract remains to be characterised. Localisation of NLGN3 protein is challenging in intestinal tissue due to the lack of target-specific antibodies. Here, we combined RNAScope in situ hybridization for Nlgn3 mRNA and immunofluorescence for markers of all enteric neurons, cholinergic submucosal neurons, non-cholinergic submucosal neurons, nitregic and calretinin-containing myenteric neurons as well as glial cells. We also developed a quantitative 3-dimensional image analysis method to measure Nlgn3 mRNA cellular expression levels in enteric neurons and glia. We show that Nlgn3 mRNA is expressed in most submucosal and myenteric neurons as well as in enteric glia. The R451C mutation reduces Nlgn3 mRNA expression levels in cholinergic, nitrergic and calretinin enteric neuronal subpopulations but does not affect Nlgn3 mRNA expression in VIPergic submucosal neurons. In summary, we show that the autism-associated R451C mutation in Nlgn3 reduces Nlgn3 mRNA expression in the mouse ENS. These findings could shed light on the pathophysiology of GI dysfunction in ASD.

neuroscience↗

bioRxiv2022

Hyperimmune bovine colostrum containing lipopolysaccharide antibodies (Imm124-E) has a non-detrimental effect on gut microbial communities in unchallenged mice.

1Enterotoxigenic Escherichia coli (ETEC) is a leading cause of bacterial diarrhea in travelers, military personnel and children in developing countries. Infection has the potential to cause long-term gastrointestinal dysfunction. Preventative treatments for ETEC-induced diarrhea exist, yet the effects of these treatments on gastrointestinal commensals in healthy individuals is unclear. Whether administration of a prophylactic preventative treatment for ETEC-induced diarrhea causes specific shifts in gut microbial populations in controlled environments is also unknown. Here we studied the effects of a hyperimmune bovine colostrum (IMM-124E) used in the manufacture of Travelan(R) (AUST L 106709) on gastrointestinal bacteria in healthy C57BL/6 mice. Using next generation sequencing, we aimed to test the onset and magnitude of potential changes to the mouse gut microbiome in response to the anti-diarrheagenic hyperimmune bovine colostrum product, rich in immunoglobulins against select ETEC strains (Travelan(R), Immuron Ltd). We engineered changes in mouse fecal and cecal bacterial communities by delivering lipopolysaccharide (LPS) antibodies derived from bovine colostrum via dietary supplementation. Holstein Friesian and Jersey cows between 28- and 35-weeks gestation stimulated by subcutaneous delivery of three important pathogenic and antigenic determinants; LPS, flagella, and colonization factor antigen (CFA), produced a hyperimmune colostrum (IMM-124E) with demonstrated beneficial effects on health via modulation of metabolic pathways and immune function. We show that in mice administered colostrum containing LPS antibodies there was an increased abundance of potentially gut-beneficial bacteria, such as Akkermansia and Desulfovibrio, without disrupting the underlying ecology of the gastrointestinal tract. Compared to controls, there was no difference in overall weight gain, body or cecal weights or small intestine length following LPS antibody colostrum supplementation. Overall, dietary supplementation with colostrum containing LPS antibodies produced subtle alterations in gut bacterial composition of mice. Primarily, Travelan(R) LPS antibody treatment decreased the ratio of Firmicutes/Bacteroidetes in gut microbial populations in unchallenged healthy mice. Further studies are required to examine the effect of Travelan(R) LPS antibody treatment to engineer the microbiome in a diseased state and during recovery.

microbiology↗

bioRxiv2019

Bacterial and fungal communities are differentially modified by melatonin in agricultural soils under abiotic stress

An extensive body of evidence from this last decade indicates that melatonin enhances plant resistance to several biotic and abiotic stressors. This has led to an interest in the use of melatonin in agriculture to reduce negative physiological effects from environmental stresses that affect yield and crop quality. However, there are no reports regarding the effects of melatonin on soil microbial communities under abiotic stress, despite the importance of microbes for plant root health and function. Three agricultural soils associated with different land usage histories (pasture, canola or wheat) were placed under abiotic stress by cadmium (100 or 280 mg/kg) or salt (4 or 7 g/kg) and treated with melatonin (0.2 and 4 mg/kg). Automated Ribosomal Intergenic Spacer Analysis (ARISA) was used to generate Operational Taxonomic Units (OTU) for microbial community analysis in each soil. Significant differences in richness ( diversity) and community structures ({beta} diversity) were observed between bacterial and fungal assemblages across all three soils, demonstrating the effect of melatonin on soil microbial communities under abiotic stress. The analysis also indicated that the microbial response to melatonin is governed by the type of soil and history. The effects of melatonin on soil microbes needs to be regarded in potential future agricultural applications.

microbiology↗