Biology subjects

Campagna, S. R.

Publications and source records attributed to Campagna, S. R..

4 recordsLinked to original sources

bioRxiv2025

The ornithine-arginine cycle supported a toxic, metalimnic Planktothrix rubescens bloom

Planktothrix rubescens is distinct from other cyanobacterial harmful algal bloom (cHAB) genera: the crimson-red cHAB thrives in the cold, low-light, nutrient-limited metalimnion. Studies have attributed this ecological success to buoyancy regulation, low-light adaptations, and the uptake of nitrogen-rich amino acids. Yet, it remains to be mechanistically determined how this cHAB maintains physiological nutrient quotas in the metalimnion due to limited in situ molecular studies. We employed metagenomics and metabolomics to investigate a toxigenic P. rubescens bloom in Meads Quarry (Knoxville, TN, USA) observed in two separate years. Our results suggest a perennial, metalimnic P. rubescens population may exist, with spring turnover facilitating seasonal migration to the epilimnion. Although P. rubescens dominated the epilimnion and metalimnion, intracellular metabolite pools grouped by depth and suggested depth-discrete partitioning of the arginine deiminase-mediated ornithine-arginine cycle (OAC, i.e., urea cycle). While the arginine influx driving the OAC is unclear, we hypothesize this input is provided via the uptake of urea or nitrogen-rich amino acids. Further, we demonstrate arginine deiminase (argE) is broadly distributed in Planktothrix genera and known microcystin producers, suggesting argE-mediated arginine recycling via the OAC may influence the fitness of toxigenic cHAB genera which require ample nitrogen to synthesize microcystins. Cumulatively, our results serve as a case study to provide insight on the metabolic pathways driving the ecological success of metalimnic P. rubescens blooms. On a broader scale, this work strengthens the case that alternative nitrogen metabolism - including urea utilization, amino acid uptake, and the OAC - is a driver of toxigenic cyanobacterial blooms in fresh waters.

bioinformatics↗

bioRxiv2025

Non-redundant cardiolipin synthases support membrane integrity and stress resilience in Bacteroides fragilis

Gut-resident bacteria must tolerate diverse membrane-disrupting agents, including bile acids, to maintain colonization. Cardiolipin is an anionic phospholipid that supports membrane integrity and stress resilience in many bacteria. However, cardiolipin synthases remain poorly characterized in the Bacteroidota, a dominant phylum of the human gut microbiota. The prevalent gut commensal Bacteroides fragilis encodes two predicted cardiolipin synthases, ClsA and ClsB. We previously identified both cls genes as bile-acid fitness factors in B. fragilis P207, but the individual contributions of ClsA and ClsB to cell physiology had remained undefined. Here we combine targeted gene deletion with high-resolution lipidomics, metabolomics, and elemental mass spectrometry to show that the two enzymes have non-redundant functions in the cell. Cardiolipin is a minor lipid in the B. fragilis membrane, and both Cls enzymes contribute to its production. clsA and clsB differ in growth-phase expression, in their effects on cell morphology, and in their associated cardiolipin species. Loss of each enzyme also produces distinct changes in fitness under several membrane-perturbing stresses and in the broader cellular metabolome, including compound classes with documented bioactivity in mammalian hosts. In contrast to the acute ion-gradient disruption caused by the secondary bile acid deoxycholate, deletion of both synthases did not measurably alter steady-state intracellular ion levels under standard growth conditions, indicating that cardiolipin loss does not perturb basal ion homeostasis under these conditions. Together, these results define non-redundant roles for two cardiolipin synthases in a common member of the human gut microbiota. ImportanceInflammatory bowel diseases affect millions of people worldwide. The gut bacterium Bacteroides fragilis is a normal member of the human intestinal microbiota that can also bloom to high abundance in inflamed guts. To survive within the gut, B. fragilis must maintain the integrity and function of its cell membrane. In this study, we characterize the functional role of two B. fragilis genes that contribute to the synthesis of the membrane lipid, cardiolipin. We find that the two cardiolipin synthase genes are not functionally interchangeable; each impacts the cells lipid pool in distinct ways and contributes differently to how B. fragilis responds to membrane stress. Our work provides insight into how a common gut bacterium adapts to conditions encountered in the intestine, and improves understanding of membrane biology in this important group of gut microbes.

microbiology↗

bioRxiv2024

Specific Bacterial Taxa and Their Metabolite, DHPS, Linked to Alzheimers Disease, Parkinsons Disease, and Amyotrophic Lateral Sclerosis.

Neurodegenerative diseases (NDDs) are multifactorial disorders frequently associated with gut dysbiosis, oxidative stress, and inflammation; however, the pathophysiological mechanisms remain poorly understood. We investigated bacterial and metabolic dyshomeostasis in the gut microbiome associated with early disease stages across three NDDs, amyotrophic lateral sclerosis (ALS), Alzheimers Disease (AD), Parkinsons Disease (PD), and healthy controls (HC) and discovered a previously unrecognized link between a microbial-derived metabolite with an unknown role in human physiology, 2,3-dihydroxypropane-1-sulfonate (DHPS), and NDDs. DHPS was downregulated in AD, ALS, and PD, while Eubacterium and Desulfovibrio, capable of metabolizing this metabolite,1-4 were increased in all disease cohorts. Additionally, select taxa within the Clostridia class had strong negative correlations to DHPS suggesting a potential role in DHPS metabolism. Hydrogen sulfide is a catabolic product of DHPS,1,5 and hydrogen sulfide promotes inflammation,6-8 oxidative stress,9 mitochondrial damage,10 and gut dysbiosis,2,11 known hallmarks of NDD. These findings suggest that cryptic sulfur metabolism via DHPS is a missing link in our current understanding of NDD onset and progression. To the best of our knowledge, we are the first to provide evidence of a conserved gut-brain axis linkage of specific bacterial taxa and their metabolism of DHPS shared by three neurodegenerative diseases.

neuroscience↗

bioRxiv2021

Metabolite discovery through global annotation of untargeted metabolomics data

Liquid chromatography-high resolution mass spectrometry (LC-MS)-based metabolomics aims to identify and quantitate all metabolites, but most LC-MS peaks remain unidentified. Here, we present a global network optimization approach, NetID, to annotate untargeted LC-MS metabolomics data. The approach aims to generate, for all experimentally observed ion peaks, annotations that match the measured masses, retention times, and (when available) MS/MS fragmentation patterns. Peaks are connected based on mass differences reflecting adducting, fragmentation, isotopes, or feasible biochemical transformations. Global optimization generates a single network linking most observed ion peaks, enhances peak assignment accuracy, and produces chemically-informative peak-peak relationships, including for peaks lacking MS/MS spectra. Applying this approach to yeast and mouse data, we identified five novel metabolites (thiamine derivatives and N-glucosyl-taurine). Isotope tracer studies indicate active flux through these metabolites. Thus, NetID applies existing metabolomic knowledge and global optimization to annotate untargeted metabolomics data, revealing novel metabolites.

bioinformatics↗