A model-driven approach to upcycling recalcitrant feedstocks in Pseudomonas putida by decoupling PHA production from nutrient limitation.

Bacterial polyhydroxyalkanoates (PHAs) have emerged as promising eco-friendly alternatives to petroleum-based plastics since they are synthesized from renewable resources and offer exceptional properties. However, their production is limited to the stationary growth phase under nutrient-limited conditions, requiring customized strategies and costly two-phase bioprocesses. In this study, we tackle these challenges by employing a model-driven approach to reroute carbon flux and remove regulatory constraints using synthetic biology. We construct a collection of Pseudomonas putida-overproducing strains at the expense of plastics and lignin-related compounds using growth-coupling approaches. PHA production was successfully achieved during growth phase, resulting in the production of up to 46% PHA/cell dry weight while maintaining a balanced carbon-to-nitrogen ratio. Our strains are additionally validated under an upcycling scenario using enzymatically hydrolyzed polyethylene terephthalate as a feedstock. These findings have the potential to revolutionize PHA production and address the global plastic crisis by overcoming the complexities of traditional PHA production bioprocesses.

Characterization of Limnospira platensis PCC 9108 R-M and CRISPR-Cas systems.

The filamentous cyanobacterium Limnospira platensis, formerly known as Arthrospira platensis or spirulina, is one of the most commercially important species of microalgae. Due to its high nutritional value, pharmacological and industrial applications it is extensively cultivated on a large commercial scale. Despite its widespread use, its precise manipulation is still under development due to the lack of effective genetic protocols. Genetic transformation of Limnospira has been attempted but the methods reported have not been generally reproducible in other laboratories. Knowledge of the transformation defense mechanisms is essential for understanding its physiology and for broadening their applications. With the aim to understand more about the genetic defenses of L. platensis, in this work we have identified the restriction-modification and CRISPR-Cas systems and we have cloned and characterized thirteen methylases. In parallel, we have also characterized the methylome and orphan methyltransferases using genome-wide analysis of DNA methylation patterns and RNA-seq. The identification and characterization of these enzymes will be a valuable resource to know how this strain avoids being genetically manipulated and for further genomics studies.

Non-atherosclerotic acute cardiac syndromes: spontaneous coronary artery dissection and Takotsubo syndrome. Comparison of long-term clinical outcomes.

BACKGROUND: Spontaneous coronary artery dissection (SCAD) and Takotsubo syndrome (TTS) constitute two common causes of nonatherosclerotic acute cardiac syndrome particularly frequent in women. Currently, there is no information comparing long-term clinical outcomes in unselected patients with these conditions. METHODS: We compared the baseline characteristics, in-hospital outcomes, and the 12-month and long-term clinical outcomes of two large prospective registries on SCAD and TTS. RESULTS: A total of 289 SCAD and 150 TTS patients were included; 89% were women. TTS patients were older with a higher prevalence of cardiovascular risk factors. Precipitating triggers were more frequent in TTS patients, while emotional triggers and depressive disorders were more common in the SCAD group. Left ventricular ejection fraction was lower in TTS patients, but SCAD patients showed higher cardiac biomarkers. In-hospital events (43.3% vs. 5.2%, P <0.01) occurred more frequently in TTS patients. TTS patients also presented more frequent major adverse events at 12-month (14.7% vs. 7.1%, HR 5.3, 95% CI: 2.4-11.7, P <0.01) and long-term (median 36 vs. 31 months, P =0.41) follow-up (25.8% vs. 9.6%, HR 4.5, 95% CI: 2.5-8.2, P <0.01). Atrial fibrillation was also more frequent in TTS patients. Moreover, TTS patients presented a higher 12-month and long-term mortality (5.6% vs. 0.7%, P =0.01; and 12.6% vs. 0.7%, P <0.01) mainly driven by noncardiovascular deaths. CONCLUSION: Compared to SCAD, TTS patients are older and present more cardiovascular risk factors but less frequent depressive disorder or emotional triggers. TTS patients have a worse in-hospital, mid-term, and long-term prognosis with higher noncardiac mortality than SCAD patients.

New strategy for bioplastic and exopolysaccharides production: Enrichment of field microbiomes with cyanobacteria.

Seven photosynthethic microbiomes were collected from field environmental samples to test their potential in polyhydroxybutyrate (PHB) and exopolysaccharides (EPS) production, both alternatives to chemical-based polymers. Microscope observations together with microbial sequence analysis revealed the microbiome enrichment in cyanobacteria after culture growth under phosphorus limitation. PHB and EPS production were studied under three culture factors (phototrophy, mixotrophy and heterotrophy) by evaluating and optimizing the effect of three parameters (organic and inorganic carbon and days under light:dark cycles) by Box-Behnken design. Results showed that optimal conditions for both biopolymers synthesis were microbiome-dependent; however, the addition of organic carbon boosted PHB production in all the tested microbiomes, producing up to 14 %dcw PHB with the addition of 1.2 g acetate·L-1 and seven days under light:dark photoperiods. The highest EPS production was 59 mg·L-1 with the addition of 1.2 g acetate·L-1 and four days under light:dark photoperiods. The methodology used is suitable for enriching microbiomes in cyanobacteria, and for testing the best conditions for bioproduct synthesis for further scale up.

Golden Standard: a complete standard, portable, and interoperative MoClo tool for model and non-model proteobacteria.

Modular cloning has become a benchmark technology in synthetic biology. However, a notable disparity exists between its remarkable development and the need for standardization to facilitate seamless interoperability among systems. The field is thus impeded by an overwhelming proliferation of organism-specific systems that frequently lack compatibility. To overcome these issues, we present Golden Standard (GS), a Type IIS assembly method underpinned by the Standard European Vector Architecture. GS unlocks modular cloning applications for most bacteria, and delivers combinatorial multi-part assembly to create genetic circuits of up to twenty transcription units (TUs). Reliance on MoClo syntax renders GS fully compatible with many existing tools and it sets the path towards efficient reusability of available part libraries and assembled TUs. GS was validated in terms of DNA assembly, portability, interoperability and phenotype engineering in α-, ß-, γ- and δ-proteobacteria. Furthermore, we provide a computational pipeline for parts characterization that was used to assess the performance of GS parts. To promote community-driven development of GS, we provide a dedicated web-portal including a repository of parts, vectors, and Wizard and Setup tools that guide users in designing constructs. Overall, GS establishes an open, standardized framework propelling the progress of synthetic biology as a whole.

Technical upgrade of an open-source liquid handler to support bacterial colony screening.

The optimization of genetically engineered biological constructs is a key step to deliver high-impact biotechnological applications. The use of high-throughput DNA assembly methods allows the construction of enough genotypic variants to successfully cover the target design space. This, however, entails extra workload for researchers during the screening stage of candidate variants. Despite the existence of commercial colony pickers, their high price excludes small research laboratories and budget-adjusted institutions from accessing such extensive screening capability. In this work we present COPICK, a technical solution to automatize colony picking in an open-source liquid handler Opentrons OT-2. COPICK relies on a mounted camera to capture images of regular Petri dishes and detect microbial colonies for automated screening. COPICK's software can then automatically select the best colonies according to different criteria (size, color and fluorescence) and execute a protocol to pick them for further analysis. Benchmark tests performed for E. coli and P. putida colonies delivers a raw picking performance over pickable colonies of 82% with an accuracy of 73.4% at an estimated rate of 240 colonies/h. These results validate the utility of COPICK, and highlight the importance of ongoing technical improvements in open-source laboratory equipment to support smaller research teams.

System metabolic engineering of Escherichia coli W for the production of 2-ketoisovalerate using unconventional feedstock.

Replacing traditional substrates in industrial bioprocesses to advance the sustainable production of chemicals is an urgent need in the context of the circular economy. However, since the limited degradability of non-conventional carbon sources often returns lower yields, effective exploitation of such substrates requires a multi-layer optimization which includes not only the provision of a suitable feedstock but the use of highly robust and metabolically versatile microbial biocatalysts. We tackled this challenge by means of systems metabolic engineering and validated Escherichia coli W as a promising cell factory for the production of the key building block chemical 2-ketoisovalerate (2-KIV) using whey as carbon source, a widely available and low-cost agro-industrial waste. First, we assessed the growth performance of Escherichia coli W on mono and disaccharides and demonstrated that using whey as carbon source enhances it significantly. Second, we searched the available literature and used metabolic modeling approaches to scrutinize the metabolic space of E. coli and explore its potential for overproduction of 2-KIV identifying as basic strategies the block of pyruvate depletion and the modulation of NAD/NADP ratio. We then used our model predictions to construct a suitable microbial chassis capable of overproducing 2-KIV with minimal genetic perturbations, i.e., deleting the pyruvate dehydrogenase and malate dehydrogenase. Finally, we used modular cloning to construct a synthetic 2-KIV pathway that was not sensitive to negative feedback, which effectively resulted in a rerouting of pyruvate towards 2-KIV. The resulting strain shows titers of up to 3.22 ± 0.07 g/L of 2-KIV and 1.40 ± 0.04 g/L of L-valine in 24 h using whey in batch cultures. Additionally, we obtained yields of up to 0.81 g 2-KIV/g substrate. The optimal microbial chassis we present here has minimal genetic modifications and is free of nutritional autotrophies to deliver high 2-KIV production rates using whey as a non-conventional substrate.

Optimized De Novo Eriodictyol Biosynthesis in Streptomyces albidoflavus Using an Expansion of the Golden Standard Toolkit for Its Use in Actinomycetes.

Eriodictyol is a hydroxylated flavonoid displaying multiple pharmaceutical activities, such as antitumoral, antiviral or neuroprotective. However, its industrial production is limited to extraction from plants due to its inherent limitations. Here, we present the generation of a Streptomyces albidoflavus bacterial factory edited at the genome level for an optimized de novo heterologous production of eriodictyol. For this purpose, an expansion of the Golden Standard toolkit (a Type IIS assembly method based on the Standard European Vector Architecture (SEVA)) has been created, encompassing a collection of synthetic biology modular vectors (adapted for their use in actinomycetes). These vectors have been designed for the assembly of transcriptional units and gene circuits in a plug-and-play manner, as well as for genome editing using CRISPR-Cas9-mediated genetic engineering. These vectors have been used for the optimization of the eriodictyol heterologous production levels in S. albidoflavus by enhancing the flavonoid-3'-hydroxylase (F3'H) activity (by means of a chimera design) and by replacing three native biosynthetic gene clusters in the bacterial chromosome with the plant genes matBC (involved in extracellular malonate uptake and its intracellular activation into malonyl-CoA), therefore allowing more malonyl-CoA to be devoted to the heterologous production of plant flavonoids in this bacterial factory. These experiments have allowed an increase in production of 1.8 times in the edited strain (where the three native biosynthetic gene clusters have been deleted) in comparison with the wild-type strain and a 13 times increase in eriodictyol overproduction in comparison with the non-chimaera version of the F3'H enzyme.

Prognostic implications of left ventricular systolic dysfunction in patients with spontaneous coronary artery dissection.

AIMS: Spontaneous coronary artery dissection (SCAD) is a relatively infrequent cause of acute coronary syndrome. Clinical features, angiographic findings, management, and outcomes of SCAD patients who present reduced left ventricular ejection fraction (LVEF) remain unknown. METHODS AND RESULTS: The Spanish multicentre prospective SCAD registry (NCT03607981), included 389 consecutive patients with SCAD. In 348 of these patients, LVEF could be assessed by echocardiography during the index admission. Characteristics and outcomes of patients with preserved LVEF (LVEF ≥50%, n = 295, 85%) were compared with those with reduced LVEF (LVEF <50%, n = 53, 15%). Mean age was 54 years and 90% of patients in both groups were women. The most frequent clinical presentation in patients with reduced LVEF was ST-segment elevation myocardial infarction (STEMI) (62% vs. 36%, P < 0.001), especially anterior STEMI. Proximal coronary segment and multi-segment involvement were also significantly more frequent in these patients. No differences were found on initial revascularization between groups. Patients with reduced LVEF significantly received more often neurohormonal antagonist therapy, and less frequently aspirin. In-hospital events were more frequent in these patients (13% vs. 5%, P = 0.01), with higher rates of death, cardiogenic shock, ventricular arrhythmia, and stroke. During a median follow-up of 28 months, the occurrence of a combined adverse event did not statistically differ between the two groups (19% vs. 12%, P = 0.13). However, patients with reduced LVEF had higher mortality (9% vs. 0.7%, P < 0.001) and readmission rates for heart failure (HF) (4% vs. 0.3%, P = 0.01). CONCLUSION: Patients with SCAD and reduced LVEF show differences in clinical characteristics and angiographic findings compared with SCAD patients with preserved LVEF. Although these patients receive specific medications at discharge, they had higher mortality and readmission rates for HF during follow-up.

New Insights on Metabolic Features of Bacillus subtilis Based on Multistrain Genome-Scale Metabolic Modeling.

Bacillus subtilis is an effective workhorse for the production of many industrial products. The high interest aroused by B. subtilis has guided a large metabolic modeling effort of this species. Genome-scale metabolic models (GEMs) are powerful tools for predicting the metabolic capabilities of a given organism. However, high-quality GEMs are required in order to provide accurate predictions. In this work, we construct a high-quality, mostly manually curated genome-scale model for B. subtilis (iBB1018). The model was validated by means of growth performance and carbon flux distribution and provided significantly more accurate predictions than previous models. iBB1018 was able to predict carbon source utilization with great accuracy while identifying up to 28 metabolites as potential novel carbon sources. The constructed model was further used as a tool for the construction of the panphenome of B. subtilis as a species, by means of multistrain genome-scale reconstruction. The panphenome space was defined in the context of 183 GEMs representative of 183 B. subtilis strains and the array of carbon sources sustaining growth. Our analysis highlights the large metabolic versatility of the species and the important role of the accessory metabolism as a driver of the panphenome, at a species level.

Highlighting the potential of Synechococcus elongatus PCC 7942 as platform to produce α-linolenic acid through an updated genome-scale metabolic modeling.

Cyanobacteria are prokaryotic organisms that capture energy from sunlight using oxygenic photosynthesis and transform CO2 into products of interest such as fatty acids. Synechococcus elongatus PCC 7942 is a model cyanobacterium efficiently engineered to accumulate high levels of omega-3 fatty acids. However, its exploitation as a microbial cell factory requires a better knowledge of its metabolism, which can be approached by using systems biology tools. To fulfill this objective, we worked out an updated, more comprehensive, and functional genome-scale model of this freshwater cyanobacterium, which was termed iMS837. The model includes 837 genes, 887 reactions, and 801 metabolites. When compared with previous models of S. elongatus PCC 7942, iMS837 is more complete in key physiological and biotechnologically relevant metabolic hubs, such as fatty acid biosynthesis, oxidative phosphorylation, photosynthesis, and transport, among others. iMS837 shows high accuracy when predicting growth performance and gene essentiality. The validated model was further used as a test-bed for the assessment of suitable metabolic engineering strategies, yielding superior production of non-native omega-3 fatty acids such as α-linolenic acid (ALA). As previously reported, the computational analysis demonstrated that fabF overexpression is a feasible metabolic target to increase ALA production, whereas deletion and overexpression of fabH cannot be used for this purpose. Flux scanning based on enforced objective flux, a strain-design algorithm, allowed us to identify not only previously known gene overexpression targets that improve fatty acid synthesis, such as Acetyl-CoA carboxylase and ß-ketoacyl-ACP synthase I, but also novel potential targets that might lead to higher ALA yields. Systematic sampling of the metabolic space contained in iMS837 identified a set of ten additional knockout metabolic targets that resulted in higher ALA productions. In silico simulations under photomixotrophic conditions with acetate or glucose as a carbon source boosted ALA production levels, indicating that photomixotrophic nutritional regimens could be potentially exploited in vivo to improve fatty acid production in cyanobacteria. Overall, we show that iMS837 is a powerful computational platform that proposes new metabolic engineering strategies to produce biotechnologically relevant compounds, using S. elongatus PCC 7942 as non-conventional microbial cell factory.

SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes.

The SEVA platform (https://seva-plasmids.com) was launched one decade ago, both as a database (DB) and as a physical repository of plasmid vectors for genetic analysis and engineering of Gram-negative bacteria with a structure and nomenclature that follows a strict, fixed architecture of functional DNA segments. While the current update keeps the basic features of earlier versions, the platform has been upgraded not only with many more ready-to-use plasmids but also with features that expand the range of target species, harmonize DNA assembly methods and enable new applications. In particular, SEVA 4.0 includes (i) a sub-collection of plasmids for easing the composition of multiple DNA segments with MoClo/Golden Gate technology, (ii) vectors for Gram-positive bacteria and yeast and [iii] off-the-shelf constructs with built-in functionalities. A growing collection of plasmids that capture part of the standard-but not its entirety-has been compiled also into the DB and repository as a separate corpus (SEVAsib) because of its value as a resource for constructing and deploying phenotypes of interest. Maintenance and curation of the DB were accompanied by dedicated diffusion and communication channels that make the SEVA platform a popular resource for genetic analyses, genome editing and bioengineering of a large number of microorganisms.

Multivessel spontaneous coronary artery dissection: Clinical features, angiographic findings, management, and outcomes.

BACKGROUND: Spontaneous coronary artery dissection (SCAD) is a rare cause of acute coronary syndrome. Multivessel (MV) SCAD is a challenging clinical presentation that might be associated to a worse prognosis compared with patients with single-vessel (SV) involvement. METHODS: The Spanish multicentre nationwide prospective SCAD registry included 389 consecutive patients. Patients were classified, according to the number of affected vessels, in SV or MV SCAD. Major adverse events (MAE) were analyzed during hospital stay and major cardiac or cerebrovascular adverse events (MACCE) at long-term clinical follow-up. RESULTS: A total of 41 patients (10.5%) presented MV SCAD. These patients had more frequently a previous history of hypothyroidism (22% vs 11%, p = 0.04) and anxiety disorder (32% vs 16%, p = 0.01). MV SCAD patients presented more often as non-ST segment elevation myocardial infarction (73% vs 52%, p = 0.01) and showed less frequently type 1 angiographic lesions (12% vs 21%, p = 0.04). An impaired initial Thrombolysis In Myocardial Infarction (TIMI) flow 0-1 was less frequent (14% vs 29%, p < 0.01) in MV SCAD. In both groups, most patients were treated conservatively (71% vs 79%, p = NS). No differences were found regarding in-hospital MAE or MACCE at late follow-up (median 29 ± 11 months). However, the rate of stroke was higher in MV SCAD patients, both in-hospital (2.4% vs 0%, p < 0.01) and at follow-up (5.1% vs 0.6%, p = 0.01). CONCLUSIONS: Patients with MV SCAD have some distinctive clinical and angiographic features. Although composite clinical outcomes, in-hospital and at long-term follow-up, were similar to those seen in patients with SV SCAD, stroke rate was significantly higher in patients with MV SCAD.

Clinical Implications of the "Broken Line" Angiographic Pattern in Patients With Spontaneous Coronary Artery Dissection.

Spontaneous coronary artery dissection (SCAD) is a rare but increasingly recognized cause of acute myocardial infarction. Coronary angiography remains the best diagnostic tool; however, clinical suspicion and experience is required to interpret angiographic findings. This study sought to assess the clinical implications of the "broken line" (BKL) angiographic pattern in a large, nationwide, cohort of patients with SCAD. The Spanish SCAD registry (NCT03607981) prospectively enrolled consecutive patients with SCAD. All angiograms were centrally analyzed and the BKL pattern was systematically assessed. The BKL angiographic pattern was found in 64 of 389 patients (16%). Patients with the BKL appearance were more frequently female (97 vs 87%, p <0.05), presented more often as intramural hematoma (83 vs 58%, p <0.001), had longer lesions (47 ± 29 vs 36 ± 22 mm, p <0.01), and had severe tortuosity (25 vs 10%, p <0.01) but showed better initial coronary flow (thrombolysis in myocardial infarction flow 2.6 ± 0.8 vs 2.1 ± 1.2, p <0.01). Patients with BKL received more frequently conservative medical management (91 vs 76%, p <0.01). At late clinical follow-up (median 29 months, interquartile range 17 to 38) predefined adverse events (death, myocardial infarction, revascularization, recurrent SCAD, or stroke) occurred less frequently (3.5 vs 15%, p <0.05) in patients with the BKL appearance. The better clinical outcomes of patients in the BKL group persisted after adjusting for potential confounders (adjusted hazard ratio 0.2, 95% confidence interval 0.1 to 0.9, p <0.05). In conclusion, patients with SCAD presenting the BKL angiographic pattern are more frequently female and present more often as intramural hematoma with longer lesions and severe vessel tortuosity but have better coronary flow. Patients with the BKL morphology have a favorable prognosis (NCT03607981).

Synechococcus elongatus PCC 7942 as a Platform for Bioproduction of Omega-3 Fatty Acids.

Alpha-linolenic acid and stearidonic acid are precursors of omega-3 polyunsaturated fatty acids, essential nutrients in the human diet. The ability of cyanobacteria to directly convert atmospheric carbon dioxide into bio-based compounds makes them promising microbial chassis to sustainably produce omega-3 fatty acids. However, their potential in this area remains unexploited, mainly due to important gaps in our knowledge of fatty acid synthesis pathways. To gain insight into the cyanobacterial fatty acid biosynthesis pathways, we analyzed two enzymes involved in the elongation cycle, FabG and FabZ, in Synechococcus elongatus PCC 7942. Overexpression of these two enzymes led to an increase in C18 fatty acids, key intermediates in omega-3 fatty acid production. Nevertheless, coexpression of these enzymes with desaturases DesA and DesB from Synechococcus sp. PCC 7002 did not improve alpha-linolenic acid production, possibly due to their limited role in fatty acid synthesis. In any case, efficient production of stearidonic acid was not achieved by cloning DesD from Synechocystis sp. PCC 6803 in combination with the aforementioned DesA and DesB, reaching maximum production at 48 h post induction. According to current knowledge, this is the first report demonstrating that S. elongatus PCC 7942 can be used as an autotrophic chassis to produce stearidonic acid.

Toward merging bottom-up and top-down model-based designing of synthetic microbial communities.

The increasing interest of microbial communities as promising biocatalyst is leading an intense effort into the development of computational frameworks assisting the analysis and rational engineering of such complex ecosystems. Here, we critically review the recent computational and model-guided advances in the system-level engineering of microbiome, including both the rational bottom-up and the evolutionary top-down approaches. Furthermore, we highlight modeling and computational methods supporting both engineering paradigms. Finally, we discuss the advantages of combining both strategies into a hybrid top-down/bottom-up (middle-out) strategy to engineer synthetic microbial communities with improved performance and scope.

Clinical outcomes in spontaneous coronary artery dissection.

OBJECTIVE: Spontaneous coronary artery dissection (SCAD) is an infrequent cause of acute coronary syndrome. Our aim was to assess adverse events at follow-up from a nationwide prospective cohort. METHODS: The Spanish Registry on SCAD (SR-SCAD) included patients from 34 hospitals. All coronary angiograms were analysed by two experts. Those cases with doubts regarding the diagnosis of SCAD were excluded. The angiographic SCAD classification by Saw et al was followed. Major adverse cardiovascular and cerebrovascular event (MACCE) was predefined as composite of death, myocardial infarction, unplanned revascularisation, SCAD recurrence or stroke. All events were assigned by a Clinical Events Committee. RESULTS: After corelab evaluation, 389 patients were included. Most patients were women (88%); median age 53 years (IQR 47-60). Most patients presented as non-ST-segment-elevation myocardial infarction (54%). A type 2 intramural haematoma (IMH) was the most frequent angiographic pattern (61%). A conservative initial management was selected in 78% of patients. At a median time of follow-up of 29 months (IQR 17-38), 46 patients (13%) presented MACCE, mainly driven by reinfarctions (7.6%) and unplanned revascularisations (6.2%). Previous history of hypothyroidism (HR 3.79; p<0.001), proximal vessel involvement (HR 2.69; p=0.009), type 2 IMH (HR 2.12; p=0.037) and dual antiplatelet therapy (DAPT) at discharge (HR 2.18; p=0.042) were independent predictors of MACCE. CONCLUSIONS: In this large prospective cohort of patients with SCAD, prognosis was overall favourable, with events mainly driven by reinfarctions or unplanned revascularisations. History of hypothyroidism, proximal vessel involvement, type 2 IMH and DAPT at discharge were associated with MACCE. TRIAL REGISTRATION NUMBER: NCT03607981.

Interrogation of Essentiality in the Reconstructed Haemophilus influenzae Metabolic Network Identifies Lipid Metabolism Antimicrobial Targets: Preclinical Evaluation of a FabH ß-Ketoacyl-ACP Synthase Inhibitor.

Expediting drug discovery to fight antibacterial resistance requires holistic approaches at system levels. In this study, we focused on the human-adapted pathogen Haemophilus influenzae, and by constructing a high-quality genome-scale metabolic model, we rationally identified new metabolic drug targets in this organism. Contextualization of available gene essentiality data within in silico predictions identified most genes involved in lipid metabolism as promising targets. We focused on the ß-ketoacyl-acyl carrier protein synthase III FabH, responsible for catalyzing the first step in the FASII fatty acid synthesis pathway and feedback inhibition. Docking studies provided a plausible three-dimensional model of FabH in complex with the synthetic inhibitor 1-(5-(2-fluoro-5-(hydroxymethyl)phenyl)pyridin-2-yl)piperidine-4-acetic acid (FabHi). Validating our in silico predictions, FabHi reduced H. influenzae viability in a dose- and strain-dependent manner, and this inhibitory effect was independent of fabH gene expression levels. fabH allelic variation was observed among H. influenzae clinical isolates. Many of these polymorphisms, relevant for stabilization of the dimeric active form of FabH and/or activity, may modulate the inhibitory effect as part of a complex multifactorial process with the overall metabolic context emerging as a key factor tuning FabHi activity. Synergies with antibiotics were not observed and bacteria were not prone to develop resistance. Inhibitor administration during H. influenzae infection on a zebrafish septicemia infection model cleared bacteria without signs of host toxicity. Overall, we highlight the potential of H. influenzae metabolism as a source of drug targets, metabolic models as target-screening tools, and FASII targeting suitability to counteract this bacterial infection. IMPORTANCE Antimicrobial resistance drives the need of synergistically combined powerful computational tools and experimental work to accelerate target identification and drug development. Here, we present a high-quality metabolic model of H. influenzae and show its usefulness both as a computational framework for large experimental data set contextualization and as a tool to discover condition-independent drug targets. We focus on ß-ketoacyl-acyl carrier protein synthase III FabH chemical inhibition by using a synthetic molecule with good synthetic and antimicrobial profiles that specifically binds to the active site. The mechanistic complexity of FabH inhibition may go beyond allelic variation, and the strain-dependent effect of the inhibitor tested supports the impact of metabolic context as a key factor driving bacterial cell behavior. Therefore, this study highlights the systematic metabolic evaluation of individual strains through computational frameworks to identify secondary metabolic hubs modulating drug response, which will facilitate establishing synergistic and/or more precise and robust antibacterial treatments.