Transcriptomic profiling of an evolved Yarrowia lipolytica strain: tackling hexanoic acid fermentation to increase lipid production from short-chain fatty acids.

BACKGROUND: Short-chain fatty acids (SCFAs) are cost-effective carbon sources for an affordable production of lipids. Hexanoic acid, the acid with the longest carbon chain in the SCFAs pool, is produced in anaerobic fermentation of organic residues and its use is very challenging, even inhibiting oleaginous yeasts growth. RESULTS: In this investigation, an adaptive laboratory evolution (ALE) was performed to improve Yarrowia lipolytica ACA DC 50109 tolerance to high hexanoic acid concentrations. Following ALE, the transcriptomic analysis revealed several genetic adaptations that improved the assimilation of this carbon source in the evolved strain compared to the wild type (WT). Indeed, the evolved strain presented a high expression of the up-regulated gene YALI0 E16016g, which codes for FAT1 and is related to lipid droplets formation and responsible for mobilizing long-chain acids within the cell. Strikingly, acetic acid and other carbohydrate transporters were over-expressed in the WT strain. CONCLUSIONS: A more tolerant yeast strain able to attain higher lipid content under the presence of high concentrations of hexanoic acid has been obtained. Results provided novel information regarding the assimilation of hexanoic acid in yeasts.

Modelling of anaerobic digestion of microalgae biomass: Effect of overloading perturbation.

Anaerobic digestion (AD) of microalgae is an intriguing approach for bioenergy production. The scaling-up of AD presents a significant challenge due to the systematic efficiency losses related to process instabilities. To gain a comprehensive understanding of AD behavior, this study assessed a modified version of the anaerobic digestion model No1 (ADM1) + Contois kinetics to represent microalgae AD impacted by overloading. To this end, two new inhibition functions were implemented: inhibition by acetate for acidogenesis/acetogenesis and total volatile fatty acids for hydrolysis. This proposed ADM1 modification (including Contois kinetics) simulated AD behavior during the stable, disturbed and recovery periods, showing that the inhibition functions described in the original ADM1 cannot explain the AD performance under one of the most common perturbations at industrial scale (overloading). The findings underscore the importance of refining the inhibitions present in original ADM1 to better capture and predict the complexities of microalgae AD against overloading.

Effect of decoupling hydraulic and solid retention times on carbohydrate-rich residue valorization into carboxylic acids.

This research assessed the effect of decoupling hydraulic retention time (HRT) and solid retention time (SRT) on the production of volatile fatty acids (VFAs) via anaerobic fermentation of beet molasses. The performance of a continuous stirred tank reactor (CSTR, STR = HTR = 30 days) and two anaerobic sequencing batch reactors (AnSBR) with decoupled STR (30 days) and HRT (20 and 10 days) was compared. Previously, a temperature study in batch reactors (25, 35, and 55 °C) revealed 25 °C as the optimal temperature to maximize the VFAs yield and the long-chain VFAs (> C4) production, being selected for the continuous reactors operation. An HRT of 20 days in AnSBR led to an enhancement in bioconversion efficiency into VFAs (55.5% chemical oxygen demand basis) compared to the CSTR (34.9%). In contrast, the CSTR allowed the production of valuable caproic acid (25.4% vs 4.1% w/w of total VFAs in AnSBR). Decreasing further the HRT to 10 days in AnSBR was detrimental in terms of bioconversion efficiency (21.7%) due to primary intermediates (lactate) accumulation. By decoupling HRT and SRT, VFAs were maximized, revealing HRT as an effective tool to drive specific conversion routes (butyrate- or lactate-fermentation).

Kinetic and Parametric Analysis of the Separation of Ultra-Small, Aqueous Superparamagnetic Iron Oxide Nanoparticle Suspensions under Quadrupole Magnetic Fields.

Superparamagnetic iron oxide nanoparticles (SPIONs) have gathered tremendous scientific interest, especially in the biomedical field, for multiple applications, including bioseparation, drug delivery, etc. Nevertheless, their manipulation and separation with magnetic fields are challenging due to their small size. We recently reported the coupling of cooperative magnetophoresis and sedimentation using quadrupole magnets as a promising strategy to successfully promote SPION recovery from media. However, previous studies involved SPIONs dispersed in organic solvents (non-biocompatible) at high concentrations, which is detrimental to the process economy. In this work, we investigate, for the first time, the magnetic separation of 20 nm and 30 nm SPIONs dispersed in an aqueous medium at relatively low concentrations (as low as 0.5 g·L-1) using our custom, permanent magnet-based quadrupole magnetic sorter (QMS). By monitoring the SPION concentrations along the vessel within the QMS, we estimated the influence of several variables in the separation and analyzed the kinetics of the process. The results obtained can be used to shed light on the dynamics and interplay of variables that govern the fast separation of SPIONs using inexpensive permanent magnets.

Cutaneotrichosporon curvatum and Yarrowia lipolytica as key players for green chemistry: efficient oil producers from food waste via the carboxylate platform.

Cutaneotrichosporon curvatum and Yarrowia lipolytica can accumulate microbial oils using short-chain fatty acids (SCFA) as carbon sources. SCFAs-rich media often contain significant amounts of nitrogen that prevent high carbon:nitrogen (C:N) ratios necessary to boost lipid production. This work assessed the intrinsic ability of C. curvatum and Y. lipolytica to produce high amounts of microbial oils from these unusual carbon sources. Results demonstrated that minor differences in SCFA concentration (only 2 g/L) had a significant effect on yeast growth and lipid production. A C:N of 80 promoted yeast growth at all SCFA concentrations and favored SCFA consumption at 19 g/L SCFAs. The different SCFA uptake preferences in C. curvatum and Y. lipolytica highlighted the importance of considering the SCFA profile to select a suitable yeast strain for microbial oils production. At the most challenging SCFA concentration (19 g/L), 57.2% ±1.6% (w/w) and 78.4 ± 0.6% (w/w) lipid content were obtained in C. curvatum and Y. lipolytica, respectively. These values are among the highest reported for wild-type strains. To circumvent the challenges associated with media with high nitrogen content, this report also proved struvite precipitation as an effective method for increasing lipid production (from 17.9 ± 3.9% (w/w) to 41.9 ± 2.6% (w/w)) after nitrogen removal in food waste-derived media.

Slight variations in SCFA concentrations have a relevant effect on yeast lipid productionHigh nitrogen availability is crucial to promote cell growth at very high SCFA concentrationsC:N effect on cell growth and lipid production is specie-specific and may depend on yeast robustnessYeast strains have diverse SCFA preferences and differently metabolize these acidsStruvite precipitation effectively removes nitrogen from real digestates increasing C:N.

Hydraulic Retention Time as an Operational Tool for the Production of Short-Chain Carboxylates via Anaerobic Fermentation of Carbohydrate-Rich Waste.

The carboxylate platform is a sustainable and cost-effective way to valorize wastes into biochemicals that replace those of fossil origin. Short-chain fatty acids (SCFAs) are intermediates generated during anaerobic fermentation (AF) and are considered high-value-added biochemicals among carboxylates. This investigation aimed to produce SCFAs through the AF of sugar beet molasses at 25 °C and semi-continuous feeding mode in completely stirred tank reactors. A particular focus was devoted to the role of hydraulic retention time (HRT) variation in SCFAs production and distribution profile. The highest SCFAs concentration (44.1 ± 2.3 gCOD/L) was reached at the HRT of 30 days. Caproic acid accounted for 32.5-35.5% (COD-concentration basis) at the long HRTs of 20 and 30 days due to the carbon chain elongation of shorter carboxylic acids. The findings of this study proved that HRT could be used to steer the anaerobic process toward the targeted SCFAs for specific uses. Furthermore, the successful operation at low-temperature conditions (i.e., 25 °C) makes the process economically promising.

Microbial co-cultures for biochemicals production from lignocellulosic biomass: A review.

Global reliance on fossil oil should shift to cleaner alternatives to get a decarbonized society. One option to achieve this ambitious goal is the use of biochemicals produced from lignocellulosic biomass (LCB). The inherent low biodegradability of LCB and the inhibitory compounds that might be released during pretreatment are two main challenges for LCB valorization. At microbiological level, constraints are mostly linked to the need for axenic cultures and the preference for certain carbon sources (i.e., glucose). To cope with these issues, this review focuses on efficient LCB conversion via the sugar platform as well as an innovative carboxylate platform taking advantage of the co-cultivation of microorganisms. This review discusses novel trends in the use of microbial communities and co-cultures aiming at different bioproducts co-generation in single reactors as well as in sequential bioprocess combination. The outlook and further perspectives of these alternatives have been outlined for future successful development.

Production of short-chain fatty acids (SCFAs) as chemicals or substrates for microbes to obtain biochemicals.

Carboxylic acids have become interesting platform molecules in the last years due to their versatility to act as carbon sources for different microorganisms or as precursors for the chemical industry. Among carboxylic acids, short-chain fatty acids (SCFAs) such as acetic, propionic, butyric, valeric, and caproic acids can be biotechnologically produced in an anaerobic fermentation process from lignocellulose or other organic wastes of agricultural, industrial, or municipal origin. The biosynthesis of SCFAs is advantageous compared to chemical synthesis, since the latter relies on fossil-derived raw materials, expensive and toxic catalysts and harsh process conditions. This review article gives an overview on biosynthesis of SCFAs from complex waste products. Different applications of SCFAs are explored and how these acids can be considered as a source of bioproducts, aiming at the development of a circular economy. The use of SCFAs as platform molecules requires adequate concentration and separation processes that are also addressed in this review. Various microorganisms such as bacteria or oleaginous yeasts can efficiently use SCFA mixtures derived from anaerobic fermentation, an attribute that can be exploited in microbial electrolytic cells or to produce biopolymers such as microbial oils or polyhydroxyalkanoates. Promising technologies for the microbial conversion of SCFAs into bioproducts are outlined with recent examples, highlighting SCFAs as interesting platform molecules for the development of future bioeconomy.

Insights into the Binding Mode of Lipid A to the Anti-lipopolysaccharide Factor ALFPm3 from Penaeus monodon: An In Silico Study through MD Simulations.

The globally expanding threat of antibiotic resistance calls for the development of new strategies for abating Gram-negative bacterial infections. The use of extracorporeal blood cleansing devices with affinity sorbents to selectively capture bacterial lipopolysaccharide (LPS), which is the major constituent of Gram-negative bacterial outer membranes and the responsible agent for eliciting an exacerbated innate immune response in the host during infection, has received outstanding interest. For that purpose, molecules that bind tightly to LPS are required to functionalize the affinity sorbents. Particularly, anti-LPS factors (ALFs) are promising LPS-sequestrating molecules. Hence, in this work, molecular dynamics (MD) simulations are used to investigate the interaction mechanism and binding pose of the ALF isoform 3 from Penaeus monodon (ALFPm3), which is referred to as "AL3" for the sake of simplicity, and lipid A (LA, the component of LPS that represents its endotoxic principle). We concluded that hydrophobic interactions are responsible for AL3-LA binding and that LA binds to AL3 within the protein cavity, where it buries its aliphatic tails, whereas the negatively charged phosphate groups are exposed to the medium. AL3 residues that are key for its interaction with LA were identified, and their conservation in other ALFs (specifically Lys39 and Tyr49) was also analyzed. Additionally, based on the MD-derived results, we provide a picture of the possible AL3-LA interaction mechanism. Finally, an in vitro validation of the in silico predictions was performed. Overall, the insights gained from this work can guide the design of novel therapeutics for treating sepsis, since they may be significantly valuable for designing LPS-sequestrating molecules that could functionalize affinity sorbents to be used for extracorporeal blood detoxification.

Genome-centric metagenomics revealed the effect of pH on the microbiome involved in short-chain fatty acids and ethanol production.

Added-value chemicals production via food waste (FWs) valorization using open-mixed cultures is an emerging approach to replace petrochemical-based compounds. Nevertheless, the effects of operational parameters on the product spectrum remain uncertain given the wide number of co-occurring species and metabolisms. In this study, the identification of 58 metagenome-assembled genomes and their investigation assessed the effect of slight pH variations on microbial dynamics and the corresponding functions when FWs were subjected to anaerobic fermentation (AF) in 1-L continuous stirred tank reactors at 25 °C. The initial pH of 6.5 promoted a microbial community involved in acetate, butyrate and ethanol production, mediated by Bifidobacterium subtile IE007 and Eubacteriaceae IE027 as main species. A slight pH decrease to 6.1 shaped microbial functions that resulted in caproate and H2 production, increasing the relevance of Eubacteriaceae IE037 role. This study elucidated the strong pH effect on product outputs when minimal variations take place in AF.

Recent progress on wastewater-based epidemiology for COVID-19 surveillance: A systematic review of analytical procedures and epidemiological modeling.

On March 11, 2020, the World Health Organization declared the coronavirus disease 2019 (COVID-19), whose causative agent is the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), a pandemic. This virus is predominantly transmitted via respiratory droplets and shed via sputum, saliva, urine, and stool. Wastewater-based epidemiology (WBE) has been able to monitor the circulation of viral pathogens in the population. This tool demands both in-lab and computational work to be meaningful for, among other purposes, the prediction of outbreaks. In this context, we present a systematic review that organizes and discusses laboratory procedures for SARS-CoV-2 RNA quantification from a wastewater matrix, along with modeling techniques applied to the development of WBE for COVID-19 surveillance. The goal of this review is to present the current panorama of WBE operational aspects as well as to identify current challenges related to it. Our review was conducted in a reproducible manner by following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines for systematic reviews. We identified a lack of standardization in wastewater analytical procedures. Regardless, the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) approach was the most reported technique employed to detect and quantify viral RNA in wastewater samples. As a more convenient sample matrix, we suggest the solid portion of wastewater to be considered in future investigations due to its higher viral load compared to the liquid fraction. Regarding the epidemiological modeling, the data-driven approach was consistently used for the prediction of variables associated with outbreaks. Future efforts should also be directed toward the development of rapid, more economical, portable, and accurate detection devices.

Phosphate limitation as crucial factor to enhance yeast lipid production from short-chain fatty acids.

Microbial lipids for chemical synthesis are commonly obtained from sugar-based substrates which in most cases is not economically viable. As a low-cost carbon source, short-chain fatty acids (SCFAs) that can be obtained from food wastes offer an interesting alternative for achieving an affordable lipid production process. In this study, SCFAs were employed to accumulate lipids using Yarrowia lipolytica ACA DC 50109. For this purpose, different amounts of SCFAs, sulfate, phosphate and carbon: phosphate ratios were used in both synthetic and real SCFAs-rich media. Although sulfate limitation did not increase lipid accumulation, phosphate limitation was proved to be an optimal strategy for increasing lipid content and lipid yields in both synthetic and real media, reaching a lipid productivity up to 8.95 g/L h. Remarkably, the highest lipid yield (0.30 g/g) was achieved under phosphate absence condition (0 g/L). This fact demonstrated the suitability of using low-phosphate concentrations to boost lipid production from SCFAs.

In silico investigation and surmounting of Lipopolysaccharide barrier in Gram-Negative Bacteria: How far has molecular dynamics Come?

Lipopolysaccharide (LPS), a main component of the outer membrane of Gram-negative bacteria, has crucial implications on both antibiotic resistance and the overstimulation of the host innate immune system. Fighting against these global concerns calls for the molecular understanding of the barrier function and immunostimulatory ability of LPS. Molecular dynamics (MD) simulations have become an invaluable tool for uncovering important findings in LPS research. While the reach of MD simulations for investigating the immunostimulatory ability of LPS has been already outlined, little attention has been paid to the role of MD simulations for exploring its barrier function and synthesis. Herein, we give an overview about the impact of MD simulations on gaining insight into the shield role and synthesis pathway of LPS, which have attracted considerable attention to discover molecules able to surmount antibiotic resistance, either circumventing LPS defenses or disrupting its synthesis. We specifically focus on the enhanced sampling and free energy calculation methods that have been combined with MD simulations to address such research. We also highlight the use of special-purpose MD supercomputers, the importance of appropriate LPS and ions parameterization to obtain reliable results, and the complementary views that MD and wet-lab experiments provide. Thereby, this work, which covers the last five years of research, apart from outlining the phenomena and strategies that are being explored, evidences the valuable insights that are gained by MD, which may be useful to advance antibiotic design, and what the prospects of this in silico method could be in LPS research.

Key role of fluorescence quantum yield in Nile Red staining method for determining intracellular lipids in yeast strains.

BACKGROUND: Microbial lipids are found to be an interesting green alternative to expand available oil sources for the chemical industry. Yeasts are considered a promising platform for sustainable lipid production. Remarkably, some oleaginous yeasts have even shown the ability to grow and accumulate lipids using unusual carbon sources derived from organic wastes, such as volatile fatty acids. Recent research efforts have been focused on developing rapid and accurate fluorometric methods for the quantification of intracellular yeast lipids. Nevertheless, the current methods are often tedious and/or exhibit low reproducibility. RESULTS: This work evaluated the reliability of different fluorescence measurements (fluorescence intensity, total area and fluorescence quantum yield) using Nile Red as lipid dye in two yeast strains (Yarrowia lipolytica ACA-DC 50109 and Cutaneotrichosporon curvatum NRRL-Y-1511). Different standard curves were obtained for each yeast specie. Fermentation tests were carried with 6-month difference to evaluate the effect of the fluorometer lamp lifetime on lipid quantification. CONCLUSIONS: Fluorescence quantum yield presented the most consistent measurements along time and the closer estimations when compared with lipids obtained by conventional methods (extraction and gravimetrical determination). The need of using fluorescence quantum yield to estimate intracellular lipids, which is not the common trend in studies focused on microbial lipid production, was stressed. The information here provided will surely enable more accurate results comparison.

Insights into cell robustness against lignocellulosic inhibitors and insoluble solids in bioethanol production processes.

Increasing yeast robustness against lignocellulosic-derived inhibitors and insoluble solids in bioethanol production is essential for the transition to a bio-based economy. This work evaluates the effect exerted by insoluble solids on yeast tolerance to inhibitory compounds, which is crucial in high gravity processes. Adaptive laboratory evolution (ALE) was applied on a xylose-fermenting Saccharomyces cerevisiae strain to simultaneously increase the tolerance to lignocellulosic inhibitors and insoluble solids. The evolved strain gave rise to a fivefold increase in bioethanol yield in fermentation experiments with high concentration of inhibitors and 10% (w/v) of water insoluble solids. This strain also produced 5% (P > 0.01) more ethanol than the parental in simultaneous saccharification and fermentation of steam-exploded wheat straw, mainly due to an increased xylose consumption. In response to the stress conditions (solids and inhibitors) imposed in ALE, cells induced the expression of genes related to cell wall integrity (SRL1, CWP2, WSC2 and WSC4) and general stress response (e.g., CDC5, DUN1, CTT1, GRE1), simultaneously repressing genes related to protein synthesis and iron transport and homeostasis (e.g., FTR1, ARN1, FRE1), ultimately leading to the improved phenotype. These results contribute towards understanding molecular mechanisms that cells might use to convert lignocellulosic substrates effectively.

Microalgae production for nitrogen recovery of high-strength dry anaerobic digestion effluent.

Dry anaerobic digestion (D-AD) generates nitrogen-rich effluents that are normally neglected in the circular bioeconomy. The high turbidity and ammonium content hamper nitrogen recovery from these effluents via biological processes, such as microalgae culture. The goal of this study was to demonstrate microalgae growth viability in high-strength D-AD effluents in order to recover nitrogen (N) as microalgae biomass. According to the experimental factorial design conducted in batch reactors, ammonium was identified as the critical inhibitory compound for microalgae growth while turbidity did not exhibit a significantly negative effect. Instead, turbidity resulted advantageous since it promoted high nitrogen uptake rates and biomass production. The presence of organic turbidity resulted in a positive effect that boosted Chlorella growth in a stream with higher ammonium (350 mg NH4+-N L-1) and turbidity (175 NTU) than the inhibition thresholds reported in the literature, reaching 98.7% of N recovery as microalgae biomass. When microalgae culture was scaled up in a photobioreactor operated in continuous mode, microalgae biomass was effectively produced while recovering 100% of N at a hydraulic retention time of 10 days. By imposing long exposure times and high turbidity, Chlorella adaptation to high-strength D-AD effluent resulted in high N uptake and biomass production. This study demonstrated not only the most influencing factor and the optimal NH4+-N and turbidity combination, but also the viability of using D-AD effluents as culture media for microalgae biomass production.

Carboxylic acids production via anaerobic fermentation: Microbial communities' responses to stepwise and direct hydraulic retention time decrease.

Carboxylic acids, traditionally produced from fossil fuels, might be generated from renewable biomass resources via anaerobic fermentation. Considering that the microbial activity of this bioprocess is ruled by the imposed hydraulic retention time (HRT), this investigation explored the relationship between process stability and microbial community. Stepwise and direct HRT reduction strategies were assessed in terms of waste bioconversion into volatile fatty acids (VFAs). Microbial community dynamics revealed a microbial specialization along the HRT decrease. The direct implementation of low HRT resulted in drastic microbial fluctuations, leading to process failure at HRT below 6 days. Stepwise strategy for HRT reduction favored microbial adaptation, supporting maximum bioconversions efficiencies (32 % VFACOD/tCODin) at low HRT values (HRT 4 days). Microbial similarity analysis revealed Clostridiales, Lactobacillales and Bacteroidales orders as keystone microorganisms involved in VFAs production, being responsible for protein degradation and propionic acid accumulation.

Statistical correlation between waste macromolecular composition and anaerobic fermentation temperature for specific short-chain fatty acid production.

To properly exploit short-chain fatty acids (SCFAs) in the chemical industry, it is of foremost importance to ensure stable SCFA profile production via anaerobic fermentation (AF). The different macromolecular distribution of food wastes (FWs) used as feedstock might be crucial for process outcome. Targeting at a specific SCFAs profile and yield, this study explored the statistical correlation between the macromolecular composition of FWs and the produced SCFAs in batch-AFs at 25 °C and 55 °C. Principal Component Analysis (PCA) revealed that the carbohydrates fraction was directly related with butyric acid accumulation, regardless of process temperature. Nevertheless, operational temperature resulted in a pH change, which ultimately affected the process fate. PCA of 25 °C-batch-AF showed a positive correlation between high carbohydrate content and longer-chain acids accumulation. By contrast, 55 °C-AF resulted in higher product specificity than at 25 °C, mainly due to butyrate-type fermentation of carbohydrates. Batch results were further validated in a semicontinuous reactor. Prevailing SCFAs and high bioconversion efficiencies relied on 3 main FWs characteristics: high carbohydrate content (>77% w/w), high carbohydrate/protein ratio (≥10) and high soluble organic matter content. Results obtained herein allowed predicting a specific SCFAs profile based on FWs composition, which is relevant for setting proper downstream technologies.

Recovery of Magnetic Catalysts: Advanced Design for Process Intensification.

The design of microdevices in which components with magnetic character must be separated and recovered from reactive media benefits from the advantages of microfluidics and meets the criteria for process intensification; however, there are open questions, such as the design of the most appropriate magnet arrangement, that need further research in order to increase the magnetic gradient exerted on the particles. Herein, we focus on the continuous recovery of magnetic microparticles, that can be used as support to facilitate the recovery of biocatalysts (magnetic microcatalysts, MMCs) from biological fluids. We analyze and compare the performance of two typical magnetophoretic microdevices for addressing bead recovery: (i) annular channels with a quadrupole orientation of the permanent magnets (quadrupole magnetic sorter, QMS) and (ii) the standard design, which consists of rectangular channels with a single permanent magnet to generate the magnetic field. To this end, an experimentally validated computational fluid dynamics (CFD) numerical model has been employed. Our results reveal that for devices with the same width and length, the micro-QMS, in comparison to a rectangular channel, could accomplish the complete particle retrieval while (i) processing more than 4 times higher fluid velocities, treating more than 360 times higher flow rates or (ii) working with smaller particles, thus reducing by 55% the particle mass. Additionally, the parallel performance of ≈300 micro-QMSs fulfills the processing of flow rates as high as 200 L·h-1 while entirely capturing the magnetic beads. Thereby, this work shows the potential of the QMS advanced design in the intensification of the recovery of catalysts supports of magnetic character.

Fighting Against Bacterial Lipopolysaccharide-Caused Infections through Molecular Dynamics Simulations: A Review.

Lipopolysaccharide (LPS) is the primary component of the outer leaflet of Gram-negative bacterial outer membranes. LPS elicits an overwhelming immune response during infection, which can lead to life-threatening sepsis or septic shock for which no suitable treatment is available so far. As a result of the worldwide expanding multidrug-resistant bacteria, the occurrence and frequency of sepsis are expected to increase; thus, there is an urge to develop novel strategies for treating bacterial infections. In this regard, gaining an in-depth understanding about the ability of LPS to both stimulate the host immune system and interact with several molecules is crucial for fighting against LPS-caused infections and allowing for the rational design of novel antisepsis drugs, vaccines and LPS sequestration and detection methods. Molecular dynamics (MD) simulations, which are understood as being a computational microscope, have proven to be of significant value to understand LPS-related phenomena, driving and optimizing experimental research studies. In this work, a comprehensive review on the methods that can be combined with MD simulations, recently applied in LPS research, is provided. We focus especially on both enhanced sampling methods, which enable the exploration of more complex systems and access to larger time scales, and free energy calculation approaches. Thereby, apart from outlining several strategies for surmounting LPS-caused infections, this work reports the current state-of-the-art of the methods applied with MD simulations for moving a step forward in the development of such strategies.