Biology subjects

Singleton, C.

Publications and source records attributed to Singleton, C..

5 recordsLinked to original sources

bioRxiv2026

QTrap-Enabled GERD Safety Analysis of Commercial Salsas

Gastroesophageal reflux disease (GERD) is a prevalent chronic disorder where dietary modifications, particularly reducing spicy foods, are a primary management strategy. Salsa, a widely consumed condiment whose spiciness comes from capsaicin, lacks standardized heat labelling, potentially leading to inconsistent capsaicin exposure for consumers. To address this, our study aimed to develop and apply an LC-MS workflow for accurate capsaicin quantification in commercially available salsas. This approach seeks to provide objective "reflux-conscious" spice classification, supporting evidence-based dietary recommendations for individuals with GERD. In the eight commercial brands we examined, we found that products labelled "mild" had significantly lower capsaicin levels as compared to "medium" or "hot", but that there was an almost 15-fold range of capsaicin within this group. Surprisingly, there was no statistical difference in capsaicin content between those groups labelled "medium" or "hot" facilitating unambiguous assignment to either category, revealing that product labelling alone is insufficient to guide consumers seeking to control capsaicin exposure in their food. The results in this study enable improved brand-specific recommendations for GERD symptom management.

pharmacology and toxicology↗

bioRxiv2024

The predicted secreted proteome of activated sludge microorganisms indicate distinct nutrient niches

In wastewater treatment plants (WWTPs) complex microbial communities process diverse chemical compounds from sewage. Secreted proteins are critical because many are the first to interact with or degrade external (macro)molecules. To better understand microbial functions in WWTPs, we predicted secreted proteomes of WWTP microbiota from more than 1000 high-quality metagenome-assembled genomes (MAGs) from 23 Danish WWTPs with biological nutrient removal. Focus was placed on examining secreted catabolic exoenzymes that target major classes of macromolecules. We demonstrate that Bacteroidota have high potential to digest complex polysaccharides, but also proteins and nucleic acids. Poorly understood activated sludge members of Acidobacteriota and Gemmatimonadota also have high capacities for extracellular polysaccharide digestion. Secreted nucleases are encoded by 61% of MAGs indicating an importance for extracellular DNA and/or RNA digestion in WWTPs. Secreted lipases were the least-common macromolecule-targeting enzymes predicted, encoded mainly by Gammaproteobacteria and Myxococcota. In contrast, diverse taxa encode extracellular peptidases, indicating that proteins are widely used nutrients. Diverse secreted multi-heme cytochromes suggest capabilities for extracellular electron-transfer by various taxa, including some Bacteroidota that encode undescribed cytochromes with >100 heme-binding motifs. Myxococcota have exceptionally large secreted protein complements, probably related to predatory lifestyles and/or complex cell cycles. Many Gammaproteobacteria MAGs (mostly former Betaproteobacteria) encode few or no secreted hydrolases, but many periplasmic substrate-binding proteins and ABC- and TRAP-transporters, suggesting they are mostly sustained by small molecules. Together, this study provides a comprehensive overview of how WWTPs microorganisms interact with the environment, providing new insights into their functioning and niche partitioning. ImportanceWastewater treatment plants are critical biotechnological systems that clean wastewater, allowing the water to reenter the environment and limit eutrophication and pollution. They are also increasingly important for recovery of resources. They function primarily by the activity of microorganisms, which act as a living sponge, taking-up and transforming nutrients, organic material and pollutants. Despite much research, many microorganisms in WWTPs are uncultivated and poorly characterized, limiting our understanding of their functioning. Here, we analyzed a large collection of high-quality metagenome-assembled genomes from WWTPs for encoded secreted enzymes and proteins, with special emphasis on those used to degrade organic material. This analysis showed highly distinct secreted proteome profiles among different major phylogenetic groups of microorganisms, thereby providing new insights into how different groups function and co-exist in activated sludge. This knowledge will contribute to a better understanding of how to efficiently manage and exploit WWTP microbiomes.

microbiology↗

bioRxiv2022

Signatures of Microbial Diversity at Multiple Scales of Resolution within Engineered Enrichment Communities

Microbial community dynamics are dictated by both abiotic environmental conditions and biotic interactions. These communities consist of individual microorganisms across the continuum of phylogenetic diversity, ranging from coexisting members of different domains of life and phyla to multiple strains with only a handful of single nucleotide variants. Ecological forces act on a shifting template of population-level diversity that is shaped by evolutionary processes. However, understanding the ecological and evolutionary forces contributing to microbial community interactions and overall ecosystem function is difficult to interrogate for complex, naturally occurring microbial communities. Here, we use two time series of lab-scale engineered enrichment microbial communities simulating phosphorus removal to explore signatures of microbial diversity at multiple phylogenetic scales. We characterized microbial community dynamics and diversity over the course of reactor start-up and long-term dynamics including periods of eubiosis and dysbiosis as informed by the intended ecosystem function of phosphorus removal. We then compared these signatures to lineages from full-scale WWTPs performing phosphorus removal. We found that enriched lineages in lab-scale bioreactors harbor less intra-population diversity than lineages from the full-scale WWTP overall. Our work establishes a foundation for using engineered enrichment microbial communities as a semi-complex model system for addressing the fundamental ecological and evolutionary processes necessary for developing stable microbiome based biotechnologies.

microbiology↗

bioRxiv2021

Re-evaluation of the phylogenetic diversity and global distribution of the genus Candidatus Accumulibacter

Candidatus Accumulibacter was the first microorganism identified as a polyphosphate-accumulating organism (PAO), important for phosphorus removal from wastewater. This genus is diverse, and the current phylogeny and taxonomic framework appears complicated, with the majority of publicly available genomes classified as "Candidatus Accumulibacter phosphatis", despite notable phylogenetic divergence. The ppk1 marker gene allows for a finer scale differentiation into different "types" and "clades", nevertheless taxonomic assignments remain confusing and inconsistent across studies. Therefore, a comprehensive re-evaluation is needed to establish a common understanding of this genus, both in terms of naming and basic conserved physiological traits. Here, we provide this re-assessment using a comparison of genome, ppk1, and 16S rRNA gene-based approaches from comprehensive datasets. We identified 15 novel species, along with the well-known Ca. A. phosphatis, Ca. A. deltensis and Ca. A. aalborgensis. To compare the species in situ, we designed new species-specific FISH probes and revealed their morphology and arrangement in activated sludge. Based on the MiDAS global survey, Ca. Accumulibacter species were widespread in WWTPs with phosphorus removal, indicating the process design as a major driver for their abundance. Genome mining for PAO related pathways and FISH-Raman microspectroscopy confirmed the potential for the PAO metabolism in all Ca. Accumulibacter species, with detection in situ of the typical PAO storage polymers. Genome annotation further revealed fine-scale differences in the nitrate/nitrite reduction pathways. This provides insights into the niche differentiation of these lineages, potentially explaining their coexistence in the same ecosystem while contributing to overall phosphorus and nitrogen removal. ImportanceCandidatus Accumulibacter is the most studied PAO organism, with a primary role in biological nutrient removal. However, the species-level taxonomy of this lineage is convoluted due to the use of different phylogenetic markers or genome sequencing. Here, we redefined the phylogeny of these organisms, proposing a comprehensive approach which could be used to address the classification of other diverse and uncultivated lineages. Using genome-resolved phylogeny, compared to 16S rRNA gene- and other phylogenetic markers phylogeny, we obtained a higher resolution taxonomy and established a common understanding of this genus. Furthermore, genome mining of gene and pathways of interest, validated in situ by application of a new set of FISH probes and Raman micromicrospectroscopy, provided additional high-resolution metabolic insights into these organisms.

microbiology↗

bioRxiv2020

Candidatus Dechloromonas phosphatis and Candidatus Dechloromonas phosphovora, two novel polyphosphate accumulating organisms abundant in wastewater treatment systems

Members of the genus Dechloromonas are often abundant in enhanced biological phosphorus removal (EBPR) systems and are recognized putative polyphosphate accumulating organisms (PAOs), but their role in phosphate (P) removal is still unclear. Here, we used 16S rRNA gene sequencing and fluorescence in situ hybridization (FISH) to investigate the abundance and distribution of Dechloromonas spp. in Danish wastewater treatment plants. Two species were abundant, novel, and uncultured, and could be targeted by existing FISH probes. Raman microspectroscopy of probe-defined organisms (FISH-Raman) revealed the levels and dynamics of important intracellular storage polymers in abundant Dechloromonas spp. in the activated sludge from four full-scale EBPR plants and from a lab-scale sequencing batch reactor fed with different carbon sources (acetate, glucose, glycine, and glutamate). Moreover, 7 distinct Dechloromonas species were determined from a set of 10 high-quality metagenome-assembled genomes (MAGs) from Danish EBPR plants, each encoding the potential for poly-P, glycogen, and polyhydroxyalkanoates (PHA) accumulation. The two most abundant species exhibited an in situ phenotype in complete accordance with the metabolic information retrieved by the MAGs, with dynamic levels of poly-P, glycogen, and PHA during feast-famine anaerobic-aerobic cycling, legitimately placing these microorganisms among the important PAOs. As no isolates are available for the two species, we propose the names Candidatus Dechloromonas phosphatis and Candidatus Dechloromonas phosphovora.

microbiology↗