Nanotherapies based on bacterial metabolism: Mechanisms, design and application

Abstract

Bacterial metabolism provides the essential materials and energy for growth and reproduction. Through complex transformations and electron transfer, bacteria convert external nutrients into useable forms and achieve pathogenicity in the human body. In recent years, with the global spread of antibiotic resistance, traditional antibiotic treatments have become increasingly ineffective and may even exacerbate the imbalance of the human microbiota. As a novel type of antibacterial agent, nanomaterials possess superior characteristics when compared with traditional antibiotics. The most significant feature is their capacity to target multiple stages of bacterial metabolism, which endows them with substantial potential in the realm of antibacterial therapy. In the early stages of nutrient entry into bacterial metabolism, nanomaterials can not only induce oxidative stress imbalance and interrupt the transformation of metabolic substances, but also hinder the energy production process by disrupting the cell membrane or interfering with the operation of the electron transport chain. Moreover, through rational and meticulous design in terms of size, surface properties, solubility, and catalytic effects, nanomaterials can exhibit even more considerable antimicrobial potential. Therefore, this article, starting from the perspective of bacterial metabolism, provides a detailed discussion on the antimicrobial mechanisms, application background, and challenges and opportunities faced by nanomaterials, with the aim of guiding future research and promoting the further development of nanomaterials in the field of antimicrobial therapy.

Graphical abstract

1. Introduction

In the 21st century, the landscape of medicine and biotechnology is undergoing a transformative shift in the treatment of bacterial-associated diseases. The global proliferation of antibiotic resistance has posed unprecedented challenges to conventional antibiotic therapy. Antimicrobial drugs, which include antibiotics, sulfonamides, and antifungals, have long been the cornerstone of treatment, with antibiotics being the most dominant due to their broad-spectrum efficacy. However, the misuse and overuse of antibiotics have led to the rapid emergence of drug-resistant bacteria, which now pose a significant threat to both ecological balance and human health. The rise of antibiotic-resistant strains has severely diminished the effectiveness of traditional antibiotics, thereby highlighting the urgent need for novel antimicrobial strategies [1,2]. Against this backdrop, targeting the intricate metabolic regulatory mechanisms within bacterial cells has emerged as a promising new frontier in research. Bacterial metabolism is a highly complex network that encompasses a vast array of biochemical reactions and regulatory pathways. These pathways not only sustain bacterial growth and reproduction but are also intricately linked to bacterial pathogenicity. Recent studies have demonstrated that by precisely modulating these energy metabolic processes, it is possible to effectively control bacterial growth and pathogenicity. This approach offers a potential alternative to traditional antibiotics and represents a significant step forward in the development of next-generation antimicrobial therapies.

As a novel type of antimicrobial agent, nanomaterials can efficiently kill bacteria, including drug-resistant strains, through rational design and application. The size effect, surface effect, and biocompatibility of nanomaterials endow them with significant antimicrobial potential. For instance, they can more easily penetrate bacterial cell membranes, carry a higher load of antimicrobial agents and surfactants, and exhibit greater targeting capabilities. Existing studies have demonstrated that the combination of nanomaterials and antibiotics has the potential to enhance bacterial susceptibility and overcome antibiotic resistance [3]. In terms of bacterial energy metabolism, nanomaterials also possess several noteworthy advantages. They can disrupt respiratory enzymes on the bacterial envelope, interfere with the activity of the electron transport chain, and inhibit the activity of redox enzymes, thereby affecting bacterial energy metabolism through multiple mechanisms. These findings provide new ideas and strategies for antimicrobial therapy[[4], [5], [6], [7]].

However, the application of nanomaterials in the field of antimicrobials is still in its infancy, and many key issues remain to be resolved. For example, the biosafety of nanomaterials, their environmental impact, and their long-term effects all require further research and evaluation. In addition, the synthesis, functionalization, and targeting of nanomaterials are also key factors in realizing their application in antimicrobial therapy[[8], [9], [10], [11]]. These studies not only contribute to our understanding of the antimicrobial mechanisms of nanomaterials but also provide a theoretical basis for the design and development of more effective nanomaterial-based antimicrobial agents. Moreover, they offer a new perspective and ideas for the therapeutic strategies of bacterial-associated diseases. By delving into the interactions between nanomaterials and bacterial energy metabolism, we hope to promote the development of nano-antimicrobial technology and provide new solutions to address the growing problem of bacterial drug resistance.

2. The energy metabolism of bacteria

2.1. The main components of bacterial energy metabolism

Bacterial growth is fundamentally dependent on the intricate metabolic processes occurring within the cell. For bacteria, the metabolism of major nutrients ultimately results in the generation of reducing equivalents and ATP, which provide the essential energy required for various cellular activities, including growth and reproduction. Bacterial energy metabolism can be categorized into three primary types based on the substrates and products involved: aerobic respiration, anaerobic respiration, and fermentation.Aerobic respiration refers to the complete oxidation of organic matter to carbon dioxide and water by bacteria in the presence of oxygen, accompanied by the release of large amounts of energy. This energy-producing process is accomplished through redox reactions in the electron transfer chain, where bacteria transfer electrons from higher energy compounds of organic matter to oxygen, generating energy while producing water. Anaerobic respiration refers to the use of other electron acceptors (e.g., sulfate, nitrate, etc.) by some bacteria in the absence of oxygen. Anaerobic respiration is similar to aerobic respiration in that the difference, in addition to the presence or absence of oxygen involved in the reaction, is in the use of different electron acceptors in the final oxidation reaction. Compared to aerobic respiration, anaerobic respiration releases less energy. Fermentation, on the other hand, is a process of partial oxidation in the complete absence of oxygen that releases energy by converting organic substrates into organic acids, alcohols, or gases. Fermentation is usually the last resort for energy production because it produces less energy compared to aerobic and anaerobic respiration. In general, bacteria choose different metabolic pathways depending on the presence or absence of oxygen in them; under aerobic conditions, bacteria usually choose aerobic respiration, while under anoxic conditions, they will turn to anaerobic respiration or fermentation.

Taking aerobic respiration as an example, the metabolism of organic compounds (such as glucose) within bacteria involves three distinct processes. The first is glycolysis, also known as the Embden-Meyerhof-Parnas (EMP) pathway. The second is the Krebs cycle (also referred to as the citric acid cycle or tricarboxylic acid cycle, TCA cycle). The third is a series of membrane-bound electron transfer oxidations coupled with oxidative phosphorylation. Glycolysis is the process by which bacteria break down simple sugar molecules like glucose to produce a small amount of ATP and intermediate products. This process occurs in the cytoplasm and does not require oxygen. During glycolysis, glucose is split into two molecules of pyruvate. Pyruvate is then further oxidized into its triphosphate form, generating a small amount of ATP and NADH (the reduced form of the coenzyme NAD+). The TCA cycle is a key step in bacterial aerobic respiration and takes place within the mitochondria-like structures in the cytoplasm. It accepts acetyl-CoA produced from glycolysis and other metabolic pathways, releasing carbon dioxide and high-energy electron carriers NADH and FADH₂ in each cycle. In this cycle, acetyl-CoA combines with oxaloacetate to form citrate, which then undergoes a series of reactions to produce multiple molecules of NADH and FADH₂, ultimately regenerating oxaloacetate. Oxidative phosphorylation is the final step in bacterial aerobic respiration. It involves transferring high-energy electrons from the TCA cycle and other metabolic pathways through the electron transport chain to oxygen, generating a large amount of ATP. Within the electron transport chain, NADH and FADH₂ release their high-energy electrons, which are then passed through a series of redox reactions to form water with oxygen molecules. The key step in this process is the transmembrane transport of protons, creating a proton gradient. Finally, this proton gradient drives the flow of protons through ATP synthase, catalyzing the conversion of ADP and inorganic phosphate into ATP. These three processes work together to oxidize organic compounds into carbon dioxide and water, while generating a large amount of ATP. This ATP provides the energy required to sustain bacterial life activities and supplies the raw materials needed for cellular synthesis.

However, various alternative metabolic pathways exist among different bacteria. These include the phosphoketolase pathway (PK pathway), which branches off from glycolysis; the oxidative pentose phosphate pathway (PPP), also known as the hexose monophosphate shunt (HMS pathway); and the Entner-Doudoroff pathway (ED pathway). Additionally, there are modified pathways of the TCA cycle, such as the glyoxylate shunt. These alternative pathways may exist independently or in combination within bacterial metabolism, serving to consume or supply intermediate compounds required at different stages [12]. Studies have shown that in bacteria cultured in vitro and those infecting hosts, these alternative metabolic pathways may replace the common EMP pathway as the primary metabolic mode. For example, the ED pathway is upregulated in Escherichia coli and Salmonella within infected hosts, while Mycobacterium tuberculosis utilizes the glyoxylate pathway to metabolize fatty acids for energy [13]. Moreover, due to evolutionary differences driven by adaptive survival, some bacteria may have incomplete common metabolic pathways. For instance, Streptococcus has an incomplete TCA cycle and lacks a functional ED pathway, relying instead on alternative reactions and enzymes [14]. Therefore, depending on the metabolic environment, bacterial metabolism may undergo hundreds of variations or adaptive adjustments. The ultimate goal is to optimize energy supply to the cell.

In addition, pyruvate or its derivatives, as the end products of the EMP, PP, and ED pathways, can be further metabolized through fermentation under anaerobic conditions. During this partial oxidation of organic compounds, energy is generated via substrate-level phosphorylation [15]. Under aerobic conditions, however, these compounds enter the TCA cycle and undergo further reactions catalyzed by various enzymes, producing electrons and reducing equivalents to fuel the operation of the respiratory chain. It is worth noting that the electron carriers in the bacterial electron transport chain are more diverse than those in eukaryotes. For aerobic and anaerobic bacteria, the nature of the terminal electron acceptor in the electron transport chain differs, leading to variations in their primary metabolic modes. For example, the aerobic respiratory chain of Pseudomonas denitrificans is highly similar to that of eukaryotic mitochondria in terms of spectrum, composition, and function. In contrast, the respiratory chain of Escherichia coli, one of the most commonly used microbial model systems, is significantly different from its mitochondrial counterpart, most notably in the absence of Complex III, which catalyzes the oxidation of ubiquinol by cytochrome c in many respiratory chains [16]. The respiratory electron transport chain varies greatly among bacteria and is even absent in some organisms [12]. Streptococcus, for instance, lacks the capacity for oxidative phosphorylation and electron transport chain function, relying entirely on substrate-level phosphorylation for energy production. As a result, most Streptococcus species are considered facultative anaerobes, susceptible to growth inhibition by oxygen [14]. Therefore, there are many differences among various bacterial species in the electron transport process of oxidative phosphorylation, which are worth investigating.

In summary, understanding bacterial metabolism requires consideration of numerous influencing factors, such as the bacterial growth environment and the species of bacteria. Under different circumstances, bacteria will adjust their metabolic processes to obtain more energy, thereby better adapting to their environment and achieving more rapid growth and reproduction.

2.2. The biological functions of bacterial energy metabolism

Bacterial energy metabolism plays an irreplaceable role in various aspects of bacterial life, including the cell cycle, adaptive growth, and motility. As unicellular organisms, bacteria conduct their metabolism at the microscopic cellular level. Even minor changes in this process can significantly impact their energy metabolism, potentially leading to metabolic disorders or even cell death.

Firstly, there is a close relationship between bacterial energy metabolism and the cell cycle. The processes of bacterial growth and division require substantial energy input, and disruptions in energy metabolism can lead to disordered cell cycles. For example, when metabolic activities are disturbed, the growth rate and cell division cycle of bacteria may be altered. Regulation of the cell cycle can be achieved at the molecular level through the mediation of metabolites or enzymes, such as those involved in DNA replication and cytoplasmic division [17].

Secondly, the regulatory mechanisms of bacterial energy metabolism vary under different growth conditions. Bacteria can adjust their metabolic pathways in response to changes in the external environment, and different bacterial species exhibit unique adaptabilities. They metabolize available nutrients and energy sources in their host environment to maintain intracellular energy balance. This regulatory mechanism not only affects bacterial growth rate and metabolic activity but may also influence their ability to withstand external stress [18]. In intracellular infection environments, bacteria display unique metabolic pathways and energy acquisition strategies. For example, the pathogenic Streptococcus mutans can sense and regulate carbohydrate utilization through its unique Catabolite Control Repression(CCR) system, thereby promoting survival and reproduction in the oral environment [19]. Streptococcus pneumoniae and Streptococcus pyogenes enhance their pathogenicity and colonization efficiency in the host through specific carbohydrate transport systems, such as ATP-binding cassette(ABC) transporters and the Phosphotransferase(PTS) System [13,20]. Intracellular pathogens, such as Salmonella enterica and Brucella abortus, metabolize more efficient carbon sources within host cells, demonstrating their adaptability to the host environment [19]. Pseudomonas aeruginosa in the airways of cystic fibrosis patients exhibits anaerobic metabolic pathways, showing metabolic adaptation to environments that are oxygen-deprived but rich in nitrates and nitrites [21]. Therefore, the type of bacterial energy metabolism may determine their growth characteristics and ability to adapt to the environment.

In addition, there is a close relationship between bacterial energy metabolism and their motility. Bacteria regulate their movement direction by sensing chemical and physical signals from the external environment, a process that typically requires substantial energy. Therefore, any disruption in bacterial energy metabolism may impair their ability to sense and respond to environmental stimuli, thereby affecting their chemotaxis. Energy taxis mediates a strategic response to changes in intracellular energy production, allowing motile bacteria to navigate autonomously toward more favorable spatial niches where their metabolic activities are enhanced. Research has shown that many compounds sensed directly by methyl-accepting chemotaxis proteins (MCPs) can influence energy metabolism [22]. In Escherichia coli, a novel sensor protein called Aer has been identified, which responds to changes in cellular energy levels (redox status) and guides bacteria toward environments that support the highest energy levels within the cell [23]. Thus, bacteria employ various strategies to navigate toward ecological niches that are conducive to growth, a process that is inseparable from energy metabolism.

Lastly, the relationship between bacterial energy metabolism and drug resistance is bidirectional. On one hand, modulating bacterial metabolism can enhance drug susceptibility. On the other hand, increased drug resistance may stem from alterations or functional impairments in certain metabolic pathways of bacteria. Studies have shown that bacteria with ample energy supply tend to exhibit stronger drug resistance. This is because robust energy metabolism helps maintain normal cellular functions and structures, thereby enhancing their ability to withstand external stress. As heterotrophic organisms, bacteria rely on exogenous substances for metabolic activities. By regulating specific metabolic pathways in bacteria, their sensitivity to antibiotics can be increased or their growth can be affected. For example, metabolic reprogramming of methicillin-resistant Staphylococcus aureus (MRSA) through uracil can boost the TCA cycle and cellular respiration, leading to increased uptake of aminoglycosides and production of reactive oxygen species (ROS) [24]. Additionally, inhibiting enzyme oxidation or the synthesis of related cofactors can disrupt essential metabolic processes in bacteria, including carbohydrate, lipid, and amino acid metabolism, thereby increasing their susceptibility to various antibiotics[[25], [26], [27]]. This, in turn, underscores the close link between increased bacterial drug resistance and specific metabolic processes.

The energy metabolism of bacteria exerts broad and profound influences on their biological functions, encompassing multiple aspects such as the cell cycle, metabolic regulation, motility, and drug resistance. These findings offer crucial insights into the survival strategies of bacteria and their capacity to combat diseases, thereby facilitating the development of novel antimicrobial therapeutic approaches and antibiotics.

3. Nanomaterials modulate bacterial metabolism

Nanomaterials (NMs) are materials with dimensions at the nanoscale, characterized by unique physicochemical properties. They have found widespread applications in biomedicine, materials science, and other fields. In the biomedical domain, nanomaterials are extensively used in disease treatment, drug delivery, and bioimaging. Significant progress has been made in recent years regarding the mechanisms by which nanomaterials affect bacterial metabolism and their applications in medicine.The nanoscale dimensions of these materials confer several advantages when used as antimicrobial agents. For instance, they can penetrate deep into bacterial cells, thereby enhancing the efficiency of cellular disruption. Additionally, due to variations in their internal groups and surface modifications, nanomaterials can exert toxicity on pathogenic bacteria through diverse antibacterial mechanisms [28]. In terms of bacterial metabolism, nanomaterials primarily influence bacteria through two mechanisms: (1) inducing the overproduction of ROS within bacterial cells, leading to oxidative stress imbalance; (2) disrupting the electron transport chain structure or respiratory enzyme activity in the bacterial cell membrane, thereby interfering with respiratory function.In this section, we will discuss how nanomaterials impact bacterial metabolism and elaborate on the relevant antibacterial mechanisms (Fig. 1).

Fig. 1.

Mechanism of nanomaterials affecting bacterial metabolism.

3.1. Nanomaterials induce oxidative stress imbalance

During bacterial energy metabolism, the generation of oxidative stress is a common occurrence, primarily due to the production of ROS during redox reactions. These species include superoxide anion (O₂⁻), hydrogen peroxide (H₂O₂), and hydroxyl radical (•OH). They can react with biomacromolecules within the cell, such as lipids, proteins, and nucleic acids, causing oxidative damage and increasing intracellular oxidative stress. To counteract this stress, bacteria typically activate a series of antioxidant defense mechanisms, including enzymes and small-molecule antioxidants, to protect biomacromolecules from damage. The survival and energy metabolism of bacteria depend on the precise balance between their antioxidant and oxidative systems. Excessive production of ROS or impairment of the antioxidant system can disrupt this balance, leading to oxidative stress. This, in turn, affects the integrity of the cell membrane and its metabolic functions, accelerating the bacterial death process[[29], [30], [31], [32], [33]]. For example, lipid peroxidation can reduce membrane fluidity, interfering with the intracellular transport of nutrients such as glucose and amino acids, thereby indirectly lowering the substrate levels for energy metabolism. Damaged cell membranes may also affect the function of cell surface receptors and enzymes, hindering processes like oxidative phosphorylation [34]. Ultimately, ROS attacks can lead to breaks in DNA or RNA strands, disrupting biosynthetic and energy metabolism processes related to nucleotide metabolism [35,36]. When facing oxidative stress, bacteria must finely regulate their antioxidant systems to maintain energy metabolism and viability. Studies have shown that nanomaterials can influence intracellular and extracellular oxidative stress processes, disrupting the redox balance and metabolic pathways of cells, and interfering with their metabolic activities and the normal functions of related enzyme systems [33]. The specific mechanisms by which nanomaterials affect intracellular oxidative stress levels in bacteria are primarily associated with ROS production. Both metal/metal oxide nanoparticles and carbon-based nanomaterials have been proven to induce intracellular ROS production. The mechanisms can generally be divided into three categories.

3.1.1. Catalytic reaction

Nanomaterials can mimic the activities of enzymes such as peroxidase (POD), oxidase (OXD), and catalase (CAT) within bacterial cells, catalyzing the generation of ROS. As emerging enzyme mimics with multifunctional and tunable catalytic activities, nanozymes can exert various enzymatic activities inside bacteria, demonstrating potential for metabolic regulation[[37], [38], [39]]. For instance, nanozymes designed from metals and metal oxides, such as copper/carbon nanozymes, can exhibit POD-like activity by catalyzing reactions with H₂O₂ to produce ROS [40]. Recently, researchers have further enhanced the activity of nanozymes through modifications. For example, a defect-rich adhesive nanozyme was constructed. Due to its lower adsorption energy for H₂O₂ and lower desorption energy for OH⁻, as well as a more exothermic reaction process, the defect edges exhibit higher intrinsic peroxidase activity compared to the pristine structure. Both in vitro and in vivo studies have confirmed that this modified nanozyme has superior antibacterial efficacy against drug-resistant Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus [41].

3.1.2. Redox reaction

Nanomaterials themselves release reductive substances that react with O₂ to form ROS. For instance, the reaction of Fe²⁺ with O₂ produces H₂O₂, which can further react with ferrous ions in the Fenton reaction to generate •OH. By co-culturing iron/iron oxide nanomaterials with bacteria, a large amount of ROS can be produced in situ through the two-electron transfer between iron ions and oxygen [42]. This process may involve indirect ROS generation via released Fe²⁺ or direct production by internalized zero-valent iron (nZVI) particles, which accumulate within bacterial cells, disrupting the intracellular redox homeostasis and mediating bacterial cell inactivation [43,44]. Further research has revealed that the mechanism by which nZVI particles inactivate bacterial cells differs depending on the environmental conditions. Under aerobic conditions, the primary inactivation mechanisms are membrane disruption and oxidative stress responses. In contrast, under anaerobic conditions, adhered nZVI/Pd particles attack functional groups such as carboxyl, ester, and amide groups, leading to the degradation of proteins and polysaccharides and ultimately causing membrane damage [45].

3.1.3. Responsive releasing ROS

Under external stimuli such as light, temperature, and ultrasound, specific components within nanomaterials undergo self-reactions to form ROS, which accumulate inside bacterial cells. Photodynamic therapy (PDT) has been proven to utilize nano-activated photosensitizers (PS) to convert molecular oxygen into ROS. Different PS, such as GaPpIX, PpIX, and water-soluble C60(OH)30 fullerol, are encapsulated into nanoparticles to target various species [46]. A polymer antimicrobial agent designed by combining silver nanoparticles with light-activated PpIX exhibits enhanced antibacterial efficacy. The silver nanoparticles attached to the micellar shell adhere to bacterial membranes, causing partial disruption that facilitates the entry of PpIX into the cell core. Upon light irradiation, ROS are generated in situ to inactivate bacteria [47]. Nanomaterials enable the precise regulation of antibacterial activity via photocatalytic gas release. An example is the NIR laser-controlled hydrogen release from PdH nanohydrides, which induces cell membrane rupture by generating H₂. This mechanism disrupts the intracellular oxidative stress equilibrium and enhances the effects of ROS [48,49]. A similar approach involves designing near-infrared laser-controlled nitric oxide-releasing gold nanostars/hollow polydopamine Janus nanoparticles. These nanoparticles induce ROS production in MRSA through two possible mechanisms: First, the photothermal effect directly triggers ROS generation, inducing bacterial oxidative stress; second, the NO released within bacterial cells interferes with bacterial metabolism, promoting ROS production. Excessive ROS lead to intracellular glutathione(GSH) depletion and DNA damage [50]. Finally, nanomaterials can also control ROS generation in the local environment through physical means. For example, an ultrasound-switchable nanozyme system can controllably produce catalytic oxygen and ultrasound-sensitized ROS during ultrasound activation [51].

In summary, the pathways by which nanomaterials affect the redox balance within bacterial cells are highly diverse. The aforementioned mechanisms can exist individually or simultaneously, and there are also ROS-independent oxidative stress pathways. For example, nanomaterials can directly oxidize proteins on the bacterial cell membrane surface. Although the structural integrity of the cell is maintained, the processes of energy transfer and oxidative phosphorylation are disrupted, hindering cellular respiration [52]. Therefore, further research is needed to explore the specific mechanisms by which nanomaterials induce oxidative stress within bacterial cells.

3.2. Nanomaterials interfere with bacterial electron transport chain

The electron transport chain (ETC) is an electron transfer system composed of a series of redox enzyme complexes arranged in a specific order. As the final stage of oxidative phosphorylation in energy metabolism, it completes the process of transferring electrons to oxygen and generating ATP. Since microbial cells lack subcellular structures, the ETC is located on the bacterial cell membrane. The vast majority of ETCs consist of enzyme complexes I, III, and IV, which are composed of various redox enzymes (such as NADH dehydrogenase, ubiquinone:cytochrome c oxidoreductase, etc.), iron-sulfur proteins, quinones, and cytochrome c. Although the composition of enzyme complexes varies among bacterial species, the chain-like electron transfer system on the membrane and the electron donors and acceptors are essentially the same. Taking the ETC of aerobic bacteria as an example, complex I catalyzes electron transfer through a chain of Fe-S centers embedded in the hydrophilic domain of the lipid membrane, providing a tunnel for electron transfer between NADH and quinone. Quinone (Q) combines with protons to form ubiquinol (QH₂), which is oxidized back to Q at a nearby binding site, triggering proton pumping across the membrane domain and the Mitchellian redox-loop mechanism of complex III. This process mediates the movement of charge through transmembrane electron transfer and ultimately delivers electrons to cytochrome c, which carries them to complex IV. The free energy generated during electron transfer is ultimately converted into the proton motive force (PMF) across the membrane, driving the synthesis of ATP from ADP and inorganic phosphate (Pi) [16]. The structural and functional integrity of these complexes on the cell membrane is crucial for the chain-like electron transfer system, which collectively completes the vital energy conversion process. Any disruption in any part of this system will lead to the breakdown of the ETC and the cessation of bacterial energy metabolism [53].

The ETC is a series of complex redox reactions within the cell, with redox enzymes being the key factors in this process. ROS-bearing groups on the surface of nanomaterials, which serve as primary sites for bacterial adhesion, not only participate in ROS generation and subsequent oxidative stress metabolism but also affect the ETC by inhibiting respiratory enzymes on the membrane. Studies have confirmed that nanomaterials can disrupt the cell membrane, leading to the inactivation of respiratory enzymes, or directly inhibit redox enzymes to interfere with the ETC. The redox enzymes in the ETC are a group of membrane-bound proteins, and disruption of the lipid bilayer may cause these proteins to detach from the membrane surface. This can further lead to the loss of structural integrity of the enzymes, resulting in their inactivation and thus inhibiting bacterial respiration. The physical disruption of the bacterial cell membrane by nanomaterials is related to their size, surface topography, surface properties, and composition. Defect-rich nanomaterials not only increase the contact area with bacteria but also enhance the active sites associated with adhesion. When surface indentations match the topography of the bacterial surface, they can generate stronger adhesion forces, making the bacterial surface rough or wrinkled and promoting membrane disruption [41]. In addition to surface structure, the surface charge of nanomaterials also plays an important role in disrupting the cell membrane. The lipid bilayer of the cell membrane is negatively charged, so many positively charged metal-based nanomaterials are more likely to form electrostatic interactions with the bacterial surface. Under the combined action of electrostatic and van der Waals forces, nanomaterials can embed themselves into the cell membrane, causing depolarization of a large number of phospholipid molecules, thereby altering membrane permeability and initiating the membrane disruption process [53]. Moreover, metal-based nanomaterials can release metal ions such as Ag⁺ and Cu⁺ during their action, which can modify membrane proteins or lipopolysaccharides on the cell membrane, leading to proton leakage from the cytoplasm to the extracellular environment and affecting the formation of proton motive force [54,55]. Nanomaterials can also directly inhibit various redox enzymes in the ETC, blocking the smooth transfer of electrons among several complexes. Redox enzymes in the ETC can be broadly classified into three categories: pyridine nucleotides, NADH dehydrogenase, and cytochromes. NADH dehydrogenase (also known as complex I) is the largest redox enzyme complex in the ETC, responsible for the oxidation of NADH and the transfer of electrons to ubiquinone. Recent studies have shown that silver nanoparticles can directly inhibit its activity by interacting with NADH dehydrogenase. This inhibition is likely due to the interaction between silver nanoparticles and the enzyme's active center, or the oxidative stress induced by silver nanoparticles, which can alter the enzyme's conformation or oxidize certain groups, thereby affecting its catalytic function [54]. In addition to NADH dehydrogenase, nanomaterials also affect the other two types of redox enzymes [53,56,57]. However, further research is needed to explore the interaction mechanisms by which nanomaterials affect redox enzyme activity and how these interactions influence cellular metabolism and physiological functions.

In addition to inhibiting enzymes on the bacterial membrane, nanomaterials can also interfere with the normal operation of the ETC by disrupting transmembrane electron transfer. In bacterial biofilms formed at infection sites, oxygen is distributed in a gradient across the biofilm due to diffusion limitations. Bacteria in the outer layers consume oxygen much faster than those in the inner layers, resulting in a situation where microorganisms in the biofilm have abundant electron donors but lack electron acceptors. Therefore, bacteria need to transfer electrons to specific electron acceptors through extracellular electron transfer (EET) pathways to achieve long-distance electron transfer[[58], [59], [60], [61]]. Since nanomaterials can reduce the interfacial resistance of electron transfer from electroactive microorganisms to extracellular acceptors and enhance electron transfer, specific electron carriers in the EET pathway can be nanomaterials in addition to bacterial-secreted electron shuttles such as flavins and phenazines. The ability of nanomaterials to mediate EET in electroactive microorganisms is closely related to their own electron transfer capabilities. Carbon-based nanomaterials and metal/metal oxide nanomaterials have advantages due to their good electrical conductivity [10,62,63]. For example, co-culturing with nano-hydroxyapatite/MoO has been shown to transfer active electrons from the bacterial respiratory chain to nanomaterials through an enhanced electron transfer mechanism, causing proton depletion in bacterial cells and disrupting the respiratory chain [64]. In addition to acting as electron carriers to interfere with electron transfer pathways, nanomaterials can also serve as electron donors, allowing electrons to flow through membrane complexes into bacteria. Since electrons are captured by the MtrCAB complex, protons on complex III cannot be pumped into complex IV to react with O₂, leading to reduced ATP production and impaired energy metabolism in bacteria [65].

In summary, the factors by which nanomaterials affect the ETC of bacteria are closely related to their structure and intrinsic properties. Unlike other cells with respiratory chains involving multiple organelles, bacterial oxidative phosphorylation is concentrated on the cell membrane, making it more susceptible to external stimuli and more sensitive to the effects of nanomaterials. Therefore, the development of novel nanomaterials targeting the ETC holds great promise.

4. The applications of nanomaterials in bacteria-associated diseases

Under normal physiological conditions, bacterial communities throughout the human body exist in a state of dynamic equilibrium. These bacteria, together with various other factors, maintain the stability of the body's microenvironment and play a crucial role in the normal functioning of organs. The onset of many diseases is accompanied by changes in the quantity or composition of bacterial communities, disrupting the existing dynamic balance and creating a pathological microenvironment. This, in turn, drives abnormal cellular behavior and ultimately leads to the characteristic manifestations of disease. This section introduces diseases caused by bacterial infections or dysbiosis, summarizes the existing nanomaterials used for treating these conditions, and provides potential design concepts for future nanomaterials aimed at combating bacterial infections and dysbiosis-related diseases.

4.1. Skin wound infections

Effective prevention and treatment of bacterial infections are crucial for wound healing and improving patient outcomes. Under normal circumstances, acute wounds such as incisions, lacerations, abrasions, and burns caused by surgery or accidental injuries typically heal in an orderly manner within 2–3 weeks. However, the healing process is susceptible to interference from both internal and external factors, such as microbial infections, diabetes, and vascular diseases. These factors can transform wounds into chronic and non-healing subtypes, prolonging the healing time to more than three months after injury. Among these factors, wound infections caused by bacterial and other microbial colonization at the wound site account for a significant portion of non-healing cases. This is especially true for diabetic patients, whose wounds are more prone to bacterial infections due to elevated glucose levels at the injury site. Moreover, toxins and metabolic products released by bacteria colonizing skin wounds can alter the microenvironment by changing pH and oxygen levels. Additionally, the body's immune response triggers local inflammatory reactions, all of which can impact the wound healing process[55,[66], [67], [68]].

Nanomaterials, with their unique physicochemical and biological properties—such as high surface-to-volume ratios, surface effects, and tunable physicochemical characteristics—have been widely applied in infection control and wound healing. Metallic nanoparticles (such as silver, gold, copper, and zinc oxide) possess high surface-to-volume ratios that allow for extensive contact and interaction with bacteria. This not only enhances antibacterial efficiency but also reduces the likelihood of bacterial resistance [69,70]. Furthermore, some nanomaterials with special optical properties, such as those based on metal oxides, carbon, and polymers, can serve as effective agents for photothermal therapy (PTT) and photodynamic therapy (PDT). These therapies kill bacteria through localized heating or controlled ROS generation in infected wounds, thereby minimizing the occurrence of bacterial resistance [71]. In addition, certain nanomaterials with adjustable shapes and functional modifications can deliver antimicrobial agents or bioactive molecules to the wound site. They can act as ideal carriers for stimuli-responsive, targeted release, and controlled-release systems [55,66,72,73] (Fig. 2, Fig. 3). These nanomaterial carriers not only facilitate the penetration of antimicrobial agents into bacterial cells but also enable the loading or grafting of antimicrobial agents onto corresponding cellular surfaces, enhancing their therapeutic efficacy. Similarly, nano-hydrogel carriers improve drug adhesion to the wound surface while providing a barrier against external stimuli and promoting healing [74]. For instance, a novel nanozyme-engineered hydrogel biomaterial can be designed. The nanozyme can mimic the activities of enzymes such as superoxide dismutase (SOD) and catalase (CAT) to generate ROS. Meanwhile, the hydrogel can serve to provide sustained release and effective regulation, thereby efficiently killing drug-resistant bacteria and promoting the healing of infected wounds [75].

Fig. 2.

(A)Multifunctional pH-switchable CuP nanozyme composite hydrogel (Alg/CuP) with mild photothermal enhanced catalysis and ion releasing activity was designed to significantly enhance the wound healing rate of various refractory wounds. (B)Schematic diagram showing the protocol to establish infection model and whole treatment process. (C)Thermal images and the corresponding photothermal heating curves of both Alg and Alg/CuP hydrogel under the irradiation of NIR light. (D)Growth of S. aureus in the wound after different treatments (n = 8). (E)Photos of the wounds with different treatments on day 0, 2, 7, and 12 (n = 6). (F)Wound size markers. (G)Infected wound closure rate with different treatments on day 2, 7, and 12 (n = 6) (∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001). (H)H&E and masson staining of wound sections after 7 and 12 days with different treatments. Adapted with permission from Ref. [55]. Copyright 2024, American Chemical Society.

Fig. 3.

(A)Scheme of the preparation process of Au NCs@PCN. (B)Under NIR radiation, high-temperature killing multidrug resistance bacteria through CDT, PDT, and PTT. (C)Bactericidal by disrupting bacterial membrane structure and protein leakage and promoting angiogenesis and epithelial cell repair by up-regulating the expression of related factors. (D)ROS fluorescence detection image processed by DCFH-DA. (E)(1–6) Pictures of crystal-violet-stained bacterial membranes of MRSA in a 24-well plate, where the scales are all 5 mm; (a–f) microscopic images of crystal-violet-stained bacterial membranes of MRSA after different treatments, where the scales are all 200 μm. (F)Quantitative analysis of ROS fluorescence. (G)Quantitative analysis of biofilm biomass at OD 590 nm. (H)Detection of protein leakage of MRSA after different treatments. (I)Thermal imaging of temperature at different time points under 808 nm laser irradiation (1.0 W/cm², 15 min). (J)Curve of temperature change per minute during treatment in vivo. (K)Body weight change curve of rats in 21 days. (L)Photographs of infectious wound healing in diabetic rats within 21 days. (M)Corresponding quantitative statistics of the wound coverage of rats under different treatments at 0, 7, 14, and 21 days. (N)H&E and Masson staining images of wound tissue slices in different treatment groups under laser irradiation. Adapted with permission from Ref. [66]. Copyright 2022, American Chemical Society.

Overall, these findings indicate that nanomaterial-based therapeutic approaches offer advantages over traditional antimicrobial strategies in wound healing applications. Nanomaterials can reduce the emergence of bacterial resistance through multiple antibacterial mechanisms and improve antibacterial efficiency through targeted drug delivery. Besides the methods mentioned above for addressing skin wound infections, the application of copper-based nanomaterials to induce a copper intoxication-like death in bacteria through the TCA cycle pathway is another viable option. Copper ions can interfere with cellular energy metabolism and redox equilibrium, ultimately triggering cell death. This mechanism thus represents a promising new direction for the development of future antimicrobial drugs [76]. However, the standalone application of nanomaterials in wound settings is limited by challenges related to safety and efficacy, necessitating further research for validation.

4.2. Gut dysbiosis

The human gut microbiota is a complex ecosystem composed of numerous bacterial species, including both beneficial and harmful bacteria. As an indispensable substrate for host health, the gut microbiota plays a crucial role in many physiological functions. It not only promotes the digestion and fermentation of indigestible polysaccharides and the production of vitamins but also maintains intestinal homeostasis. Additionally, it is essential for the development and differentiation of the intestinal epithelium and the gut-associated lymphoid tissue (GALT). Moreover, the composition of the gut microbiota affects the absorption of nutrients and trace elements from food in the gut, and toxins secreted by various bacteria can be absorbed by the small intestinal mucosa into the bloodstream, reaching various parts of the body. Therefore, as an important component of human and animal physiology, the gut microbiota plays a vital role in maintaining host health. Recent studies have shown that gut dysbiosis can impact energy metabolism, inflammatory responses, nutrient digestion and absorption, immune status, and the onset and progression of many diseases. However, the gut microbiota is susceptible to various exogenous stimuli. Substances entering the body through the digestive tract can interact with gut bacteria over extended periods, affecting their structure and abundance[[77], [78], [79], [80], [81]]. Gut dysbiosis can lead to impaired intestinal barriers and trigger a range of diseases, such as inflammatory bowel disease (IBD). Therefore, strategies that effectively modulate the gut microbiota to restore a healthy intestinal microenvironment hold great potential in therapeutic applications [82].

In recent years, the widespread use of nanomaterials in food and pharmaceuticals has increased their likelihood of entering the human body through the digestive tract, where they can accumulate in the gastrointestinal tract and significantly impact host health. On the one hand, nanomaterials may contribute to the restoration of gut microbiota balance by promoting the proliferation of beneficial bacteria, thereby enhancing intestinal barrier function and reducing the recurrence of inflammation [82,83]. Research indicates that, due to the low absorption rate of nanomaterials through the intestinal mucosa into the bloodstream, their primary effects are mediated through alterations in gut microbiota structure or interactions with bacteria, thereby reducing the incidence of systemic diseases [[84], [85], [86]]. Exposure to silver nanoparticles (Ag NPs) and silver nanowires (Ag NWs) over a short period (14 days) has been shown to inhibit the proliferation of Gram-negative bacteria, altering microbial community structure and reducing gut microbiota diversity in mice [87]. Researchers have also developed a multifunctional nanozyme based on two-dimensional nanomaterials—Bi₂Se₃ nanodisks—which has the potential to regulate gut microbiota, increase the ratio of Firmicutes to Bacteroidetes, inhibit Proteobacteria, and restore intestinal homeostasis [88] (Fig. 4). Reports have indicated that TiO₂ nanoparticles (NPs) can compromise the integrity of Escherichia coli cell membranes in the dark, leading to osmotic stress. In the absence of light, TiO₂ NPs can also destroy bacterial cell walls and induce cell death by generating ROS [89]. Additionally, acid-resistant enteric pathogens can bypass the acid barrier of the small intestine, colonize, and infect the gut. A pH-triggered dual-biological-functional self-assembling peptide (SAP) has been designed. Changes in pH conditions may trigger the transformation of the nano-peptide from a nanosphere to a nanofiber microstructure. By disrupting bacterial membrane integrity, the SAP demonstrates significant antimicrobial activity against Escherichia coli, Salmonella enterica serovar Typhimurium, Listeria monocytogenes, and Bacillus cereus. The SAP exhibits excellent therapeutic efficacy and good biosafety, avoiding the destruction of the gut microbiota by broad-spectrum antibiotics. This establishes a new therapeutic strategy for peptide-based nanomaterials targeting gastrointestinal bacterial infections [90]. Furthermore, nanomaterials, as encapsulation materials, have shown great potential in improving the encapsulation of probiotics. Oral administration of probiotics is widely recognized as beneficial for gut and systemic health. However, due to the loss of probiotic viability during gastrointestinal transit, leading to poor intestinal delivery, nanomaterials can be developed to achieve the delivery and controlled release of probiotics, thereby enhancing their efficacy after oral administration [91].

Fig. 5.

(A)Schematic illustration showing the working principles of HA-JNPs@Cef to treat H2O2-secreting S. pneumoniae infection. (B)The synthesis process of HA-JNPs@Cef. (C)TEM image and of Fhn NPs, JNPs, and HA-JNPs@Cef. (D)Experimental design of pneumonia model and treatment. The mice with pneumonia were treated since day 5 and sacrificed for analysis on day 11 (n = 6). (E)The CFU of S. pneumoniae in lungs. (F)H&E-stained histological sections of lungs of different groups. Green arrows represent neutrophils. Adapted with permission from Ref. [99]. Copyright 2024, Elsevier.

Fig. 6.

(A)Synthesis and characterization of drug-loaded Mg-based micromotors. a Schematic preparation of the micromotors. b Schematic of in vivo propulsion and drug delivery of the Mg-based micromotors in a mouse stomach. c Time-lapse images of the propulsion of the drug-loaded Mg-based micromotors in simulated gastric fluid (pH ∼1.3). d Schematic dissection of a drug-loaded micromotor consisting of a Mg core, a TiO2 shell coating, a drug-loaded PLGA layer, and a chitosan layer. e Scanning electron microscopy (SEM) image of a drug-loaded Mg-based micromotor. f, g Energy-dispersive X-ray spectroscopy (EDX) images illustrating the distribution of f magnesium and g titanium in the micromotor. h–k Microscopy images of dye-loaded Mg-based micromotor. (B)Schematic displaying the loading clarithromycin (CLR) onto the Mg-based micromotors. PLGA polymer dissolved in ethyl acetate is mixed with CLR, and the solution is deposited over the Mg-TiO2 microparticles resulting in the formation of a thin PLGA-CLR coating. (C)Microscope images showing the PLGA-CLR film over the Mg-based micromotors. (D)Mouse body weight log from day 0 to day 6 of the toxicity study. (E)In vivo toxicity evaluation of the Mg-based micromotors by histological staining with hematoxylin and eosin (H&E). Adapted with permission from Ref. [101]. Copyright 2017, the Authors, published by Springer Nature.

Fig. 4.

(A)A Schematic illustration of the preparation of Bi2Se3 nanodiscs and scavenging RONS for IBD therapy. (B)Protocol for acclimatization and treatment. (C)Corresponding mouse photographs with different treatments. (D)Different treatments for the colon with corresponding photographs. (E)Body weight of different mice. (F)Colon length of different mice. (G)Spleen vs body mass ratio of different mice. (H)Staining of colon section slices with H&E. (I)Immunofluorescence staining of ROS, TNF-α and IL-6. (J)IL-6 levels in RAW264.7 macrophages subjected to different treatments. (K)Visualization of dead and live HUVECs by calcein-AM and PI staining. (L)TNF-α levels in RAW264.7 macrophages subjected to different treatments. (M)Confocal image of DAF-FM DA -stained NCM460 treated with H2O2 (1 mM). (N)A confocal image of NCM460 cells stained with DCFH-DA after being treated with H2O2 (1 mM). Adapted with permission from Ref. [88]. Copyright 2023, Elsevier.

On the other hand, if nanomaterials persist in the body for extended periods or their metabolites exhibit biological activity, they may exert a sustained impact on the structure of the gut microbial community and may even trigger new ecological imbalances. Carbon dots (CDs) have garnered significant attention as an excellent antimicrobial nanomaterial, particularly in the treatment of diseases caused by infections, such as periodontitis and stomatitis. CDs derived from ε-poly-L-lysine (PL-CDs) negatively regulate the growth of Lactobacillus rhamnosus by increasing the production of ROS and reducing antioxidant activity, thereby compromising the permeability and integrity of the cell membrane. PL-CDs also tend to inhibit cell viability and accelerate apoptosis. In vivo studies via gavage have demonstrated that PL-CDs can induce inflammatory infiltration and barrier damage in mice. Additionally, PL-CDs increase the ratio of Firmicutes to Bacteroidota (F/B) and the relative abundance of the Lachnospiraceae family, while decreasing the relative abundance of Muribaculaceae. These findings suggest that PL-CDs may cause pathological damage to the gut by inhibiting the growth of probiotics and simultaneously activating intestinal inflammation, inevitably leading to gut microbiota dysbiosis [92]. Secondly, nanomaterials typically exhibit high surface activity, enabling them to readily interact with the gut microbiota and induce the production of harmful substances by bacteria. These substances can enter the bloodstream through the gastrointestinal mucosa, thereby affecting systemic health. Experimental evidence has shown that oral administration of TiO₂ NPs leads to increased secretion of lipopolysaccharides (LPS) by the gut microbiota of rats, resulting in elevated LPS levels in the serum and inducing oxidative stress and immune-inflammatory responses throughout the intestinal system. In vitro experiments have also observed significant changes in bacterial metabolites within the microbiota, particularly in the production of short-chain fatty acids, demonstrating that TiO₂ NPs can influence the production of microbial metabolites through interactions with the gut microbiota [93].

In summary, nanomaterials can alter the abundance and structure of gut microbiota by promoting the colonization of beneficial bacteria and inhibiting the proliferation of harmful bacteria. They may also cause changes in microbial metabolism, potentially exerting adverse effects on the host. However, current research on the impact of nanomaterials on gut microbiota is largely limited to animal or in vitro studies, and further exploration is needed in the complex human environment. Future research should continue to investigate the effects of nanomaterials on human gut microbiota, elucidate the connections between cellular pathways and host diseases, provide new insights into the safety assessment of nanomaterials, and contribute scientific evidence for addressing public health issues related to chronic metabolic diseases associated with gut dysbiosis.

4.3. Others

In addition to the two common diseases mentioned above, there are numerous other diseases associated with bacterial infections. Overall, these conditions can be categorized based on the body site where they occur or the specific organs and systems they affect. For a more detailed summary, please refer to Table 1.

Table 1.

Application of nanomaterials in bacteria-associated diseases.

Type of diseases	System or Organ	Diseases	Pathogenic Bacteria Species	Types of Nanomaterials	Advantages of Application	Ref.
Bacterial Infectious Disease	Central Nervous System	Neonatal Meningitis	E. coli	PLGA Nanoparticles	high stability of VoNPs(Recombinant Protein OmpAVac (Vo))	[94]
	Respiratory System	Pneumonia	Streptococcus、Haemophilus influenzae type B、baumanii、pseudomonas aeruginosa	Nanomotor、Nanocomposites	excellent enzyme activity, antibacterial activity, good biocompatibility, low drug resistance, prevention of infection	[[95], [96], [97], [98], [99]] (Fig. 5)
	Digestive System	Intestinal Tract	E. coli、salmonella、Shigella、campylobacter jejuni、clostridium difficile	antimicrobial peptide + nanotechnology、drug delivery system based on chitosan	pH responsive nanostructure transformation, high stability of drug delivery	[90,100]
		Stomach	H pylori	synthetic nano/micromotors、nanoparticles (NPs)	efficient drug delivery, body harmless, immunosensor	[[101], [102], [103]] (Fig. 6)
	Skeletal System	Osteomyelitis	S. aureus、Streptococcus、enterococcus	Nanocomposites、gold nanoparticles (GNPs)	biocompatibility, low cytotoxicity, high specificity, delivery vector	[[104], [105], [106]]
		Necrotizing Fasciitis	pyogenic streptococcus、S. aureus、Bacteroides、Enterobacterales、vibrio vulnificus、Aeromonas hydrophila	nanoflower-shaped molybdenum disulfide (MoS2) and tubular carbon nanotubes (CNTs)	Microwave thermotherapy(MTT)	[107]
	Skin and Soft Tissue	Skin Wound Infection	Gram-positive cocci、Gram negative bacilli、Streptococcus、Enterobacteriaceae	Two-dimensional (2D) nanomaterials	uniform shape, large surface area, stable surface charge	[108]
		Soft Tissue Infection	S. aureus、pseudomonas aeruginosa、Streptococcus、enterococcus	magnetic composite nanoplatform、nanoparticles	Photodynamics Therapy (PDT),low biotoxicity, good skin permeability and low drug resistance	[[109], [110], [111]]
	Eyes	Eye Wound Infection	S. aureus、pseudomonas aeruginosa、Streptococcus、E. coli	nanomaterials	small size, simple preparation, good degradability, strong targeting, little stimulation to biological tissue	[112]
		keratitis	CNS、S. aureus、pseudomonas aeruginosa	gold nanoclusters (GNCs) 、NDDS、artificial nanoplatforms	excellent antibacterial effect, Chemokinetic therapy(CDT),excellent enzyme activity	[[113], [114], [115]]
	Oral Cavity	Periodontitis	Porphyromonas gingivalis、Actinobacillus actinomycetemcomitans、Prevotella intermedius、Fusobacterium nucleatum、Streptococcus thermophilus	Nanoparticles 、NDDS、Nanozymes	clearance of excess ROS,excellent enzyme activity, low drug resistance	[[116], [117], [118]]
	Urogenital System	Urinary Tract Infection	E. coli、Enterococcus faecalis	NDDS、nanoprobes	biosensors, strong targeting,low drug resistance	[[119], [120], [121]]
		Gonorrhea	Neisseria gonorrhoeae	Nanoparticles	strong targeting	[122]
Dysbiosis-Related Diseases	Digestive System	Irritable Bowel Syndrome (IBS)	lactic acid bacteria、Bifidobacterium	NDDS	strong targeting, ensure probiotic activity, sustained release	[9,123]
		Crohn's Disease	Salmonella、E. coli、Bacterooides fragilis、Clostridium Prazmowski	NDDS	strong targeting, drug sustained release, fewer side effects	[124]
		Obesity、Metabolic Disease	Bacteroides thetaiotaomicron、Bacteroides、Phylum Firmicutes	–	–	[[125], [126], [127]]
	Skin	Acne	Propionibacterium acnes、Staphylococcus epidermidis、S. aureus、malassezia	Nanomaterials	low drug resistance, Immunoregulatory activity	[128]
		Eczema、Atopic Dermatitis	S. aureus	amorphous silica particles	high stability, surface functionalization, shape variable	[129,130]
	Urogenital System	Vaginal Infection	Gardnerella vaginalis、anaerobic bacteria	Myrtle-Functionalized Nanofibers	regulation of cell population behavior, selective antibacterial	[131]

5. Factors related to the influence of nanomaterials on bacteria

After delving into the role of nanomaterials in bacterial-related diseases, we now turn to analyze the factors influencing the interactions between these nanomaterials and bacteria. The intrinsic properties of nanomaterials, as well as the characteristics of bacteria, collectively determine the success or failure of antibacterial efficacy. The physicochemical attributes of nanomaterials, such as size, shape, and surface charge, directly impact their modes of interaction with bacteria, including adsorption, penetration, and internalization. Meanwhile, the species, physiological state, and antibiotic resistance of bacteria dictate their sensitivity and response to nanomaterials. Understanding how these factors influence the antibacterial effects of nanomaterials is crucial for designing more effective antibacterial strategies. The following sections will discuss these relevant factors from the perspectives of both nanomaterials and bacteria, providing a basis for the design of future antibacterial nanomaterials.

5.1. Aspects of nanomaterials

5.1.1. Size

The antibacterial mechanisms of nanomaterials are closely related to their size. Smaller nanoparticles can more easily penetrate biological barriers and interfere with internal metabolic processes. Moreover, smaller nanoparticles tend to have higher surface activity and a larger contact area, making them more likely to interact with bacterial cell membranes. This interaction can lead to the disruption of the bacterial cell membrane or interference with metabolic pathways [132]. In addition, smaller nanomaterials can increase the production of ROS, thereby disrupting the redox balance within bacterial cells and affecting their metabolic processes [133]. For example, graphene oxide (GO) has a rich abundance of oxygen-containing functional groups on its surface, making it an excellent electron acceptor. When GO comes into contact with bacterial cells, it can extract electrons from the cell membrane. The transfer of electrons to GO triggers the generation of ROS within the bacteria. Therefore, compared with larger GO sheets, smaller GO sheets with a larger surface area induce a greater oxidative effect [134]. In contrast, relatively larger nanomaterials, although capable of interacting with bacterial cell membranes, have a smaller specific surface area and a relatively limited contact area with the cell membrane. As a result, their ability to damage the cell membrane and interfere with intracellular metabolic processes is weaker. Instead, they more often encapsulate bacteria, thereby impeding their membrane transport [132]. Nanomaterials with diameters less than 100 nm, due to their unique small size and surface effects, as well as tunable physicochemical properties, are more advantageous for controlling bacterial infections and promoting wound healing [135,136]. Notably, metal nanoparticles with intrinsic antibacterial properties, especially metal nanoclusters (NCs), can be extremely small, composed of a few to several metal atoms, and exhibit superior antibacterial efficacy [72,137]. For instance, 8-nm ZnO nanoparticles can kill 95 % of Staphylococcus aureus at a low concentration of 1 mM, while larger ZnO nanoparticles (50–70 nm) can only kill 40–50 % of S. aureus at a higher concentration of 5 mM [138]. Ultrasmall gold nanoclusters (AuNCs, <2 nm) can diffuse through the small pores in bacterial cell walls more easily than larger gold nanoparticles (AuNPs), leading to higher intracellular uptake and broad-spectrum antibacterial activity. In studies using MHA as a ligand, both AuNPs and AuNCs were tested at the same concentration against Gram-positive (S. aureus) and Gram-negative (Escherichia coli) bacteria [139]. The results showed that AuNPs had a minimal bactericidal effect, killing only 3 % of the bacterial population, whereas AuNCs effectively killed approximately 95 % of the bacterial population after 2 h of exposure [139]. Similar findings have been reported for silver nanoclusters (AgNCs), which exhibit better antibacterial activity compared to traditional silver nanoparticles (AgNPs) [140,141](Fig. 7). Additionally, the size of nanomaterials is associated with their dispersibility and phagocytosis. For example, the antibacterial effect of gold nanoparticles against S. aureus is size-dependent and correlates with macrophage phagocytosis in vivo [142,143].

Fig. 7.

(A)A schematic depicting the morphology and surface properties of AgNPs (#1 and #2) and AgNCs. (B)Initial interaction structure of the AgNPs, AgNCs, and the bacterial membrane. (C)Interaction energy between AgNPs/AgNCs and the LPS/DPPE molecules. The negative value represents the attraction interaction, and the positive value indicates the repulsion interaction. (D)Representative TEM images showing the interaction of AgNCs and AgNPs with P. aeruginosa cells after 6 h of exposure. Blue arrowheads indicate agglomerated particles outside cells, red arrowheads denote AgNCs inside cells, and orange arrows point at cell debris. The enlarged images show the detailed interplay between AgNCs, AgNPs, and bacteria. (E)Characterization of as-synthesized Au NCs and Au NPs. (F)Optical images of Au nanoparticle suspension and TEM analysis of Au nanoparticles. TEM analysis for the intracellular locations of Au nanoparticles in RAW264.7 cells incubated with 200 μg/mL Au nanoparticles for 48h. The red arrows indicate nanoparticles. A-D)Adapted with permission from Ref. [141]. Copyright 2020, the Authors, published by Springer Nature. E)Adapted with permission from Ref. [139]. Copyright 2020, the Authors, published by KeAi Publishing. F-G)Adapted with permission from Ref. [143]. Copyright 2023, the Authors, published by Elsevier.

The size of nanomaterials plays a significant role in their antibacterial efficacy. Based on the theories discussed above, it might seem logical to reduce the volume of nanomaterials as much as possible to improve their antibacterial performance. However, there is a valid concern that smaller-sized nanomaterials may not be readily recognized by the body's immune system. When an excessive amount of nanomaterials enters the human body, it may lead to damage in other tissues or organs. Therefore, additional experimental research is necessary to confirm and guide the size design of nanomaterials. By controlling the size of nanomaterials within a reasonable range, satisfactory therapeutic effects can be achieved.

5.1.2. Surface properties

The surface properties of nanomaterials, including surface charge, topography, and aggregation behavior, may influence bacterial nutrient uptake and metabolic pathway selection by affecting bacterial adsorption and attachment through various pathways(Fig. 8).

Fig. 8.

(A)Aggregated nanoparticles enter into cells largely and are regarded as autophagic cargos. (B)Schematic Illustration for Tween-SPIONs Crossing the BBB in the Presence of a Magnet. (C)Subcellular distribution of the Tween-SPIONs in the frontal cortex in the presence of EMF. (a)SPIONs enter the brain by crossing BBB. Asp: astrocyte processes, End: endothelial cell. (b)Higher magnification of the figure; the inset shows the size of SPIONs. (c)Nanoparticle clusters were found near the axons of neurons. (d)EDS analysis of electron-dense black clusters shows the presence of Fe. A)Adapted with permission from Ref. [142]. Copyright 2015, Macmillan Publishers Limited, published by Springer Nature. B-C)Adapted with permission from Ref. [144]. Copyright 2016, American Chemical Society.

5.1.2.1. Charge

The surface charge is a key factor influencing the adsorption and adhesion of nanomaterials. Most bacterial surfaces carry a negative charge, especially Gram-positive bacteria, which possess a unique cell wall component called wall teichoic acid (WTA). Composed of repeating polyphosphoglycerol units with pyrophosphate termini, WTA forms a polyanionic network. Due to this structure, the cell membranes of Gram-positive bacteria exhibit a substantial negative charge, facilitating the binding of cationic molecules. In contrast, Gram-negative bacteria have a surface negative charge that accounts for only about 30 %, but they still maintain an overall negatively charged surface structure [145]. Therefore, designing nanomaterials with a positive charge can enhance their initial interaction with the negatively charged bacterial membrane through electrostatic and van der Waals forces. This increases bacterial adhesion and attachment, allowing for further internalization and more effective exertion of the nanomaterials' antibacterial properties [140,146,147]. Furthermore, when nanomaterials electrostatically bind to the bacterial cell wall and cell membrane, membrane damage occurs, leading to changes in membrane potential, membrane depolarization, and loss of integrity. These alterations subsequently result in transport imbalance, impaired respiration, disruption of energy transduction, or cell lysis. Research has shown that positively charged nanomaterials can interact with LPS in the bacterial outer membrane, thereby altering membrane potential and fluidity. This interaction, in turn, inhibits the activity of some membrane-bound enzymes or transporters that are dependent on the membrane potential [148]. Nanoparticles synthesized from positively charged natural or synthetic polymers also serve as effective antibacterial agents and carriers for anionic drugs. Researchers have developed new pH-responsive antibacterial nano-carrier platforms by utilizing pH-cleavable chemical bonds (such as ester, Schiff base, and hydrazone bonds) or pH-ionizable groups (such as zwitterions, chitosan, and metal-organic frameworks). These platforms enable the nano-carriers to degrade or alter their surface charge under acidic pH conditions to release antibacterial agents or switch from a negative to a positive charge to effectively kill bacteria [149,150]. Therefore, for bacterial infections caused by Gram-positive bacteria, designing nanomaterials with a positive charge can enhance antibacterial efficacy. The rational design of the surface charge of nanomaterials is thus a noteworthy consideration [151].

5.1.2.2. Surface topography

The surface topography of nanomaterials is another critical factor influencing their interactions with bacteria. Generally, the surface topography of nanomaterials determines their surface area and the number of active sites. Previous studies have shown that, compared to homogeneous shapes, star-shaped and flower-shaped nanoparticles with polygonal structures provide more contact points. This allows them to adsorb more effectively onto bacterial surfaces, thereby increasing the chances of contact between the antibacterial agent and bacterial cells[143,[152], [153], [154]]. These uniquely shaped nanoparticles may penetrate bacterial cell walls or membranes with their sharp edges, enhancing membrane permeability. Leveraging these characteristics, researchers have designed nanozymes with sharp edges, rough surfaces, spiky or virus-like serrated surfaces, which exhibit strong binding affinity to bacterial membranes, facilitating membrane disruption, separation, and inactivation of respiratory enzymes. This ultimately inhibits bacterial respiration, leading to the cessation of energy metabolism and loss of cell viability [41]. In addition, the tunable shapes and functional modifications of nanomaterials enable them to deliver antimicrobial agents or bioactive molecules to the desired sites of action. For example, preparing nanomaterials with different shapes (such as nanorods and nanospheres) embedded in carriers like hydrogels can achieve controlled release effects [155,156]. When combined with environment-responsive carriers, these nanomaterials can enable the self-assembly of chimeric peptides into nanofibers at pH 7.4 and transform them into nanoparticles in the acidic biofilm infection microenvironment (pH = 5.0), thereby enhancing penetration and killing efficiency against bacterial biofilms [157].

Beyond the previously discussed aspects, the functional modification of nanomaterials offers additional possibilities. For example, surface modification with suitable ligands enables nanomaterials to competitively bind to enzyme receptors or transporters on the bacterial membrane, thereby inhibiting their functions and consequently hindering bacterial respiration or nutrient transport. For instance, certain nanomaterials modified with carbohydrates can interact with mannose transporters on the bacterial membrane, blocking the normal transport of mannose and thereby affecting bacterial energy metabolism and growth[[158], [159], [160]]. Furthermore, ligand-functionalized nanomaterials can interact with enzymes on the bacterial membrane, thereby influencing enzyme activity. For example, when zinc is used as a ligand, it can dissociate into zinc ions that interact with the thiol groups of respiratory enzymes in the bacterial envelope, inhibiting respiration while inducing the production of large amounts of ROS within bacterial cells [161,162]. Therefore, through rational design of the surface topography of nanomaterials, their antibacterial efficacy can be significantly enhanced [151,163].

5.1.2.3. Aggregation behavior

In the environment, nanomaterials may undergo aggregation or agglomeration, which affects their contact and interaction with bacteria, thereby influencing bacterial metabolism. When nanoparticles are reduced to the nanoscale, their surfaces accumulate a large number of positive and negative charges, leading to charge aggregation that renders the nanoparticles highly unstable and prone to clustering. In addition to charge, the surface energy of nanoparticles, van der Waals forces, and various chemical bonds also contribute to their aggregation. The agglomeration behavior of nanoparticles reduces their surface area, diminishing contact and interaction with bacteria and consequently decreasing the efficiency of nanomaterials [164]. Therefore, exploring methods to prevent nanoparticle aggregation and enhance their delivery to the site of action is an important area of research.

Researchers have addressed this issue by coating nanoparticles with hydrophilic polymers, such as polyethylene glycol (PEG) and polylactic acid. This approach not only prevents the immune system from recognizing and clearing the nanoparticles when they enter the bloodstream but also ensures better dispersion and delivery to sites where they can interact with bacteria [165]. However, nanoparticle aggregation also has its advantages. By using environmentally responsive materials in mixed systems to control nanoparticle assembly, novel nanomaterials with tunable antibacterial properties can be developed [166,167]. Overall, it remains challenging to isolate and analyze the regulatory effects of nanoparticle aggregation on antibacterial performance. Nevertheless, nanoparticle aggregation is undoubtedly a potential parameter for optimization.

5.1.3. Solubility and concentration

The solubility of nanomaterials allows them to release ions or compounds that can influence bacterial metabolism, especially in the case of metal nanomaterials. The metal nanoparticles or ions they release can disrupt the structure of proteins, DNA, and lipids through thiol bonding or by inducing oxidative stress, or interfere with transmembrane electron transport, ultimately leading to bacterial death[28,[168], [169], [170], [171], [172]]. For example, when AgNPs dissolve in aqueous solutions, Ag⁺ ions interact with microbes and exhibit various antibacterial mechanisms. One mechanism involves Ag⁺ ions binding to sulfur- and phosphorus-containing groups in bacterial cell wall and membrane proteins, causing protein dysfunction [173,174]. Ag⁺ ions can also form pores in microbial membranes by binding to negatively charged regions, leading to the efflux of cytoplasmic contents, dissipation of the proton gradient across the membrane [175,176]. Intracellular Ag⁺ ions can interfere with the function of the bacterial electron transport chain, interact with bacterial DNA and RNA, and inhibit cell division [28,168]. Environmental factors such as pH, temperature, and light conditions can affect the stability and solubility of nanomaterials, thereby influencing their metabolic effects on bacteria. Additionally, the solubility of nanomaterials in the environment affects the concentration of released metal ions, which in turn influences antibacterial performance. High concentrations of metal ions may exert cytotoxic effects, posing risks to normal tissues [177,178]. To mitigate these adverse effects, researchers have employed strategies such as combining metal nanomaterials with antibiotics or coating them with biomolecules to develop antibacterial agents with controlled-release properties and enhanced safety[[179], [180], [181], [182]].

5.1.4. Catalytic effect

Nanomaterials can influence bacterial metabolic pathways, including inhibiting or activating specific metabolic enzymes and inducing stress responses in bacteria. Some nanozymes can regulate the levels of ROS by mimicking the activity of redox enzymes, thereby affecting bacteria [11,183]. For example, certain nanozymes can kill bacteria by generating ROS radicals that cleave bacterial nucleic acids, inactivate proteins, and disrupt the integrity of cell membranes. Additionally, nanozymes can degrade various molecules in biofilm matrices, including polysaccharides, proteins, extracellular DNA, and lipids, to kill multidrug-resistant bacteria and eliminate biofilms[[184], [185], [186]]. Beyond redox enzyme-like activities, nanomaterials also possess catalytic activities related to light and heat. For instance, TiO₂ can produce ROS under light conditions, which can damage bacterial cell membranes and internal structures, thereby affecting bacterial metabolic activities [187]. Moreover, some nanomaterials with special optical properties, such as those based on metal oxides, carbon, and polymer-based materials, can serve as effective agents for PTT and PDT. These therapies kill bacteria through localized heating or controlled ROS generation in infected wounds without the issue of bacterial resistance [71,188,189]. However, the catalytic activity of nanozymes themselves is not stable, and their material design is complex. Therefore, developing simpler, more convenient, and efficient methods for rapid synthesis of these materials, or combining nanozymes with other antimicrobial agents, will be the future direction for the rational use of nanozyme antibacterial effects[[190], [191], [192]].

5.1.5. Nano-drug delivery systems(NDDSs)

To enhance the targeting of drugs and deliver them to specific sites where they can act on bacteria, researchers have developed nano-drug delivery systems (NDDSs) that combine the advantages of both nanomaterials and antimicrobial agents. These systems use nanomaterials to encapsulate drugs or serve as scaffolds for drug loading and controlled release. This allows the drugs to dissolve and be released in specific environments or to be absorbed more rapidly. NDDSs first leverage the size and surface effects of nanomaterials, enabling easier penetration of cellular barriers and precise control over drug release. Second, nanomaterials can carry or encapsulate drugs to specific sites, enhancing drug stability while reducing damage to normal cells [157,193,194]. For example, Trusek et al. developed a novel enzyme-responsive GO nanocomposite hydrogel. This system chemically binds antibiotics to GO via an enzyme-cleavable peptide, releasing the antibiotics from the hydrogel in the presence of the specific enzyme produced by bacteria, thereby achieving controlled drug delivery [195](Fig. 9). Based on their primary matrix components, NDDSs can be divided into two main categories: one is organic nanoparticle-based delivery systems, including liposomes and polymer nanoparticles, which typically exhibit good biocompatibility and biodegradability and are suitable for loading and controlled release of various drugs. The other category is inorganic nanoparticle-based delivery systems, such as metal and metal oxide nanoparticles, which, with their unique physicochemical properties, show great potential in imaging, diagnostics, and photothermal therapy[[196], [197], [198]]. Regardless of the type of nanomaterial delivery system, the goal is to achieve high-efficiency antibacterial activity. Therefore, future antimicrobial drug design can benefit from the rational design and application of these systems [199,200].

Fig. 9.

(A)Schetches illustrating the strategy adopted for synthesising Lyz-AuNPs and the experimental plan. (B)Optical characterisation of the solution containing Lyz-AuNPs complexes. (C)Lysozyme activity assay performed on the Lyz-AuNPs complexes made up of 100 nm AuNPs. (D)Fe‐SAC with peroxidase mimics activities and photothermal performance against bacteria. (E)Agar plate photographs of MRSA bacterial colonies by Fe‐SAC under NIR‐I irradiation; PBS was as a control. (F)Relative bacterial viability of MRSA. (G)Live/dead staining of MRSA. SEM images of MRSA following various therapies. (H)SEM images of MRSA following various therapies. (I)Schematic of the experimental procedure for wound infection and treatment. (J)Photographs of MRSA‐infected wounds. (K)Representation of wound healing trace in real‐time and (L) corresponding pictures of the MRSA colonies for every group under treatment were obtained on the 10th day of the assay. (M) Quantitative statistics of the relative wound size in a time‐dependent manner. The mice's body weight was recorded while they were receiving treatment. (N)Histologic changes were examined using H&E staining and Gram staining. A-C)Adapted with permission from Ref. [166]. Copyright 2020, Elsevier. D-N)Adapted with permission from Ref. [188]. Copyright 2024, the Authors, published by Wiley-VCH.

5.2. Aspects of bacteria

5.2.1. Species and characteristics

Different types of bacteria exhibit varying sensitivities to nanomaterials. For example, Gram-positive and Gram-negative bacteria are distinguished by their unique cellular structures. The cellular structure of Gram-negative bacteria is more complex, comprising three main layers: the inner membrane (IM), the peptidoglycan cell wall (PG), and the outer membrane (OM), with the OM being the outermost layer. Unlike Gram-positive bacteria, the OM of Gram-negative bacteria provides an additional layer of protection against harmful external substances, such as antibiotics and disinfectants. Proteins within the OM mediate the uptake of essential small molecules by the cell, while the cytoplasmic membrane, enveloped by the OM, acts as a filtering barrier through porins, allowing the passive diffusion of specific small molecules [201,202].

These bacteria also develop resistance by using efflux pumps to expel antibiotics that have entered the cells. Nanomaterials can overcome these barriers through various mechanisms. For instance, nanomaterials can serve as carriers for efflux pump inhibitors, thereby enhancing the stability and delivery efficiency of the inhibitors and consequently augmenting the antibacterial efficacy of antibiotics. Furthermore, nanomaterials can target outer membrane proteins, disrupting the integrity of the outer membrane and enhancing the permeability of antibiotics [3].

In contrast, Gram-positive bacteria are characterized by a thick and continuous peptidoglycan cell wall, lacking the OM structure. This cell wall is composed of alternating layers of MurNAc and GlcNAc, with a thickness significantly greater than that of Gram-negative bacteria and containing teichoic acids. Although it has long been believed that Gram-positive bacteria lack porins, recent studies suggest that they may possess similar structures, albeit with potentially different functions and distributions. These porins may be involved in the transport of specific molecules or ions, although their exact roles remain unclear[[203], [204], [205]]. Nanomaterials can enhance the permeability of antibiotics by disrupting the structure of biofilms. For instance, some nanoparticles are capable of generating highly toxic ROS, which directly degrade the extracellular polysaccharides and extracellular DNA within biofilms, thereby exposing bacteria to antibiotics. Additionally, nanomaterials can target the cell wall synthesis pathway, interfering with the synthesis of peptidoglycan and consequently weakening the integrity of the cell wall, thereby enhancing the efficacy of antibiotics [3].

After understanding the impact of different bacterial species and their characteristics on the effects of nanomaterials, we may be able to design specific nanomaterials to modulate the composition and proportion of microbial communities within the human body. In most bacterial infectious diseases, there is usually an imbalance of the microbiota or overgrowth of pathogenic bacteria. Therefore, controlling the proportion of specific bacteria using nanomaterials while avoiding damage to beneficial bacteria may become a new approach for future antimicrobial therapies.

5.2.2. Physiological state

In addition to bacterial species and structure, their growth stages and metabolic states also influence their response to nanomaterials. Bacteria at different growth stages may exhibit varying sensitivity to nanomaterials. Some studies have shown that bacteria in the exponential growth phase are more susceptible to certain nanomaterials than those in the stationary phase. For example, titanium dioxide nanotube (TNT) arrays exert different effects on Escherichia coli at various growth stages. During the lag phase (0–2 h), TNT arrays inhibit initial bacterial adhesion. In the logarithmic phase (4–12 h), TNT arrays not only suppress bacterial proliferation but also kill bacteria through physical means. In the stationary phase (beyond 12 h), the antimicrobial efficacy of TNT arrays may be weakened due to excessive bacterial overgrowth on the TNT surface, leading to biofilm formation and an increase in bacterial numbers [206]. Moreover, under different oxidative stress conditions, bacteria exhibit distinct survival states, which can alter their size, morphology, and metabolism, thereby affecting their response to nanomaterials[[207], [208], [209], [210]](Fig. 10).

Fig. 10.

(A)Presence of cell division sites. B. subtilis ΔspoIIE cells encoding divIVA-gfp reporter were incubated for 14 days in starvation buffer. (B)To avoid bias, the captured phase contrast images were used to select approximately 100 cells per sample, and the number of cells containing a midcell DivIVA-GFP signal, indicative of cell division, were counted. (C)Average change in cell length was calculated for approximately 100 individual cells for each time point. (D)Cell growth under deep starvation conditions. B. subtilis ΔspoIIE cells (strain DG001) were incubated for 14 days in starvation buffer. Adapted with permission from Ref. [207]. Copyright 2019, the Authors, published by Springer Nature.

As is well known, bacteria in biofilms are more resistant to nanomaterials than their planktonic counterparts. The unique physiological properties and microenvironment of biofilms enhance their resistance to antimicrobial agents, a characteristic that also applies to nanomaterials [157,211,212]. The energy metabolism of planktonic bacteria and biofilm bacteria differs significantly. Planktonic bacteria, which are usually in a free-suspended state, depend mainly on the oxidation and degradation of dissolved organic matter (DOM) for their energy metabolism. In contrast, biofilm bacteria are embedded within extracellular polymeric substances (EPS), forming complex three-dimensional structures. They maintain their energy metabolism through metabolic exchange; for example, internal cells provide amino acids to external cells, while external cells supply fatty acids to internal cells. The respiration and metabolism of biofilm bacteria are restricted by EPS, but they also use EPS to protect themselves from environmental stress. EPS, characterized by its dense structure and low drug permeability, assists internal bacteria in maintaining metabolic homeostasis and growth conditions, leading to persistent infections in the host [213]. For instance, prosthetic joint infection is a major complication following joint replacement surgery. Pseudomonas aeruginosa and Staphylococcus aureus, as the primary pathogens, have garnered significant clinical attention. When they form biofilms on the surface of implants, antibiotic resistance increases, resulting in persistent infections in humans [214]. Therefore, targeted interventions against bacterial metabolic pathways, aimed at disrupting their metabolic homeostasis, have emerged as a novel therapeutic strategy for eradicating bacterial biofilms and combating infections. Researchers have developed a biofilm microenvironment (BME)-responsive self-assembled copper-doped polyoxometalate cluster (Cu-POM). Within the high-glutathione environment of biofilms, Cu-POM can generate ROS to destroy bacteria. Moreover, driven by PTT, Cu-POM can enter bacterial cells, inhibit the TCA cycle, limit bacterial energy acquisition, promote the accumulation of intracellular peroxides, and thereby cause bacterial death and biofilm disruption. Meanwhile, the highly biocompatible BTO@MMSa nanosystem can target infected sites and rapidly generate ROS under ultrasound (US) irradiation to kill bacteria and accelerate wound healing [215]. Other researchers have proposed the concept of nanopore-enhanced biofilm electron transport (NBET), in which nanopores with atomic vacancies and biofilms act as electron donors and acceptors, respectively, thereby enhancing the high electron transport capacity between nanomaterials and biofilms. Electron transport effectively disrupts key components of biofilms (proteins, polysaccharides involved in intercellular adhesion, and extracellular DNA) and significantly downregulates the expression of genes associated with biofilm formation [216].

In addition, bacteria can regulate the formation and disassembly of biofilms through quorum sensing (QS). Quorum sensing is a communication mechanism by which bacteria coordinate group behavior through the secretion and perception of signaling molecules. This mechanism controls processes such as biofilm formation, the production of virulence factors, and the synthesis of secondary metabolites, enabling bacteria to adapt to environmental changes [217]. The interference of nanomaterials with quorum sensing can be categorized into several mechanisms: interference with signal synthesis and secretion, alteration of the conformation of bacterial enzymes or membrane receptors, and acting as nanocarriers [218]. At the transcriptional level, nanomaterials primarily disrupt QS-regulated genes through direct damage, ROS-mediated oxidative damage, and the chelation of released metal ions, thereby inhibiting the transcription process. Metal-based nanomaterials or their dissolved metal ions, when adsorbed on the bacterial cell membrane, can bind with high affinity to the amino (-NH) and carboxyl (-COOH) groups of membrane receptor proteins, leading to structural and functional disruption of the membrane receptors. For QS-related membrane receptors with similar groups, nanomaterials may also disrupt receptor structure through similar mechanisms, thereby impairing the binding capacity of receptors with QS signaling molecules [218]. Researchers have used nanoparticle chemodynamic therapy (CDT) to interfere with metabolic processes such as galactose metabolism in MRSA bacteria, disrupting the transport systems on the MRSA surface, affecting quorum sensing, and inhibiting biofilm formation, thereby achieving effective antibacterial effects [219]. Moreover, nanocarriers can infiltrate biofilms. With their excellent loading capacity and designability, nanocarrier systems can enhance the stability and targeted delivery efficiency of traditional quorum sensing inhibitors (QSIs). By targeting various stages of the quorum sensing pathway, they disrupt bacterial communication and better exert QS regulatory functions, providing a new therapeutic strategy for infection control [217].

These findings reveal the potential mechanisms by which nanomaterials affect bacteria at different growth stages. Understanding how to leverage bacterial growth and survival states is of great significance and may guide the future design and application of antimicrobial nanomaterials.

5.2.3. Antibiotic resistance

At present, the overuse of antibiotics has led to the rapid spread and dissemination of bacterial resistance in the environment. Due to their inherent resistance mechanisms, resistant bacteria may respond differently to certain nanomaterials compared to their susceptible counterparts. As a new type of antimicrobial agent, nanomaterials have the ability to evade existing mechanisms associated with acquired resistance. Bacterial resistance is primarily generated through alterations in antibiotic targets. For example, modifications to the cell wall can confer resistance to vancomycin, while changes in ribosomes can enable resistance to tetracyclines. Bacteria also degrade antibiotics by enhancing the activity of enzymes such as β-lactamase and overexpress efflux pumps to expel a variety of antibiotics. Some pathogens, like Chlamydia pneumoniae, evade antibiotic effects by residing within host cells [6,220,221]. The antibacterial strategies of nanomaterials against antibiotic resistance can be categorized into the following approaches: (1)For multidrug-resistant bacteria such as MRSA, nanomaterials can serve as carriers for β-lactamase inhibitors, targeting the active sites of the enzyme to inhibit its activity. They can also target efflux pump proteins on the cell membrane and inhibit their function. (2)For bacteria that develop resistance through biofilm formation, such as Pseudomonas aeruginosa, nanomaterials can generate highly toxic ROS to directly degrade the extracellular polysaccharides and extracellular DNA within the biofilm. Additionally, they can target specific components of the biofilm (such as extracellular polysaccharides and extracellular DNA) to enhance the antibacterial efficacy of antibiotics. (3)For bacteria that utilize quorum sensing, such as Staphylococcus aureus, nanomaterials can target the QS system to reduce biofilm formation and bacterial virulence. They can also act as carriers for QS inhibitors, targeting QS signaling molecules to disrupt bacterial group behavior [3].

Compared with traditional antibiotics, antibacterial therapies utilizing nanomaterials have been proven to offer significant advantages. Researchers have demonstrated that gold nanoparticles outperform levofloxacin in treating gastrointestinal infections [222]. Copper single-atom nanozymes (Cu-NC) exhibit superior antibacterial activity against Staphylococcus aureus compared to vancomycin [223]. Silver nanoparticles display strong bactericidal effects against multidrug-resistant Acinetobacter baumannii, a strain that exhibits high resistance to various traditional antibiotics such as piperacillin, cefuroxime, and others [224]. Moreover, nanomaterials have shown excellent antibacterial activity against a variety of resistant bacteria, including MRSA and extended-spectrum β-lactamase-producing Escherichia coli (ESBL E. coli) [219,225]. Lastly, nanomaterials, when used as targeted carriers in combination with antibiotics and antimicrobial peptides, can offer more advantages and superior antibacterial effects [215,226].

In summary, the impact of nanomaterials on bacteria is a complex process that involves multiple physicochemical properties of nanomaterials as well as the species and physiological characteristics of bacteria(Fig. 11). These interactions determine the effectiveness of antibacterial efficacy, highlighting the importance of considering these factors when designing antimicrobial nanomaterials. Given the diverse types of bacteria and varying infection environments, the factors influencing the antibacterial effects of nanomaterials are often multifaceted and may interact with each other. For instance, when designing a more multifunctional nanomaterial, the addition of extra components may lead to an increase in the nanomaterial's size and a decrease in its solubility. A thorough understanding of these relationships can guide us in optimizing the performance of nanomaterials. However, when designing antibacterial nanomaterials, several principles are worth noting, such as targeting, functionality, and safety. Regarding targeting, we can design receptor ligands or surface morphologies with positive or negative charges to enable better binding of nanomaterials to specific bacteria and thus exert more targeted effects. In terms of functionality, smaller nanomaterials, with their larger surface area and enhanced ability to penetrate bacterial biofilms, tend to have higher antibacterial efficiency. Moreover, the antibacterial effects of nanomaterials can be further enhanced through photothermal effects and ultrasound assistance. Lastly, concerning safety, biocompatible materials should be selected to minimize toxicity to living organisms, taking into account the aforementioned factors.

Fig. 11.

Factors related to the influence of nanomaterials on bacteria.

Therefore, we aim to design nanomaterials with stronger targeting capabilities within a safe range, thereby enhancing their antibacterial efficacy while reducing the development of bacterial resistance. This approach is expected to provide more effective solutions for future infection control and treatment.

6. Future and perspectives

In this review, we have thoroughly explored the applications of nanomaterials in modulating bacterial metabolism and their underlying mechanisms. Research has shown that nanomaterials interact with bacteria through multiple pathways, including direct physical damage, generation of ROS, and interference with energy metabolism, thereby effectively inhibiting bacterial growth and reproduction. These findings reveal the potential of nanomaterials as antibacterial agents, especially in the context of the diminishing efficacy of traditional antibiotics. The size, shape, and surface properties of nanomaterials significantly influence their antibacterial effects, providing guidance for the design and synthesis of novel nano-antimicrobial materials. Moreover, nanomaterials synthesized by microorganisms have garnered attention due to their environmental friendliness and biocompatibility, offering new pathways for green synthesis of nanomaterials. However, the environmental release and biosafety of nanomaterials remain critical issues requiring in-depth investigation. Therefore, future research should focus on the long-term effects, ecotoxicity, and safety assessments of nanomaterials in clinical applications.

The biocompatibility assessment of nanomaterials is a complex process influenced by multiple factors, among which the long-term accumulation of nanomaterials, damage to normal cells in the body, and overactivation of the immune system are several major concerns. Owing to their small size and large specific surface area, nanomaterials can easily enter the body and accumulate over the long term. For example, some nanoparticles that deposit in the lungs may trigger chronic inflammatory responses, and long-term exposure can even lead to severe diseases such as pulmonary fibrosis [227]. In addition, nanomaterials may be distributed to other organs such as the liver and spleen through the bloodstream, potentially affecting the function of other normal cells. When nanomaterials exist in the body as foreign objects over the long term, they often tend to overactivate the body's immune system, increasing the risk of autoimmune diseases or affecting the body's immune defense against pathogens [228,229]. Therefore, using biocompatible raw materials, maintaining a safe concentration and release stability in the body, and enhancing the degradation capability of the materials are issues that need to be addressed in the synthesis of nanomaterials.

Moreover, the green and sustainable synthesis of nanomaterials is an important developmental direction in this field. When nanomaterials enter the environment such as water bodies and soil, they are likely to have negative impacts on aquatic and soil microorganisms, flora and fauna, and consequently affect the functioning of ecosystems. To this end, we should consider developing biodegradable nanomaterials and avoid using heavy metal elements that cause severe ecological damage to address the environmental and biological safety issues of nanomaterials. In addition, studies have shown that ecotoxicity is often related to the type and exposure dose of nanomaterials, so the excessive use of nanomaterials should also be strictly controlled [97,230,231]. However, the limitations of these methods also need to be fully considered, including synthesis efficiency, the ability for large-scale production, and the consistency and stability of the final product.

Although many studies have analyzed the excellent effects of nanomaterials in antibacterial therapy, the translation of laboratory research into actual clinical applications still faces many challenges and opportunities, including regulatory barriers and considerations for clinical trials. On the one hand, the regulatory framework for nanomedicine is still being continuously improved. Regulatory authorities for pharmaceuticals in various countries have set strict requirements for the safety, efficacy, and quality control of nanomedicine. However, there is a huge gap in the work and opinions on the safety of nanomaterial use and requirements among different organizations around the world. This restricts the regulation of nanomaterials and hinders their safer production and utilization [232]. On the other hand, the evaluation cycle for clinical trials of nanomedicine is relatively long, and the success rate is relatively low. The main reasons include appropriate patient selection, dose optimization, efficacy evaluation criteria, and model drug selection. We know that the treatment outcomes of bacterial-related diseases are usually influenced by multiple factors. The immune capacity of patients themselves varies, which poses a dilemma for the evaluation of antibacterial therapy. In addition, the rational use of nanomaterials is also crucial. The mode of action, dosage, and duration of the drug often need to go through many trials and comparisons, which poses great difficulties for the implementation of clinical trials. Therefore, clinical trials need to be strictly designed, and the implementation difficulty may become one of the barriers to the development of antibacterial therapy using nanomaterials [233]. We look forward to opportunities such as smart responsive systems, integration of multidisciplinary technologies, patient screening and personalized therapy, and simplified nano-design to provide new directions for the clinical translation of nanotherapy. Through interdisciplinary cooperation and technological innovation, it is hoped that these challenges can be overcome to promote the transition of nanotherapy from the laboratory to the clinic and bring new hope to patients.

Finally, the targeting ability of nanomaterials is one of the key advantages in antibacterial therapy, especially when combined with photodynamic and photothermal strategies to achieve extraordinary therapeutic effects. These strategies can precisely target the infected area and achieve synergistic antibacterial effects in various modes, especially showing strong capabilities in eliminating biofilms [41,55,63,157,188]. In addition, they can also be combined with existing antibiotics, antimicrobial peptides, and other components to achieve combined therapeutic effects. The current design concepts for targeting are usually limited to ligand binding, light, heat, or ultrasound assistance, etc. However, it is difficult to predict whether this approach will cause imperceptible damage to other cells in the body after long-term action. Therefore, in addition to further exploring the application of these strategies in the treatment of diseases caused by drug-resistant bacteria and their potential in regulating the wound microenvironment, promoting wound healing, and activating the immune system, future research also needs to focus on their safety.

Overall, nanomaterials have important research and application value in the field of bacterial metabolism regulation and antibacterial therapy. In the future, the development of nanomaterials needs to be jointly promoted by multidisciplinary collaboration, while ensuring their safety and efficacy in clinical applications.

CRediT authorship contribution statement

Jiaping Chen: Writing – review & editing, Writing – original draft. Yanli Zhang: Writing – review & editing, Writing – original draft, Visualization. Xin Luo: Software, Resources, Project administration. Yuting Zeng: Validation, Supervision, Resources. Ping Xiao: Project administration, Methodology, Investigation. Xian Ding: Formal analysis, Data curation, Conceptualization. Sijie Qiu: Methodology, Investigation, Funding acquisition. Qianlin Li: Project administration, Methodology, Investigation, Funding acquisition. Qianwen Deng: Validation, Software, Project administration, Methodology. Simin Wang: Software, Project administration, Methodology, Funding acquisition. Ruofei Lin: Validation, Investigation, Formal analysis, Data curation. Xiuwen Chen: Resources, Investigation, Formal analysis. Dehong Yang: Writing – original draft, Visualization, Resources. Wenjuan Yan: Conceptualization.

Vocabulary

Nanomaterials: Nanomaterials are materials with nanoscale in at least one dimension, allowing them to exhibit special physical, chemical, and biological properties.

Bacterial metabolism: Bacterial metabolism encompasses the biochemical processes that enable bacteria to convert nutrients into energy and essential biomolecules. Bacteria can adapt their metabolism to various environments, utilizing different pathways like glycolysis, fermentation, or the TCA cycle to optimize their growth and survival.

Glycolysis: Glycolysis is a central metabolic pathway that converts glucose into pyruvate through a series of enzymatic reactions, generating ATP as an energy source. This process occurs in the cytoplasm of cells and does not require oxygen, making it a crucial energy pathway under both aerobic and anaerobic conditions.

The TCA cycle: The tricarboxylic acid cycle, also known as the citric acid cycle or Krebs cycle, is a central metabolic pathway that oxidizes organic molecules to produce energy and biosynthetic intermediates. It consists of a series of enzyme-catalyzed reactions that convert acetyl-CoA into carbon dioxide, generating high-energy molecules like NADH and FADH₂, which are used in the electron transport chain to produce ATP.

ROS: Reactive oxygen species are highly reactive molecules derived from molecular oxygen, including superoxide radicals, hydrogen peroxide, and hydroxyl radicals. They play crucial roles in cellular signaling, stress responses, and can cause oxidative damage to biomolecules.

ETC: The electron transport chain is a series of protein complexes and electron carriers located in the cell membrane that transfer electrons through a series of redox reactions. This process generates a proton gradient across the membrane, which drives ATP synthesis through oxidative phosphorylation, providing energy for cellular functions.

Declaration of competing interest

The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Wenjuan Yan reports financial support was provided by National Natural Science Foundation of China. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Data availability

No data was used for the research described in the article.