MetaboMAPS: Pathway sharing and multi-omics data visualization in metabolic context

Optimisation of surfactin yield in Bacillus using data-efficient active learning and high-throughput mass spectrometry

Integration of machine learning and high throughput measurements are essential to drive the next generation of the design-build-test-learn (DBTL) cycle in synthetic biology. Here, we report the use of active learning in combination with metabolomics for optimising production of surfactin, a complex lipopeptide resulting from a non-ribosomal assembly pathway. We designed a media optimisation algorithm that iteratively learns the yield landscape and steers the media composition toward maximal production. The algorithm led to a 160 % yield increase after three DBTL runs as compared to an M9 baseline. Metabolomics data helped to elucidate the underpinning biochemistry for yield improvement and revealed Pareto-like trade-offs in production of other lipopeptides from related pathways. We found positive associations between organic acids and surfactin, suggesting a key role of central carbon metabolism, as well as system-wide anisotropies in how metabolism reacts to shifts in carbon and nitrogen levels. Our framework offers a novel data-driven approach to improve yield of biological products with complex synthesis pathways that are not amenable to traditional yield optimisation strategies.

Effects of Early Life Exposures to the Aryl Hydrocarbon Receptor Ligand TCDF on Gut Microbiota and Host Metabolic Homeostasis in C57BL/6J Mice

BACKGROUND

Exposure to persistent organic pollutants (POPs) and disruptions in the gastrointestinal microbiota have been positively correlated with a predisposition to factors such as obesity, metabolic syndrome, and type 2 diabetes; however, it is unclear how the microbiome contributes to this relationship.

OBJECTIVE

This study aimed to explore the association between early life exposure to a potent aryl hydrocarbon receptor (AHR) agonist and persistent disruptions in the microbiota, leading to impaired metabolic homeostasis later in life.

METHODS

This study used metagenomics, nuclear magnetic resonance (NMR)- and mass spectrometry (MS)-based metabolomics, and biochemical assays to analyze the gut microbiome composition and function, as well as the physiological and metabolic effects of early life exposure to 2,3,7,8-tetrachlorodibenzofuran (TCDF) in conventional, germ-free (GF), and Ahr-null mice. The impact of TCDF on Akkermansia muciniphila (A. muciniphila) in vitro was assessed using optical density (OD 600), flow cytometry, transcriptomics, and MS-based metabolomics.

RESULTS

TCDF-exposed mice exhibited lower abundances of A. muciniphila, lower levels of cecal short-chain fatty acids (SCFAs) and indole-3-lactic acid (ILA), as well as lower levels of the gut hormones glucagon-like peptide 1 (GLP-1) and peptide YY (PYY), findings suggestive of disruption in the gut microbiome community structure and function. Importantly, microbial and metabolic phenotypes associated with early life POP exposure were transferable to GF recipients in the absence of POP carry-over. In addition, AHR-independent interactions between POPs and the microbiota were observed, and they were significantly associated with growth, physiology, gene expression, and metabolic activity outcomes of A. muciniphila, supporting suppressed activity along the ILA pathway.

CONCLUSIONS

These data obtained in a mouse model point to the complex effects of POPs on the host and microbiota, providing strong evidence that early life, short-term, and self-limiting POP exposure can adversely impact the microbiome, with effects persisting into later life with associated health implications. https://doi.org/10.1289/EHP13356.

Catabolic Network of the Fermentative Gut Bacterium Phocaeicola vulgatus (Phylum Bacteroidota) from a Physiologic-Proteomic Perspective

INTRODUCTION

Phocaeicola vulgatus (formerly Bacteroides vulgatus) is a prevalent member of human and animal guts, where it influences by its dietary-fiber-fueled, fermentative metabolism the microbial community as well as the host health. Moreover, the fermentative metabolism of P. vulgatus bears potential for a sustainable production of bulk chemicals. The aim of the present study was to refine the current understanding of the P. vulgatus physiology.

METHODS

P. vulgatus was adapted to anaerobic growth with 14 different carbohydrates, ranging from hexoses, pentoses, hemicellulose, via an uronic acid to deoxy sugars. These substrate-adapted cells formed the basis to define the growth stoichiometries by quantifying growth/fermentation parameters and to reconstruct the catabolic network by applying differential proteomics.

RESULTS

The determination of growth performance revealed, e.g., doubling times (h) from 1.39 (arabinose) to 14.26 (glucuronate), biomass yields (gCDW/mmolS) from 0.01 (fucose) to 0.27 (α-cyclodextrin), and ATP yields (mMATP/mMC) from 0.21 (rhamnose) to 0.60 (glucuronate/xylan). Furthermore, fermentation product spectra were determined, ranging from broad and balanced (with xylan: acetate, succinate, formate, and propanoate) to rather one sided (with rhamnose or fucose: mainly propane-1,2-diol). The fermentation network serving all tested compounds is composed of 56 proteins (all identified), with several peripheral reaction sequences formed with high substrate specificity (e.g., conversion of arabinose to d-xylulose-3-phosphate) implicating a fine-tuned regulation. By contrast, central modules (e.g., glycolysis or the reaction sequence from PEP to succinate) were constitutively formed. Extensive formation of propane-1,2-diol from rhamnose and fucose involves rhamnulokinase (RhaB), rhamnulose-1-phosphate kinase (RhaD), and lactaldehyde reductase (FucO). Furthermore, Sus-like systems are apparently the most relevant uptake systems and a complex array of transmembrane electron-transfer systems (e.g., Na+-pumping Rnf and Nqr complexes, fumarate reductase) as well as F- and V-type ATP-synthases were detected.

CONCLUSIONS

The present study provides insights into the potential contribution of P. vulgatus to the gut metabolome and into the strain's biotechnological potential for sustainable production of short-chain fatty acids and alcohols.

Membrane Adaptations and Cellular Responses of Sulfolobus acidocaldarius to the Allylamine Terbinafine

Cellular membranes are essential for compartmentalization, maintenance of permeability, and fluidity in all three domains of life. Archaea belong to the third domain of life and have a distinct phospholipid composition. Membrane lipids of archaea are ether-linked molecules, specifically bilayer-forming dialkyl glycerol diethers (DGDs) and monolayer-forming glycerol dialkyl glycerol tetraethers (GDGTs). The antifungal allylamine terbinafine has been proposed as an inhibitor of GDGT biosynthesis in archaea based on radiolabel incorporation studies. The exact target(s) and mechanism of action of terbinafine in archaea remain elusive. Sulfolobus acidocaldarius is a strictly aerobic crenarchaeon thriving in a thermoacidophilic environment, and its membrane is dominated by GDGTs. Here, we comprehensively analyzed the lipidome and transcriptome of S. acidocaldarius in the presence of terbinafine. Depletion of GDGTs and the accompanying accumulation of DGDs upon treatment with terbinafine were growth phase-dependent. Additionally, a major shift in the saturation of caldariellaquinones was observed, which resulted in the accumulation of unsaturated molecules. Transcriptomic data indicated that terbinafine has a multitude of effects, including significant differential expression of genes in the respiratory complex, motility, cell envelope, fatty acid metabolism, and GDGT cyclization. Combined, these findings suggest that the response of S. acidocaldarius to terbinafine inhibition involves respiratory stress and the differential expression of genes involved in isoprenoid biosynthesis and saturation.

IDARE2-Simultaneous Visualisation of Multiomics Data in Cytoscape

Visual integration of experimental data in metabolic networks is an important step to understanding their meaning. As genome-scale metabolic networks reach several thousand reactions, the task becomes more difficult and less revealing. While databases like KEGG and BioCyc provide curated pathways that allow a navigation of the metabolic landscape of an organism, it is rather laborious to map data directly onto those pathways. There are programs available using these kind of databases as a source for visualization; however, these programs are then restricted to the pathways available in the database. Here, we present IDARE2 a cytoscape plugin that allows the visualization of multiomics data in cytoscape in a user-friendly way. It further provides tools to disentangle highly connected network structures based on common properties of nodes and retains structural links between the generated subnetworks, offering a straightforward way to traverse the splitted network. The tool is extensible, allowing the implementation of specialised representations and data format parsers. We present the automated reproduction of the original IDARE nodes using our tool and show examples of other data being mapped on a network of E. coli. The extensibility is demonstrated with two plugins that are available on github. IDARE2 provides an intuitive way to visualise data from multiple sources and allows one to disentangle the often complex network structure in large networks using predefined properties of the network nodes.

Utilization of Phenol as Carbon Source by the Thermoacidophilic Archaeon Saccharolobus solfataricus P2 Is Limited by Oxygen Supply and the Cellular Stress Response

Present in many industrial effluents and as common degradation product of organic matter, phenol is a widespread compound which may cause serious environmental problems, due to its toxicity to animals and humans. Degradation of phenol from the environment by mesophilic bacteria has been studied extensively over the past decades, but only little is known about phenol biodegradation at high temperatures or low pH. In this work we studied phenol degradation in the thermoacidophilic archaeon Saccharolobus solfataricus P2 (basonym: Sulfolobus solfataricus) under extreme conditions (80°C, pH 3.5). We combined metabolomics and transcriptomics together with metabolic modeling to elucidate the organism’s response to growth with phenol as sole carbon source. Although S. solfataricus is able to utilize phenol for biomass production, the carbon source induces profound stress reactions, including genome rearrangement as well as a strong intracellular accumulation of polyamines. Furthermore, computational modeling revealed a 40% higher oxygen demand for substrate oxidation, compared to growth on glucose. However, only 16.5% of oxygen is used for oxidation of phenol to catechol, resulting in a less efficient integration of carbon into the biomass. Finally, our data underlines the importance of the phenol meta-degradation pathway in S. solfataricus and enables us to predict enzyme candidates involved in the degradation processes downstream of 2-hydroxymucconic acid.

Metabolic impact of persistent organic pollutants on gut microbiota

Emerging evidence supports that exposure to persistent organic pollutants (POPs) can impact the interaction between the gut microbiota and host. Recent efforts have characterized the relationship between gut microbiota and environment pollutants suggesting additional research is needed to understand potential new avenues for toxicity. Here, we systematically examined the direct effects of POPs including 2,3,7,8-tetrachlorodibenzofuran (TCDF), 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), and polychlorinated biphenyls (PCB-123 and PCB-156) on the microbiota using metatranscriptomics and NMR- and mass spectrometry-based metabolomics combined with flow cytometry and growth rate measurements (OD₆₀₀). This study demonstrated that (1) POPs directly and rapidly affect isolated cecal bacterial global metabolism that is associated with significant decreases in microbial metabolic activity; (2) significant changes in cecal bacterial gene expression related to tricarboxylic acid (TCA) cycle as well as carbon metabolism, carbon fixation, pyruvate metabolism, and protein export were observed following most POP exposure; (3) six individual bacterial species show variation in lipid metabolism in response to POP exposure; and (4) PCB-153 (non-coplanar)has a greater impact on bacteria than PCB-126 (coplanar) at the metabolic and transcriptional levels. These data provide new insights into the direct role of POPs on gut microbiota and begins to establish possible microbial toxicity endpoints which may help to inform risk assessment.