Effects of oxygen on biofilm formation and the AtlA autolysin of Streptococcus mutans

Rapid assembly of biofilms from DNA released by SOS-inducing drugs in enteric bacteria

The SOS response is a bacterial stress response activated by DNA damage in many types of bacteria. SOS-inducing antibiotics trigger the rapid release of DNA into the extracellular medium in many strains. Surprisingly, the DNA released in this way contains greater amounts of single-stranded DNA (ssDNA) than double-stranded DNA (dsDNA). In this study, we observed that addition of DNA-binding proteins following induction of the SOS response in Enterobacter cloacae decreased the amount of DNA measurable in the supernatant medium, but increased the amount of DNA deposited as a biofilm at the air-fluid interface. Bacteria incorporated into the biofilms survived the stress of dessication much better than did planktonic bacteria, with over a 400-fold increase in survival in the biofilm-bound bacteria. SOS-inducing drugs also triggered DNA release in Proteus mirabilis, with ssDNA again being more abundant than dsDNA in the culture supernatants. Addition of urea in this urease-producing organism triggered the formation of struvite crystals (magnesium ammonium phosphate), with the crystals, Proteus bacteria, and extracellular DNA forming mixed biofilms. Last, we tested the effect of inhibitors of the SOS response, such as zinc acetate. We also tested an inhibitor of the generalized stress response, dequalinium, which also indirectly inhibits the SOS response, and found it had a strong ability to inhibit biofilm formation.

Characterization of MreCD in Streptococcus mutans

Background

Activities that control cell shape and division are critical for the survival of bacteria. However, little is known about the circuitry controlling these processes in the dental caries pathogen Streptococcus mutans.

Methodology

We designed experiments to characterize two genes, mreC and mreD, in S. mutans. Assays included cell morphology imaging, protein interaction analysis, transcriptomics, proteomics, and biofilm studies to generate a comprehensive understanding of the role of MreCD in S. mutans.

Results

Consistent with mreCD participating in cell elongation, cells lacking these genes were found to be rounder than wild-type cells. Using bacterial two-hybrid assays, interactions between MreCD and several other proteins implicated in cell elongation were observed. Further characterization, using proteomics, revealed that the surface-associated proteome is different in mutants lacking mreCD. Consistent with these changes we observed altered sucrose-mediated biofilm architecture. Loss of mreCD also had a noticeable impact on bacteriocin gene expression, which could account in part for the observation that mreCD mutants had a diminished capacity to compete with commensal streptococci.

Conclusion

Our results provide evidence that cell elongation proteins are required for normal S. mutans physiology and establish a foundation for additional examination of these and related proteins in this organism.

Constructing two bifunctional tooth-targeting antimicrobial peptides for caries management: an in vitro study

OBJECTIVES

Caries is a significant public health challenge. Herein, novel tooth-targeting antimicrobial peptides (HABPs@AMPs) were developed by combining the antimicrobial peptide DJK-5 with hydroxyapatite (HA) binding peptides, providing a potential new strategy for caries management.

MATERIALS AND METHODS

The minimal inhibitory concentration (MIC100) and minimal biofilm inhibitory concentration (MBIC100) values of HABPs@AMPs were determined via micro-broth dilution and crystal violet staining. The affinities of the peptides for HA were measured by mass depletion, and the abilities of peptides to inhibit Streptococcus mutans (S. mutans) biofilm formation and kill 3-day-old S. mutans biofilms were evaluated in HA disk and tooth slice biofilm models through confocal laser scanning microscopy. Biocompatibility with human gingival fibroblasts was evaluated via CCK8 assays.

RESULTS

The best performing peptides, DJK-5@SVA and SVA@DJK-5 exhibited MIC100 and MBIC100 values of 31.25 µg/mL, similar to DJK-5. DJK-5@linker2@YSL had the highest affinity for HA, followed by YSL@DJK-5, DJK-5@linker1@YSL, and DJK-5@SVA. Moreover, the biofilms on HABPs@DJK-5 coated surfaces had more dead bacteria by volume than those in the DJK-5 and SVA groups (p < 0.05). DJK-5@SVA outperformed SVA@DJK-5 and DJK-5 in killing 3-day-old S. mutans biofilms (p < 0.05). With the exception of established biofilms on tooth slices, DJK-5@SVA exhibited greater killing efficiency in the bottom half of the biofilms than in the top half. The CCK-8 assay results confirmed peptides' biocompatibility.

CONCLUSIONS

DJK-5@SVA with good affinity for HA, has excellent biocompatibility and efficacy against S. mutans biofilms.

CLINICAL RELEVANCE

HABPs@AMPs with effective inhibitory effects on the growth of S. mutans and biofilm formation, contributing to intraoral targeted application AMPs and providing a new strategy for caries management.

An optimized caries model of Streptococcus mutans in rats and its application for evaluating prophylactic vaccines

Dental caries is a prevalent oral disease that mainly results from Streptococcus mutans. Susceptibility to S. mutans decreased rapidly after weaning in a well-known rat model. However, owing to the lack of time to establish protective immunity ahead of challenge, the weaning rat model is suboptimal for assessing prophylactic vaccines against S. mutans infection. In this study, we found that, in adult rats, S. mutans cultured under air-restricted conditions showed dramatically increased colonization efficacy and accelerated development of dental caries compared with those cultured under air-unrestricted conditions. We propose that S. mutans cultured under air-restricted conditions can be used to develop an optimal caries model, especially for the evaluation of prophylactic efficacy against S. mutans. Therefore, we used the anti-caries vaccine, KFD2-rPAc, to reevaluate the protection against the challenge of S. mutans. In immunized rats, rPAc-specific protective antibodies were robustly elicited by KFD2-rPAc before the challenge. In addition to inhibiting the initial and long-term colonization of S. mutans in vivo, KFD2-rPAc immunization showed an 83% inhibitory efficacy against the development of caries, similar to that previously evaluated in a weaning rat model. These results demonstrate that culturing under air-restricted conditions can promote S. mutans infection in adult rats, thereby helping establish a rat infection model to evaluate the prophylactic efficacy of vaccines and anti-caries drugs.

Essential genes for Haemophilus parainfluenzae survival and biofilm growth

Haemophilus parainfluenzae (Hp) is a Gram-negative, highly prevalent, and abundant commensal in the human oral cavity, and an infrequent extraoral opportunistic pathogen. Hp occupies multiple niches in the oral cavity, including the supragingival plaque biofilm. Little is known about how Hp interacts with its neighbors in healthy biofilms nor its mechanisms of pathogenesis as an opportunistic pathogen. To address this, we identified the essential genome and conditionally essential genes in in vitro biofilms aerobically and anaerobically. Using transposon insertion sequencing (TnSeq) with a highly saturated mariner transposon library in two strains, the ATCC33392 type-strain (Hp 392) and oral isolate EL1 (Hp EL1), we show that the essential genomes of Hp 392 and Hp EL1 are composed of 395 (20%) and 384 (19%) genes, respectively. The core essential genome, consisting of 341 (17%) essential genes conserved between both strains, was composed of genes associated with genetic information processing, carbohydrate, protein, and energy metabolism. We also identified conditionally essential genes for aerobic and anaerobic biofilm growth, which were associated with carbohydrate and energy metabolism in both strains. RNAseq analysis determined that most genes upregulated during anaerobic growth are not essential for Hp 392 anaerobic survival. The completion of this library and analysis under these conditions gives us a foundational insight into the basic biology of H. parainfluenzae in differing oxygen conditions, similar to its in vivo habitat. This library presents a valuable tool for investigation into conditionally essential genes for an organism that lives in close contact with many microbial species in the human oral habitat.IMPORTANCEHaemophilus parainfluenzae is a highly abundant human commensal microbe, present in most healthy individuals where it colonizes the mouth. H. parainfluenzae correlates with good oral health and may play a role in preservation of healthy host status. Also, H. parainfluenzae can cause opportunistic infections outside of the oral cavity. To date, little is known about how H. parainfluenzae colonizes the human host, despite being such a frequent and abundant part of our human microbiome. Here, we demonstrate the creation and use of a powerful tool, a TnSeq library, used to identify genes necessary for both the outright growth of this organism and also genes conditionally essential for growth in varying oxygen status which it can encounter in the human host. This tool and these data serve as a foundation for further study of this relatively unknown organism that may play a role in preserving human health.

Topical oxygen therapy as a novel strategy to promote wound healing and control the bacteria in implantology, oral surgery and periodontology: A review

Globally, oral infections and inflammatory lesions persist as substantial public health concerns, necessitating the introduction of novel oral treatment protocols. Oral diseases are linked to various causative factors, with dental plaque/biofilm resulting from inadequate hygiene practices playing a predominant role. The strategic implementation of novel topical therapies holds promise for effectively controlling the biofilms, addressing oral infections and promoting enhanced oral wound healing. This review aims to providing a comprehensive overview of the available evidence pertaining to the potential efficacy of topical oxygen and lactoferrin-releasing biomaterials, exemplified by the blue®m formula, as novel oral care interventions within the scope of contemporary implantology, oral surgery and periodontology.

Essential genes for Haemophilus parainfluenzae survival and biofilm growth

Haemophilus parainfluenzae ( Hp ) is a Gram-negative, pleomorphic rod, highly prevalent and abundant as a commensal in the human oral cavity, and an infrequent extraoral opportunistic pathogen. Hp occupies multiple niches in the oral cavity, including the tongue dorsum, keratinized gingiva, and the supragingival plaque biofilm. As a member of the HACEK group, Hp is also known to cause infective endocarditis. Additionally, case reports have identified Hp as the causative agent of meningitis, septic arthritis, chronic osteomyelitis, septicemia, and a variety of other infectious diseases. Little is known about how Hp interacts with its neighbors in the healthy biofilm nor about its mechanisms of pathogenesis as an extraoral opportunistic pathogen. To address these unknowns, we identified the essential genomes of two Hp strains and the conditionally essential genes for their growth in in vitro biofilms aerobically and anaerobically. Using transposon insertion sequencing (TnSeq) with a highly saturated mariner transposon library in two strains, the ATCC33392 type-strain ( Hp 392) and a commensal oral isolate EL1 ( Hp EL1), we show that the essential genome of Hp 392 and Hp EL1 is composed of 395 and 384 genes, respectively. The core essential genome, consisting of 341 essential genes conserved between both strains, was composed of genes associated with genetic information processing, carbohydrate, protein, and energy metabolism. We also identified conditionally essential genes for aerobic and anaerobic biofilm growth, which were associated with carbohydrate and energy metabolism in both strains of Hp . Additionally, RNAseq analysis determined that most genes upregulated during anaerobic growth are not essential for Hp 392 anaerobic biofilm survival. The completion of this library and analysis under these conditions gives us a foundational insight into the basic biology of H. parainfluenzae in differing oxygen conditions, similar to its in vivo oral habitat. Further, the creation of this library presents a valuable tool for further investigation into conditionally essential genes for an organism that lives in close contact with many microbial species in the human oral habitat.

Iron coatings on carbonate rocks shape the attached bacterial aquifer community

Most studies of groundwater ecosystems target planktonic microbes, which are easily obtained via water samples. In contrast, little is known about the diversity and function of microbes adhering to rock surfaces, particularly to consolidated rocks. To investigate microbial attachment to rock surfaces, we incubated rock chips from fractured aquifers in limestone-mudstone alternations in bioreactors fed with groundwater from two wells representing oxic and anoxic conditions. Half of the chips were coated with iron oxides, representing common secondary mineralization in fractured rock. Our time-series analysis showed bacteria colonizing the chips within two days, reaching cell numbers up to 4.16 × 105 cells/mm2 after 44 days. Scanning electron microscopy analyses revealed extensive colonization but no multi-layered biofilms, with chips from oxic bioreactors more densely colonized than from anoxic ones. Estimated attached-to-planktonic cell ratios yielded values of up to 106: 1 and 103: 1, for oxic and anoxic aquifers, respectively. We identified distinct attached and planktonic communities with an overlap between 17 % and 42 %. Oxic bioreactors were dominated by proteobacterial genera Aquabacterium and Rhodoferax, while Rheinheimera and Simplicispira were the key players of anoxic bioreactors. Motility, attachment, and biofilm formation traits were predicted in major genera based on groundwater metagenome-assembled genomes and reference genomes. Early rock colonizers appeared to be facultative autotrophs, capable of fixing CO2 to synthesize biomass and a biofilm matrix. Late colonizers were predicted to possess biofilm degrading enzymes such as beta-glucosidase, beta-galactosidase, amylases. Fe-coated chips of both bioreactors featured more potential iron reducers and oxidizers than bare rock chips. As secondary minerals can also serve as energy source, they might favor primary production and thus contribute to subsurface ecosystem services like carbon fixation. Since most subsurface microbes seem to be attached, their contribution to ecosystem services should be considered in future studies.

N-acyl homoserine lactone signaling modulates bacterial community associated with human dental plaque

N-acyl homoserine lactones (AHLs) are small diffusible signaling molecules that mediate a cell density-dependent bacterial communication system known as quorum sensing (QS). AHL-mediated QS regulates gene expression to control many critical bacterial behaviors including biofilm formation, pathogenicity, and antimicrobial resistance. Dental plaque is a complex multispecies oral biofilm formed by successive colonization of the tooth surface by groups of commensal, symbiotic, and pathogenic bacteria, which can contribute to tooth decay and periodontal diseases. While the existence and roles of AHL-mediated QS in oral microbiota have been debated, recent evidence indicates that AHLs play significant roles in oral biofilm development and community dysbiosis. The underlying mechanisms, however, remain poorly characterized. To better understand the importance of AHL signaling in dental plaque formation, we manipulated AHL signaling by adding AHL lactonases or exogenous AHL signaling molecules. We find that AHLs can be detected in dental plaque grown under 5% CO2 conditions, but not when grown under anaerobic conditions, and yet anaerobic cultures are still responsive to AHLs. QS signal disruption using lactonases leads to changes in microbial population structures in both planktonic and biofilm states, changes that are dependent on the substrate preference of the used lactonase but mainly result in the increase in the abundance of commensal and pioneer colonizer species. Remarkably, the opposite manipulation, that is the addition of exogenous AHLs increases the abundance of late colonizer bacterial species. Hence, this work highlights the importance of AHL-mediated QS in dental plaque communities, its potential different roles in anaerobic and aerobic parts of dental plaque, and underscores the potential of QS interference in the control of periodontal diseases.

Genetic characterization of glyoxalase pathway in oral streptococci and its contribution to interbacterial competition

Objectives

To analyze contributions to microbial ecology of Reactive Electrophile Species (RES), including methylglyoxal, generated during glycolysis.

Methods

Genetic analyses were performed on the glyoxalase pathway in Streptococcus mutans (SM) and Streptococcus sanguinis (SS), followed by phenotypic assays and transcription analysis.

Results

Deleting glyoxalase I (lguL) reduced RES tolerance to a far greater extent in SM than in SS, decreasing the competitiveness of SM against SS. Although SM displays a greater RES tolerance than SS, lguL-null mutants of either species showed similar tolerance; a finding consistent with the ability of methylglyoxal to induce the expression of lguL in SM, but not in SS. A novel paralogue of lguL (named gloA2) was identified in most streptococci. SM mutant ∆gloA2SM showed little change in methylglyoxal tolerance yet a significant growth defect and increased autolysis on fructose, a phenotype reversed by the addition of glutathione, or by the deletion of a fructose: phosphotransferase system (PTS) that generates fructose-1-phosphate (F-1-P).

Conclusions

Fructose contributes to RES generation in a PTS-specific manner, and GloA2 may be required to degrade certain RES derived from F-1-P. This study reveals the critical roles of RES in fitness and interbacterial competition and the effects of PTS in modulating RES metabolism.

Bacterial biofilms in the human body: prevalence and impacts on health and disease

Bacterial biofilms can be found in most environments on our planet, and the human body is no exception. Consisting of microbial cells encased in a matrix of extracellular polymers, biofilms enable bacteria to sequester themselves in favorable niches, while also increasing their ability to resist numerous stresses and survive under hostile circumstances. In recent decades, biofilms have increasingly been recognized as a major contributor to the pathogenesis of chronic infections. However, biofilms also occur in or on certain tissues in healthy individuals, and their constituent species are not restricted to canonical pathogens. In this review, we discuss the evidence for where, when, and what types of biofilms occur in the human body, as well as the diverse ways in which they can impact host health under homeostatic and dysbiotic states.

Dysbiome and Its Role in Surgically Relevant Medical Disease

Several surgically relevant conditions are directly or indirectly influenced by the human microbiome. Different microbiomes may be found within, or along, specific organs and intra-organ variation is common. Such variations include those found along the course of the gastrointestinal tract as well as those on different regions of the skin. A variety of physiologic stressors and care interventions may derange the native microbiome. A deranged microbiome is termed a dysbiome and is characterized by decreased diversity and an increase in the proportion of potentially pathogenic organisms; the elaboration of virulence factors coupled with clinical consequences defines a pathobiome. Specific conditions such as Clostridium difficile colitis, inflammatory bowel disease, obesity, and diabetes mellitus are tightly linked to a dysbiome or pathobiome. Additionally, massive transfusion after injury appears to derange the gastrointestinal microbiome as well. This review explores what is known about these surgically relevant clinical conditions to chart how non-surgical interventions may support surgical undertakings or potentially reduce the need for operation.

Potential therapeutic targets for combating Mycoplasma genitalium

Mycoplasma genitalium (M. genitalium) has emerged as a sexually transmitted infection (STI) all over the world in the last three decades. It has been identified as a cause of male urethritis, and there is now evidence that it also causes cervicitis and pelvic inflammatory disease in women. However, the precise role of M. genitalium in diseases such as pelvic inflammatory disease, and infertility is unknown, and more research is required. It is a slow-growing organism, and with the advent of the nucleic acid amplification test (NAAT), more studies are being conducted and knowledge about the pathogenicity of this organism is being elucidated. The accumulation of data has improved our understanding of the pathogen and its role in disease transmission. Despite the widespread use of single-dose azithromycin in the sexual health field, M. genitalium is known to rapidly develop antibiotic resistance. As a result, the media frequently refer to this pathogen as the "new STI superbug." Despite their rarity, antibiotics available today have serious side effects. As the cure rates for first-line antimicrobials have decreased, it is now a challenge to determine the effective antimicrobial therapy. In this review, we summarise recent M. genitalium research and investigate potential therapeutic targets for combating this pathogen.

The effect of active oxygen-containing toothpaste on Streptococcus mutans and white spot lesions: An in-vivo randomized controlled trial

INTRODUCTION

Fixed appliances limit patients' ability to clean their teeth, thus making orthodontic patients highly susceptible to developing white spot lesions (WSLs). Using patient compliance would be one of the simplest methods to prevent WSLs.

METHODS

A parallel trial design with 34 patients that met the eligibility criteria were randomized to experimental (received Blue M oxygen for health toothpaste) and control (received Colgate Total fluoridated toothpaste) groups. The eligibility criteria were that the patients should be aged 13-30 years, on fixed mechanotherapy, had undergone therapeutic extraction of all first premolars, had completed leveling and aligning, and had satisfactory oral hygiene (assessed using pretreatment and current Simplified Oral Hygiene Index scores). The objectives were to assess the effects of active oxygen-containing toothpaste on Streptococcus mutans (SM) and WSLs in patients undergoing fixed mechanotherapy. The random allocation sequence was generated using the RAND function in Microsoft Excel. The sequence generated was sealed in opaque white envelopes. The investigators and the participants were blinded until allocation. Blinding of the first author (J.A.G.) who dispensed the toothpaste or the participants was not possible. The outcome assessment was blinded by coding the plaque specimens sent for real-time polymerase chain reaction (RT-PCR) to ensure that the final data assessment was blinded. The study setting was the Department of Orthodontics and Dentofacial Orthopedics, Sri Ramachandra Institute of Higher Education and Research (SRIHER) University. The primary outcome was SM counts, which were analyzed using RT-PCR. The secondary outcome was WSL assessment, performed using DIAGNOdent and International Caries Detection and Assessment System (ICDAS) II criteria at baseline and after 4 weeks. The data were subjected to statistical analysis.

RESULTS

Thirty-four patients were randomized to 17 per group and analyzed. RT-PCR showed lower SM in the experimental group (Ct = 32.25 ± 10.6) than in the control group (Ct = 30.9 ± 10.49). However, this was not statistically significant (P = 0.70). ICDAS scores remained the same from baseline and after 4 weeks for both groups. The DIAGNOdent values were in tandem with the ICDAS scores and showed minimal change for the 2 groups (P >0.05). A strong positive correlation was observed for DIAGNOdent and ICDAS scores (τb >0.30). No harms or adverse effects were observed or reported by the patients during the experimental period.

CONCLUSIONS

The active oxygen-containing toothpaste showed a greater inhibitory effect on SM than the fluoridated toothpaste. However, this effect was minimal. Both kinds of toothpaste showed negligible effects on WSLs. Thus, active oxygen-containing toothpaste is as effective as fluoridated toothpaste.

REGISTRATION

The Trial was registered in the Controlled Trials Registry India (CTRI/2021/10/037458).

PROTOCOL

The full protocol can be obtained from any of the authors via e-mail.

FUNDING

The project was self-funded.

Effects of free and nano encapsulated bovine lactoferrin on the viability and acid production by Streptococcus mutans biofilms

Tooth decay is one of the most common diseases that humans face during their lifetime. Streptococcus mutans is one of the most critical factors of early tooth decay. These bacteria may produce biofilms in the mouth, which are more resistant to antimicrobial agents. S. mutans may also demineralize tooth enamel by producing lactic acid. In this study, the effect of nanoliposomes containing lactoferrin at three different concentrations (1.5, 3, and 6 mg ml^-1 l) on the biofilm formed by S. mutans was investigated. Nanoliposomes were prepared using the thin-layer hydration method. An active attachment model (AAA) was used to evaluate biofilm and lactic acid production. The results showed that nano encapsulated lactoferrin could reduce CFU of biofilm more effectively than free lactoferrin. Lactoferrin-containing nanoliposomes also significantly reduced lactic acid production by S. mutans. Therefore, nano encapsulated lactoferrin may be used along with other dental caries control methods to increase anti caries efficacy.

Variation in adhesion of Streptococcus mutans and Porphyromonas gingivalis in saliva-derived biofilms on raw materials of orthodontic brackets

Objective

To evaluate differences in the adhesion levels of the most common oral pathogens, Streptococcus mutans and Porphyromonas gingivalis, in human saliva-derived microcosm biofilms with respect to time and raw materials of orthodontic brackets.

Methods

The samples were classified into three groups of bracket materials 1) monocrystalline alumina ceramic (CR), 2) stainless steel metal (SS), and 3) polycarbonate plastic (PL), and a hydroxyapatite (HA) group was used to mimic the enamel surface. Saliva was collected from a healthy donor, and saliva-derived biofilms were grown on each sample. A real-time polymerase chain reaction was performed to quantitatively evaluate differences in the attachment levels of total bacteria, S. mutans and P. gingivalis at days 1 and 4.

Results

Adhesion of S. mutans and P. gingivalis to CR and HA was higher than the other bracket materials (SS = PL < CR = HA). Total bacteria demonstrated higher adhesion to HA than to bracket materials, but no significant differences in adhesion were observed among the bracket materials (CR = SS = PL < HA). From days 1 to 4, the adhesion of P. gingivalis decreased, while that of S. mutans and total bacteria increased, regardless of material type.

Conclusions

The higher adhesion of oral pathogens, such as S. mutans and P. gingivalis to CR suggests that the use of CR brackets possibly facilitates gingival inflammation and enamel decalcification during orthodontic treatment.

Nutrients, temperature, and oxygen mediate microbial antibiotic resistance in sea bass (Lateolabrax maculatus) ponds

Antibiotic resistance genes (ARGs) have drawn increasing attention as novel environmental pollutants because of the threat they impose on human and animal health. The sea bass (Lateolabrax maculatus) is the third most cultured marine fish in China. Therefore, a study of ARG pollution in the sea bass culture environment is of great significance for the healthy and sustainable development of the sea bass industry. Here, we systematic investigated the contents of 23 antibiotic resistance-related genes (ARRGs), including 19 ARGs and four mobile genetic elements, and analyzed bacterial community composition and environmental parameters in sea bass ponds. The relative abundance (ARRG copies/16S ribosomal RNA gene copies) of ARRGs was up to 3.83 × 10^-2. Sul1 was the most abundant ARRG, followed by ereA, intI-1, sul2, dfrA1, and aadA. Both the ARRG changes and aquatic microbiota succession were mainly driven by water temperature (WT), dissolved oxygen (DO), and NO₃^-. WT is positively correlated with the most ARGs and some of the top 38 Operational Taxonomic Units (OTUs) belonging to the orders of Frankiales, Micrococcales, Chitinophagales, and Sphingomonadales. Furthermore, WT is negatively related with some other OTUs of the orders Frankiales, Xanthomonadales, Micrococcales, and Rhizobiales. However, DO and NO₃^- have the opposite function with WT on specific taxa and ARGs. These results indicate that sea bass ponds are reservoirs of ARGs, and are driven mainly by the nutrient, temperature, and oxygen with inducing specific microbial taxa. The regulation of environmental factors (increasing DO and NO₃^-) can be conducted to reduce drug resistance risk in aquaculture ponds. Therefore, environmental factors and specific taxa could be the indicators of ARG contamination and can be used to establish an antibiotic elimination system and consequently realize a sustainable aquaculture industry.

Bacteroides thetaiotaomicron uses a widespread extracellular DNase to promote bile-dependent biofilm formation

Biofilms are communities of surface-attached bacteria exhibiting biofilm-specific properties. Although anaerobic biofilms impact health, industry, and environment, they are mostly studied in aerobic bacterial species. Here, we studied biofilm formation in Bacteroides thetaiotaomicron, an anaerobic gut symbiont degrading diet sugars and contributing to gut maturation. Although B. thetaiotaomicron adhesion contributes to intestinal colonization, little is known about the determinants of its biofilm capacities. We identified that bile is a physiologically relevant gut signal inducing biofilm formation in B. thetaiotaomicron and other gut Bacteroidales. Moreover, we showed that, in contrast to the known scaffolding role of extracellular DNA, bile-dependent biofilm requires a DNase degrading matrix DNA, thus revealing a previously unrecognized factor contributing to the adhesion capacity of major gut symbionts.

Bacteroides thetaiotaomicron is a gut symbiont that inhabits the mucus layer and adheres to and metabolizes food particles, contributing to gut physiology and maturation. Although adhesion and biofilm formation could be key features for B. thetaiotaomicron stress resistance and gut colonization, little is known about the determinants of B. thetaiotaomicron biofilm formation. We previously showed that the B. thetaiotaomicron reference strain VPI-5482 is a poor in vitro biofilm former. Here, we demonstrated that bile, a gut-relevant environmental cue, triggers the formation of biofilm in many B. thetaiotaomicron isolates and common gut Bacteroidales species. We determined that bile-dependent biofilm formation involves the production of the DNase BT3563 or its homologs, degrading extracellular DNA (eDNA) in several B. thetaiotaomicron strains. Our study therefore shows that, although biofilm matrix eDNA provides a biofilm-promoting scaffold in many studied Firmicutes and Proteobacteria, BT3563-mediated eDNA degradation is required to form B. thetaiotaomicron biofilm in the presence of bile.

Gut biofilms: Bacteroides as model symbionts to study biofilm formation by intestinal anaerobes

Bacterial biofilms are communities of adhering bacteria that express distinct properties compared to their free-living counterparts, including increased antibiotic tolerance and original metabolic capabilities. Despite the potential impact of the biofilm lifestyle on the stability and function of the dense community of micro-organisms constituting the mammalian gut microbiota, the overwhelming majority of studies performed on biofilm formation by gut bacteria focused either on minor and often aerobic members of the community or on pathogenic bacteria. In this review, we discuss the reported evidence for biofilm-like structures formed by gut bacteria, the importance of considering the anaerobic nature of gut biofilms and we present the most recent advances on biofilm formation by Bacteroides, one of the most abundant genera of the human gut microbiota. Bacteroides species can be found attached to food particles and colonizing the mucus layer and we propose that Bacteroides symbionts are relevant models to probe the physiology of gut microbiota biofilms.

Redox Sensing Modulates the Activity of the ComE Response Regulator of Streptococcus mutans

Streptococcus mutans, a dental pathogen, encodes the ComDE two-component system comprised of a histidine kinase (ComD) and a response regulator (ComE). This system is necessary for production of bacteriocins and development of genetic competence. ComE interacts with its cognate promoters to activate the transcription of bacteriocin and competence-related genes. Previous transcriptomic studies indicated that expressions of bacteriocin genes were upregulated in the presence of oxygen. To understand the relationship between the aerobic condition and bacteriocin expression, we analyzed the S. mutans ComE sequence and its close homologs. Surprisingly, we noticed the presence of cysteine (Cys) residues located at positions 200 and 229, which are highly conserved among the ComE homologs. Here, we investigated the role of Cys residues of S. mutans ComE in the activation of bacteriocin transcription using the PnlmA promoter that expresses bacteriocin NlmA. We constructed both single mutants and double mutants by replacing the Cys residues with serine and performed complementation assays. We observed that the presence of Cys residues is essential for PnlmA activation. With purified ComE mutant proteins, we found that ComE double mutants displayed a nearly 2-fold lower association rate than wild-type ComE. Furthermore, 1-anilinonaphthalene-8-sulfonic acid (ANS) fluorescence studies indicated that the double mutants displayed wider conformation changes than wild-type ComE. Finally, we demonstrated that close streptococcal ComE homologs successfully activate the PnlmA expression in vivo. This is the first report suggesting that S. mutans ComE and its homologs can sense the oxidation status of the cell, a phenomenon similar to the AgrA system of Staphylococcus aureus but with different outcomes. IMPORTANCE Streptococci are an important species that prefer to grow under anaerobic or microaerophilic environments. Studies have shown that streptococci growth in an aerobic environment generates oxidative stress responses by activating various defense systems, including production of antimicrobial peptides called bacteriocins. This study highlights the importance of a two-component response regulator (ComE) that senses the aerobic environment and induces bacteriocin production in Streptococcus mutans, a dental pathogen. We believe increased bacteriocin secretion under aerobic conditions is necessary for survival and colonization of S. mutans in the oral cavity by inhibiting other competing organisms. Redox sensing by response regulator might be a widespread phenomenon since two other ComE homologs from pathogenic streptococci that inhabit diverse environmental niches also perform a similar function.

Subtractive Genomics Approach for Identification of Novel Therapeutic Drug Targets in Mycoplasma genitalium

Mycoplasma genitalium infection is a sexually transmitted infection that causes urethritis, cervicitis, and pelvic inflammatory disease (PID) in men and women. The global rise in antimicrobial resistance against recommended antibiotics for the treatment of M. genitalium infection has triggered the need to explore novel drug targets against this pathogen. The application of a bioinformatics approach through subtractive genomics has proven highly instrumental in predicting novel therapeutic targets against a pathogen. This study aimed to identify essential and non-homologous proteins with unique metabolic pathways in the pathogen that could serve as novel drug targets. Based on this, a manual comparison of the metabolic pathways of M. genitalium and the human host was done, generating nine pathogen-specific metabolic pathways. Additionally, the analysis of the whole proteome of M. genitalium using different bioinformatics databases generated 21 essential, non-homologous, and cytoplasmic proteins involved in nine pathogen-specific metabolic pathways. The further screening of these 21 cytoplasmic proteins in the DrugBank database generated 13 druggable proteins, which showed similarity with FDA-approved and experimental small-molecule drugs. A total of seven proteins that are involved in seven different pathogen-specific metabolic pathways were finally selected as novel putative drug targets after further analysis. Therefore, these proposed drug targets could aid in the design of potent drugs that may inhibit the functionality of these pathogen-specific metabolic pathways and, as such, lead to the eradication of this pathogen.

Biofilm Formation, Production of Matrix Compounds and Biosorption of Copper, Nickel and Lead by Different Bacterial Strains

Bacterial biofilms play a key role in metal biosorption from wastewater. Recently, Enterobacter asburiae ENSD102, Enterobacter ludwigii ENSH201, Vitreoscilla sp. ENSG301, Acinetobacter lwoffii ENSG302, and Bacillus thuringiensis ENSW401 were shown to form air–liquid (AL) and solid–air–liquid (SAL) biofilms in a static condition at 28 and 37°C, respectively. However, how environmental and nutritional conditions affect biofilm formation; production of curli and cellulose; and biosorption of copper (Cu), nickel (Ni), and lead (Pb) by these bacteria have not been studied yet. In this study, E. asburiae ENSD102, E. ludwigii ENSH201, and B. thuringiensis ENSW401 developed the SAL biofilms at pH 8, while E. asburiae ENSD102 and Vitreoscilla sp. ENSG301 constructed the SAL biofilms at pH 4. However, all these strains produced AL biofilms at pH 7. In high osmolarity and ½-strength media, all these bacteria built fragile AL biofilms, while none of these strains generated the biofilms in anaerobic conditions. Congo red binding results showed that both environmental cues and bacterial strains played a vital role in curli and cellulose production. Calcofluor binding and spectrophotometric results revealed that all these bacterial strains produced significantly lesser amounts of cellulose at 37°C, pH 8, and in high osmotic conditions as compared to the regular media, at 28°C, and pH 7. Metal biosorption was drastically reduced in these bacteria at 37°C than at 28°C. Only Vitreoscilla sp. ENSG301 and B. thuringiensis ENSW401 completely removed (100%) Cu and Ni at an initial concentration of 12.5 mg l^–1, while all these bacteria totally removed (100%) Pb at concentrations of 12.5 and 25 mg l^–1 at pH 7 and 28°C. At an initial concentration of 100 mg l^–1, the removal of Cu (92.5 to 97.8%) and Pb (89.3 to 98.3%) was the highest at pH 6, while it was higher (84.7 to 93.9%) for Ni at pH 7. Fourier transform infrared spectroscopy results showed metal-unloaded biomass biofilms contained amino, hydroxyl, carboxyl, carbonyl, and phosphate groups. The peak positions of these groups were shifted responding to Cu, Ni, and Pb, suggesting biosorption of metals. Thus, these bacterial strains could be utilized to remove Cu, Ni, and Pb from aquatic environment.

Prospective bioremediation of toxic heavy metals in water by surfactant exopolysaccharide of Ochrobactrum pseudintermedium using cost-effective substrate

Globally, the underlying peril of cumulative toxicity of heavy metals in water bodies contaminated by industrial effluents is a matter of great concern to the environmentalists. Heavy metals like lead, cadmium, and nickel are particularly liable for this. Such toxic water is not only hazardous to human health but also harmful to aquatic animals. Remedial measures are being taken by physico-chemical techniques, but most of them are neither eco-friendly nor cost-effective. Biological means like bioaccumulation of heavy metals by viable bacteria are often tedious. In the present study, biosorption of heavy metals is successfully expedited by surfactant exopolysaccharide (SEPS) of Ochrobactrum pseudintermedium C1 as a simple, safe, and economically sustainable option utilizing an easily available and cost-effective substrate like molasses extract. Its efficacy in bioremediation of toxic heavy metals like cadmium, nickel, and lead have been studied by UV-Vis spectrophotometry and verified by inductively coupled plasma-atomic emission spectroscopy (ICP-AES). FTIR and zeta potential studies have also been carried out to explore this novel biosorption potential. Results are conclusive and promising. Moreover, this particular SEPS alone can remediate all these three toxic heavy metals in water. For futuristic applications, it might be a prospective and cost-effective resource for bioremediation of toxic heavy metals in aqueous environment.

Screening for phagocytosis resistance-related genes via a transposon mutant library of Streptococcus suis serotype 2

Streptococcus suis

serotype 2 (SS2) is a serious zoonotic pathogen which causes symptoms of streptococcal toxic shock syndrome (STSS) and septicemia; these symptoms suggest that SS2 may have evade innate immunity. Phagocytosis is an important innate immunity process where phagocytosed pathogens are killed by lysosome enzymes, reactive oxygen, and nitrogen species, and acidic environments in macrophages following engulfment. A previously constructed mutant SS2 library was screened, revealing 13 mutant strains with decreased phagocytic resistance. Through inverse PCR, the transposon insertion sites were determined. Through bioinformatic analysis, the 13 disrupted genes were identified as Cps2F, 3 genes belonging to ABC transporters, WalR, TehB, rpiA, S-transferase encoding gene, prs, HsdM, GNAT family N-acetyltransferase encoding gene, proB, and upstream region of DnaK. Except for the capsular polysaccharide biosynthesis associated Cps2F, the other genes had not been linked to a role in anti-phagocytosis. The survival ability in macrophages and whole blood of randomly picked mutant strains were significantly impaired compared with wild-type ZY05719. The virulence of the mutant strains was also attenuated in a mouse infection model. In the WalR mutant, the transcription of HP1065 decreased significantly compared with wild-type strain, indicating WalR might regulated HP1065 expression and contribute to the anti-phagocytosis of SS2. In conclusion, we identified 13 genes that influenced the phagocytosis resistant ability of SS2, and many of these genes have not been reported to be associated with resistance to phagocytosis. Our work provides novel insight into resistance to phagocytosis, and furthers our understanding of the pathogenesis mechanism of SS2.

Influence of the incubation temperature and total dissolved solids concentration on the biofilm and spore formation of dairy isolates of Geobacillus stearothermophilus

Geobacillus species are an important contaminant in the dairy industry and their presence is often considered as an indicator of poor plant hygiene with the potential to cause spoilage. They can form heat resistant spores that adhere to surfaces of processing equipment and germinate to form biofilms. Therefore, strategies aimed towards preventing or controlling biofilm formation in the dairy industry are desirable. In this study we demonstrate that the preferred temperature for biofilm and spore formation among Geobacillus stearothermophilus A1, D1, P3 and ATCC 12980 was 65°C. Increasing the total dissolved milk solids concentration to 20% (w/v) caused an apparent delay in the onset of biofilm and spore formation to detectable concentrations among all the strains at 55°C. Compared to the onset time of the biofilm formation of A1 in 10% (w/v) reconstituted skim milk, addition of milk protein (whey protein and sodium caseinate) caused an apparent delay in the onset of biofilm formation to detectable concentrations by an average of 10 h at 55°C. This study proposes that temperature and total dissolved solids concentration have a cumulative effect on the biofilm and spore formation of G. stearothermophilus A1, D1, P3 and ATCC 12980. In addition, the findings from this study may indicate that preconditioning of stainless-steel surface with adsorbed milk proteins may delay the onset of biofilm and spore formation of thermophilic bacteria during milk powder manufacture.IMPORTANCE The thermophilic bacilli, Geobacillus stearothermophilus is a predominant spoilage bacterium in milk powder manufacturing plants. If their numbers exceed the accepted levels, this may incur financial loses by lowering the price of the end product. Furthermore, they can form heat resistant spores which adhere to processing surfaces and can germinate to form biofilms. Previously conducted research had highlighted the variation in the spore and biofilm formation among three specific strains of G. stearothermophilus isolated from a milk powder manufacturing plant in New Zealand. The significance of our research is demonstrating the effect of two abiotic factors namely temperature and total dissolved solids concentration on the biofilm and spore formation of these three dairy isolates, leading to modifications in the thermal processing steps aimed towards controlling the biofilm and spore formation of G. stearothermophilus in the dairy industry.

Spatial Correlations and Distribution of Competence Gene Expression in Biofilms of Streptococcus mutans

Streptococcus mutans is an important pathogen in the human oral biofilm. It expresses virulent behaviors that are linked to its genetic competence regulon, which is controlled by comX. Expression of comX is modulated by two diffusible signaling peptides, denoted CSP and XIP, and by other environmental cues such as pH and oxidative stress. The sensitivity of S. mutans competence to environmental inputs that may vary on microscopic length scales raises the question of whether the biofilm environment creates microniches where competence and related phenotypes are concentrated, leading to spatial clustering of S. mutans virulence behaviors. We have used two-photon microscopy to characterize the spatial distribution of comX expression among individual S. mutans cells in biofilms. By analyzing correlations in comX activity, we test for spatial clustering that may suggest localized competence microenvironments. Our data indicate that both competence-signaling peptides diffuse efficiently through the biofilm. XIP elicits a population-wide response. CSP triggers a Poisson-like, spatially random comX response from a subpopulation of cells that is homogeneously dispersed. Our data indicate that competence microenvironments if they exist are small enough that the phenotypes of individual cells are not clustered or correlated to any greater extent than occurs in planktonic cultures.

Halomonas icarae sp. nov., a moderately halophilic bacterium isolated from beach soil in India

A moderately halophilic, Gram-stain-negative, aerobic bacterium, strain D1-1^T, belonging to the genus Halomonas, was isolated from soil sampled at Pentha beach, Odisha, India. Phylogenetic trees reconstructed based on 16S rRNA genes and multilocus sequence analysis of gyrB and rpoD genes revealed that strain D1-1^T belonged to the genus Halomonas and was most closely related to Halomonas alimentaria YKJ-16^T (98.1 %) followed by Halomonas ventosae Al12^T (97.5 %), Halomonas sediminicola CPS11^T (97.5 %), Halomonas fontilapidosi 5CR^T (97.4 %) and Halomonas halodenitrificans DSM 735^T (97.2 %) on the basis of 16S rRNA gene sequence similarity. Sequence identities with other species within the genus were lower than 97.0 %. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of 22.4-30 % and 79.5-85.4 % with close relatives of H. halodenitrificans DSM 735^T, H. alimentaria YKJ-16^T, H. ventosae Al12^T and H. fontilapidosi 5CR^T were lower than the threshold recommended for species delineation (70 % and 95-96 % for dDDH and ANI, respectively). Further, strain D1-1^T formed yellow-coloured colonies; cells were rod-shaped, motile with optimum growth at 30 °C (range, 4-45 °C) and 2-8 % NaCl (w/v; grew up to 24 % NaCl). The major fatty acids were summed feature 8 (C_18 : 1  ω7c/C_18 : 1  ω6c), summed feature 3 (C_16 : 1  ω7c/C_16 : 1  ω6c) and C_16 : 0 and the main respiratory quinone was ubiquinone Q-9 in line with description of the genus. Based on its chemotaxonomic and phylogenetic characteristics and genome uniqueness, strain D1-1^T represents a novel species in the genus Halomonas, for which we propose the name Halomonas icarae sp. nov., within the family Halomonadaceae. The type strain is D1-1^T (=JCM 33602^T=KACC 21317^T=NAIMCC-B-2254^T).

Assessment of the aerobic glass beads fixed biofilm reactor (GBs-FBR) for the treatment of simulated methylene blue wastewater

The present research is focused on the application of glass beads (GBs) in fixed biofilm reactor (FBR) for the treatment of simulated methylene blue (MB) wastewater for 9 weeks under aerobic conditions. The COD of MB wastewater showed a reduction of 86.48% from 2000 to 270.4 mg/L, and BOD was declined up to 97.7% from 1095.5 to 25.03 mg/L. A drastic increase in the pH was observed until the 3rd week (8.5 to 8.28), and later, marginal changes between 8.30 ± 0.02 were noticed. A dramatic fluctuation was observed in ammonia concentration which increased (74.25 mg/L) up till the 2nd week, and from the 3rd week it started declining. In the 9th week, the ammonia concentration dropped to 16.5 mg/L. The color intensity increased significantly up till the 2nd week (259,237.46 Pt/Co) of the experiment and started decreasing slowly thereafter. The SEM-EDX analysis has shown the maximum quantity of carbon content in the GBs without biofilm, and then in the GB samples of 1st, and 9th-week old aerobic biofilms. Furthermore, Raman spectroscopy results revealed that the 9th-week GBs has a fine and strong MB peak and matched with that of the MB stock solution. Overall, the results have shown that the GBs filter media were suitable for the development of active biofilm communities for the treatment of dye wastewater. Thus, GBs-FBR system can be used for wastewater treatment to solve the current problem of industrial pollution in many countries and to protect the aquatic environment from dye pollution caused by the textile industry.

Association between the gut and oral microbiome with obesity

In recent decades, obesity has become one of the most common lifestyle-associated disorders. Obesity is a major contributing factor for several other lifestyles associated disorders such as type 2 diabetes mellitus, hypertension, and cardiovascular disease. Although genetics and lifestyle have been directly implicated in the onset and progression of obesity, recent studies have established that gut microbiome plays a crucial role in obesity progression. A higher proportion of Firmicutes and a skewed Firmicutes/Bacteroidetes ratio may contribute to gut dysbiosis and subsequent disturbances in the overall body metabolisms. Like gut microbiome, the oral cavity of humans also harbors a characteristic microbial population called "oral microbiome". The oral microbiome has also been implicated in the development of obesity due to its modulating effects on the gut microbiome. Due to its critical role in obesity, alteration in the gut microbiome has been suggested as one of the therapeutic strategies to manage obesity itself. For example, fecal microbiome transfer, or the use of probiotics and prebiotics have been suggested. These therapies not only restore the gut microbiome to the "pre-obese stage" but also ameliorate many functional aspects of the metabolic syndrome such as systemic inflammation, insulin resistance, and fat accumulation. However, the efficacy and safety of some of the methods have not been tested for their long-term implications, and further research in this area is warranted to understand the molecular mechanisms involved in this process completely.

Combinatorial effects of trans-cinnamaldehyde with fluoride and chlorhexidine on Streptococcus mutans

AIMS

The aim of this study was to investigate the effects of trans-cinnamaldehyde (TC) and its synergistic activity with chlorhexidine (CHX) and fluoride against Streptococcus mutans.

METHODS AND RESULTS

Streptococcus mutans UA159 was treated with TC alone and in combination with CHX or sodium fluoride. The synergy profile was analysed using the Zero Interaction Potency model. TC showed strong synergism (synergy score of 21·697) with CHX, but additive effect (synergy score of 5·298) with fluoride. TC and the combinations were tested for acid production (glycolytic pH drop) and biofilm formation by S. mutans, and nitric oxide production in macrophages. TC significantly inhibited sucrose-dependent biofilm formation and acid production by S. mutans. Mechanistic studies were carried out by qRT-PCR-based transcriptomic studies which showed that TC acts by impairing genes related to metabolism, quorum sensing, bacteriocin expression, stress tolerance and biofilm formation.

CONCLUSIONS

trans-Cinnamaldehyde potentiates CHX and sodium fluoride in inhibiting S. mutans biofilms and virulence through multiple mechanisms. This study sheds significant new light on the potential to develop TC as an anti-caries treatment.

SIGNIFICANCE AND IMPACT OF THE STUDY

Oral diseases were classified as a 'silent epidemic' in the US Surgeon General's Report on Oral Health. Two decades later, >4 billion people are still affected worldwide by caries, having significant effects on the quality of life. There is an urgent need to develop novel compounds and strategies to combat dental caries. Here, we prove that TC downregulates multiple pathways and potentiates the CHX and fluoride to prevent S. mutans biofilms and virulence. This study sheds significant new light on the potential to develop TC in combination with CHX or fluoride as novel treatments to arrest dental caries.

Monoclonal Antibodies Specific to the Extracellular Domain of Histidine Kinase YycG of Staphylococcus epidermidis Inhibit Biofilm Formation

Staphylococcus epidermidis is frequently associated with biofilm-related infections. Biofilms drastically reduce the efficacy of conventional antibiotics and the host immune system. In S. epidermidis biofilm formation, a major role is played by the YycG/YycF two-component system, and previous findings have indicated that inhibitors targeting the cytoplasmic HATPase_c domain of YycG kinase in S. epidermidis exhibit bactericidal and biofilm-killing activities. Therefore, we hypothesized that monoclonal antibodies (mAbs) against YycG extracellular (YycG_ex) domain would block the signal transduction and influence the biofilm formation of S. epidermidis. In this study, we screened out two YycG_ex-specific mAbs showing the highest affinity for the target, mAbs 2F3 and 1H1. These mAbs inhibited S. epidermidis biofilm formation in a dose-dependent manner, and at a concentration of 160 μg/mL, mAbs 2F3 and 1H1 caused 78.3 and 93.1% biofilm reduction, respectively, relative to normal mouse IgG control. When co-cultivated with YycG_ex mAbs, S. epidermidis cells showed diminished initial-adherence capacity, and the antibody treatment further led to a marked decrease in the synthesis of polysaccharide intercellular adhesin and in the transcriptional level of genes encoding proteins involved in biofilm formation. Lastly, we determined that the epitopes recognized by the two YycG_ex mAbs are located within aa 59–70 of the YycG_ex domain. It indicates that the YycG_ex domain may be a potential candidate as a vaccine for the prevention of S. epidermidis biofilm infections.

Guardian genes ensuring subsistence of oral Streptococcus mutans

Despite the substantial research advancements on oral diseases, dental caries remains a major healthcare burden. A disease of microbial dysbiosis, dental caries is characterised by the formation of biofilms that assist demineralisation and destruction of the dental hard tissues. While it is well understood that this is a multi-kingdom biofilm-mediated disease, it has been elucidated that acid producing and acid tolerant bacteria play pioneering roles in the process. Specifically, Streptococcus mutans houses major virulence pathways that enable it to thrive in the oral cavity and cause caries. This pathogen adheres to the tooth substrate, forms biofilms, resists external stress, produces acids, kills closely related species, and survives the acid as well as the host clearance mechanisms. For an organism to be able to confer such virulence, it requires a large and complex gene network which synergise to establish disease. In this review, we have charted how these multi-faceted genes control several caries-related functions of Streptococcus mutans. In a futuristic thinking approach, we also briefly discuss the potential roles of omics and machine learning, to ease the study of non-functional genes that may play a major role and enable the integration of experimental data.

Environmental Triggers of lrgA Expression in Streptococcus mutans

The cidAB and lrgAB operons of Streptococcus mutans encode proteins that are structurally similar to the bacteriophage lambda family of holin-antiholin proteins, which are believed to facilitate cell death in other bacterial species. Although their precise function is not known, cidAB and lrgAB are linked to multiple virulence traits of S. mutans, including oxidative stress tolerance, biofilm formation, and autolysis. Here we investigate the regulation of lrgAB which in S. mutans shows a complex dependence on growth conditions that is not fully understood. By combining single-cell imaging of a fluorescent gene reporter with microfluidic control of the extracellular environment, we identify specific environmental cues that trigger lrgA expression and characterize cell-to-cell heterogeneity in lrgA activity. We find that the very abrupt activation of lrgA at stationary phase is tightly synchronized across the population. This activation is controlled by a small number of inputs that are sensitive to growth phase: extracellular pyruvate, glucose, and molecular oxygen. Activation of lrgA appears to be self-limiting, so that strong expression of lrgA is confined to a short interval of time. lrgA is programmed to switch on briefly at the end of exponential growth, as glucose and molecular oxygen are exhausted and extracellular pyruvate is available. Our findings are consistent with studies of other bacteria showing that homologs of lrgAB participate, with input from lytST, in the reimport of pyruvate for anaerobic fermentative growth.

Homeostatic control of cell wall hydrolysis by the WalRK two-component signaling pathway in Bacillus subtilis

Bacterial cells are encased in a peptidoglycan (PG) exoskeleton that protects them from osmotic lysis and specifies their distinct shapes. Cell wall hydrolases are required to enlarge this covalently closed macromolecule during growth, but how these autolytic enzymes are regulated remains poorly understood. Bacillus subtilis encodes two functionally redundant D,L-endopeptidases (CwlO and LytE) that cleave peptide crosslinks to allow expansion of the PG meshwork during growth. Here, we provide evidence that the essential and broadly conserved WalR-WalK two component regulatory system continuously monitors changes in the activity of these hydrolases by sensing the cleavage products generated by these enzymes and modulating their levels and activity in response. The WalR-WalK pathway is conserved among many Gram-positive pathogens where it controls transcription of distinct sets of PG hydrolases. Cell wall remodeling in these bacteria may be subject to homeostatic control mechanisms similar to the one reported here.

Characterization of LrgAB as a stationary phase-specific pyruvate uptake system in Streptococcus mutans

BACKGROUND

Our recent '-omics' comparisons of Streptococcus mutans wild-type and lrgAB-mutant revealed that this organism undergoes dynamic cellular changes in the face of multiple exogenous stresses, consequently affecting its comprehensive virulence traits. In this current study, we further demonstrate that LrgAB functions as a S. mutans pyruvate uptake system.

RESULTS

S. mutans excretes pyruvate during growth as an overflow metabolite, and appears to uptake this excreted pyruvate via LrgAB once the primary carbon source is exhausted. This utilization of excreted pyruvate was tightly regulated by glucose levels and stationary growth phase lrgAB induction. The degree of lrgAB induction was reduced by high extracellular levels of pyruvate, suggesting that lrgAB induction is subject to negative feedback regulation, likely through the LytST TCS, which is required for expression of lrgAB. Stationary phase lrgAB induction was efficiently inhibited by low concentrations of 3FP, a toxic pyruvate analogue, without affecting cell growth, suggesting that accumulated pyruvate is sensed either directly or indirectly by LytS, subsequently triggering lrgAB expression. S. mutans growth was inhibited by high concentrations of 3FP, implying that pyruvate uptake is necessary for S. mutans exponential phase growth and occurs in a Lrg-independent manner. Finally, we found that stationary phase lrgAB induction is modulated by hydrogen peroxide (H₂O₂) and by co-cultivation with H₂O₂-producing S. gordonii.

CONCLUSIONS

Pyruvate may provide S. mutans with an alternative carbon source under limited growth conditions, as well as serving as a buffer against exogenous oxidative stress_. Given the hypothesized role of LrgAB in cell death and lysis, these data also provide an important basis for how these processes are functionally and mechanically connected to key metabolic pathways such as pyruvate metabolism.

Transcriptional regulatory module analysis reveals that bridge proteins reconcile multiple signals in extracellular electron transfer pathways

Shewanella oneidensis MR-1 shows remarkable respiratory versatility with a large variety of extracellular electron acceptors (termed extracellular electron transfer, EET). To utilize the various electron acceptors, the bacterium must employ complex regulatory mechanisms to elicit the relevant EET pathways. To investigate the relevant mechanisms, we integrated EET genes and related transcriptional factors (TFs) into transcriptional regulatory modules (TRMs) and showed that many bridge proteins in these modules were signal proteins, which generally contained one or more signal processing domains (eg, GGDEF, EAL, PAS, etc.). Since Shewanella has to respond to diverse environmental conditions despite encoding few EET-relevant TFs, the overabundant signal proteins involved in the TRMs can help decipher the mechanism by which these microbes elicit a wide range of condition-specific responses. By combining proteomic data and protein bioinformatic analysis, we demonstrated that diverse signal proteins reconciled the different EET pathways, and we discussed the functional roles of signal proteins involved in the well-known MtrCAB pathway. Additionally, we showed that the signal proteins SO_2145 and SO_1417 played central roles in triggering EET pathways in anaerobic environments. Taken together, our results suggest that signal proteins have a profound impact on the transcriptional regulation of EET genes and thus have potential applications in microbial fuel cells.

Interacting proteins of the essential two-component system YycFG in Bacillus subtilis

Two-component signal transduction systems (TCSs) play a major role in adaption and survival of microorganisms in a dynamic and sometimes dangerous environment. YycFG is an essential TCS for many Gram-positive bacteria, such as Bacillus subtilis, which regulates many important biological processes. However, its functional essentiality remains largely unknown. Here, we report several YycFG interacting proteins through coimmunoprecipitation (Co-IP) and mass spectrometry (MS) analyses. We engineered the B. subtilis genome by a knock-in approach to express YycG with a C-terminal Flag and YycF with an N-terminal HA tag. Immunoprecipitated fractions using anti-Flag or anti-HA agarose were subjected to MS analyses. A total of 41 YycG interacting proteins and four YycF interacting proteins were identified, most of which are involved in cellular metabolic processes, including cell wall synthesis and modification. The interactions of YycG with AsnB and FabL, as examples, were further validated in vitro. This study provided a clue that YycFG may be directly involved in regulation of bacterial central metabolic pathways.

Roles of two-component regulatory systems in antibiotic resistance

Two-component regulatory systems (TCSs) are a major mechanism by which bacteria sense and respond to changes in their environment. TCSs typically consist of two proteins that bring about major regulation of the cell genome through coordinated action mediated by phosphorylation. Environmental conditions that activate TCSs are numerous and diverse and include exposure to antibiotics as well as conditions inside a host. The resulting regulatory action often involves activation of antibiotic defenses and changes to cell physiology that increase antibiotic resistance. Examples of resistance mechanisms enacted by TCSs contained in this review span those found in both Gram-negative and Gram-positive species and include cell surface modifications, changes in cell permeability, increased biofilm formation, and upregulation of antibiotic-degrading enzymes.

Effect of Chloroaluminium phthalocyanine in cationic nanoemulsion on photoinactivation of multispecies biofilm

BACKGROUND

Photosensitizers in nanocarriers have been investigated for antimicrobial Photodynamic Therapy (aPDT). However, most studies are focused against microorganisms in planktonic or monospecies biofilm. Thus, this in vitro study evaluated the effect of aPDT using Chloroaluminium phthalocyanine (ClAlPc) in cationic nanoemulsion (NE) against Candida albicans, Candida glabrata and Streptococcus mutans grown as multispecies biofilm.

METHODS

Standard suspensions of each microorganism were added into wells of a microtiter plate for biofilm growth for 48 h in a candle jar. The biofilms were incubated with ClAlPc in cationic NE at 31.8 μM for 30 min and illuminated with red light fluence of 39.3 J/cm² (P+L+ group). Additional samples were treated only with photosensitizer (P+L-) or red light (P-L+) or neither (P-L-, control group). aPDT efficacy was assessed by colony quantification, biofilm's metabolic activity, total biomass, and confocal microscopy. Data were analyzed by ANOVA/Welch and post-hoc Tukey/Games-Howell tests (α = 0.05).

RESULTS

aPDT (P+L+) reduced the colony count in 1.30 to 2.24 lg₁₀ and the metabolic activity in 53.7% compared with the control group (P-L-). The total biomass showed no statistical difference among the groups. The confocal microscopy analyzes showed uptake of the PS in the biofilm, and dead cells were observed in the biofilm treated with aPDT.

CONCLUSION

aPDT mediated by ClAlPc in cationic NE promoted photoinactivation of the multispecies biofilm, which was confirmed by colony quantification, metabolic activity, and confocal microscopy. However, the total biomass of the biofilm was not affected by the treatment.

Cell-gel interactions of in-gel propagating bacteria

Objective

Our immediate objective is to test the data-suggested possibility that in-agarose gel bacterial propagation causes gel fiber dislocation and alteration of cell distribution. We also test the further effect of lowering water activity. We perform these tests with both Gram-negative and Gram-positive bacteria. Data are obtained via electron microscopy of thin sections, which provides the first images of both bacteria and gel fibers in gel-supported bacterial lawns. The long-term objective is analysis of the effects of in-gel propagation on the DNA packaging of phages.

Results

We find that agarose gel-supported cells in lawns of Escherichia coli and Lysinibacillus (1) are primarily in clusters that increase in size with time and are surrounded by gel fibers, and (2) sometimes undergo gel-induced, post-duplication rotation and translation. Bacterial growth-induced dislocation of gel fibers is observed. One reason for clustering is that clustering promotes growth by increasing the growth-derived force applied to the gel fibers. Reactive force exerted by gel on cells explains cell movement. Finally, addition to growth medium of 0.94 M sucrose causes cluster-associated E. coli cells to become more densely packed and polymorphic. Shape is determined, in part, by neighboring cells, a novel observation to our knowledge.

The role of two-component regulatory system in β-lactam antibiotics resistance

The irrational use of antibiotics in agriculture and in the medical field has led to a variety of pathogenic microorganisms that produce drug resistance and even multidrug resistance. B-lactam is one of the most widely used antibiotics to treat infectious diseases. Resistance to β-lactam resistance can be primarily due to the presence β-lactamase, mutation of β-lactam targets and overexpression of efflux pumps. Two-component regulatory systems are composed of histidine kinase and response regulator that regulate gene expression under different environmental conditions. In this review, we summarized the mechanisms by which β-lactam resistance is developed and the role of the two-component regulatory system in β-lactam resistance.

Two-component signal transduction systems in oral bacteria

We present an overview of how members of the oral microbiota respond to their environment by regulating gene expression through two-component signal transduction systems (TCSs) to support conditions compatible with homeostasis in oral biofilms or drive the equilibrium toward dysbiosis in response to environmental changes. Using studies on the sub-gingival Gram-negative anaerobe Porphyromonas gingivalis and Gram-positive streptococci as examples, we focus on the molecular mechanisms involved in activation of TCS and species specificities of TCS regulons.

Remodeling of the Streptococcus mutans proteome in response to LrgAB and external stresses

The Streptococcus mutans Cid/Lrg system represents an ideal model to study how this organism withstands various stressors encountered in the oral cavity. Mutation of lrgAB renders S. mutans more sensitive to oxidative, heat, and vancomycin stresses. Here, we have performed a comprehensive proteomics experiment using label-free quantitative mass spectrometry to compare the proteome changes of wild type UA159 and lrgAB mutant strains in response to these same stresses. Importantly, many of identified proteins showed either a strikingly large fold-change, or were completely suppressed or newly induced in response to a particular stress condition. Notable stress proteome changes occurred in a variety of functional categories, including amino acid biosynthesis, energy metabolism, protein synthesis, transport/binding, and transcriptional/response regulators. In the non-stressed growth condition, mutation of lrgAB significantly altered the abundance of 76 proteins (a fold change >1.4, or <0.6, p-value <0.05) and several of these matched the stress proteome of the wild type strain. Interestingly, the statistical correlation between the proteome changes and corresponding RNA-seq transcriptomic studies was relatively low (rho(ρ) <0.16), suggesting that adaptation to a new environment may require radical proteome turnover or metabolic remodeling. Collectively, this study reinforces the importance of LrgAB to the S. mutans stress response.

AtlA Mediates Extracellular DNA Release, Which Contributes to Streptococcus mutans Biofilm Formation in an Experimental Rat Model of Infective Endocarditis

Host factors, such as platelets, have been shown to enhance biofilm formation by oral commensal streptococci, inducing infective endocarditis (IE), but how bacterial components contribute to biofilm formation in vivo is still not clear. We demonstrated previously that an isogenic mutant strain of Streptococcus mutans deficient in autolysin AtlA (ΔatlA) showed a reduced ability to cause vegetation in a rat model of bacterial endocarditis. However, the role of AtlA in bacterial biofilm formation is unclear. In this study, confocal laser scanning microscopy analysis showed that extracellular DNA (eDNA) was embedded in S. mutans GS5 floes during biofilm formation on damaged heart valves, but an ΔatlA strain could not form bacterial aggregates. Semiquantification of eDNA by PCR with bacterial 16S rRNA primers demonstrated that the ΔatlA mutant strain produced dramatically less eDNA than the wild type. Similar results were observed with in vitro biofilm models. The addition of polyanethol sulfonate, a chemical lysis inhibitor, revealed that eDNA release mediated by bacterial cell lysis is required for biofilm initiation and maturation in the wild-type strain. Supplementation of cultures with calcium ions reduced wild-type growth but increased eDNA release and biofilm mass. The effect of calcium ions on biofilm formation was abolished in ΔatlA cultures and by the addition of polyanethol sulfonate. The VicK sensor, but not CiaH, was found to be required for the induction of eDNA release or the stimulation of biofilm formation by calcium ions. These data suggest that calcium ion-regulated AtlA maturation mediates the release of eDNA by S. mutans, which contributes to biofilm formation in infective endocarditis.

The two-component system VicRK regulates functions associated with Streptococcus mutans resistance to complement immunity

Streptococcus mutans, a dental caries pathogen, can promote systemic infections upon reaching the bloodstream. The two-component system (TCS) VicRK_Sm of S. mutans regulates the synthesis of and interaction with sucrose-derived exopolysaccharides (EPS), processes associated with oral and systemic virulence. In this study, we investigated the mechanisms by which VicRK_Sm affects S. mutans susceptibility to blood-mediated immunity. Compared with parent strain UA159, the vicK_Sm isogenic mutant (UAvic) showed reduced susceptibility to deposition of C3b of complement, low binding to serum immunoglobulin G (IgG), and low frequency of C3b/IgG-mediated opsonophagocytosis by polymorphonuclear cells in a sucrose-independent way (P<.05). Reverse transcriptase quantitative polymerase chain reaction analysis comparing gene expression in UA159 and UAvic revealed that genes encoding putative peptidases of the complement (pepO and smu.399) were upregulated in UAvic in the presence of serum, although genes encoding murein hydrolases (SmaA and Smu.2146c) or metabolic/surface proteins involved in bacterial interactions with host components (enolase, GAPDH) were mostly affected in a serum-independent way. Among vicK_Sm -downstream genes (smaA, smu.2146c, lysM, atlA, pepO, smu.399), only pepO and smu.399 were associated with UAvic phenotypes; deletion of both genes in UA159 significantly enhanced levels of C3b deposition and opsonophagocytosis (P<.05). Moreover, consistent with the fibronectin-binding function of PepO orthologues, UAvic showed increased binding to fibronectin. Reduced susceptibility to opsonophagocytosis was insufficient to enhance ex vivo persistence of UAvic in blood, which was associated with growth defects of this mutant under limited nutrient conditions. Our findings revealed that S. mutans employs mechanisms of complement evasion through peptidases, which are controlled by VicRK_Sm.

Anti-bacterial and Anti-biofilm Evaluation of Thiazolopyrimidinone Derivatives Targeting the Histidine Kinase YycG Protein of Staphylococcus epidermidis

Staphylococcus epidermidis is one of the most important opportunistic pathogens in nosocomial infections. The main pathogenicity associated with S. epidermidis involves the formation of biofilms on implanted medical devices, biofilms dramatically decrease the efficacy of conventional antibiotics and the host immune system. This emphasizes the urgent need for designing novel anti-staphylococcal biofilm agents. Based on the findings that compound 5, targeting the histidine kinase domain of S. epidermidis YycG, possessed bactericidal activity against staphylococci, 39 derivatives of compound 5 with intact thiazolopyrimidinone core structures were newly designed, 7 derivatives were further screened to explore their anti-bacterial and anti-biofilm activities. The seven derivatives strongly inhibited the growth of S. epidermidis and Staphylococcus aureus in the minimal inhibitory concentration range of 1.56–6.25 μM. All the derivatives reduced the proportion of viable cells in mature biofilms. They all displayed low cytotoxicity on mammalian cells and were not hemolytic to human erythrocytes. The biofilm inhibition activities of four derivatives (H5-32, H5-33, H5-34, and H5-35) were further investigated under shearing forces, they all led to significant decreases in the biofilm formation of S. epidermidis. These results were suggestive that the seven derivatives of compound 5 have the potential to be developed into agents for eradicating biofilm-associated infections.

Modification of the Streptococcus mutans transcriptome by LrgAB and environmental stressors

The Streptococcus mutans Cid/Lrg system is central to the physiology of this cariogenic organism, affecting oxidative stress resistance, biofilm formation and competence. Previous transcriptome analyses of lytS (responsible for the regulation of lrgAB expression) and cidB mutants have revealed pleiotropic effects on carbohydrate metabolism and stress resistance genes. In this study, it was found that an lrgAB mutant, previously shown to have diminished aerobic and oxidative stress growth, was also much more growth impaired in the presence of heat and vancomycin stresses, relative to wild-type, lrgA and lrgB mutants. To obtain a more holistic picture of LrgAB and its involvement in stress resistance, RNA sequencing and bioinformatics analyses were used to assess the transcriptional response of wild-type and isogenic lrgAB mutants under anaerobic (control) and stress-inducing culture conditions (aerobic, heat and vancomycin). Hierarchical clustering and principal components analyses of all differentially expressed genes revealed that the most distinct gene expression profiles between S. mutans UA159 and lrgAB mutant occurred during aerobic and high-temperature growth. Similar to previous studies of a cidB mutant, lrgAB stress transcriptomes were characterized by a variety of gene expression changes related to genomic islands, CRISPR-C as systems, ABC transporters, competence, bacteriocins, glucosyltransferases, protein translation, tricarboxylic acid cycle, carbohydrate metabolism/storage and transport. Notably, expression of lrgAB was upregulated in the wild-type strain under all three stress conditions. Collectively, these results demonstrate that mutation of lrgAB alters the transcriptional response to stress, and further support the idea that the Cid/Lrg system acts to promote cell homeostasis in the face of environmental stress.