Natural-Product Antibiotics: Cues for Modulating Bacterial Biofilm Formation

Antibiotics shape the core microbial community distribution between floc and biofilm in an endogenous partial denitrification system: Insight from metabolic pathway

The response mechanism of microorganisms in partial denitrification (PD) system under antibiotic stress, particularly microbial energy metabolism and electron transfer, remain inadequately understood. This knowledge gap hinders the establishment of ecological links between microbial dynamics and macro-level reactor performance. To address this, moving bed biofilm reactors were employed to investigate the dynamic changes of microbial community and metabolism under sulfadiazine (SDZ) and ciprofloxacin (CIP) stress. Results showed that dosing 2 mg/L SDZ or CIP accelerated nitrite accumulation, achieving this milestone 15 days earlier than in the control group. At the end of the operational phase, nitrate removal efficiencies reached 90.3 ± 18.3 % (Control), 83.5 ± 16.2 % (SDZ-treated) and 93.9 ± 12.4 % (CIP-treated), with nitrate-to nitrite-transformation rates of 61.3 ± 12.7 %, 65.6 ± 13.1 % and 58.0 ± 21.2 %, respectively. The abundances of energy supply related genes, i.e., sucC and PK were higher in the CIP-treated group, while those in the other two groups were similar. The promoted tricarboxylic acid cycle and glycolysis led to NADH and ATP accumulation, accelerating nitrogen metabolism and benefiting early nitrite accumulation in the antibiotic-stressed system. More importantly, increasing antibiotics concentration from 2 mg/L to 4 mg/L induced selective migration of Thauera from floc to biofilm (abundance in floc reduced to < 2.01 %). Metagenomic sequencing indicated that the higher abundance of narGHI in biofilms, compared to flocs, was crucial for maintaining stable PD performance under antibiotic stress. The electron transport related genes, such as IDH1, DLD and DLAT, were more abundant in biofilms than in flocs after SDZ and CIP addition. These findings provide a theoretical basis for understanding the response mechanism of PD consortia to antibiotic.

Halogen anion modulated metal-organic frameworks with enhanced nanozyme activities for bacterial biofilm disruption

There is an urgent need to develop new nanozymes with enhanced catalytic activities to combat bacterial infections, which have become increasingly challenging due to the misuse of antibiotics and the difficulties of new antibiotic discovery. Here, we employed a new strategy against bacterial biofilms by introducing halide anions to modulate the crystal facets of ZIF-L metal-organic frameworks (MOFs) and then loading chloroquine to form Ch@ZIF-L. The modulation of crystal facets significantly enhanced the oxidase activities of ZIF-L, which can be significantly changed by modulation of its crystal facets, with the hexagonal ZIF-L (ZIF-L-H-Cl) structure showing the highest oxidase activity. At pH 6.0, over 80% of chloroquine was released from Ch@ZIF-L-H-Cl within 8 hours, altering the DNA conformation of bacterial biofilms and disrupting the extracellular polymeric substances (EPSs). The generation of singlet oxygen catalyzed by ZIF-L-H-Cl can effectively kill bacteria at the infected wound site. The composite nanozyme of Ch@ZIF-L-H-Cl, when treated at 100 μg mL-1, exhibited no adverse effects on normal cell growth or hemolysis. Our in vivo experiments demonstrated an 85% reduction of the wound area by day 8 and a rapid recovery of body weight in mice with wounds infected with Staphylococcus aureus (S. aureus) biofilms. Furthermore, substantial reductions in bacterial counts were observed in both wounds and blood samples in the mice, highlighting the great potential of Ch@ZIF-L-H-Cl in combating bacterial biofilm infections.

Natural sideromycins and siderophore-conjugated natural products as inspiration for novel antimicrobial agents

The widespread emergence of multidrug-resistant (MDR) Gram-negative pathogens has posed a major challenge to clinical anti-infective therapy, and new effective treatments are urgently needed. A promising "Trojan horse" strategy involves conjugating antibiotics to siderophore molecules; the resulting siderophore-antibiotic conjugates (SACs) deliver antibiotics directly into cells by hijacking the sophisticated iron transport systems of Gram-negative bacteria, bypassing the outer membrane permeability barrier to enhance uptake and antibacterial efficacy. The clinical release of the first siderophore-antibiotic conjugate, cefiderocol, has aroused tremendous interest in the field among researchers and pharmaceutical companies. To date, most of the reported SACs have focused on the conjugation of siderophores to traditional antibacterial drugs. However, these antibacterial agents designed on the basis of the traditional antibiotic skeleton theoretically bear the risk of cross-resistance caused by shared molecular scaffolds. In this case, exploring novel natural product antibacterial conjugate scaffolds to circumvent the risk of early cross-resistance represents a presumably more sustainable approach for the development of SACs. In this review, we systematically summarize the research progress on siderophore-natural product conjugates as novel antimicrobial agents reported since 2010. Additionally, we propose challenges to be overcome and prospects for future development in this field.

Moonlighting antibiotics: the extra job of modulating biofilm formation

The widespread use of antibiotics to treat bacterial infections has led to the common perception that their only function is to inhibit growth or kill bacteria. However, it has become clear that when antibiotics reach susceptible bacteria at non-lethal concentrations, they perform additional functions that significantly impact bacterial physiology, shaping both individual and collective behaviors. A key bacterial behavior influenced by sub-lethal antibiotic doses is biofilm formation, a multicellular, surface-associated mode of growth. This review explores different contexts in which natural and clinical antibiotics act as modulators of bacterial biofilm formation. We discuss cases that provide mechanistic insights into antibiotic modes of action, highlighting emerging common patterns and novel findings that pave the way for future research.

Photoimmunologic Therapy of Stubborn Biofilm via Inhibiting Bacteria Revival and Preventing Reinfection

Stubborn biofilm infections pose serious threats to public health. Clinical practices highly rely on mechanical debridement and antibiotics, which often fail and lead to persistent and recurrent infections. The main culprits are 1) persistent bacteria reviving, colonizing, and rejuvenating biofilms, and 2) secondary pathogen exposure, particularly in individuals with chronic diseases. Addressing how to inhibit persistent bacteria revival and prevent reinfection simultaneously is still a major challenge. Herein, an oligo-ethylene glycol-modified lipophilic cationic photosensitizer (PS), TBTCP-PEG7, is developed. It effectively eradicates Methicillin-Resistant Staphylococcus aureus (MRSA) under light irradiation. Furthermore, TBTCP-PEG7-mediated photodynamic therapy (PDT) not only conquers stubborn biofilm infections by downregulating the two-component system (TCS), quorum sensing (QS), and virulence factors, thereby reducing intercellular communication, inhibiting persistent bacterial regrowth and biofilm remodeling but also prevents reinfection by upregulating heat shock protein-related genes to induce immunogenetic cell death (ICD) and establish immune memory. In vivo, TBTCP-PEG7 efficiently eradicates MRSA biofilm adhered to medical catheters, stimulates angiogenesis, reduces inflammatory factor expression, and accelerates wound healing. Furthermore, ICD promotes short-term immune and long-term immunological memory for coping with secondary infections. This two-pronged strategy not only effectively overcomes stubborn, persistent and recurrent biofilm infection, but also provides theoretical guidance for designing the next generation of antibacterial materials.

A stable dual functional superhydrophobic coating to inhibit Proteus mirabilis colonization, migration, and encrustation formation for urinary catheter applications

Catheter-associated urinary tract infections are some of the most common hospital-acquired infections. Proteus mirabilis, a common pathogen associated with urinary tract infections, has swarming motility and has pili on its surface for adhesion and flagella for upward movement. Migration of P. mirabilis along the catheter surface can lead to ascending urinary tract infection. However, there is currently a lack of effective strategies to inhibit or delay the colonization, migration, and encrustation formation of P. mirabilis in urinary catheters. This study developed a method for constructing a stable superhydrophobic coating on the surface of urinary catheters using a layer-by-layer approach. The adhesion and deposition of polydopamine were enhanced by pre-coating a liquid bandage film on the polydimethylsiloxane surface, resulting in a multilayer micro-nano composite structure on the catheter surface. This structure was combined with copper ions and superhydrophobic modifiers, ultimately resulting in a highly stable superhydrophobic coating. The coating retains its superhydrophobic properties after prolonged incubation, friction tests, and tape peeling tests. Importantly, the coating demonstrates excellent efficacy in inhibiting P. mirabilis colonization, migration, and encrustation formation. This study offers novel insights into developing biomedical superhydrophobic coatings with enhanced stability and efficacy in inhibiting urinary tract bacterial infections.

Surfactin facilitates establishment of Bacillus subtilis in synthetic communities

Soil bacteria are prolific producers of a myriad of biologically active secondary metabolites. These natural products play key roles in modern society, finding use as anti-cancer agents, as food additives, and as alternatives to chemical pesticides. As for their original role in interbacterial communication, secondary metabolites have been extensively studied under in vitro conditions, revealing many roles including antagonism, effects on motility, niche colonization, signaling, and cellular differentiation. Despite the growing body of knowledge on their mode of action, biosynthesis, and regulation, we still do not fully understand the role of secondary metabolites on the ecology of the producers and resident communities in situ. Here, we specifically examine the influence of Bacillus subtilis-produced cyclic lipopeptides during the assembly of a bacterial synthetic community, and simultaneously, explore the impact of cyclic lipopeptides on B. subtilis establishment success in a synthetic community propagated in an artificial soil microcosm. We found that surfactin production facilitates B. subtilis establishment success within multiple synthetic communities. Although neither a wild type nor a cyclic lipopeptide non-producer mutant had a major impact on the synthetic community composition over time, both the B. subtilis and the synthetic community metabolomes were altered during co-cultivation. Overall, our work demonstrates the importance of surfactin production in microbial communities, suggesting a broad spectrum of action of this natural product.

Bacillus lipopeptides as key players in rhizosphere chemical ecology

Microbial natural products are widely explored for their therapeutic potential. Understanding the underlying evolutionary and adaptive forces driving their production remains a fundamental question in biology. Amphiphilic cyclic lipopeptides (CLPs), a prominent category of bacterial specialized metabolites, show strong antimicrobial activity, particularly against phytopathogens. It is thus assumed that these compounds are deployed by soil- or rhizosphere-dwelling bacteria as microbial weapons in competitive natural environments. Here, we challenge this reductionist perspective and present evidence that Bacillus CLPs are prominent chemical mediators of ecological interactions. They help Bacillus to communicate, compete, defend against predators, or cooperate and establish mutualistic relationships with other (micro)organisms. Additional parallel examples are highlighted in other genera, such as Pseudomonas. This broader perspective underscores the need for further investigation into the role of CLPs in shaping the adaptive strategies of key rhizobacterial species.

High-generation tetracyclines shifted microbial community composition and induced the emergence of antibiotic resistant bacteria in soil

Tetracyclines (TCs) have been widely detected in agricultural soil due to their widespread use in animal husbandry. The impact of low-generation TCs, i.e., the first- and second- generations, on soil ecosystem has attracted widespread attention. However, the dynamic response of soil microbial community to high-generation TCs, i.e., the third- and fourth- generations, remains largely unknown. Herein, we characterized the variations in the composition, diversity and succession of microbial community and the proliferation of antibiotic resistance genes (ARGs) under the stress of four generations of TCs in brown soil and red soil. The results demonstrated that the exposure of low- and high- generation TCs consistently decreased the alpha diversity and stimulated the succession rate of microbial community in soil. High-generation TCs strongly shifted microbial community composition by reducing community resilience. The complexity of microbial networks and cross-module associations were strengthened to cope with the stress of high-generation TCs in soil. The abundance of ARGs was exacerbated by 1.75 times in response to the fourth-generation TCs compared to control in brown soil. The potential bacterial hosts of ARGs were more diverse in brown soil exposed to high-generation TCs, but the dominant hosts were not changed. These results highlight the potential ecological risk of the newly developed antibiotics, which is helpful for a comprehensive risk assessment of emerging contaminants.

The Epiphyte Bacillus sp. G2112 Produces a Large Diversity of Nobilamide Peptides That Promote Biofilm Formation in Pseudomonads and Mycobacterium aurum

Bacillus sp. G2112, an isolate from cucumber plants that inhibited plant pathogens, produces not only surfactins, iturins, and fengycins common to many Bacillus spp., but also a large variety of N-acyl-(depsi)peptides related to A-3302-B and nobilamides. Four known and fourteen previously unreported nobilamide peptides were characterized using high-resolution mass spectrometry, tandem mass spectrometry, and NMR. The stereochemistry of the amino acids of nobilamide peptides was determined using Marfey's method. The diversity of nobilamide peptides from Bacillus sp. G2112 resulted from the incorporation of different acyl groups and amino acids in the sequence. The peptides occur in linear or cyclic form. In addition, a truncated N-acetylpentapeptide was produced. Agar diffusion assays with selected nobilamide peptides against plant pathogens and human pathogens revealed that A-3302-B and its N-acyl homologs, A-3302-A and nobilamide J, exhibited powerful antibiotic activity (at 5 µg/hole) against Lysinibacillus sphaericus that can cause severe sepsis and bacteremia in patients. Moreover, nobilamide peptides from Bacillus sp. G2112 strongly promoted biofilm formation in the Gram-positive Mycobacterium aurum and Gram-negative pseudomonads. Structurally diverse nobilamides from Bacillus sp. G2112, whether linear or cyclic, penta and heptapeptides, induced biofilm formation, suggesting that the common N-acetyl-D-Phe-D-Leu-L-Phe-D-allo-Thr-L-Val amino acid sequence motif is important for the biofilm-inducing activity.

Glyphosate effects on growth and biofilm formation in bee gut symbionts and diverse associated bacteria

Biofilm formation is a common adaptation enabling bacteria to thrive in various environments and withstand external pressures. In the context of host-microbe interactions, biofilms play vital roles in establishing microbiomes associated with animals and plants and are used by opportunistic microbes to facilitate survival within hosts. Investigating biofilm dynamics, composition, and responses to environmental stressors is crucial for understanding microbial community assembly and biofilm regulation in health and disease. In this study, we explore in vivo colonization and in vitro biofilm formation abilities of core members of the honey bee (Apis mellifera) gut microbiota. Additionally, we assess the impact of glyphosate, a widely used herbicide with antimicrobial properties, and a glyphosate-based herbicide formulation on growth and biofilm formation in bee gut symbionts as well as in other biofilm-forming bacteria associated with diverse animals and plants. Our results demonstrate that several strains of core bee gut bacterial species can colonize the bee gut, which probably depends on their ability to form biofilms. Furthermore, glyphosate exposure elicits variable effects on bacterial growth and biofilm formation. In some instances, the effects correlate with the bacteria's ability to encode a susceptible or tolerant version of the enzyme inhibited by glyphosate in the shikimate pathway. However, in other instances, no such correlation is observed. Testing the herbicide formulation further complicates comparisons, as results often diverge from glyphosate exposure alone, suggesting that co-formulants influence bacterial growth and biofilm formation. These findings highlight the nuanced impacts of environmental stressors on microbial biofilms, with both ecological and host health-related implications.

IMPORTANCE

Biofilms are essential for microbial communities to establish and thrive in diverse environments. In the honey bee gut, the core microbiota member Snodgrassella alvi forms biofilms, potentially aiding the establishment of other members and promoting interactions with the host. In this study, we show that specific strains of other core members, including Bifidobacterium, Bombilactobacillus, Gilliamella, and Lactobacillus, also form biofilms in vitro. We then examine the impact of glyphosate, a widely used herbicide that can disrupt the bee microbiota, on bacterial growth and biofilm formation. Our findings demonstrate the diverse effects of glyphosate on biofilm formation, ranging from inhibition to enhancement, reflecting observations in other beneficial or pathogenic bacteria associated with animals and plants. Thus, glyphosate exposure may influence bacterial growth and biofilm formation, potentially shaping microbial establishment on host surfaces and impacting health outcomes.

Emerging Issues and Initial Insights into Bacterial Biofilms: From Orthopedic Infection to Metabolomics

Bacterial biofilms, enigmatic communities of microorganisms enclosed in an extracellular matrix, still represent an open challenge in many clinical contexts, including orthopedics, where biofilm-associated bone and joint infections remain the main cause of implant failure. This study explores the scenario of biofilm infections, with a focus on those related to orthopedic implants, highlighting recently emerged substantial aspects of the pathogenesis and their potential repercussions on the clinic, as well as the progress and gaps that still exist in the diagnostics and management of these infections. The classic mechanisms through which biofilms form and the more recently proposed new ones are depicted. The ways in which bacteria hide, become impenetrable to antibiotics, and evade the immune defenses, creating reservoirs of bacteria difficult to detect and reach, are delineated, such as bacterial dormancy within biofilms, entry into host cells, and penetration into bone canaliculi. New findings on biofilm formation with host components are presented. The article also delves into the emerging and critical concept of immunometabolism, a key function of immune cells that biofilm interferes with. The growing potential of biofilm metabolomics in the diagnosis and therapy of biofilm infections is highlighted, referring to the latest research.

Pectic homogalacturonan sensed by Bacillus acts as host associated cue to promote establishment and persistence in the rhizosphere

Bacillus velezensis isolates are among the most promising plant-associated beneficial bacteria used as biocontrol agents. However, various aspects of the chemical communication between the plant and these beneficials, determining root colonization ability, remain poorly described. Here we investigated the molecular basis of such interkingdom interaction occurring upon contact between Bacillus velezensis and its host via the sensing of pectin backbone homogalacturonan (HG). We showed that B. velezensis stimulates key developmental traits via a dynamic process involving two conserved pectinolytic enzymes. This response integrates transcriptional changes leading to the switch from planktonic to sessile cells, a strong increase in biofilm formation, and an accelerated sporulation dynamics while conserving the potential to efficiently produce specialized secondary metabolites. As a whole, we anticipate that this response of Bacillus to cell wall-derived host cues contributes to its establishment and persistence in the competitive rhizosphere niche and ipso facto to its activity as biocontrol agent.

Mupirocin enhances the biofilm formation of Staphylococcus epidermidis in an atlE-dependent manner

The pathogenicity of Staphylococcus epidermidis is largely attributed to its exceptional ability to form biofilms. Here, we report that mupirocin, an antimicrobial agent widely used for staphylococcal decolonization and anti-infection, strongly stimulates the biofilm formation of S. epidermidis. Although the polysaccharide intercellular adhesin (PIA) production was unaffected, mupirocin significantly facilitated extracellular DNA (eDNA) release by accelerating autolysis, thereby positively triggering cell surface attachment and intercellular agglomeration during biofilm development. Mechanistically, mupirocin regulated the expression of genes encoding for the autolysin AtlE as well as the programmed cell death system CidA-LrgAB. Critically, through gene knockout, we found out that deletion of atlE, but not cidA or lrgA, abolished the enhancement of biofilm formation and eDNA release in response to mupirocin treatment, indicating that atlE is required for this effect. In Triton X-100 induced autolysis assay, mupirocin treated atlE mutant displayed a slower autolysis rate compared with the wild-type strain and complementary strain. Therefore, we concluded that subinhibitory concentrations of mupirocin enhance the biofilm formation of S. epidermidis in an atlE dependent manner. This induction effect could conceivably be responsible for some of the more unfavourable outcomes of infectious diseases.

Assembly of an active microbial consortium by engineering compatible combinations containing foreign and native biocontrol bacteria of kiwifruit

Assembling functional bacterial biocontrol consortia is expected to expand the scope and efficiency of biocontrol agents. Generally, bacterial interspecies interactions lead to incompatibility events, as bacteria can produce antibacterial compounds and/or assemble contact-dependent killing (CDK) devices. Here, we aimed to assemble a bacterial consortium comprising Lysobacter enzymogenes OH11 and Bacillus safensis ZK-1 for the synergistic control of bacterial and fungal diseases of kiwifruit. ZK-1, a native kiwifruit biocontrol bacterium, is effective against Pseudomonas syringae pv. actinidiae (Psa) that causes bacterial kiwifruit canker, but has weak antifungal activity. OH11 is a foreign kiwifruit biocontrol agent with strong antifungal activity. While OH11 was unable to produce anti-Gram-negative metabolites, this strain could utilize type IV secretion system as an antibacterial CDK weapon. We first observed that OH11 could inhibit growth of ZK-1 by generating diffusible anti-Gram-positive antibiotic WAP-8294A2, whereas ZK-1 failed to generate diffusible antibacterial compound to inhibit growth of OH11. To disrupt this interspecies incompatibility, we generated a transgenic OH11-derived strain, OH11W, by deleting the WAP-8294A2 biosynthetic gene and found that OH11W did not kill ZK-1. We further observed that when OH11W and ZK-1 were co-inoculated on agar plates, no CDK effect was observed between them, whereas co-culture of OH11W or ZK-1 with Psa on agar plates resulted in Psa killing, suggesting L. enzymogenes and B. safensis assemble antibacterial CDK weapons against bacterial pathogens, and these CDK weapons did not affect the compatibility between OH11W and ZK-1. Based on these findings, we assembled an OH11W/ZK-1 dependent consortium that was shown to be functional in controlling bacterial canker and several representative fungal diseases of kiwifruit.

Antibacterial and antibiofilm efficacy of the preferred fractions and compounds from Euphorbia humifusa (herba euphorbiae humifusae) against Staphylococcus aureus

ETHNOPHARMACOLOGICAL RELEVANCE

Euphorbia humifusa Willd., known as Di-Jin-Cao in Chinese, has long been utilized as a traditional herb for the treatment of furuncles and carbuncles mainly caused by Staphylococcus aureus infection. Despite extensive chemical and pharmacological studies reported previously for E. humifusa, the antibacterial and antibiofilm activities against S. aureus as well as the related mechanism of action (MoA) remain largely obscure.

AIM OF THE STUDY

To investigate the antibacterial and antibiofilm activities of the preferred fractions and compounds from E. humifusa against S. aureus and assess the associated MoA.

MATERIALS AND METHODS

The bioactive fractions and compounds were obtained from the 75% ethanol extract of E. humifusa (75%-EEEH) with the assistance of the related antibacterial and antibiofilm screening. Their antibacterial activities were determined using the broth microdilution method, whilst the inhibition of biofilm formation and the disruption of preformed biofilm were assessed by crystal violet staining and confocal laser scanning microscopy (CLSM). To achieve more effective therapies, the combinatory effects of different components were also studied. The biofilm metabolic activities of isolated compounds were evaluated by 2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide (XTT) reduction assay. The scanning electron microscopy (SEM) and quantitative real-time polymerase chain reaction (qRT-PCR) were employed to explore the antibiofilm mechanism.

RESULTS

Fractions DJC06 and DJC07 collected from the ethyl acetate extract of the 75%-EEEH exhibited antibacterial activity (MIC = 256 μg/mL) against S. aureus and further separation of these two fractions led to the isolation and characterization of 22 compounds. Among the isolates, luteolin (LU), quercetin (QU), and kaempferol (KA) are the verified components associated with the antibacterial and antibiofilm activities by displaying individual or combinational MIC values of 8-128 μg/mL and 70.9-99.7% inhibition for biofilm formation. Importantly, QU and KA can work in synergy with LU to significantly enhance the efficacy via destroying cell integrity, increasing membrane permeability, and down-regulating the biofilm-related gene expression.

CONCLUSIONS

The preferred fractions and compounds from E. humifusa exerted desired antibacterial and antibiofilm efficacy against S. aureus via a MoA involving cell morphology disruption and altered genes expression. The findings herein not only support its traditional use in the treatment of furuncles and carbuncles, but reveal E. humifusa is a potential source for producing promising antibiofilm alternatives against S. aureus and highlight the isolated components (LU, QU, KA) that can potentiate the efficacy when used in synergy.

Plant-associated Bacillus mobilizes its secondary metabolites upon perception of the siderophore pyochelin produced by a Pseudomonas competitor

Bacillus velezensis is considered as model species for plant-associated bacilli providing benefits to its host such as protection against phytopathogens. This is mainly due to the potential to secrete a wide range of secondary metabolites with specific and complementary bioactivities. This metabolite arsenal has been quite well defined genetically and chemically but much remains to be explored regarding how it is expressed under natural conditions and notably how it can be modulated upon interspecies interactions in the competitive rhizosphere niche. Here, we show that B. velezensis can mobilize a substantial part of its metabolome upon the perception of Pseudomonas, as a soil-dwelling competitor. This metabolite response reflects a multimodal defensive strategy as it includes polyketides and the bacteriocin amylocyclicin, with broad antibiotic activity, as well as surfactin lipopeptides, contributing to biofilm formation and enhanced motility. Furthermore, we identified the secondary Pseudomonas siderophore pyochelin as an info-chemical, which triggers this response via a mechanism independent of iron stress. We hypothesize that B. velezensis relies on such chelator sensing to accurately identify competitors, illustrating a new facet of siderophore-mediated interactions beyond the concept of competition for iron and siderophore piracy. This phenomenon may thus represent a new component of the microbial conversations driving the behavior of members of the rhizosphere community.

Effects of daphnetin on biofilm formation and motility of pseudomonas aeruginosa

Introduction

Pseudomonas aeruginosa is a common clinical opportunistic pathogen. Antibiotic resistance of P. aeruginosa is frequent, and it affects the clinical curative effect and leads to recurrent infections, disease progression, and difficult treatment, especially in cystic fibrosis patients. The drug-resistance mechanism of P. aeruginosa is complex, and biofilms play an important role. Given the widespread antibiotic resistance of P. aeruginosa, the discovery of a drug that can prevent or eradicate biofilm formation is imperative. Daphnetin (DAP), a coumarin derivative, is a safe, non-toxic, natural compound with antibacterial and anti-biofilm properties. Herein, this study highlights the bacterial motility effects, antibacterial effect, pyocyanin production, and anti-biofilm potential of DAP against P. aeruginosa.

Methods

In this study, the minimal inhibitory concentration of DAP against P. aeruginosa was determined using the microdilution method. The antibiofilm activity of DAP against P. aeruginosa was determined using crystal violet staining, colony-forming unit enumeration, and scanning electron microscopy. The effect of DAP on P. aeruginosa motility was detected using the swimming, swarming, and twitching agar plates to measure the diameter of the concentric area.

Results

We found that DAP at concentrations of 0.445–1.781 mg/mL and 0.89–1.781 mg/mL can effectively inhibit biofilm formation and eradicate the formed biofilm of P. aeruginosa, respectively. DAP reduced pyocyanin production and inhibited bacterial motility of P. aeruginosa.

Discussion

In conclusion, our results support the conclusion that DAP can effectively eradicate formed biofilm and inhibit biofilm formation, bacterial motility, and pyocyanin production of P. aeruginosa and may represent a natural anti-biofilm therapeutic agent.

Caffeic Acid Phenethyl Ester (CAPE) Inhibits Cross-Kingdom Biofilm Formation of Streptococcus mutans and Candida albicans

Streptococcus mutans and Candida albicans exhibit strong cariogenicity through cross-kingdom biofilm formation during the pathogenesis of dental caries. Caffeic acid phenethyl ester (CAPE), a natural compound, has potential antimicrobial effects on each species individually, but there are no reports of its effect on this dual-species biofilm. This study aimed to explore the effects of CAPE on cariogenic biofilm formation by S. mutans and C. albicans and the related mechanisms. The effect of CAPE on planktonic cell growth was investigated, and crystal violet staining, the anthrone-sulfuric acid assay and confocal laser scanning microscopy were used to evaluate biofilm formation. The structures of the formed biofilms were observed using scanning electron microscopy. To explain the antimicrobial effect of CAPE, quantitative real-time PCR (qRT-PCR) was applied to monitor the relative expression levels of cariogenic genes. Finally, the biocompatibility of CAPE in human oral keratinocytes (HOKs) was evaluated using the CCK-8 assay. The results showed that CAPE suppressed the growth, biofilm formation and extracellular polysaccharides (EPS) synthesis of C. albicans and S. mutans in the coculture system of the two species. The expression of the gtf gene was also suppressed by CAPE. The efficacy of CAPE was concentration dependent, and the compound exhibited acceptable biocompatibility. Our research lays the foundation for further study of the application of the natural compound CAPE as a potential antimicrobial agent to control dental caries-associated cross-kingdom biofilms. IMPORTANCE Severe dental caries is a multimicrobial infectious disease that is strongly induced by the cross-kingdom biofilm formed by S. mutans and C. albicans. This study aimed to investigate the potential of caffeic acid phenethyl ester (CAPE) as a natural product in the prevention of severe caries. This study clarified the inhibitory effect of CAPE on cariogenic biofilm formation and the control of cariogenic genes. It deepens our understanding of the synergistic cariogenic effect of S. mutans and C. albicans and provides a new perspective for the prevention and control of dental caries with CAPE. These findings may contribute to the development of CAPE as a promising antimicrobial agent targeting this caries-related cross-kingdom biofilm.

Cyclic AMP and biofilms reveal the synergistic proliferation strategy of Pseudomonas aeruginosa and Escherichia coli under the costimulation of high concentrations of microplastics and enrofloxacin

Microplastics (MPs) provide attachment sites for biofilm formation of microorganisms, which can promote their resistance to environmental stress has been proved. However, the effect of MPs on synergy survival among microorganisms under antibiotic stress remains unclear. In the present study, the proliferation of Escherichia coli and Pseudomonas aeruginosa was assessed under enrofloxacin stress with the influence of MPs. Here, MPs reduced the growth speed of E. coli and enhanced that of P. aeruginosa, especially at 12 h, but the final value of OD₆₀₀ and CFU of both bacteria not be influenced. E. coli was enrofloxacin sensitive (MIC = 0.25 μg/mL), and a high MP concentration in the presence of enrofloxacin notably enhanced the biofilm formation ability of P. aeruginosa, but proliferation decreased. In the coculture system, the proliferation of E. coli (increased 1.42-fold) and P. aeruginosa (increased 1.06-fold) both increased under enrofloxacin stress (0.25 μg/mL) with high-concentration MP addition. P. aeruginosa may provide the biofilm matrix for E. coli to resist the stress of enrofloxacin. The high concentration of cyclic AMP secreted by E. coli may slightly inhibited biofilm formation, leading to a decrease in the fitness cost of P. aeruginosa; thus, the proliferation of P. aeruginosa increased. The present study is the first to show that MP combined with antibiotics stimulates the metabolic cooperation of bacteria to promote proliferation.

Novel Antibiofilm Inhibitor Ginkgetin as an Antibacterial Synergist against Escherichia coli

As an opportunistic pathogen, Escherichia coli (E. coli) forms biofilm that increases the virulence of bacteria and antibiotic resistance, posing a serious threat to human and animal health. Recently, ginkgetin (Gin) has been discovered to have antiinflammatory, antioxidant, and antitumor properties. In the present study, we evaluated the antibiofilm and antibacterial synergist of Gin against E. coli. Additionally, Alamar Blue assay combined with confocal laser scanning microscope (CLSM) and crystal violet (CV) staining was used to evaluate the effect of antibiofilm and antibacterial synergist against E. coli. Results showed that Gin reduces biofilm formation, exopolysaccharide (EPS) production, and motility against E. coli without limiting its growth and metabolic activity. Furthermore, we identified the inhibitory effect of Gin on AI-2 signaling molecule production, which showed apparent anti-quorum sensing (QS) properties. The qRT-PCR also indicated that Gin reduced the transcription of curli-related genes (csgA, csgD), flagella-formation genes (flhC, flhD, fliC, fliM), and QS-related genes (luxS, lsrB, lsrK, lsrR). Moreover, Gin showed obvious antibacterial synergism to overcome antibiotic resistance in E. coli with marketed antibiotics, including gentamicin, colistin B, and colistin E. These results suggested the potent antibiofilm and novel antibacterial synergist effect of Gin for treating E. coli infections.

Design, Synthesis, and Application of Carbon Dots With Synergistic Antibacterial Activity

The diversity of bacteria and their ability to acquire drug resistance lead to many challenges in traditional antibacterial methods. Photothermal therapies that convert light energy into localized physical heat to kill target microorganisms do not induce resistance and provide an alternative for antibacterial treatment. However, many photothermal materials cannot specifically target bacteria, which can lead to thermal damage to normal tissues, thus seriously affecting their biological applications. Here, we designed and synthesized bacteria-affinitive photothermal carbon dots (BAPTCDs) targeting MurD ligase that catalyzes the synthesis of peptidoglycan (PG) in bacteria. BAPTCDs presented specific recognition ability and excellent photothermal properties. BAPTCDs can bind to bacteria very tightly due to their chiral structure and inhibit enzyme activity by competing with D-glutamic acid to bind to MurD ligases, thus inhibiting the synthesis of bacterial walls. It also improves the accuracy of bacteria treatment by laser irradiation. Through the synergy of biochemical and physical effects, the material offers outstanding antibacterial effects and potentially contributes to tackling the spread of antibiotic resistance and facilitation of antibiotic stewardship.

Prevalence of Escherichia coli strains in horticultural farms from Argentina: antibiotic resistance, biofilm formation, and phylogenetic affiliation

Escherichia coli is the bacteria most commonly used as an indicator of fecal contamination in agricultural environments. Moreover, E. coli is categorized as a priority pathogen due to its widespread antibiotic resistance. This study aimed to characterize E. coli strains isolated from 10 horticultural farms. Isolates were obtained from samples of vegetable crops (n = 62), the surrounding soil (n = 62), poultry litter (n = 8), and groundwater (n = 6). Phyllo-grouping assignment was performed on the total of E. coli isolates. Antibiograms and quantification of the minimal inhibitory concentration (MIC) were performed with antibiotics commonly used in humans. Biofilm formation capacity was studied by quantifying cells attached to culture tubes. Overall, 21 E. coli isolates were obtained. Three phylogenetic groups (A, B1, and C) and two Escherichia clade IV and IV-V were identified in the collection by polymerase chain reaction. Sixty-seven percent of the E. coli isolates were resistant to amoxicillin-clavulanic acid and/or ampicillin. Amoxicillin MIC values ranged from 11.9 to >190.5 µg/mL and ampicillin MIC values ranged from 3 to >190.5 µg/mL. All the E. coli isolates, resistant and non-resistant, had biofilm forming capacity. The presence of phenotypic resistance on fresh produce and environmental matrices could present significant opportunities for contamination that result in health risks for consumers. To the authors' best knowledge, this is the first environmental assessment of resistant E. coli occurrence in horticultural farms in South America.

Nanophysical Antimicrobial Strategies: A Rational Deployment of Nanomaterials and Physical Stimulations in Combating Bacterial Infections

The emergence of bacterial resistance due to the evolution of microbes under antibiotic selection pressure, and their ability to form biofilm, has necessitated the development of alternative antimicrobial therapeutics. Physical stimulation, as a powerful antimicrobial method to disrupt microbial structure, has been widely used in food and industrial sterilization. With advances in nanotechnology, nanophysical antimicrobial strategies (NPAS) have provided unprecedented opportunities to treat antibiotic-resistant infections, via a combination of nanomaterials and physical stimulations. In this review, NPAS are categorized according to the modes of their physical stimulation, which include mechanical, optical, magnetic, acoustic, and electrical signals. The biomedical applications of NPAS in combating bacterial infections are systematically introduced, with a focus on their design and antimicrobial mechanisms. Current challenges and further perspectives of NPAS in the clinical treatment of bacterial infections are also summarized and discussed to highlight their potential use in clinical settings. The authors hope that this review will attract more researchers to further advance the promising field of NPAS, and provide new insights for designing powerful strategies to combat bacterial resistance.

Exploration of BAY 11-7082 as a Potential Antibiotic

Exposure of the Gram-negative pathogen Pseudomonas aeruginosa to subinhibitory concentrations of antibiotics increases the formation of biofilms. We exploited this phenotype to identify molecules with potential antimicrobial activity in a biofilm-based high-throughput screen. The anti-inflammatory compound BAY 11-7082 induced dose-dependent biofilm stimulation, indicative of antibacterial activity. We confirmed that BAY 11-7082 inhibits the growth of P. aeruginosa and other priority pathogens, including methicillin-resistant Staphylococcus aureus (MRSA). We synthesized 27 structural analogues, including a series based on the related scaffold 3-(phenylsulfonyl)-2-pyrazinecarbonitrile (PSPC), 10 of which displayed increased anti-Staphylococcal activity. Because the parent molecule inhibits the NLR Family Pyrin Domain Containing 3 (NLRP3) inflammasome, we measured the ability of select analogues to reduce interleukin-1β (IL-1β) production in mammalian macrophages, identifying minor differences in the structure-activity relationship for the anti-inflammatory and antibacterial properties of this scaffold. Although we could evolve stably resistant MRSA mutants with cross-resistance to BAY 11-7082 and PSPC, their lack of shared mutations suggested that the two molecules could have multiple targets. Finally, we showed that BAY 11-7082 and its analogues synergize with penicillin G against MRSA, suggesting that this scaffold may serve as an interesting starting point for the development of antibiotic adjuvants.

Lipopeptide Interplay Mediates Molecular Interactions between Soil Bacilli and Pseudomonads

Some Bacillus species, such as B. velezensis, are important members of the plant-associated microbiome, conferring protection against phytopathogens. However, our knowledge about multitrophic interactions determining the ecological fitness of these biocontrol bacteria in the competitive rhizosphere niche is still limited. Here, we investigated molecular mechanisms underlying interactions between B. velezensis and Pseudomonas as a soil-dwelling competitor. Upon their contact-independent in vitro confrontation, a multifaceted macroscopic outcome was observed and characterized by Bacillus growth inhibition, white line formation in the interaction zone, and enhanced motility. We correlated these phenotypes with the production of bioactive secondary metabolites and identified specific lipopeptides as key compounds involved in the interference interaction and motile response. Bacillus mobilizes its lipopeptide surfactin not only to enhance motility but also to act as a chemical trap to reduce the toxicity of lipopeptides formed by Pseudomonas. We demonstrated the relevance of these unsuspected roles of lipopeptides in the context of competitive tomato root colonization by the two bacterial genera.

IMPORTANCE Plant-associated Bacillus velezensis and Pseudomonas spp. represent excellent model species as strong producers of bioactive metabolites involved in phytopathogen inhibition and the elicitation of plant immunity. However, the ecological role of these metabolites during microbial interspecies interactions and the way their expression may be modulated under naturally competitive soil conditions has been poorly investigated. Through this work, we report various phenotypic outcomes from the interactions between B. velezensis and 10 Pseudomonas strains used as competitors and correlate them with the production of specific metabolites called lipopeptides from both species. More precisely, Bacillus overproduces surfactin to enhance motility, which also, by acting as a chemical trap, reduces the toxicity of other lipopeptides formed by Pseudomonas. Based on data from interspecies competition on plant roots, we assume this would allow Bacillus to gain fitness and persistence in its natural rhizosphere niche. The discovery of new ecological functions for Bacillus and Pseudomonas secondary metabolites is crucial to rationally design compatible consortia, more efficient than single-species inoculants, to promote plant health and growth by fighting economically important pathogens in sustainable agriculture.

Defining the Expression, Production, and Signaling Roles of Specialized Metabolites during Bacillus subtilis Differentiation

Bacterial specialized (or secondary) metabolites are structurally diverse molecules that mediate intra- and interspecies interactions by altering growth and cellular physiology and differentiation. Bacillus subtilis, a Gram-positive model bacterium commonly used to study biofilm formation and sporulation, has the capacity to produce more than 10 specialized metabolites. Some of these B. subtilis specialized metabolites have been investigated for their role in facilitating cellular differentiation, but only rarely has the behavior of multiple metabolites been simultaneously investigated. In this study, we explored the interconnectivity of differentiation (biofilm and sporulation) and specialized metabolites in B. subtilis. Specifically, we interrogated how development influences specialized metabolites and vice versa. Using the sporulation-inducing medium DSM, we found that the majority of the specialized metabolites examined are expressed and produced during biofilm formation and sporulation. Additionally, we found that six of these metabolites (surfactin, ComX, bacillibactin, bacilysin, subtilosin A, and plipastatin) are necessary signaling molecules for proper progression of B. subtilis differentiation. This study further supports the growing body of work demonstrating that specialized metabolites have essential physiological functions as cell-cell communication signals in bacteria. IMPORTANCE Bacterially produced specialized metabolites are frequently studied for their potential use as antibiotics and antifungals. However, a growing body of work has suggested that the antagonistic potential of specialized metabolites is not their only function. Here, using Bacillus subtilis as our model bacterium, we demonstrated that developmental processes such as biofilm formation and sporulation are tightly linked to specialized metabolite gene expression and production. Additionally, under our differentiation-inducing conditions, six out of the nine specialized metabolites investigated behave as intraspecific signals that impact B. subtilis physiology and influence biofilm formation and sporulation. Our work supports the viewpoint that specialized metabolites have a clear role as cell-cell signaling molecules within differentiated populations of bacteria.

Holomycin, an Antibiotic Secondary Metabolite, Is Required for Biofilm Formation by the Native Producer Photobacterium galatheae S2753

While the effects of antibiotics on microorganisms are widely studied, it remains less well understood how antibiotics affect the physiology of the native producing organisms. Here, using a marine bacterium, Photobacterium galatheae S2753, that produces the antibiotic holomycin, we generated a holomycin-deficient strain by in-frame deletion of hlmE, the core gene responsible for holomycin production. Mass spectrometry analysis of cell extracts confirmed that the ΔhlmE strain did not produce holomycin and that the mutant was devoid of antibacterial activity. Biofilm formation of the ΔhlmE strain was significantly reduced compared to that of wild-type S2753 and was restored in an hlmE complementary mutant. Consistent with this, exogenous holomycin, but not its dimethylated and less antibacterial derivative, S,S'-dimethyl holomycin, restored the biofilm formation of the ΔhlmE strain. Furthermore, zinc starvation was found to be essential for both holomycin production and biofilm formation of S2753, although the molecular mechanism remains elusive. Collectively, these data suggest that holomycin promotes biofilm formation of S2753 via its ene-disulfide group. Lastly, the addition of holomycin at subinhibitory concentrations also enhanced the biofilms of four other Vibrionaceae strains. P. galatheae likely gains an ecological advantage from producing holomycin as both an antibiotic and a biofilm stimulator, which facilitates nutrition acquisition and protects P. galatheae from environmental stresses. Studying the function of antibiotic compounds in the native producer will shed light on their roles in nature and could point to novel bioprospecting strategies.IMPORTANCE Despite the societal impact of antibiotics, their ecological functions remain elusive and have mostly been studied by exposing nonproducing bacteria to subinhibitory concentrations. Here, we studied the effects of the antibiotic holomycin on its native producer, Photobacterium galatheae S2753, a Vibrionaceae bacterium. Holomycin provides a distinct advantage to S2753 both as an antibiotic and by enhancing biofilm formation in the producer. Vibrionaceae species successfully thrive in global marine ecosystems, where they play critical ecological roles as free-living, symbiotic, or pathogenic bacteria. Genome mining has demonstrated that many have the potential to produce several bioactive compounds, including P. galatheae To unravel the contribution of the microbial metabolites to the development of marine microbial ecosystems, better insight into the function of these compounds in the producing organisms is needed. Our finding provides a model to pursue this and highlights the ecological importance of antibiotics to the fitness of the producing organisms.

The New Antibacterial Properties of the Plants: Quo vadis Studies of Anti-virulence Phytochemicals?

The recent increase in bacterial resistance to antibiotics has motivated the resurgence of the study of natural antimicrobial products. For centuries, plants have been recognized for their bactericidal properties. However, in the last two decades, it has been reported that several plant derived metabolites at growth subinhibitory concentrations also tend to have anti-virulence properties, since they reduce the expression of factors that cause damage and the establishment of pathogenic bacteria. In this area of study, plants have been positioned as one of the main natural sources of anti-virulence molecules, but only a small portion of the plant species that exist have been investigated. Also, anti-virulence studies have been primarily focused on analyzing the ability of extracts and compounds to inhibit quorum sensing and biofilms formation in vitro. This mini-review discusses the current panorama, the trends in the study of anti-virulence phytochemicals, as well as their potential for the development of antibacterial therapies.

Natural and Enantiopure Alkylglycerols as Antibiofilms Against Clinical Bacterial Isolates and Quorum Sensing Inhibitors of Chromobacterium violaceum ATCC 12472

Resistance mechanisms occur in almost all clinical bacterial isolates and represent one of the most worrisome health problems worldwide. Bacteria can form biofilms and communicate through quorum sensing (QS), which allow them to develop resistance against conventional antibiotics. Thus, new therapeutic candidates are sought. We focus on alkylglycerols (AKGs) because of their recently discovered quorum sensing inhibition (QSI) ability and antibiofilm potential. Fifteen natural enantiopure AKGs were tested to determine their effect on the biofilm formation of other clinical bacterial isolates, two reference strains and their QSI was determined using Chromobacterium violaceum ATCC 12472. The highest biofilm inhibition rates (%) and minimum QS inhibitory concentration were determined by a microtiter plate assay and ciprofloxacin was used as the standard antibiotic. At subinhibitory concentrations, each AKG reduced biofilm formation in a concentration-dependent manner against seven bacterial isolates, with values up to 97.2%. Each AKG displayed QSI at different levels of ability without affecting the growth of C. violaceum. AKG (2S)-3-O-(cis-13’-docosenyl)-1,2-propanediol was the best QS inhibitor (20 μM), while (2S)-3-O-(cis-9’-hexadecenyl)-1,2-propanediol was the least effective (795 μM). The results showed for the first time the QSI activity of this natural AKG series and suggest that AKGs could be promising candidates for further studies on preventing antimicrobial resistance.

Preparation of AAEK-functionalized cellulose film with antibacterial and anti-adhesion activities

Bacterial adhesion infection caused by medical materials in clinical application has become a serious threat, and it urgently needs new strategies to deal with these clinical challenges. The purpose of this study is to explore the effectiveness of surface-decorated aryl (β-amino) ethyl ketones (AAEK), a promising sorting enzyme A (SrtA) inhibitor of Staphylococcus aureus, to improve the anti-adhesion ability of biomaterials. AAEK was covalently grafted onto cellulose films (CF) via copper-catalyzed azide-alkyne 1, 3-dipolar cycloaddition click reaction. The data of contact angle measurements, ATR-FTIR and XPS proved the successful covalent attachment of AAEK-CF, and the antimicrobial efficacy of AAEK coating was assessed by CFUs, crystal violet staining, scanning electron microscopy and Living/Dead bacteria staining assay. The results illustrated that AAEK-CF exhibited excellent anti-adhesion ability to Staphylococcus aureus, and significantly reduced the number of bacteria adhering to the film. More importantly, AAEK-CF could hinder the formation of bacterial biofilm. Furthermore, AAEK-CF indicated no cytotoxicity to mammalian cells, and the cells could grow normally on the modified surface. Hence, our present work demonstrated that the grafting of the SrtA inhibitor-AAEK onto cellulose films enabled to combat bacterial biofilm formation in biomedical applications.

On the possible ecological roles of antimicrobials

The Introduction of antibiotics into the clinical use in the middle of the 20th century had a profound impact on modern medicine and human wellbeing. The contribution of these wonder molecules to public health and science is hard to overestimate. Much research has informed our understanding of antibiotic mechanisms of action and resistance at inhibitory concentrations in the lab and in the clinic. Antibiotics, however, are not a human invention as most of them are either natural products produced by soil microorganisms or semisynthetic derivatives of natural products. Because we use antibiotics to inhibit the bacterial growth, it is generally assumed that growth inhibition is also their primary ecological function in the environment. Nevertheless, multiple studies point to diverse nonlethal effects that are exhibited at lower levels of antibiotics. Here we review accumulating evidence of antibiosis and of alternative functions of antibiotics exhibited at subinhibitory concentrations. We also speculate on how these effects might alter phenotypes, fitness, and community composition of microbes in the context of the environment and suggest directions for future research.

Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance

A multitude of factors, such as drug misuse, lack of strong regulatory measures, improper sewage disposal, and low-quality medicine and medications, have been attributed to the emergence of drug resistant microbes. The emergence and outbreaks of multidrug resistance to last-line antibiotics has become quite common. This is further fueled by the slow rate of drug development and the lack of effective resistome surveillance systems. In this review, we provide insights into the recent advances made in computational approaches for the surveillance of antibiotic resistomes, as well as experimental formulation of combinatorial drugs. We explore the multiple roles of antibiotics in nature and the current status of combinatorial and adjuvant-based antibiotic treatments with nanoparticles, phytochemical, and other non-antibiotics based on synergetic effects. Furthermore, advancements in machine learning algorithms could also be applied to combat the spread of antibiotic resistance. Development of resistance to new antibiotics is quite rapid. Hence, we review the recent literature on discoveries of novel antibiotic resistant genes though shotgun and expression-based metagenomics. To decelerate the spread of antibiotic resistant genes, surveillance of the resistome is of utmost importance. Therefore, we discuss integrative applications of whole-genome sequencing and metagenomics together with machine learning models as a means for state-of-the-art surveillance of the antibiotic resistome. We further explore the interactions and negative effects between antibiotics and microbiomes upon drug administration.

Natural products as inspiration for the development of bacterial antibiofilm agents

Natural products have historically been a rich source of diverse chemical matter with numerous biological activities, and have played an important role in drug discovery in many areas including infectious disease. Synthetic and medicinal chemistry have been, and continue to be, important tools to realize the potential of natural products as therapeutics and as chemical probes. The formation of biofilms by bacteria in an infection setting is a significant factor in the recalcitrance of many bacterial infections, conferring increased tolerance to many antibiotics and to the host immune response, and as yet there are no approved therapeutics for combatting biofilm-based bacterial infections. Small molecules that interfere with the ability of bacteria to form and maintain biofilms can overcome antibiotic tolerance conferred by the biofilm phenotype, and have the potential to form combination therapies with conventional antibiotics. Many natural products with anti-biofilm activity have been identified from plants, microbes, and marine life, including: elligic acid glycosides, hamamelitannin, carolacton, skyllamycins, promysalin, phenazines, bromoageliferin, flustramine C, meridianin D, and brominated furanones. Total synthesis and medicinal chemistry programs have facilitated structure confirmation, identification of critical structural motifs, better understanding of mechanistic pathways, and the development of more potent, more accessible, or more pharmacologically favorable derivatives of anti-biofilm natural products.

Hormetic Promotion of Biofilm Growth by Polyvalent Bacteriophages at Low Concentrations

Interactions between bacteriophages (phages) and biofilms are poorly understood despite their broad ecological and water quality implications. Here, we report that biofilm exposure to lytic polyvalent phages at low concentrations (i.e., 10²-10⁴ phages/mL) can counterintuitively promote biofilm growth and densification (corroborated by confocal laser scanning microscopy (CLSM)). Such exposure hormetically upregulated quorum sensing genes (by 4.1- to 24.9-fold), polysaccharide production genes (by 3.7- to 9.3-fold), and curli synthesis genes (by 4.5- to 6.5-fold) in the biofilm-dwelling bacterial hosts (i.e., Escherichia coli and Pseudomonas aeruginosa) relative to unexposed controls. Accordingly, the biofilm matrix increased its polysaccharide and extracellular DNA content relative to unexposed controls (by 41.8 ± 2.3 and 81.4 ± 2.2%, respectively), which decreased biofilm permeability and increased structural integrity. This contributed to enhanced resistance to disinfection with chlorine (bacteria half-lives were 6.08 ± 0.05 vs 3.91 ± 0.03 min for unexposed controls) and to subsequent phage infection (biomass removal was 18.2 ± 1.2 vs 32.3 ± 1.2% for unexposed controls), apparently by mitigating diffusion of these antibacterial agents through the biofilm. Overall, low concentrations of phages reaching a biofilm may result in unintended biofilm stimulation, which might accelerate biofouling, biocorrosion, or other biofilm-related water quality problems.

Secondary Effects of Antibiotics on Microbial Biofilms

Biofilms are assemblages of microorganisms attached to each other, or to a surface, and encased in a protective, self-produced matrix. Such associations are now recognized as the predominant microbial growth mode. The physiology of cells in biofilms differs from that of the planktonic cells on which most research has been conducted. Consequently, there are significant gaps in our knowledge of the biofilm lifestyle. Filling this gap is particularly important, given that biofilm cells may respond differently to antibiotics than do planktonic cells of the same species. Understanding the effects of antibiotics on biofilms is of paramount importance for clinical practice due to the increased levels of antibiotic resistance and resistance dissemination in biofilms. From a wider environmental perspective antibiotic exposure can alter the ecology of biofilms in nature, and hence disrupt ecosystems. Biofilm cells display increased resilience toward antibiotics. This resilience is often explained by mechanisms and traits such as decreased antibiotic penetration, metabolically inactive persister cells, and intrinsic resistance by members of the biofilm community. Together, these factors suggest that cells in biofilms are often exposed to subinhibitory concentrations of antimicrobial agents. Here we discuss how cells in biofilms are affected by the presence of antibiotics at subinhibitory concentrations, and the possible ramifications of such secondary effects for healthcare and the environment.

Bacillus Responses to Plant-Associated Fungal and Bacterial Communities

Some members of root-associated Bacillus species have been developed as biocontrol agents due to their contribution to plant protection by directly interfering with the growth of pathogens or by stimulating systemic resistance in their host. As rhizosphere-dwelling bacteria, these bacilli are surrounded and constantly interacting with other microbes via different types of communications. With this review, we provide an updated vision of the molecular and phenotypic responses of Bacillus upon sensing other rhizosphere microorganisms and/or their metabolites. We illustrate how Bacillus spp. may react by modulating the production of secondary metabolites, such as cyclic lipopeptides or polyketides. On the other hand, some developmental processes, such as biofilm formation, motility, and sporulation may also be modified upon interaction, reflecting the adaptation of Bacillus multicellular communities to microbial competitors for preserving their ecological persistence. This review also points out the limited data available and a global lack of knowledge indicating that more research is needed in order to, not only better understand the ecology of bacilli in their natural soil niche, but also to better assess and improve their promising biocontrol potential.

Roles of Organohalide-Respiring Dehalococcoidia in Carbon Cycling

The class Dehalococcoidia within the Chloroflexi phylum comprises the obligate organohalide-respiring genera Dehalococcoides, Dehalogenimonas, and “Candidatus Dehalobium.” Knowledge of the unique ecophysiology and biochemistry of Dehalococcoidia has been largely derived from studies with enrichment cultures and isolates from sites impacted with chlorinated pollutants; however, culture-independent surveys found Dehalococcoidia sequences in marine, freshwater, and terrestrial biomes considered to be pristine (i.

The class Dehalococcoidia within the Chloroflexi phylum comprises the obligate organohalide-respiring genera Dehalococcoides, Dehalogenimonas, and “Candidatus Dehalobium.” Knowledge of the unique ecophysiology and biochemistry of Dehalococcoidia has been largely derived from studies with enrichment cultures and isolates from sites impacted with chlorinated pollutants; however, culture-independent surveys found Dehalococcoidia sequences in marine, freshwater, and terrestrial biomes considered to be pristine (i.e., not impacted with organohalogens of anthropogenic origin). The broad environmental distribution of Dehalococcoidia, as well as other organohalide-respiring bacteria, supports the concept of active halogen cycling and the natural formation of organohalogens in various ecosystems. Dechlorination reduces recalcitrance and renders organics susceptible to metabolic oxidation by diverse microbial taxa. During reductive dechlorination, hydrogenotrophic organohalide-respiring bacteria, in particular Dehalococcoidia, can consume hydrogen to low consumption threshold concentrations (<0.3 nM) and enable syntrophic oxidation processes. These functional attributes and the broad distribution imply that Dehalococcoidia play relevant roles in carbon cycling in anoxic ecosystems.

Environmental stress perception activates structural remodeling of extant Streptococcus mutans biofilms

Transcription regulators from the LexA-like Protein Superfamily control a highly diverse assortment of genetic pathways in response to environmental stress. All characterized members of this family modulate their functionality and stability via a strict coordination with the coprotease function of RecA. Using the LexA-like protein IrvR from Streptococcus mutans, we demonstrate an exception to the RecA paradigm and illustrate how this evolutionary innovation has been coopted to diversify the stress responsiveness of S. mutans biofilms. Using a combination of genetics and biophysical measurements, we demonstrate how non-SOS stresses and SOS stresses each trigger separate regulatory mechanisms that stimulate production of a surface lectin responsible for remodeling the viscoelastic properties of extant biofilms during episodes of environmental stress. These studies demonstrate how changes in the external environment or even anti-biofilm therapeutic agents can activate biofilm-specific adaptive mechanisms responsible for bolstering the integrity of established biofilm communities. Such changes in biofilm community structure are likely to play central roles in the notorious recalcitrance of biofilm infections.

The manifold roles of microbial ribosomal peptide-based natural products in physiology and ecology

The ribosomally synthesized and posttranslationally modified peptides (RiPPs), also called ribosomal peptide natural products (RPNPs), form a growing superfamily of natural products that are produced by many different organisms and particularly by bacteria. They are derived from precursor polypeptides whose modification by various dedicated enzymes helps to establish a vast array of chemical motifs. RiPPs have attracted much interest as a source of potential therapeutic agents, and in particular as alternatives to conventional antibiotics to address the bacterial resistance crisis. However, their ecological roles in nature are poorly understood and explored. The present review describes major RiPP actors in competition within microbial communities, the main ecological and physiological functions currently evidenced for RiPPs, and the microbial ecosystems that are the sites for these functions. We envision that the study of RiPPs may lead to discoveries of new biological functions and highlight that a better knowledge of how bacterial RiPPs mediate inter-/intraspecies and interkingdom interactions will hold promise for devising alternative strategies in antibiotic development.

An Ag-loaded photoactive nano-metal organic framework as a promising biofilm treatment

Surface biofilm inhibition is still currently a considerable challenge. Among other organisms, Staphylococcus aureus is notable for its ability to form a strong biofilm with proved resistance to chemotherapy. Contamination of high-touch surfaces with S. aureus biofilm not only promotes disease spread but also generates tremendous health-associated costs. Therefore, development of new bactericidal and antiadhesive surface coatings is a priority. Considering that metal-organic frameworks (MOFs) have recently emerged as promising antibacterial agents, we originally report here the synthesis of a multi-active silver-containing nanoscaled MOF composite as a potential surface coating against S. aureus biofilm owing to a triple effect: intrinsic bactericide activity of the MOF, biocidal character of silver nanoparticles (AgNPs), and photoactivity after UVA irradiation. AgNPs were successfully entrapped within the benchmarked nanoscaled porous photoactive titanium(IV) aminoterephthalate MIL-125(Ti)NH₂ using a simple and efficient impregnation-reduction method. After complete characterization of the composite thin film, its antibacterial and anti-adherent properties were fully evaluated. After UVA irradiation, the composite coating exhibited relevant bacterial inhibition and detachment, improved ligand-to-cluster charge transfer, and steady controlled delivery of Ag⁺. These promising results establish the potential of this composite as an active coating for biofilm treatment on high-touch surfaces (e.g., surgical devices, door knobs, and rail bars). STATEMENT OF SIGNIFICANCE: Surface contamination due to bacterial biofilm formation is still a demanding issue, as it causes severe disease spread. One possible solution is the development of antifouling and antibacterial surface coatings. In this work, we originally propose the use of photoactive metal-organic frameworks (MOFs) for biofilm treatment. The novelty of this work relies on the following: i) the treatment of strongly contaminated surfaces, as previous studies with MOFs have exclusively addressed biofilm prevention; ii) this pioneering work reports both antiadherent effect, which removes the biofilm, and bacterial inhibition; iii) our original successful strategy has never been proposed thus far, involving the multi-active combination of 1) intrinsic antibacterial effect of a photoactive titanium-based nanoMOF, 2) immobilization of biocide silver nanoparticles, and 3) improved anti-bioadherent effect upon irradiation of the composite coating.

Assessing the impact of curcumin on dual-species biofilms formed by Streptococcus mutans and Candida albicans

Streptococcus mutans and Candida albicans are often isolated from plaques associated with early childhood caries. However, there are limited studies examining how these microorganisms interact with one another and how best to manage them. Recent studies have shown that curcumin (CUR), a natural compound, has the potential to independently control both of these microorganisms. The purpose of this study was to investigate how S. mutans and C. albicans respond in mono‐ and dual‐species biofilms challenged with CUR. Quantitative biofilm biomass and viability were first evaluated and supported by live–dead PCR to assess biofilm composition. Confocal laser scanning microscopy (CLSM) was used to evaluate the exopolysaccharide (EPS) content and thickness of the biofilms, and the structure of the biofilms and morphology of the cells were observed by scanning electron microscopy (SEM). Quantitative real‐time PCR (qRT‐PCR) was applied to assess relative gene expression. The 50% minimum biofilm eradication concentration (MBEC₅₀) of CUR against S. mutans and C. albicans was 0.5 mM. The biomass and viability decreased after treatment with CUR both in dual‐species biofilms and in mono‐species biofilm. CUR inhibited S. mutans and C. albicans in both mono‐ and dual‐species biofilms. Streptococcus mutans was more sensitive to CUR in dual‐species biofilm than in mono‐species biofilms, whereas C. albicans was less sensitive in dual‐species biofilms. EPS production was decreased by CUR in both mono‐ and dual‐species biofilms, which coincided with the downregulation of glucosyltransferase and quorum sensing‐related gene expression of S. mutans. In C. albicans, the agglutinin‐like sequence family of C. albicans was also downregulated in dual‐species biofilms. Collectively, these data show the potential benefit of using a natural antimicrobial, CUR, to control caries‐related dual‐species plaque biofilms.

Thiostrepton Hijacks Pyoverdine Receptors To Inhibit Growth of Pseudomonas aeruginosa

Pseudomonas aeruginosa is a biofilm-forming opportunistic pathogen and is intrinsically resistant to many antibiotics. In a high-throughput screen for molecules that modulate biofilm formation, we discovered that the thiopeptide antibiotic thiostrepton (TS), which is considered to be inactive against Gram-negative bacteria, stimulated P. aeruginosa biofilm formation in a dose-dependent manner. This phenotype is characteristic of exposure to antimicrobial compounds at subinhibitory concentrations, suggesting that TS was active against P. aeruginosa Supporting this observation, TS inhibited the growth of a panel of 96 multidrug-resistant (MDR) P. aeruginosa clinical isolates at low-micromolar concentrations. TS also had activity against Acinetobacter baumannii clinical isolates. The expression of Tsr, a 23S rRNA-modifying methyltransferase from TS producer Streptomyces azureus, in trans conferred TS resistance, confirming that the drug acted via its canonical mode of action, inhibition of ribosome function. The deletion of oligopeptide permease systems used by other peptide antibiotics for uptake failed to confer TS resistance. TS susceptibility was inversely proportional to iron availability, suggesting that TS exploits uptake pathways whose expression is increased under iron starvation. Consistent with this finding, TS activity against P. aeruginosa and A. baumannii was potentiated by the FDA-approved iron chelators deferiprone and deferasirox and by heat-inactivated serum. Screening of P. aeruginosa mutants for TS resistance revealed that it exploits pyoverdine receptors FpvA and FpvB to cross the outer membrane. We show that the biofilm stimulation phenotype can reveal cryptic subinhibitory antibiotic activity, and that TS has activity against select multidrug-resistant Gram-negative pathogens under iron-limited growth conditions, similar to those encountered at sites of infection.

Targeting S. mutans biofilms: a perspective on preventing dental caries

The prevalence of biofilm diseases, and dental caries in particular, have encouraged extensive research on S. mutans biofilms, including methods of preventing its formation. Numerous small molecules with specific anti-biofilm activity against this pathogen have been isolated and synthesized. Generally, these molecules can be characterized into three categories: sucrose-dependent anti-adhesion, sucrose-independent anti-adhesion and cellular signaling interference. This review aims to provide an overview of the current small molecule strategies used for targeting S. mutans biofilms, and a perspective of the future for the field.

Review of Catheter-Associated Urinary Tract Infections and In Vitro Urinary Tract Models

Catheter-associated urinary tract infections (CAUTIs) are one of the most common nosocomial infections and can lead to numerous medical complications from the mild catheter encrustation and bladder stones to the severe septicaemia, endotoxic shock, and pyelonephritis. Catheters are one of the most commonly used medical devices in the world and can be characterised as either indwelling (ID) or intermittent catheters (IC). The primary challenges in the use of IDs are biofilm formation and encrustation. ICs are increasingly seen as a solution to the complications caused by IDs as ICs pose no risk of biofilm formation due to their short time in the body and a lower risk of bladder stone formation. Research on IDs has focused on the use of antimicrobial and antibiofilm compounds, while research on ICs has focused on preventing bacteria entering the urinary tract or coming into contact with the catheter. There is an urgent need for in vitro urinary tract models to facilitate faster research and development for CAUTI prevention. There are currently three urinary tract models that test IDs; however, there is only a single very limited model for testing ICs. There is currently no standardised urinary tract model to test the efficacies of ICs.

Mechanisms of biofilm stimulation by subinhibitory concentrations of antimicrobials

Biofilms are a typical mode of growth for most microorganisms and provide them with a variety of survival benefits. Biofilms can pose medical and industrial challenges due to their increased tolerance of antimicrobials and disinfectants. Exposure of bacteria to subinhibitory concentrations of those compounds can further exacerbate the problem, as they provoke physiological changes that lead to increased biofilm production and potential therapeutic failure. The protected niche of a biofilm provides conditions that promote selection for persisters and resistant mutants. In this review we discuss our current understanding of the mechanisms underlying biofilm stimulation in response to subinhibitory antimicrobials, and how we might exploit this 'anti-antibiotic' phenotype to treat biofilm-related infections and discover new compounds.

Development of Molecularly Imprinted Polymers To Block Quorum Sensing and Inhibit Bacterial Biofilm Formation

Bacterial biofilms are responsible for most clinical infections and show increased antimicrobial resistance. In this study, molecularly imprinted polymers (MIPs) were developed to specifically capture prototypical quorum sensing autoinducers [i.e., N-(3-oxododecanoyl)-l-homoserine lactone (3-oxo-C₁₂AHL)], interrupt quorum sensing, and subsequently inhibit biofilm formation of Pseudomonas aeruginosa, an important human nosocomial pathogen. The synthesis of MIPs was optimized by considering the amount and type of the functional monomers itaconic acid (IA) and 2-hydroxyethyl methacrylate (HEMA). IA-based MIPs showed high adsorption affinity toward 3-oxo-C₁₂AHL with an imprinting factor of 1.68. Compared to IA-based MIPs, the adsorption capacity of HEMA-based MIPs was improved fivefold. HEMA-based MIPs significantly reduced biofilm formation (by ∼65%), whereas biofilm suppression by IA-based MIPs was neutralized because of increased bacterial attachment. The developed MIPs represent promising alternative biofilm intervention agents that can be applied to surfaces relevant to clinical settings and food processing equipment.