Biology subjects

Bess, E. N.

Publications and source records attributed to Bess, E. N..

7 recordsLinked to original sources

bioRxiv2026

Metabolomic Investigations Reveal Lignin Deconstruction by Human Gut Microbiota

Lignin is a polyphenolic dietary fiber whose role in human nutrition has been debated for over a century. Herein, we reveal the ability of human gut microbiota to deconstruct lignin in anaerobic conditions. Quantitative 13C-tracing mass spectrometric analyses showed that sustained microbial deconstruction of lignin feeds into a pathway for the biosynthetic production of enterolignans. We used 2D NMR to characterize the microbe-induced structural changes in the lignin polymer. Untargeted mass spectrometry demonstrated that human gut microbiota not only deconstruct lignin but also that they do so on rapid timescales. While most existing reports of anaerobic lignin metabolism have solely focused on the production of small metabolites, we additionally profiled the deconstruction of large lignin oligomers. Moreover, we identified the putative structure of a large lignin oligomer and traced its metabolism to downstream metabolites. Collectively, we provide a compelling body of evidence to support the hypothesis that human gut microbiota deconstruct lignin and to establish the human gut microbiome in the paradigm of anaerobic lignin deconstruction.

microbiology↗

bioRxiv2025

A Validated LC-MS/MS Method for Quantifying Phenolic Acids, Lignans, and Enterolignans from Human Fecal Samples

The human gut microbiome is home to numerous small molecules that impact health. Three prominent classes of molecules in this environment include phenolic acids, lignans, and enterolignans, which have been linked to anti-inflammatory and anti-oxidant effects as well as protection from cancer, cardiovascular disease, and neurodegeneration. The abundance of these molecules in the gut microbiome as well as their biological significance motivated the development of the LC-MS/MS method reported herein, which provides a simple, robust, and high-throughput approach to simultaneously quantify a 17-membered panel of phenolic acids, lignans, and enterolignans in human fecal microbiome samples. This method employs liquid-liquid extraction, which allows for cost-effective sample preparation by using common laboratory materials. Additionally, fecal samples are lyophilized prior to extraction to mitigate confounding effects introduced by variability in water content that exists across individuals samples. Inclusion of 0.1% acetic acid in the chromatographic solvents optimized peak shape and signal intensity. Plastic microcentrifuge tubes imparted substantial interferences for some analytes, which was resolved through use of glass vials. Using this method, 60% of human fecal samples from 10 individuals showed that phenolic acids bearing a catechol motif were in significantly greater abundance than were guaiacols. As specific gut bacteria can transform guaiacols into redox-active catechols, determination of guaiacol:catechol ratios in fecal samples may afford a biomarker of gut microbiota anti-oxidant potential. For the Table of Contents only O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/673557v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@11985a6org.highwire.dtl.DTLVardef@955d08org.highwire.dtl.DTLVardef@ee39aorg.highwire.dtl.DTLVardef@180a0d3_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Multiomic Analysis Reveals Molecular Pathways Associated with Intestinal Aggregation of α-Synuclein

Aggregates of the protein -synuclein may initially form in the gut before propagating to the brain in Parkinsons disease. Indeed, our prior work supports that enteroendocrine cells, specialized intestinal epithelial cells, could play a key role in the development of this disease. Enteroendocrine cells natively express -synuclein and synapse with enteric neurons as well as the vagus nerve. Severing the vagus nerve reduces the load of -synuclein aggregates in the brain, suggesting that this nerve is a conduit for gut-to-brain spread. Enteroendocrine cells line the gut lumen, as such, they are in constant contact with metabolites of the gut microbiota. We previously found that when enteroendocrine cells are exposed to nitrite--a potent oxidant produced by gut bacterial Enterobacteriaceae--a biochemical pathway is initiated that results in -synuclein aggregation. Here, we determined that dopamine production is critical to this mechanism of nitrite-induced -synuclein aggregation. Using enteroendocrine cells, we modulated dopamine biosynthesis and profiled the cellular proteome and lipidome. Proteomic signatures in dopamine-free cells were distinctly different than in enteroendocrine cells, highlighting pathways relevant to intestinal development of Parkinsons disease. Intriguingly, we observed that enteroendocrine cells maintain viability upon exposure to nitrite and in the presence of -synuclein aggregates. This cellular robustness suggests that dopamine-producing enteroendocrine cells may be a reservoir of toxic -synuclein aggregates, which can spread through a prion-like process. As a possible antidote, our findings show that benserazide--a chemical inhibitor of dopamine biosynthesis--limits formation of these aggregates in enteroendocrine cells. These studies lay a foundation for mechanistically informed therapeutic targets to prevent intestinal formation of -synuclein aggregates before they spread to the brain. For Table of Contents Use Only O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/672706v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1668b83org.highwire.dtl.DTLVardef@1515382org.highwire.dtl.DTLVardef@41b1d2org.highwire.dtl.DTLVardef@1018049_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

Discovery of a Gut Bacterial Metabolic Pathway that Drives α-Synuclein Aggregation and Neurodegeneration

Parkinsons disease (PD) etiology is associated with aggregation and accumulation of -synuclein (- syn) proteins in midbrain dopaminergic neurons. Emerging evidence suggests that in certain subtypes of PD, -syn aggregates originate in the gut and subsequently spread to the brain. However, the mechanisms that instigate -syn aggregation in the gut have remained elusive. In the brain, the aggregation of -syn is induced by oxidized dopamine. Such a mechanism has not been explored in the gastrointestinal (GI) tract, a niche harboring 46% of the bodys dopamine reservoirs. Here, we report that gut bacteria Enterobacteriaceae induce -syn aggregation. More specifically, our in vitro data indicate that respiration of nitrate by Escherichia coli K-12 yields nitrite, a potent oxidizing agent that creates an oxidizing redox potential in the bacterial environment. In these conditions, Fe2+ was oxidized to Fe3+, enabling formation of dopamine-derived quinones and -syn aggregates. Exposing nitrite, but not nitrate, to enteroendocrine STC-1 cells induced aggregation of -syn that is natively expressed in these cells, which line the intestinal tract. Finally, we examined the in vivo relevance of bacterial nitrate respiration to the formation of -syn aggregates using Caenorhabditis elegans models of PD. We discovered that nematodes exposed to nitrate-reducing E. coli K-12 displayed significantly enhanced neurodegeneration as compared to an E. coli K-12 mutant that could not respire nitrate. This neurodegenerative effect was absent when -syn was mutated to prevent interactions with dopamine-derived quinones. Taken together, our findings indicate that gut bacterial nitrate reduction may be critical to initiating intestinal - syn aggregation. Table of Contents Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/495350v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@258b2org.highwire.dtl.DTLVardef@d3b42org.highwire.dtl.DTLVardef@ad6b1borg.highwire.dtl.DTLVardef@152d39b_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2019

A widely distributed metalloenzyme class enables gut microbial metabolism of host- and diet-derived catechols

Catechol dehydroxylation is a central chemical transformation in the gut microbial metabolism of plant- and host-derived small molecules. However, the molecular basis for this transformation and its distribution among gut microorganisms are poorly understood. Here, we characterize a molybdenum-dependent enzyme from the prevalent human gut bacterium Eggerthella lenta that specifically dehydroxylates catecholamine neurotransmitters available in the human gut. Our findings suggest that this activity enables E. lenta to use dopamine as an electron acceptor under anaerobic conditions. In addition to characterizing catecholamine dehydroxylation, we identify candidate molybdenum-dependent enzymes that dehydroxylate additional host-and plant-derived small molecules. These gut bacterial catechol dehydroxylases are specific in their substrate scope and transcriptional regulation and belong to a distinct group of largely uncharacterized molybdenum-dependent enzymes that likely mediate both primary and secondary metabolism in multiple environments. Finally, we observe catechol dehydroxylation in the gut microbiotas of diverse mammals, suggesting that this chemistry is present in habitats beyond the human gut. Altogether, our data reveal the molecular basis of catechol dehydroxylation among gut bacteria and suggest that the chemical strategies that mediate metabolism and interactions in the human gut are relevant to a broad range of species and habitats.

microbiology↗

bioRxiv2018

The Genetic Basis for the Cooperative Bioactivation of Plant Lignans by a Human Gut Bacterial Consortium

Plant-derived lignans, consumed daily by most individuals, are inversely associated with breast cancer; however, their bioactivity is only exerted following gut bacterial conversion to enterolignans. Here, we dissect a four-species bacterial consortium sufficient for all four chemical reactions in this pathway. Comparative genomics and heterologous expression experiments identified the first enzyme in the pathway. Transcriptional profiling (RNAseq) independently identified the same gene and linked a single genomic locus to each of the remaining biotransformations. Remarkably, we detected the complete bacterial lignan metabolism pathway in the majority of human gut microbiomes. Together, these results are an important step towards a molecular genetic understanding of the gut bacterial bioactivation of lignans and other plant secondary metabolites to downstream metabolites relevant to human disease.\n\nOne Sentence SummaryBess et al. provide a first step towards elucidating the molecular genetic basis for the cooperative gut bacterial bioactivation of plant lignans, consumed daily by most individuals, to phytoestrogenic enterolignans.

microbiology↗

bioRxiv2018

Illuminating the microbiome’s dark matter: a functional genomic toolkit for the study of human gut Actinobacteria

Despite the remarkable evolutionary and metabolic diversity found within the human microbiome, the vast majority of mechanistic studies focus on two phyla: the Bacteroidetes and the Proteobacteria. Generalizable tools for studying the other phyla are urgently needed in order to transition microbiome research from a descriptive to a mechanistic discipline. Here, we focus on the Coriobacteriia class within the Actinobacteria phylum, detected in the distal gut of 90% of adult individuals around the world, which have been associated with both chronic and infectious disease, and play a key role in the metabolism of pharmaceutical, dietary, and endogenous compounds. We established, sequenced, and annotated a strain collection spanning 14 genera, 8 decades, and 3 continents, with a focus on Eggerthella lenta. Genome-wide alignments revealed inconsistencies in the taxonomy of the Coriobacteriia for which amendments have been proposed. Re-sequencing of the E. lenta type strain from multiple culture collections and our laboratory stock allowed us to identify errors in the finished genome and to identify point mutations associated with antibiotic resistance. Analysis of 24 E. lenta genomes revealed an \"open\" pan-genome suggesting we still have not fully sampled the genetic and metabolic diversity within this bacterial species. Consistent with the requirement for arginine during in vitro growth, the core E. lenta genome included the arginine dihydrolase pathway. Surprisingly, glycolysis and the citric acid cycle was also conserved in E. lenta despite the lack of evidence for carbohydrate utilization. We identified a species-specific marker gene and validated a multiplexed quantitative PCR assay for simultaneous detection of E. lenta and specific genes of interest from stool samples. Finally, we demonstrated the utility of comparative genomics for linking variable genes to strain-specific phenotypes, including antibiotic resistance and drug metabolism. To facilitate the continued functional genomic analysis of the Coriobacteriia, we have deposited the full collection of strains in DSMZ and have written a general software tool (ElenMatchR) that can be readily applied to novel phenotypic traits of interest. Together, these tools provide a first step towards a molecular understanding of the many neglected but clinically-relevant members of the human gut microbiome.

microbiology↗