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Pollution from plastics is a global problem that threatens the biosphere for a host of reasons, including the time scale that it takes for most plastics to degrade. Biodegradation is an ideal solution for remediating bioplastic waste as it does not require the high temperatures necessary for thermal degradation and does not introduce additional pollutants into the environment. Numerous organisms can scavenge for bioplastics, such as polylactic acid (PLA) or poly‐(R)‐hydroxybutyrate (PHB), which they can use as an energy source. Recently, a promiscuous PHBase from the thermophilic soil bacterium Lihuaxuella thermophila (LtPHBase) was identified. LtPHBase can accommodate many substrates, including PHB granules and films and PHB block copolymers, as well as the unrelated polymers polylactic acid (PLA) and polycaprolactone (PCL). LtPHBase uses the expected Ser–His–Asp catalytic triad for hydrolysis at an optimal enzyme activity near 70°C. Here, the 1.75 Å resolution crystal structure of apo LtPHBase is presented and its chemical stability is profiled. Knowledge of its substrate preferences was extended to different‐sized PHB granules. It is shown that LtPHBase is highly resistant to unfolding, with barriers typical for thermophilic enzymes, and shows a preference for low‐molecular‐mass PHB granules. These insights have implications for the long‐term potential of LtPHBase as an industrial PHB hydrolase and shed light on the evolutionary role that this enzyme plays in bacterial metabolism. [ABSTRACT FROM AUTHOR]

The rise in osteomyelitis and periprosthetic joint infections, in combination with increasing life expectancy and the prevalence of diabetes, underscores the urgent need for rapid and accurate diagnostic tools. Conventional culture‐based methods are often time‐consuming and prone to false‐negatives, leading to prolonged and inappropriate antibiotic treatments. This study aims to improve osteomyelitis diagnostics by decreasing the time to detection and the time to an antibiotic susceptibility result to enable a targeted treatment using isothermal microcalorimetry (IMC). IMC measures heat flow in real‐time, providing insights into bacterial metabolism without the need for labeling. Using clinical isolates from bone infections, assessing their response to antibiotics through IMC, we demonstrated that IMC could detect bacteria within 4 h and determine antimicrobial susceptibility profiles within 2–22 h (median 4.85, range 1.28–21.78). This is significantly faster than traditional methods. A decision tree, based on antibiotic susceptibility, accurately categorized pathogens, achieving high accuracy (74–100%), sensitivity (100%), and specificity (65–100%). These findings suggest that IMC could redefine diagnostics of bone and joint infections and potentially infections in general, offering timely and precise treatment guidance, thereby improving patient outcomes and reducing health care burdens. Further optimization and clinical validation are needed to fully integrate IMC into routine diagnostics. [ABSTRACT FROM AUTHOR]

Summary: Escherichia coli (E. coli) biofilm is the major cause of its high lethality in foodborne illness. Controlling E. coli biofilm formation is a critical way to reduce foodborne diseases. Here, chiral borneol isomers (L‐borneol, D‐borneol, and isoborneol) were identified as E. coli chemorepellents, which reduced reversible adhesion at the initial stage of biofilm formation. Borneols directly inhibited biofilm production and their inhibitory capacities were associated with the chiral stereochemical structures (L‐borneol > D‐borneol > isoborneol). A transcriptomic study revealed the inhibitory mechanism of borneols was attributed to the bacterial motility intention and motility energy system. The most effective isomer, L‐borneol, reduced bacterial energy metabolism and increased E. coli chemotaxis motility intention through the up‐regulation of genes associated with flagellar assembly and bacterial chemotaxis pathways. This work demonstrates that borneols are biofilm inhibitors and supports the potential of borneols as a stereochemical antimicrobial strategy to reduce foodborne pathogenic bacterial contamination. [ABSTRACT FROM AUTHOR]

The flexible acquisition of substrates from nutrient pools is critical for microbes to prevail in competitive environments. To acquire glucose from diverse glycoside and disaccharide substrates, many free‐living and symbiotic bacteria have developed, alongside hydrolysis, a non‐hydrolytic pathway comprised of four biochemical steps and conferred from a single glycoside utilization gene locus (GUL). Mechanistically, this pathway integrates within the framework of oxidation and reduction at the glucosyl/glucose C3, the eliminative cleavage of the glycosidic bond and the addition of water in two consecutive lyase‐catalyzed reactions. Here, based on study of enzymes from the phytopathogen Agrobacterium tumefaciens, we reveal a conserved Mn2+ metallocenter active site in both lyases and identify the structural requirements for specific catalysis to elimination of 3‐keto‐glucosides and water addition to the resulting 2‐hydroxy‐3‐keto‐glycal product, yielding 3‐keto‐glucose. Extending our search of GUL‐encoded putative lyases to the human gut commensal Bacteroides thetaiotaomicron, we discover a Ca2+ metallocenter active site in a putative glycoside hydrolase‐like protein and demonstrate its catalytic function in the eliminative cleavage of 3‐keto‐glucosides of opposite (α) anomeric configuration as preferred by the A. tumefaciens enzyme (β). Structural and biochemical comparisons reveal the molecular‐mechanistic origin of 3‐keto‐glucoside lyase stereo‐complementarity. Our findings identify a basic set of GUL‐encoded lyases for glucoside metabolism and assign physiological significance to GUL genetic diversity in the bacterial domain of life. [ABSTRACT FROM AUTHOR]

Riboswitches are structured ribonucleic acid (RNA) segments that act as specific sensors for small molecules in bacterial metabolism. Due to the flexible nature of these highly charged macromolecules, molecular dynamics simulations are instrumental to investigating the mechanistic details of their regulatory function. In the present study, the guanidine‐I riboswitch serves as an example of how atomistic simulations can shed light on the effect of ions on the structure and dynamics of RNA and on ligand binding. Relying on two orthologous crystal structures from different bacterial species, it is demonstrated how the ion setup crucially determines whether the simulation yields meaningful insights into the conformational stability of the RNA, functionally relevant residues and RNA‐ligand interactions. The ion setup in this context includes diffuse ions in solution and bound ions associated directly with the RNA, in particular a triad of 2 Mg2+ ions and a K+ ion in close proximity to the guanidinium binding site. A detailed investigation of the binding pocket reveals that the K+ from the ion triad plays a decisive role in stabilizing the ligand binding by stabilizing important localized interactions, which in turn contribute to the overall shape of the folded state of the RNA. [ABSTRACT FROM AUTHOR]

A strategy for vaccine design involves identifying proteins that could be involved in pathogen–host interactions. The aim of this proteomic study was to determine how iron limitation affects the protein expression of Tenacibaculum dicentrarchi, with a primary focus on virulence factors and proteins associated with iron uptake. The proteomic analysis was carried out using two strains of T. dicentrarchi grown under normal (control) and iron‐limited conditions, mimicking the host environment. Our findings revealed differences in the proteins expressed by the type strain CECT 7612T and the Chilean strain TdCh05 of T. dicentrarchi. Nonetheless, both share a common response to iron deprivation, with an increased expression of proteins associated with iron oxidation and reduction metabolism (e.g., SufA, YpmQ, SufD), siderophore transport (e.g., ExbD, TonB‐dependent receptor, HbpA), heme compound biosynthesis, and iron transporters under iron limitation. Proteins involved in gliding motility, such as GldL and SprE, were also upregulated in both strains. A negative differential regulation of metabolic proteins, particularly those associated with amino acid biosynthesis, was observed under iron limitation, reflecting the impact of iron availability on bacterial metabolism. Additionally, the TdCh05 strain exhibited unique proteins associated with gliding motility machinery and phage infection control compared to the type strain. These groups of proteins have been identified as virulence factors within the Flavobacteriaceae family, including the genus Tenacibaculum. These results build upon our previous report on iron acquisition mechanisms and could lay the groundwork for future studies aimed at elucidating the role of some of the described proteins in the infectious process of tenacibaculosis, as well as in the development of potential vaccines. [ABSTRACT FROM AUTHOR]

Electrochemistry with purines as indicators may be a promising new method for antibiotic activity testing. However, the traditional electrochemical detection method (S‐LSV) requires a long accumulation time for purines and has low signal intensity. High‐temperature treatment of bacterial samples may significantly enhance the signal intensity and speed of detection. However, this process may also impact the structure and metabolism of bacteria. Further research is necessary to determine how electrochemical signals respond to antibiotic antibacterial activity. In this paper, the electrochemical detection method based on heat‐treated Escherichia coli (E. coli, H‐LSV) was used to investigate the effects of 11 antibiotics with four different antibacterial mechanisms on the electrochemical behavior of E. coli. The results showed that compared to the S‐LSV, the electrochemical signal of E. coli detected by the H‐LSV increased by 362%, and showed a strong linear relationship with bacterial counts up to 1.88×108 CFU/mL, with a detection limit of 1.15×106 CFU/mL. The electrochemical signal consistently correlated with changes in viable E. coli counts following treatment with the four different antibacterial mechanisms. HPLC analysis further confirmed that the changes in purine contents in bacteria after antibiotic treatment were consistent with the trends in electrochemical signals. The evaluation of antibiotic antibacterial ability by H‐LSV showed good consistency with results from plate counting and turbidity methods, but was closer to the results of plate counting. The inhibition rates of antibiotics on E. coli detected by H‐LSV and S‐LSV also showed high consistency, indicating that short‐term high‐temperature treatment of E. coli did not affect the response of the bacterium to the inhibitory activity of antibiotics. [ABSTRACT FROM AUTHOR]

Infection is the most common complication after orthopedic surgery and can result in prolonged ailments such as chronic wounds, enlarged bone defects, and osteomyelitis. Iron, which is essential for bacterial metabolism and immune cell functions, is extremely important. Bacteria harness iron from nearby cells to promote biofilm formation, ensuring their survival. Iron deficiency within the infection microenvironment (IME) consequently hampers macrophage function, enabling further dissemination of the infection and hindering macrophage polarization to the M2 phenotype. Therefore, a novel approach is proposed to regulate macrophage polarization, aiming to restore the inflammatory immune environment. A composite hydrogel derived from natural polymers is developed to address infections and manage iron metabolism in macrophages. This IME‐responsive hydrogel, named FCL‐ECMH, is synthesized by encapsulating vermiculite functional core layers within a decellularized extracellular matrix hydrogel. It is noteworthy that FCL‐ECMH can produce reactive oxygen species within the IME. Supplementary photothermal treatment enhances bacterial iron uptake, leading to ferroptosis‐like death. This process also rejuvenates the iron‐enriched macrophages around the IME, thereby enhancing their antibacterial and tissue repair functions. In vivo experiments confirmed the antibacterial and repair‐promoting capabilities of FCL‐ECMH, indicating its potential for clinical applications. [ABSTRACT FROM AUTHOR]

Infection is among the most common factors that impede wound healing, yet standard treatments routinely fail to resolve chronic wound infections. The chronic wound environment is largely hypoxic/anoxic, and wounds are predominantly colonised by facultative and obligate anaerobic bacteria. Oxygen (O2) limitation is an underappreciated driver of microbiota composition and behaviour in chronic wounds. In this perspective article, we examine how anaerobic bacteria and their distinct physiologies support persistent, antibiotic‐recalcitrant infections. We describe the anaerobic energy metabolisms bacteria rely on for long‐term survival in the wound environment, and why many antibiotics become less effective under hypoxic conditions. We also discuss obligate anaerobes, which are among the most prevalent taxa to colonise chronic wounds, yet their potential roles in influencing the microbial community and wound healing have been overlooked. All of the most common obligate anaerobes found in chronic wounds are opportunistic pathogens. We consider how these organisms persist in the wound environment and interface with host physiology to hinder wound healing processes or promote chronic inflammation. Finally, we apply our understanding of anaerobic physiologies to evaluate current treatment practices and to propose new strategies for treating chronic wound infections. [ABSTRACT FROM AUTHOR]

Summary: Multiple sclerosis (MS) is an autoimmune disease of the central nervous system, affecting nearly 2 million people worldwide. The etiology of MS is multifactorial: Approximately 30% of the MS risk is genetic, which implies that the remaining ~70% is environmental, with a number of factors proposed. One recently implicated risk factor for MS is the composition of the gut microbiome. Numerous case–control studies have identified changes in gut microbiota composition of people with MS (pwMS) compared with healthy control individuals, and more recent studies in animal models have begun to identify the causative microbes and underlying mechanisms. Here, we review some of these mechanisms, with a specific focus on the role of host genetic variation, dietary inputs, and gut microbial metabolism, with a particular emphasis on short‐chain fatty acid and tryptophan metabolism. We put forward a model where, in an individual genetically susceptible to MS, the gut microbiota and diet can synergize as potent environmental modifiers of disease risk and possibly progression, with diet‐dependent gut microbial metabolites serving as a key mechanism. We also propose that specific microbial taxa may have divergent effects in individuals carrying distinct variants of MS risk alleles or other polymorphisms, as a consequence of host gene‐by‐gut microbiota interactions. Finally, we also propose that the effects of specific microbial taxa, especially those that exert their effects through metabolites, are highly dependent on the host dietary intake. What emerges is a complex multifaceted interaction that has been challenging to disentangle in human studies, contributing to the divergence of findings across heterogeneous cohorts with differing geography, dietary preferences, and genetics. Nonetheless, this provides a complex and individualized, yet tractable, model of how the gut microbiota regulate susceptibility to MS, and potentially progression of this disease. Thus, we conclude that prophylactic or therapeutic modulation of the gut microbiome to prevent or treat MS will require a careful and personalized consideration of host genetics, baseline gut microbiota composition, and dietary inputs. [ABSTRACT FROM AUTHOR]

Chassis strains, derived from Streptomyces coelicolor M145, deleted for one or more of its four main specialized metabolites biosynthetic pathways (CPK, CDA, RED and ACT), in various combinations, were constructed for the heterologous expression of specialized metabolites biosynthetic pathways of various types and origins. To determine consequences of these deletions on the metabolism of the deleted strains comparative lipidomic and metabolomic analyses of these strains and of the original strain were carried out. These studies unexpectedly revealed that the deletion of the peptidic clusters, RED and/or CDA, in a strain deleted for the ACT cluster, resulted into a great increase in the triacylglycerol (TAG) content, whereas the deletion of polyketide clusters, ACT and CPK had no impact on TAG content. Low or high TAG content of the deleted strains was correlated with abundance or paucity in amino acids, respectively, reflecting high or low activity of oxidative metabolism. Hypotheses based on what is known on the bio‐activity and the nature of the precursors of these specialized metabolites are proposed to explain the unexpected consequences of the deletion of these pathways on the metabolism of the bacteria and on the efficiency of the deleted strains as chassis strains. [ABSTRACT FROM AUTHOR]

Objectives: Reflecting the need for an effective support for the daily oral hygiene routine of patients experiencing (symptoms of) gum inflammation, a new mouthwash has been developed containing an amine + zinc lactate + fluoride system. The in vitro efficacy of this product was assessed using traditional laboratory methods, as well as novel experimentation. Materials and Methods: This mouthwash has been evaluated in a series of laboratory tests including two short interval kill tests (SIKTs), a 12‐h (longer term) biofilm regrowth assay, a plaque glycolysis assay, and an aerobic, repeated exposure biofilm model, as well as tests for soft tissue uptake and LPS neutralization. Results: Several laboratory studies demonstrate that a mouthwash containing an amine + zinc lactate + fluoride system provides short‐term and long‐term antibacterial activity. While the immediate efficacy of this formula has been shown to be driven by the presence of the amine, zinc lactate provides a long‐term antibacterial effect, as well as is able to inhibit bacterial metabolism. Conclusions: This research provides the basis for understanding the mode of action of this new mouthwash formulation and explains the previously observed clinical efficacy of this formula against plaque and gingivitis. [ABSTRACT FROM AUTHOR]

Biofilms, comprised of cells embedded in extracellular matrix (ECM), enable bacterial surface colonization and contribute to pathogenesis and biofouling. Yet, antibacterial surfaces are mainly evaluated for their effect on bacterial cells rather than the ECM. Here, a method is presented to separately quantify amounts and distribution of cells and ECM in Salmonella biofilms grown on electroactive poly(3,4‐ethylenedioxythiophene):polystyrenesulfonate (PEDOT:PSS). Within a custom‐designed biofilm reactor, biofilm forms on PEDOT:PSS surfaces electrically addressed with a bias potential and simultaneous recording of the resulting current. The amount and distribution of cells and ECM in biofilms are analyzed using a fluorescence‐based spectroscopic mapping technique and fluorescence confocal microscopy combined with advanced image processing. The study shows that surface charge leads to upregulated ECM production, leaving the cell counts largely unaffected. An altered texture is also observed, with biofilms forming small foci or more continuous structures. Supported by mutants lacking ECM production, ECM is identified as an important target when developing antibacterial strategies. Also, a central role for biofilm distribution is highlighted that likely influences antimicrobial susceptibility in biofilms. This work provides yet a link between conductive polymer materials and bacterial metabolism and reveals for the first time a specific effect of electrochemical addressing on bacterial ECM formation. [ABSTRACT FROM AUTHOR]

Bacterial infections pose a major concern for the medical community, especially regarding wound healing. Traditional passive antibiotic therapies can be cytotoxic and lead to bacterial resistance, posing a continuing challenge to treat. Based on precision therapy, a novel targeted‐delivery nanosystem is developed to efficiently eliminate bacteria and promote bacteria‐infected wound healing. Macrophage membranes pre‐activated by Staphylococcus aureus (MMSa) are prepared. In doing so, Toll‐like receptors (TLRs), a typical pathogen‐associated molecular pattern (PAMP), are significantly higher than normal macrophage membranes (MM0). Subsequently, MMSa are coated onto ultrasound‐triggered piezocatalytic nano‐barium titanate (BaTiO3, BTO) surfaces, and these two components are assembled to form a novel targeting delivery nanosystem, namely BTO@MMSa. The in vitro and in vivo results demonstrate that the biocompatible BTO@MMSa nanosystem can target infected areas and rapidly generate reactive oxygen species (ROS) to kill bacteria under ultrasound (US) irradiation, as well as accelerate wound healing. Furthermore, prokaryotic RNA‐seq transcriptomics reveals that changes in bacterial membrane function and substance, and energy metabolism are responsible for the targeted antibacterial ability of BTO@MMSa with US. Compared to widely reported unselective antibacterial agents, this novel targeted delivery nanosystem has potential for precise bacterial infection treatment by using macrophage membrane functions. [ABSTRACT FROM AUTHOR]

Different international agencies recognize that antibiotic resistance is one of the most severe human health problems that humankind is facing. Traditionally, the introduction of new antibiotics solved this problem but various scientific and economic reasons have led to a shortage of novel antibiotics at the pipeline. This situation makes mandatory the implementation of approaches to preserve the efficacy of current antibiotics. The concept is not novel, but the only action taken for such preservation had been the 'prudent' use of antibiotics, trying to reduce the selection pressure by reducing the amount of antibiotics. However, even if antibiotics are used only when needed, this will be insufficient because resistance is the inescapable outcome of antibiotics' use. A deeper understanding of the alterations in the bacterial physiology upon acquisition of resistance and during infection will help to design improved strategies to treat bacterial infections. In this article, we discuss the interconnection between antibiotic resistance (and antibiotic activity) and bacterial metabolism, particularly in vivo, when bacteria are causing infection. We discuss as well how understanding evolutionary trade‐offs, as collateral sensitivity, associated with the acquisition of resistance may help to define evolution‐based therapeutic strategies to fight antibiotic resistance and to preserve currently used antibiotics. [ABSTRACT FROM AUTHOR]

Iron is an essential element for microbial survival and secondary metabolism. However, excess iron availability and overloaded secondary metabolites can hinder microbial growth and survival. Microorganisms must tightly control iron homeostasis and secondary metabolism. Our previous studies have found that the stringent starvation protein A (SspA) positively regulates prodiginine biosynthesis by activating iron uptake in Pseudoalteromonas sp. strain R3. It is believed that the interaction between SspA and the small nucleotide ppGpp is important for iron to exert regulation functions. However, the roles of ppGpp in iron absorption and prodiginine biosynthesis, and the underlying relationship between ppGpp and SspA in strain R3 remain unclear. In this study, we found that ppGpp accumulation in strain R3 could be induced by limiting iron. In addition, ppGpp not only positively regulated iron uptake and prodiginine biosynthesis via increasing the SspA level but also directly repressed iron uptake and prodiginine biosynthesis independent of SspA, highlighting the finding that ppGpp can stabilize both iron levels and prodiginine production. Notably, the abolishment of ppGpp significantly increased prodiginine production, thus providing a theoretical basis for manipulating prodiginine production in the future. This dynamic ppGpp‐mediated interaction between iron uptake and prodiginine biosynthesis has significant implications for understanding the roles of nutrient uptake and secondary metabolism for the survival of bacteria in unfavorable environments. [ABSTRACT FROM AUTHOR]

The modern food industry is undergoing a rapid change with the trend of production of plant‐based food products that are more sustainable and have less impact on nature. Plant‐based dairy analogues have been increasingly popular due to their suitability for individuals with milk protein allergy or lactose intolerance and those preferring a plant‐based diet. Nevertheless, plant‐based products still have insufficient nutritional quality, undesirable structure, and earthy, green, and bean‐like flavor compared to dairy products. In addition, most plant‐based foods contain lesser amounts of essential nutrients, antinutrients limiting the bioavailability of some nutrients, and allergenic proteins. Novel processing technologies can be applied to have a homogeneous and stable structure. On the other hand, fermentation of plant‐based matrix with lactic acid bacteria can provide a solution to most of these problems. Additional nutrients can be produced and antinutrients can be degraded by bacterial metabolism, thereby increasing nutritional value. Allergenic proteins can be hydrolyzed reducing their immunoreactivity. In addition, fermentation has been found to reduce undesired flavors and to enhance various bioactivities of plant foods. However, the main challenge in the production of fermented plant‐based dairy analogues is to mimic familiar dairy‐like flavors by producing the major flavor compounds other than organic acids, yielding a flavor profile similar to those of fermented dairy products. Further studies are required for the improvement of the flavor of fermented plant‐based dairy analogues through the selection of special microbial cultures and formulations. [ABSTRACT FROM AUTHOR]

The cosmopolitan marine Roseobacter clade is of global biogeochemical importance. Members of this clade produce sulfur‐containing amino lipids (SALs) involved in biofilm formation and marine surface colonization processes. Despite their physiological relevance and abundance, SALs have only been explored through genomic mining approaches and lipidomic studies based on mass spectrometry, which left the relative and absolute structures of SALs unresolved, hindering progress in biochemical and functional investigations. Herein, we report the structural revision of a new group of SALs, which we named cysteinolides, using a combination of analytical techniques, isolation and degradation experiments and total synthetic efforts. Contrary to the previously proposed homotaurine‐based structures, cysteinolides are composed of an N,O‐acylated cysteinolic acid‐containing head group carrying various different (α‐hydroxy)carboxylic acids. We also performed the first validated targeted‐network based analysis, which allowed us to map the distribution and structural diversity of cysteinolides across bacterial lineages. Beyond offering structural insight, our research provides SAL standards and validated analytical data. This information holds significance for forthcoming investigations into bacterial sulfonolipid metabolism and biogeochemical nutrient cycling within marine environments. [ABSTRACT FROM AUTHOR]

Gut microbiota is linked to human metabolic diseases. The previous work showed that leucine deprivation improved metabolic dysfunction, but whether leucine deprivation alters certain specific species of bacterium that brings these benefits remains unclear. Here, this work finds that leucine deprivation alters gut microbiota composition, which is sufficient and necessary for the metabolic improvements induced by leucine deprivation. Among all the affected bacteria, B. coccoides is markedly increased in the feces of leucine‐deprived mice. Moreover, gavage with B. coccoides improves insulin sensitivity and reduces body fat in high‐fat diet (HFD) mice, and singly colonization of B. coccoides increases insulin sensitivity in gnotobiotic mice. The effects of B. coccoides are mediated by metabolizing tryptophan into indole‐3‐acetic acid (I3AA) that activates the aryl hydrocarbon receptor (AhR) in the liver. Finally, this work reveals that reduced fecal B. coccoides and I3AA levels are associated with the clinical metabolic syndrome. These findings suggest that B. coccoides is a newly identified bacterium increased by leucine deprivation, which improves metabolic disorders via metabolizing tryptophan into I3AA. [ABSTRACT FROM AUTHOR]

Background: The bacteriocins, particularly derived from lactic acid bacteria, currently exhibit potential as a promising food preservative owing to their low toxicity and potent antimicrobial activity. This study aimed to evaluate the efficacy of lactocin 63, produced by Lactobacillus coryniformis, in inhibiting the deterioration of Lateolabrax japonicas during chilled storage, while also investigating its underlying inhibitory mechanism. The measurement of total viable count, biogenic amines, and volatile organic compounds were conducted, along with high‐throughput sequencing and sensory evaluation. Results: The findings demonstrated that treatment with lactocin 63 resulted in a notable retardation of bacterial growth in L. japonicas fish fillet during refrigerated storage compared with the water‐treated and nisin‐treated groups. Moreover, lactocin 63 effectively maintained the microbial flora balance in the fish fillet and inhibited the proliferation and metabolic activity of specific spoilage microorganisms, particularly Shewanella, Pseudomonas, and Acinetobacter. Furthermore, the production of unacceptable volatile organic compounds (e.g. 1‐octen‐3‐ol, hexanal, nonanal), as well as the biogenic amines derived from the bacterial metabolism, could be hindered, thus preventing the degradation in the quality of fish fillets and sustaining relatively high sensory quality. Conclusion: The results of this study provide valuable theoretical support for the development and application of lactocin 63, or other bacteriocins derived from lactic acid bacteria, as potential bio‐preservatives in aquatic food. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Hematoma, a risk factor of implant‐associated infections (IAIs), creates a Fe‐rich environment following implantation, which proliferates the growth of pathogenic bacteria. Fe metabolism is a major vulnerability for pathogens and is crucial for several fundamental physiological processes. Herein, a deferiprone (DFP)‐loaded layered double hydroxide (LDH)‐based nanomedicine (DFP@Ga‐LDH) that targets the Fe‐rich environments of IAIs is reported. In response to acidic changes at the infection site, DFP@Ga‐LDH systematically interferes with bacterial Fe metabolism via the substitution of Ga3+ and Fe scavenging by DFP. DFP@Ga‐LDH effectively reverses the Fe/Ga ratio in Pseudomonas aeruginosa, causing comprehensive interference in various Fe‐associated targets, including transcription and substance metabolism. In addition to its favorable antibacterial properties, DFP@Ga‐LDH functions as a nano‐adjuvant capable of delaying the emergence of antibiotic resistance. Accordingly, DFP@Ga‐LDH is loaded with a siderophore antibiotic (cefiderocol, Cefi) to achieve the antibacterial nanodrug DFP@Ga‐LDH‐Cefi. Antimicrobial and biosafety efficacies of DFP@Ga‐LDH‐Cefi are validated using ex vivo human skin and mouse IAI models. The pivotal role of the hematoma‐created Fe‐rich environment of IAIs is highlighted, and a nanoplatform that efficiently interferes with bacterial Fe metabolism is developed. The findings of the study provide promising guidance for future research on the exploration of nano‐adjuvants as antibacterial agents. [ABSTRACT FROM AUTHOR]

Coherent anti‐Stokes Raman scattering (CARS) microscopy has demonstrated a powerful platform for label‐free, non‐invasive, and chemically specific imaging of biological samples. However, the non‐resonant background limits its ability to detect weak Raman signals. Here, an approach to eliminate the non‐resonant background in CARS using delay modulation (DM) is presented, which is enabled by an acousto‐optic modulator and spectral focusing. The results demonstrate that DM‐CARS reduces the non‐resonant background by 10 times and improves detection sensitivity by 100‐fold over normal CARS. It also shows that DM‐CARS has potential applications in tracking heavy water metabolism in bacteria for antimicrobial susceptibility testing and imaging liver tumor tissues. Furthermore, a handheld DM‐CARS device has also demonstrated for in vivo imaging, which can be beneficial in various applications. [ABSTRACT FROM AUTHOR]

The permanently anoxic waters in meromictic lakes create suitable niches for the growth of bacteria using sulphur metabolisms like sulphur oxidation. In Lake Pavin, the anoxic water mass hosts an active cryptic sulphur cycle that interacts narrowly with iron cycling, however the metabolisms of the microorganisms involved are poorly known. Here we combined metagenomics, single‐cell genomics, and pan‐genomics to further expand our understanding of the bacteria and the corresponding metabolisms involved in sulphur oxidation in this ferruginous sulphide‐ and sulphate‐poor meromictic lake. We highlighted two new species within the genus Sulfurimonas that belong to a novel clade of chemotrophic sulphur oxidisers exclusive to freshwaters. We moreover conclude that this genus holds a key‐role not only in limiting sulphide accumulation in the upper part of the anoxic layer but also constraining carbon, phosphate and iron cycling. [ABSTRACT FROM AUTHOR]

Paenibacillus polymyxa is a non‐pathogenic, Gram‐positive bacterium endowed with a rich and versatile metabolism. However interesting, this bacterium has been seldom used for bioproduction thus far. In this study, we engineered P. polymyxa for isobutanol production, a relevant bulk chemical and next‐generation biofuel. A CRISPR‐Cas9‐based genome editing tool facilitated the chromosomal integration of a synthetic operon to establish isobutanol production. The 2,3‐butanediol biosynthesis pathway, leading to the main fermentation product of P. polymyxa, was eliminated. A mutant strain harbouring the synthetic isobutanol operon (kdcA from Lactococcus lactis, and the native ilvC, ilvD and adh genes) produced 1 g L−1 isobutanol under microaerobic conditions. Improving NADPH regeneration by overexpression of the malic enzyme subsequently increased the product titre by 50%. Network‐wide proteomics provided insights into responses of P. polymyxa to isobutanol and revealed a significant metabolic shift caused by alcohol production. Glucose‐6‐phosphate 1‐dehydrogenase, the key enzyme in the pentose phosphate pathway, was identified as a bottleneck that hindered efficient NADPH regeneration through this pathway. Furthermore, we conducted culture optimization towards cultivating P. polymyxa in a synthetic minimal medium. We identified biotin (B7), pantothenate (B5) and folate (B9) to be mutual essential vitamins for P. polymyxa. Our rational metabolic engineering of P. polymyxa for the production of a heterologous chemical sheds light on the metabolism of this bacterium towards further biotechnological exploitation. [ABSTRACT FROM AUTHOR]

Robust bacterial metabolism and the immunosuppression on peripheral immune cells cause biofilm‐associated infections (BAIs) extremely refractory to be eradicated via antibiotics alone. Herein, hierarchical mesoporous UiO‐66 metal–organic framework is decorated with selenite, polypyrrole, and macrophage membrane (MM) to develop a biomimetic nanosphere (USPM). Following the recruitment of USPM to the biofilm microenvironment (BME) via the pathogen‐targeting ability derived from MM. The BME‐responsive USPM can precisely release selenite to penetrate the loosened biofilm in synergy with near‐infrared‐induced mild photothermal therapy (mPTT). Selenite can quickly react with reducing substances to generate hydrogen selenide (H2Se) inside the biofilm. H2Se can competitively inhibit bacterial metabolic processes and disrupt biofilm metabolic homeostasis by cascade amplification effects. Furthermore, H2Se inside the biofilm further sensitizes photothermia to exert a precise local photothermal effect. Outside the biofilm, USPM can simultaneously promote the phagocytosis and autophagy of macrophages to kill and decompose the phagocytosed bacteria. Finally, the well‐decomposed bacterial antigens in macrophages can be presented to antigen‐presenting cells to arouse adaptive immune responses and enhance anti‐biofilm effectiveness further. Such powerful mPTT‐enhanced bacterial metabolic disruption and macrophagic autophagy‐promoted adaptive immune activation suggest an alternative therapeutic strategy to cure refractory BAIs. [ABSTRACT FROM AUTHOR]

Green manufacture of steroid precursors from diosgenin by microbial replacing multistep chemical synthesis has been elusive. It is currently limited by the lack of strain and degradation mechanisms. Here, we demonstrated the feasibility of this process using a novel strain Mycolicibacterium sp. HK‐90 with efficiency in diosgenin degradation. Diosgenin degradation by strain HK‐90 involves the selective removal of 5,6‐spiroketal structure, followed by the oxygenolytic cleavage of steroid nuclei. Bioinformatic analyses revealed the presence of two complete steroid catabolic gene clusters, SCG‐1 and SCG‐2, in the genome of strain HK‐90. SCG‐1 cluster was found to be involved in classic phytosterols or cholesterol catabolic pathway through the deletion of key kstD1 gene, which promoted the mutant m‐∆kstD1 converting phytosterols to intermediate 9α‐hydroxyandrostenedione (9‐OHAD). Most impressively, global transcriptomics and characterization of key genes suggested SCG‐2 as a potential gene cluster encoding diosgenin degradation. The gene inactivation of kstD2 in SCG‐2 resulted in the conversion of diosgenin to 9‐OHAD and 9,16‐dihydroxy‐pregn‐4‐ene‐3,20‐dione (9,16‐(OH)2‐PG) in mutant m‐ΔkstD2. Moreover, the engineered strain mHust‐ΔkstD1,2,3 with a triple deletion of kstDs was constructed, which can stably accumulate 9‐OHAD by metabolizing phytosterols, and accumulate 9‐OHAD and 9,16‐(OH)2‐PG from diosgenin. Diosgenin catabolism in strain mHust‐ΔkstD1,2,3 was revealed as a progression through diosgenone, 9,16‐(OH)2‐PG, and 9‐OHAD to 9α‐hydroxytestosterone (9‐OHTS). So far, this work is the first report on genetically engineered strain metabolizing diosgenin to produce 21‐carbon and 19‐carbon steroids. This study presents a promising biosynthetic platform for the green production of steroid precursors, and provide insights into the complex biochemical mechanism of diosgenin catabolism. [ABSTRACT FROM AUTHOR]

Viruses exist anywhere on earth where there is life, and among them, virus‐encoded auxiliary metabolic genes (AMGs) can maintain ecosystem balance and play a major role in the global ecosystem. Although the function of AMGs has been widely reported, the genetic diversity of AMGs in natural ecosystems is still poorly understood. Exploring the genetic diversity of viral community‐wide AMGs is essential to gain insight into the complex interactions between viruses and hosts. In this article, we studied the phylogenetic tree, principal co‐ordinates analysis (PCoA), α diversity, and metabolic pathways of viral auxiliary metabolism genes involved in the pentose phosphate pathway (PPP) through metagenomics, and the changes of metabolites and genes of host bacteria were further studied by using Pseudomonas mandelii SW‐3 and its lytic phage based on metabolic flow and AMGs expression. We found that the viral AMGs in the Napahai plateau wetland were created by a combination of various external forces, which contributed to the rich genetic diversity, uniqueness, and differences of the virus, which promoted the reproduction of offspring and better adaptation to the environment. Overall, this study systematically describes the genetic diversity of AMGs associated with the PPP in plateau wetland ecosystems and further expands the understanding of phage–host unique interactions. [ABSTRACT FROM AUTHOR]

We investigated seasonal net community production (NCP) variations in the productive Amundsen Sea Polynya, integrating observational data and ecosystem modeling. NCP estimates (NCPO2/Ar) from in situ O2/Ar data during the austral summer (January‐March) from 2011 to 2018 were compared with those from a one‐dimensional ecosystem model. Early January saw the highest NCPO2/Ar values ranging from 115 to 139 mmol O2 m−2 d−1 among observations. Over the summer, NCPO2/Ar gradually decreased, reaching 40 mmol O2 m−2 d−1 by late February. Late summer values, though one‐third of early January, remained notably positive, indicating net autotrophy. This persisted despite sea surface temperature dropping from >−0.4°C in January to −1.33°C in late February. Refining NCPO2/Ar, we modified bacterial dynamics in our ecosystem model. Significantly improved model performance resulted from two key modifications. First, we introduced bacterial uptake dependency on Phaeocystis primary production. Second, we heightened temperature‐dependent bacterial respiration and production approximately fifteenfold. These changes revealed NCP's remarkable sensitivity to minor temperature fluctuations (<1°C). Furthermore, modified bacterial dynamics delayed the net primary production peak by 2 weeks, underlining the importance of phytoplankton‐bacteria interaction in the ocean carbon cycle. Model results estimated annual NCP in the Amundsen Sea Polynya at 4.04 mol C m−2, aligning with summer NCP estimates (0.2–5.9 mol C m−2) in observational study. Our study advances NCP understanding in polar regions, emphasizing comprehensive observations, including bacterial processes, for understanding intricate biotic interactions. These findings align with past observations on bacterial metabolism and Phaeocystis ecological properties in the Antarctic oceans. Plain Language Summary: Our study delved into the seasonal changes in productivity in the Amundsen Sea Polynya, a bustling region near Antarctica. We combined real‐world observations with computer modeling to unravel these patterns. In early January, this area was super productive, generating lots of oxygen. As summer progressed, productivity slowly declined, but it remained positive even in late summer, despite a significant drop in ocean temperature. This suggested that the ecosystem continued to thrive. To refine our model, we adjusted how bacteria interacted in the ecosystem. The results were fascinating. When we made bacteria more reliant on a specific algae, Phaeocystis, and more sensitive to temperature, our model better matched real‐world conditions. This revealed that even minor water temperature changes, less than 1°C, could significantly impact this ecosystem. Furthermore, altering bacterial dynamics led to a 2‐week delay in the peak period of ocean plant growth, highlighting the crucial role of the interaction between tiny plants called phytoplankton and bacteria in the ocean's carbon cycle. Our study provides valuable insights into polar regions, emphasizing the need for comprehensive observations that include bacterial activities. Understanding these intricate interactions is vital for grasping the bigger picture of life in these remote and extreme environments. Key Points: Net community production in the Amundsen Sea Polynya was investigated by integrating observational data with ecosystem modelingPhaeocystis‐driven nutrient remineralization by bacteria stimulates phytoplankton growthBacterial respiration peaks within specific temperature range, affecting carbon cycling in Antarctic polynyas [ABSTRACT FROM AUTHOR]

Rhizopus microsporus often lives in association with bacterial and viral symbionts that alter its biology. This fungal model represents an example of the complex interactions established among diverse organisms in functional holobionts. We constructed a Genome‐Scale Model (GSM) of the fungal‐bacterial‐viral holobiont (iHol). We employed a constraint‐based method to calculate the metabolic fluxes to decipher the metabolic interactions of the symbionts with their host. Our computational analyses of iHol simulate the holobiont's growth and the production of the toxin rhizoxin. Analyses of the calculated fluxes between R. microsporus in symbiotic (iHol) versus asymbiotic conditions suggest that changes in the lipid and nucleotide metabolism of the host are necessary for the functionality of the holobiont. Glycerol plays a pivotal role in the fungal‐bacterial metabolic interaction, as its production does not compromise fungal growth, and Mycetohabitans bacteria can efficiently consume it. Narnavirus RmNV‐20S and RmNV‐23S affected the nucleotide metabolism without impacting the fungal‐bacterial symbiosis. Our analyses highlighted the metabolic stability of Mycetohabitans throughout its co‐evolution with the fungal host. We also predicted changes in reactions of the bacterial metabolism required for the active production of rhizoxin. This iHol is the first GSM of a fungal holobiont. [ABSTRACT FROM AUTHOR]

The human gut is an anoxic environment that harbours a multitude of microorganisms that not only contribute to food digestion. The microbiome is also involved in malfunctions such as diseases, inflammation processes or development of obesity, but it is also involved in processes that increase the human well‐being. Both, the good and the bad, are mediated by fermentation end products of bacterial metabolism, among others. However, despite a steadily growing knowledge of 'who lives out there', little in known of 'what do they do out there'. The genus Blautia is commonly found in the gut and associated with human well‐being, but the exploration of their metabolic potential has just started. We demonstrate that B. schinkii grows on glycerol by producing acetate and ethanol. Transcriptome studies and biochemical analyses revealed a glycerol dehydrogenase and dihydroxyacetone kinase that funnel the substrate into glycolysis. Consequently, cells also grew on dihydroxyacetone. Cells could be adapted to grow at high (up to 1.5 M) glycerol concentrations but then only ethanol was formed. Ethanol production from glycerol is not only of relevance for the human host but also for potential bioindustrial production of bioethanol from waste glycerol. [ABSTRACT FROM AUTHOR]

With the emerging problem of antimicrobial resistance, the world is facing a slow but dangerous pandemic. While the discovery of novel antibiotics is reaching a nearly exhaustive end, new concepts for anti‐infective drugs are emerging. So‐called pathoblockers aim to de‐weaponize bacteria rather than just killing them. As the target of these molecules is typically located intracellularly, however, hitherto almost unnoticed biological barriers are emerging such as the biofilm matrix, the bacterial cell envelope, efflux pumps, and eventual bacterial metabolism. This leads to a new paradigm that is to maximize bacterial bioavailability. To overcome the bacterial barriers, especially when further optimization of the active molecules is not possible, functional materials are needed to engineer innovative delivery systems. Those may not only enable novel anti‐infective molecules to reach their targets, but will also improve the bacterial bioavailability of existing anti‐infectives. Additionally, there is a need for better infection models that allow studying drug effects on both the bacteria and the host in a relevant manner as needed for rational anti‐infective drug development. [ABSTRACT FROM AUTHOR]

This study aimed to investigate the role of the gut microbiota (GM)–bile acid (BA)–fibroblast growth factor (FGF) 19 axis in patients with atrial fibrillation (AF). Gut bacterial metabolisms of BAs were determined in an AF metagenomic dataset. The composition of faecal BAs pools was characterized by targeted metabolomics in an independent AF cross‐sectional cohort. Circulating levels of FGF19 were measured by ELISA. In vitro cell experiments were conducted to validate the regulatory role of FGF19 in atrial cardiomyocytes stimulated with palmitic acid. First, metagenomic profiling revealed that gut microbial biotransformation from primary to secondary BAs was dysregulated in AF patients. Second, the proportion of secondary BAs decreased in the faeces of patients with AF. Also, eight BAs were identified as AF‐associated BAs, including seven AF‐enriched BAs (ursodeoxycholic acid, chenodeoxycholic acid, etc.), and AF‐decreased dehydrolithocholic acid. Third, reduced levels of circulating FGF19 were observed in patients with AF. Subsequently, FGF19 was found to protect against palmitic acid‐induced lipid accumulation and dysregulated signalling in atrial cardiomyocytes, including attenuated phosphorylation of YAP and Ca2+/calmodulin‐dependent protein kinases II and secretion of interleukin‐1β, mediated via peroxisome proliferator‐activated receptor α. Our data found decreased levels of secondary BAs and circulating FGF19, resulting in the impaired protective function of FGF19 against lipid accumulation in atrial cardiomyocytes. [ABSTRACT FROM AUTHOR]

Objective: To characterize the bacterial community from different oral niches (buccal mucosa and saliva) in oral lichen planus (OLP) patients. Subjects and Methods: This preliminary study analyzed site‐specific (mucosa and saliva) microbial landscape of 20 OLP patients and 10 healthy controls. Results: The microbial diversity was similar between OLP patients and healthy controls in both salivary and mucosal communities. However, the topological properties of co‐occurrence networks of salivary and mucosal microbiome were different between healthy controls and OLP patients. SparCC analysis inferred three and five keystone taxa in the salivary and mucosal microbial networks of healthy controls, respectively. However, in the salivary and mucosal bacterial networks of OLP patients, only one hub OTU and three OTUs were identified as keystone taxa, respectively. In addition, analysis of community cohesion revealed that mucosal microbial community in OLP patients had lower stability than that in healthy controls. In final, correlation assay showed that the clinical severity of OLP was positively associated with the relative abundance of Rothia in saliva but negatively associated with that of Porphyromonas on mucosa. Conclusions: The salivary and mucosal bacterial communities of OLP patients differ in terms of composition, the genera associated with OLP severity, and co‐occurrence patterns. [ABSTRACT FROM AUTHOR]

Drug resistance to antibacterial and anticancer drugs is one of the most important global problems in the treatment field that is constantly expanding and hinders the recovery and survival of patients. Therefore, it is necessary to identify compounds that have antibacterial and anticancer properties or increase the effectiveness of existing drugs. One of these approaches is using natural compounds that have few side effects and are effective. Gallic acid (GA) has been identified as one of the most important plant polyphenols that health‐promoting effects in various aspects such as bacterial and viral infections, cancer, inflammatory, neuropsychological, gastrointestinal, and metabolic disease. Various studies have shown that GA inhibits bacterial growth by altering membrane structure, and bacterial metabolism, and inhibits biofilm formation. Also, GA inhibits cancer cell growth by targeting different signaling pathways in apoptosis, increasing reactive oxygen species (ROS) production, targeting the cell cycle, and inhibiting oncogenes and matrix metalloproteinases (MMPs) expression. Due to the powerful function of GA against bacteria and cancer cells. In this review, we describe the latest findings in the field of the sources and chemical properties of GA, its pharmacological properties and bioavailability, the antibacterial and anticancer activities of GA, and its derivatives alone, in combination with other drugs and in the form of nanoformulation. This review can be a comprehensive perspective for scientists to use medicinal compounds containing GA in future research and expand its clinical applications. [ABSTRACT FROM AUTHOR]

Aquatic microbial responses to changes in the amount and composition of dissolved organic carbon (DOC) are of fundamental ecological and biogeochemical importance. Parallel factor (PARAFAC) analysis of excitation–emission fluorescence spectra is a common tool to characterize DOC, yet its ability to predict bacterial production (BP), bacterial respiration (BR), and bacterial growth efficiency (BGE) vary widely, potentially because inorganic nutrient limitation decouples microbial processes from their dependence on DOC composition. We used 28‐d bioassays with water from 19 lakes, streams, and rivers in northern Sweden to test how much the links between bacterial metabolism and fluorescence PARAFAC components depend on experimental additions of inorganic nutrients. We found a significant interaction effect between nutrient addition and fluorescence on carbon‐specific BP, and weak evidence for influence on BGE by the same interaction (p = 0.1), but no corresponding interaction effect on BR. A practical implication of this interaction was that fluorescence components could explain more than twice as much of the variability in carbon‐specific BP (R2 = 0.90) and BGE (R2 = 0.70) after nitrogen and phosphorus addition, compared with control incubations. Our results suggest that an increased supply of labile DOC relative to ambient phosphorus and nitrogen induces gradually larger degrees of nutrient limitation of BP, which in turn decouple BP and BGE from fluorescence signals. Thus, while fluorescence does contain precise information about the degree to which DOC can support microbial processes, this information may be hidden in field studies due to nutrient limitation of bacterial metabolism. [ABSTRACT FROM AUTHOR]

Heterotrophic bacteria play a vital role in the marine carbon cycle and viruses are an important regulator of bacterial metabolism and community composition. It remains unclear about how bacteria‐virus interactions vary with environmental conditions in oceans. In this study, bacterial metabolic activity and community composition were examined in three treatments with different viral pressure (control, virus‐rich and virus‐reduced) through bioassay experiments at three stations with different environmental conditions in the shelf of the northern South China Sea. Our results showed that bacteria‐virus interactions varied with environmental conditions. Viral lysis mediated bacterial growth rate (BGR) and production by shaping bacterial community composition. Furthermore, the effect of viral lysis on bacterial growth rate and production was reduced in substrate‐rich waters compared to substrate‐low waters. However, the opposite pattern occurred for viral regulation on bacterial respiration and carbon demand, likely since viral lysis dramatically mitigated the maintenance respiration of bacteria. Consequently, viral lysis to greater extent mitigated bacterial carbon processing in substrate‐rich environments than in substrate‐low environments. Our findings provided new insights into bacteria‐virus interactions, and improved our understanding of the role microbial processes in carbon cycling in oceans. Plain Language Summary: Heterotrophic bacteria play important roles in marine biogeochemical cycle and their viruses manipulate these processes. We found that viral regulation of bacterial metabolism varied with environmental conditions and the two aspects of bacterial metabolism responded differently to viral lysis. The reductions of bacterial growth rate and production caused by viral lysis increased from nearshore to offshore seawaters, while viral regulations on bacterial respiration and carbon demand showed the opposite pattern. The reasons for differences in the regulation of bacterial metabolism by virus varied with environmental conditions may be that high substrate supply in nearshore waters improved antiviral defense and dramatically mitigated the maintenance respiration of bacteria. In general, viral lysis to greater extent mitigated bacterial carbon processing in substrate‐rich environments than in substrate‐low environments. Our study provided new insights into the interactions of bacterial metabolism with viruses, and improved our understanding of marine carbon cycle in contrasting trophic environments. Key Points: Viral lysis reduced bacterial growth rate and production less in the substrate‐rich waters than oligotrophic watersVirus‐induced losses in bacterial respiration and carbon demand decreased offshoreViral lysis mitigated bacterial carbon processing more in substrate‐rich environments than in oligotrophic environments [ABSTRACT FROM AUTHOR]

Certain f‐block elements—the lanthanides—have biological relevance in the context of methylotrophic bacteria. The respective strains incorporate these 4 f elements into the active site of one of their key metabolic enzymes, a lanthanide‐dependent methanol dehydrogenase. In this study, we investigated whether actinides, the radioactive 5 f elements, can replace the essential 4 f elements in lanthanide‐dependent bacterial metabolism. Growth studies with Methylacidiphilum fumariolicum SolV and the Methylobacterium extorquens AM1 ΔmxaF mutant demonstrate that americium and curium support growth in the absence of lanthanides. Moreover, strain SolV favors these actinides over late lanthanides when presented with a mixture of equal amounts of lanthanides together with americium and curium. Our combined in vivo and in vitro results establish that methylotrophic bacteria can utilize actinides instead of lanthanides to sustain their one‐carbon metabolism if they possess the correct size and a +III oxidation state. [ABSTRACT FROM AUTHOR]

Lipid droplets (LDs) are dynamic and versatile organelles present in most eukaryotic cells. LDs consist of a hydrophobic core of neutral lipids, a phospholipid monolayer coat, and a variety of associated proteins. LDs are formed at the endoplasmic reticulum and have diverse roles in lipid storage, energy metabolism, membrane trafficking, and cellular signaling. In addition to their physiological cellular functions, LDs have been implicated in the pathogenesis of several diseases, including metabolic disorders, cancer, and infections. A number of intracellular bacterial pathogens modulate and/or interact with LDs during host cell infection. Members of the genera Mycobacterium, Legionella, Coxiella, Chlamydia, and Salmonella exploit LDs as a source of intracellular nutrients and membrane components to establish their distinct intracellular replicative niches. In this review, we focus on the biogenesis, interactions, and functions of LDs, as well as on their role in lipid metabolism of intracellular bacterial pathogens. [ABSTRACT FROM AUTHOR]

In food manufacturing and processing, food matrix complexity usually makes it difficult to detect unwanted subprocesses, which can impact the quality of the final product. In the case of wine alcoholic fermentation, the main process is the conversion of sugars into ethanol and carbon dioxide, but the presence of some unwanted microorganisms could lead to wine contamination by production of undesired minor compounds. In the study we present, an intentional contamination of the vinification process by the addition of acetic acid bacteria was studied using a portable Fourier transform infrared (FT‐IR) spectrometer. ANOVA simultaneous component analysis (ASCA) was used to unravel these minor variability sources. However, as the subprocess is two orders of magnitude lower in concentration than the main process, different methodologies were used to enhance the ASCA results, such as to select a specific spectral region related to acetic acid bacteria metabolism, to divide the process in time intervals related to the different phases, or to unfold the data matrix in different ways. In addition, spectral preprocessing was optimized to scale up small peaks related to the subprocess. Our results show that several methodologies to build ASCA models can be applied to emphasize and better characterize bacteria contamination subprocesses. Sugar to ethanol reaction in wine alcoholic fermentation hinders other undesired compound spectroscopic detection.Acetic acid bacteria contamination was studied by coupling a portable Fourier transform infrared spectrometer and ANOVA simultaneous component analysis.Selection of a specific spectral region, division of the process in time intervals, and different unfolding of the data matrix were applied to emphasize bacteria contamination. [ABSTRACT FROM AUTHOR]

Multidrug efflux pumps are among the main Pseudomonas aeruginosa antibiotic‐resistance determinants. Besides, efflux pumps are also involved in other relevant activities of bacterial physiology, including the quorum sensing‐mediated regulation of bacterial virulence. Nevertheless, despite the relevance of efflux pumps in bacterial physiology, their interconnection with bacterial metabolism remains obscure. The effect of several metabolites on the expression of P. aeruginosa efflux pumps, and on the virulence and antibiotic resistance of this bacterium, was studied. Phenylethylamine was found to be both inducer and substrate of MexCD‐OprJ, an efflux pump involved in P. aeruginosa antibiotic resistance and in extrusion of precursors of quorum‐sensing signals. Phenylethylamine did not increase antibiotic resistance; however, the production of the toxin pyocyanin, the tissue‐damaging protease LasB and swarming motility were reduced in the presence of this metabolite. This decrease in virulence potential was mediated by a reduction of lasI and pqsABCDE expression, which encode the proteins that synthesise the signalling molecules of two quorum‐sensing regulatory pathways. This work sheds light on the interconnection between virulence and antibiotic‐resistance determinants, mediated by bacterial metabolism, and points to phenylethylamine as an anti‐virulence metabolite to be considered in the study of therapies against P. aeruginosa infections. [ABSTRACT FROM AUTHOR]

The ability of a bacterium to successfully colonize its host is dependent on proper adaptation to its local environment. Environmental cues are diverse in nature, ranging from ions to bacterial‐produced signals, and to host immune responses that can also be exploited by the bacteria as cues. Simultaneously, bacterial metabolism must be matched to the carbon and nitrogen sources available at a given time and location. While initial characterization of a bacterium's response to a given environmental cue or its ability to utilize a particular carbon/nitrogen source requires study of the signal in question in isolation, actual infection poses a situation where multiple signals are present concurrently. This perspective focuses on the untapped potential in uncovering and understanding how bacteria integrate their response to multiple concurrent environmental cues, and in elucidating the possible intrinsic coordination of bacterial environmental response with its metabolism. [ABSTRACT FROM AUTHOR]

The soil bacterium Pseudomonas putida KT2440 has been shown to produce selenium nanoparticles aerobically from selenite; however, the molecular actors involved in this process are unknown. Here, through a combination of genetic and analytical techniques, we report the first insights into selenite metabolism in this bacterium. Our results suggest that the reduction of selenite occurs through an interconnected metabolic network involving central metabolic reactions, sulphur metabolism, and the response to oxidative stress. Genes such as sucA, D2HGDH and PP_3148 revealed that the 2‐ketoglutarate and glutamate metabolism is important to convert selenite into selenium. On the other hand, mutations affecting the activity of the sulphite reductase decreased the bacteria's ability to transform selenite. Other genes related to sulphur metabolism (ssuEF, sfnCE, sqrR, sqr and pdo2) and stress response (gqr, lsfA, ahpCF and sadI) were also identified as involved in selenite transformation. Interestingly, suppression of genes sqrR, sqr and pdo2 resulted in the production of selenium nanoparticles at a higher rate than the wild‐type strain, which is of biotechnological interest. The data provided in this study brings us closer to understanding the metabolism of selenium in bacteria and offers new targets for the development of biotechnological tools for the production of selenium nanoparticles. [ABSTRACT FROM AUTHOR]

Osteomyelitis is a destructive disease of bone tissue caused by infection with pathogenic microorganisms. Because of the complex and long‐term abnormal conditions, osteomyelitis is one of the refractory diseases in orthopedics. Currently, anti‐infective therapy is the primary modality for osteomyelitis therapy in addition to thorough surgical debridement. However, bacterial resistance has gradually reduced the benefits of traditional antibiotics, and the development of advanced antibacterial agents has received growing attention. This review introduces the main targets of antibacterial agents for treating osteomyelitis, including bacterial cell wall, cell membrane, intracellular macromolecules, and bacterial energy metabolism, focuses on their mechanisms, and predicts prospects for clinical applications. [ABSTRACT FROM AUTHOR]

Isoprene (2‐methyl‐1,3‐butadiene) is emitted to the atmosphere each year in sufficient quantities to rival methane (>500 Tg C yr−1), primarily due to emission by trees and other plants. Chemical reactions of isoprene with other atmospheric compounds, such as hydroxyl radicals and inorganic nitrogen species (NOx), have implications for global warming and local air quality, respectively. For many years, it has been estimated that soil‐dwelling bacteria consume a significant amount of isoprene (~20 Tg C yr−1), but the mechanisms underlying the biological sink for isoprene have been poorly understood. Studies have indicated or confirmed the ability of diverse bacterial genera to degrade isoprene, whether by the canonical iso‐type isoprene degradation pathway or through other less well‐characterized mechanisms. Here, we review current knowledge of isoprene metabolism and highlight key areas for further research. In particular, examples of isoprene‐degraders that do not utilize the isoprene monooxygenase have been identified in recent years. This has fascinating implications both for the mechanism of isoprene uptake by bacteria, and also for the ecology of isoprene‐degraders in the environments. [ABSTRACT FROM AUTHOR]

Bacterial viruses are the most abundant biological entities in soil ecosystems. Owing to the advent of metagenomics and viromics approaches, an ever‐increasing diversity of virus‐encoded auxiliary metabolic genes (AMGs) have been identified in soils, including those involved in the transformation of carbon, phosphorus, and sulfur, degradation of organic pollutants, and antibiotic resistance, among other processes. These viral AMGs can alter soil biogeochemical processes and metabolic activities by interfering with bacterial host metabolism. It is recognized that viral AMGs compensate for host bacterial metabolism outputs by encoding accessory functional genes and are favourable for the hosts' adaptation to stressed soil environments. The eco‐evolutionary mechanisms behind this fascinating diversity of viral AMGs in soil microbiomes have begun to emerge, such as horizontal gene transfer, lytic‐lysogenic conversion, and single‐nucleotide polymorphisms. In this mini‐review, we summarize recent advances in the diversity and function of virus‐encoded AMGs in the soil environment, especially focusing on the evolutionary significance of AMGs involved in virus‐host interactions. This mini‐review also sheds light on the existing gaps and future perspectives that could have major significance for viral AMGs research in soils. [ABSTRACT FROM AUTHOR]

Although bulk bacterial metabolism in response to temperature has been determined for different oceanic regions, the impact of temperature on the functional diversity of dissolved organic matter (DOM) utilization has been largely unexplored. Here, we hypothesized that besides modifying the rates of carbon utilization, temperature can also alter the diversity of substrates utilized. The patterns of utilization of 31 model DOM compounds (as represented in Biolog EcoPlate™) by bacterioplankton were assessed using inocula from surface waters of the southern Bay of Biscay continental shelf over 1 year. Bacteria utilized more polymers and carbohydrates in late spring and summer than in winter, likely reflecting changes in substrate availability linked to the release and accumulation of DOM in phytoplankton post‐bloom conditions. Seawater temperature correlated positively with the number of substrates utilized (i.e. functional richness) and this relationship was maintained in monthly experimental incubations spanning 3°C below and above in situ values. The enhancement of functional richness with experimental warming displayed a unimodal response to ambient temperature, peaking at 16°C. This temperature acted as a threshold separating nutrient‐sufficient from nutrient‐deficient conditions at the study site, suggesting that trophic conditions will be critical in the response of microbial DOM utilization to future warming. [ABSTRACT FROM AUTHOR]

Soluble fragments of peptidoglycan called muropeptides are released from the cell wall of bacteria as part of their metabolism or as a result of biological stresses. These compounds trigger immune responses in mammals and plants. In bacteria, they play a major role in the induction of antibiotic resistance. The development of efficient methods to produce muropeptides is, therefore, desirable both to address their mechanism of action and to design new antibacterial and immunostimulant agents. Herein, we engineered the peptidoglycan recycling pathway of Escherichia coli to produce N‐acetyl‐β‐D‐glucosaminyl‐(1→4)‐1,6‐anhydro‐N‐acetyl‐β‐D‐muramic acid (GlcNAc‐anhMurNAc), a common precursor of Gram‐negative and Gram‐positive muropeptides. Inactivation of the hexosaminidase nagZ gene allowed the efficient production of this key disaccharide, providing access to Gram‐positive muropeptides through subsequent chemical peptide conjugation. E. coli strains deficient in both NagZ hexosaminidase and amidase activities further enabled the in vivo production of Gram‐negative muropeptides containing meso‐diaminopimelic acid, a rarely available amino acid. [ABSTRACT FROM AUTHOR]

22 Moreno, R., Fonseca, P. & Rojo, F. (2010) The Crc global regulator inhibits the Pseudomonas putida pWW0 toluene/xylene assimilation pathway by repressing the translation of regulatory and structural genes. Many bacterial species have biotechnological applications, for example in the production of compounds of interest by fermentation or biotransformation, the handling of waste and the decontamination of polluted sites. For example, when different types of carbon sources are present, and in varying abundance, regulatory responses may prioritize one compound over the rest, resulting in a distribution of metabolite fluxes that may - or may not - be compatible with the microorganism's biotechnological use. [Extracted from the article]

Lactic acid bacteria (LAB) play pivotal roles in the preservation and fermentation of forage crops in spontaneous or inoculated silages. Highlights of silage LAB over the past decades include the discovery of the roles of LAB in silage bacterial communities and metabolism and the exploration of functional properties. The present article reviews published literature on the effects of LAB on the succession, structure, and functions of silage microbial communities involved in fermentation. Furthermore, the utility of functional LAB in silage preparation including feruloyl esterase‐producing LAB, antimicrobial LAB, lactic acid bacteria with high antioxidant potential, pesticide‐degrading LAB, lactic acid bacteria producing 1,2‐propanediol, and low‐temperature‐tolerant LAB have been described. Compared with conventional LAB, functional LAB produce different effects; specifically, they positively affect animal performance, health, and product quality, among others. In addition, the metabolic profiles of ensiled forages show that plentiful probiotic metabolites with but not limited to antimicrobial, antioxidant, aromatic, and anti‐inflammatory properties are observed in silage. Collectively, the current knowledge on the roles of LAB in crop silage indicates there are great opportunities to develop silage not only as a fermented feed but also as a vehicle of delivery of probiotic substances for animal health and welfare in the future. [ABSTRACT FROM AUTHOR]

Microbially induced calcium carbonate precipitation (MICP) is a promising method for eco-friendly solutions in geotechincal engineering. MICP involves highly coupled processes in geochemistry and bacterial metabolism that take place in a porous medium. Advancement of these processes drives calcite crystal growth which leads to a decrease in porosity and permeability of the medium. Mathematical models are being developed and used to predict the fate of system at different conditions. Micro-scale and local bio-geochemical evolution and its role on the overall macroscopic fate of MICP needs further investigation. In this work, a pore-scale reactive transport model of MICP for biocementation is developed in a closed system. MICP is simulated in a sample porous geometry in 2D using a native geochemical solver and a lattice Boltzmann solver that handles diffusive transport. We present reactive-transport factors to up-scale pore-scale effects and quantify the efficiency of MICP at different stages of the process. Our results show that pore-scale effects on the average concentration of urea and calcium are not significant after the initial 20% of urea have been consumed. On the other hand, the pH evolution in the system is significantly affected by pore-scale effects. We also explored effects of biomass density and biomass distribution on the reactive transport factors, as well as the effect of the urea to calcium ratio on the resulting crystallization patterns. We found that a higher ratio of rate of ureolysis to rate of precipitation leads to more nucleation sites and more uniform calcite precipitation in the geometry. [ABSTRACT FROM AUTHOR]