Search Results (72)

The detection of colony-forming units (CFUs) is a time-consuming but essential task in mulberry bacterial blight research. To overcome the problem of inaccurate small-target detection and high computational consumption in mulberry bacterial blight colony detection task, a mulberry bacterial blight colony dataset (MBCD) consisting of 310 images and 23,524 colonies is presented. Based on the MBCD, a colony detection model named Colony-YOLO is proposed. Firstly, the lightweight backbone network StarNet is employed, aiming to enhance feature extraction capabilities while reducing computational complexity. Next, C2f-MLCA is designed by embedding MLCA (Mixed Local Channel Attention) into the C2f module of YOLOv8 to integrate local and global feature information, thereby enhancing feature representation capabilities. Furthermore, the Shape-IoU loss function is implemented to prioritize geometric consistency between predicted and ground truth bounding boxes. Experiment results show that the Colony-YOLO achieved an mAP of 96.1% on MBCDs, which is 4.8% higher than the baseline YOLOv8n, with FLOPs and Params reduced by 1.8 G and 0.8 M, respectively. Comprehensive evaluations demonstrate that our method excels in detection accuracy while maintaining lower complexity, making it effective for colony detection in practical applications. Full article

Mycobacterium tuberculosis is a formidable pathogen capable of establishing persistent infections within macrophages. To survive and thrive within the host environment, it has evolved intricate regulatory networks, including a diverse array of transcription factors that enable adaptation to various stresses encountered within the host. However, the mechanisms by which transcription factors regulate biofilm formation in M. tuberculosis remain incompletely understood. This study aimed to investigate the role of serC, encoding phosphoserine aminotransferase, and its regulation by NapR, a transcription factor, in mycobacterial physiology. NapR regulates serC through directly binding to its promoter. Notably, the regulatory effect and corresponding phenotypes vary due to distinct binding affinities of NapR for the serC promoter in different mycobacterial species. In Mycobacterium smegmatis, NapR_Msm positively regulates biofilm formation, growth on solid media, and the transition from microcolonies to microcolonies by activating serC_Msm. In the BCG vaccine, on the contrary, NapR_BCG represses serC_BCG, thus negatively regulating colony size and alleviating the growth inhibition caused by high concentrations of serine. Furthermore, proteomic analysis suggested NapR serves as a global transcriptional regulator in BCG vaccine strains by simultaneously modulating four metabolic pathways. These findings underscore the complex and strain-specific regulatory mechanisms governing serine metabolism in mycobacteria and provide valuable insights into the interplay between metabolism, gene regulation, and bacterial physiology. Full article

Although bioremediation is considered the most environmentally friendly and sustainable technique for remediating contaminated soil and water, it is most effective when combined with physicochemical methods, which allow for the preliminary removal of large quantities of pollutants. This allows microorganisms to efficiently eliminate the remaining contaminants. In addition to requiring the necessary genes and degradation pathways for specific substrates, as well as tolerance to adverse environmental conditions, microorganisms may perform below expectations. One typical reason for this is the high toxicity of xenobiotics present in large concentrations, stemming from the vulnerability of bacteria introduced to a contaminated site. This is especially true for planktonic bacteria, whereas bacteria within biofilms or microcolonies have significant advantages over their planktonic counterparts. A physical matrix is essential for the formation, maintenance, and survival of bacterial biofilms. By providing such a matrix for bacterial immobilization, the formation of biofilms can be facilitated and accelerated. Therefore, bioremediation combined with bacterial immobilization offers a comprehensive solution for environmental cleanup by harnessing the specialized metabolic activities of microorganisms while ensuring their retention and efficacy at target sites. In many cases, such bioremediation can also eliminate the need for physicochemical methods that are otherwise required to initially reduce contaminant concentrations. Then, it will be possible to use microorganisms for the remediation of higher concentrations of xenobiotics, significantly reducing costs while maintaining a rapid rate of remediation processes. This review explores the benefits of bacterial immobilization, highlighting materials and processes for developing an optimal immobilization matrix. It focuses on the following four key areas: (i) the types of organic pollutants impacting environmental and human health, (ii) the bacterial strains used in bioremediation processes, (iii) the types and benefits of immobilization, and (iv) the immobilization of bacterial cells on various carriers for targeted pollutant degradation. Full article

Background: Biofilm formation in Helicobacter pylori (H. pylori) helps bacteria survive antibiotic exposure and supports bacterial colonization and persistence in the stomach. Most of the published articles have focused on one aspect of the biofilm. Therefore, we conducted the current study to better understand the mechanism of biofilm formation, how the biofilm contributes to antibiotic resistance, and how the biofilm modifies the medication delivery mechanism. Methods: We conducted a literature review analysis of the published articles on the Helicobacter pylori biofilm between 1998 and 2024 from the PubMed database to retrieve eligible articles. After applying the inclusion and exclusion criteria, two hundred and seventy-three articles were eligible for our study. Results: The results showed that biofilm formation starts as adhesion and progresses through micro-colonies, maturation, and dispersion in a planktonic form. Moreover, specific genes modulate each phase of biofilm formation. Few studies have shown that mechanisms, such as quorum sensing and diffusible signal factors, enhance coordination among bacteria when switching from biofilm to planktonic states. Different protein expressions were also observed between planktonic and biofilm strains, and the biofilm architecture was supported by exopolysaccharides, extracellular DNA, and outer membrane vesicles. Conclusions: This infrastructure is responsible for the increased survival of bacteria, especially in harsh environments or in the presence of antibiotics. Therefore, understanding the biofilm formation for H. pylori is crucial. This study illustrates biofilm formation in H. pylori to help improve the treatment of H. pylori infection. Full article

Campylobacter jejuni plays a significant role in human health, food production, and veterinary practice. Biofilm formation is a likely mechanism explaining the survival of C. jejuni in seemingly unfavourable environments, but the underlying mechanisms are poorly understood. We propose a mathematical model to unify various observations regarding C. jejuni biofilm formation. Specifically, we present a cellular automaton with stochastic dynamics that describes both the probability of biofilm initiation and its subsequent growth. Our model incorporates fundamental processes such as cell rearrangement, diffusion of chemical compounds, accumulation of extracellular material, cell growth, lysis, and deactivation due to nutrient scarcity. The model predicts an optimal nutrient concentration that enhances population survival, revealing a trade-off where higher nutrient levels may harm individual cells but benefit the overall population. Our results suggest that the lower biofilm accumulation observed experimentally in aerobic conditions compared to microaerobic conditions may be due to a reduced surface invasion probability of individual cells. However, cells that do manage to invade can generate microcolonies of a similar size under both aerobic and microaerobic conditions. These findings provide new insights into the survival probability and size of C. jejuni biofilms, suggesting potential targets for controlling its biofilm formation in various environments. Full article

Biofilms are accumulations of microorganisms in an extracellular polymeric substance matrix which are composed of polysaccharides, proteins, lipids, and nucleic acids. Many bacteria can switch between a planktonic form and a biofilm form. The planktonic bacteria have relatively high cell growth and reproduction rates and have a reduced likelihood of survival but can adapt to occupy new habitats. The biofilm state appears to be a natural and predominant state of bacteria. The need for the formation of bacterial biofilm is that it enhances the tolerance of bacteria to harsh environmental conditions, thereby allowing bacteria to avoid being washed away by water flow or the bloodstream by simply attaching to a surface or tissue, and the EPS matrix protects bacteria cells, in deeper layers, against antimicrobial agents, probably by limiting the diffusion of these agents. Biofilm formation steps are initial contact/attachment to the surface, followed by micro-colony formation, maturation and formation of the architecture of the biofilm, and finally detachment/dispersion of the biofilm. Once formed, biofilm restricts bacterial mobility and increases cell density. Secretions of autoinducers into the environment are critical for cross-signaling between bacteria. This cross-talk is called quorum sensing (QS). Quorum sensing is a cell–cell communication mechanism between bacteria that allows specific processes to be controlled, such as biofilm formation and virulence factor expression. Bacterial quorum sensing signaling mainly consists of acyl-homoserine lactones (produced by Gram-negatives), autoinducing peptides (produced by Gram-positives), and autoinducer-2 (produced by both Gram-negatives and Gram-positives). Therefore, this review is aimed at how bacterial biofilms work and are formed. Full article

Enterococcus faecalis is a bacterial pathogen that can cause opportunistic infections. Studies indicate that initial biofilm formation plays a crucial regulatory role in these infections, as well as in colonising and maintaining the gastrointestinal tract as a commensal member of the microbiome of most land animals. It has long been thought that vegetation of endocarditis resulting from bacterial attachment to the endocardial endothelium requires some pre-existing tissue damage, and in animal models of experimental endocarditis, mechanical valve damage is typically induced by cardiac catheterisation preceding infection. This section reviews historical and contemporary animal model studies that demonstrate the ability of E. faecalis to colonise the undamaged endovascular endothelial surface directly and produce robust microcolony biofilms encapsulated within a bacterially derived extracellular matrix. This report reviews both previous and current animal model studies demonstrating the resilient capacity of E. faecalis to colonise the undamaged endovascular endothelial surface directly and produce robust microcolony biofilms encapsulated in a bacterially derived extracellular matrix. The article also considers the morphological similarities when these biofilms develop on different host sites, such as when E. faecalis colonises the gastrointestinal epithelium as a commensal member of the common vertebrate microbiome, lurking in plain sight and transmitting systemic infection. These phenotypes may enable the organism to survive as an unrecognised infection in asymptomatic subjects, providing an infectious resource for subsequent clinical process of endocarditis. Full article

Saxispiralis lemnorum MUM 23.14 is an extremotolerant microcolonial black fungus, originally isolated from a biodeteriorated limestone artwork in Portugal. This recently introduced species belongs to the Aeminiaceae family, representing the second member of this monophyletic clade. This fungus exhibits a unique set of characteristics, including xerophily, cold tolerance, high UV radiation tolerance, and an exceptional ability to thrive in NaCl concentrations of up to 30% while also enduring pH levels ranging from 5 to 11. To gain insights into its genomic traits associated with stress resistance mechanisms, specialization, and their potential implications in stone biodeterioration, we conducted a comprehensive genome sequencing and analysis. This draft genome not only marks the first for the Saxispiralis genus but also the second for the Aeminiaceae family. Furthermore, we performed two comparative genomic analyses: one focusing on the closest relative within the Aeminiaceae family, Aeminium ludgeri, and another encompassing the genome of different extremotolerant black fungi. In this study, we successfully achieved high genome completeness for S. lemnorum and confirmed its close phylogenetic relationship to A. ludgeri. Our findings revealed traits contributing to its extremophilic nature and provided insights into potential mechanisms contributing to stone biodeterioration. Many traits are common to both Aeminiaceae species and are shared with other black fungi, while numerous unique traits may be attributed to species-specific characteristics. Full article

The extracellular polymeric substance (EPS) plays a key factor in biofilm formation. However, the research on the importance of each EPS fraction is mainly concentrated in the activated sludge field. In this study, biofilms were cultivated under different hydrodynamic conditions in indoor flumes, and the important regulatory effects of dissolved EPS (SB-EPS), loosely bound EPS (LB-EPS), and tightly bound EPS (TB-EPS) on biofilm formation were investigated. The results indicated that the ratios of soluble EPS (S-EPS), loosely bound EPS (LB-EPS), and tightly bound EPS (TB-EPS) were 27:74:108 in the turbulent flow, 38:48:71 in the transitional flow, and 89:51:51 in the laminar flow. Regarding proportion, TB-EPS and LB-EPS were secreted more in the turbulent flow, while S-EPS was secreted slightly more in the laminar flow. S-EPS lacks the structural strength provided by bound EPS. Under the special bonding effects of LB-EPS and TB-EPS, many microcolonies join to form biofilms. The polysaccharide content in the EPS of biofilms remained dominant under all conditions. Polysaccharides are the core of biofilm formation, which enhance bacterial aggregation and make biofilm dense. Through the mutual verification of the results in the microscopic and macroscopic fields, the mechanism of biofilm formation was further elucidated, especially, in Stage IV, due to the special bonding effects of LB-EPS and TB-EPS, many colonies adhere to the mature biofilm. Further studies are required to investigate the extracellular polysaccharides and proteins in EPS along with their properties in biofilms. Full article

With an impressive ability to survive in harsh environments, black fungi are an ecological group of melanized fungi that are widely recognized as a major contributor to the biodeterioration of stone cultural heritage materials. As part of the ongoing efforts to study the fungal diversity thriving in a deteriorated limestone funerary art piece at the Lemos Pantheon, a national monument located in Águeda, Portugal, two isolates of an unknown microcolonial black fungus were retrieved. These isolates were thoroughly studied through a comprehensive analysis based on a multi-locus phylogeny of a combined dataset of ITS rDNA, LSU, and rpb2, along with morphological, physiological, and ecological characteristics. Based on the data obtained from this integrative analysis, we propose a new genus, Saxispiralis gen. nov., and a new species, Saxispiralis lemnorum sp. nov., in the recently described Aeminiaceae family (order Mycosphaerellales). Prior to this discovery, this family only had one known genus and species, Aeminium ludgeri, also isolated from deteriorated limestone. Additionally, considering the isolation source of the fungus and to better understand its potential contribution to the overall stone monument biodeterioration, its in vitro biodeteriorative potential was also evaluated. This work represents a significant contribution to the understanding of the fungal diversity involved in the biodeterioration of limestone heritage. Full article

Candida albicans is a pathobiont of the gastrointestinal tract. It can contribute to the diversity of the gut microbiome without causing harmful effects. When the immune system is compromised, C. albicans can damage intestinal cells and cause invasive disease. We hypothesize that a therapeutic approach against C. albicans infections can rely on the antimicrobial properties of probiotic bacteria. We investigated the impact of the probiotic strain Escherichia coli Nissle 1917 (EcN) on C. albicans growth and its ability to cause damage to intestinal cells. In co-culture kinetic assays, C. albicans abundance gradually decreased over time compared with C. albicans abundance in the absence of EcN. Quantification of C. albicans survival suggests that EcN exerts a fungicidal activity. Cell-free supernatants (CFS) collected from C. albicans-EcN co-culture mildly altered C. albicans growth, suggesting the involvement of an EcN-released compound. Using a model of co-culture in the presence of human intestinal epithelial cells, we further show that EcN prevents C. albicans from damaging enterocytes both distantly and through direct contact. Consistently, both C. albicans’s filamentous growth and microcolony formation were altered by EcN. Taken together, our study proposes that probiotic-strain EcN can be exploited for future therapeutic approaches against C. albicans infections. Full article

Improving the management of children with asthma associated with mycoplasma infection is important. Aim: To study the duration of the persistence of antigens, and DNA in a free state, in the structures of circulating immune complexes (CICs) and living cells of Mycoplasma pneumoniae (Mpn) and Mycoplasma hominis (Mh) in children with asthma. In total, 205 children with asthma from 1 to 14 years were observed. The reaction of aggregate-hemagglutination (AHAA), the direct immunofluorescence reaction (DIF), the reaction of the polymerase chain reaction (PCR), and the culture method were used. In addition, 47 children were re-examined 1.5 months after the treatment of mycoplasma infection with azithromycin. The number of samples positive for antigens and DNA in the free state and in the structures of CICs significantly decreased. Then, 50 blood serum samples containing Mh antigens, and 50 samples containing Mpn antigens were analyzed by culture method. Mh was isolated in 21 (65.5%) of 32 samples containing DNA. Mpn was isolated from antigen-positive samples in nine cases. The presented data indicate the long-term persistence of antigens, and DNA of mycoplasma cells in the free state, in the structure of CICs, as well as in the form of “microcolonies”. A high level of CICs can be used to predict the course of the disease and the response to therapy. Full article

The objective of this research was to encapsulate probiotics by alginate hydrogel beads based on an in situ cultivation method and investigate the influences on the cell loading capacity, surface and internal structure of hydrogel beads and in vitro gastrointestinal digestion property of cells. Hydrogel beads were prepared by extrusion and cultured in MRS broth to allow probiotics to grow inside. Up to 10.34 ± 0.02 Log CFU/g of viable cell concentration was obtained after 24 h of in situ cultivation, which broke through the bottleneck of low viable cell counts in the traditional extrusion method. Morphology and rheological analyses showed that the structure of the eventually formed probiotic hydrogel beads can be loosed by the existence of hydrogen bond interaction with water molecules and the internal growth of probiotic microcolonies, while it can be tightened by the acids metabolized by the probiotic bacteria during cultivation. In vitro gastrointestinal digestion analysis showed that great improvement with only 1.09 Log CFU/g of loss in viable cells was found after the entire 6 h of digestion. In conclusion, the current study demonstrated that probiotic microcapsules fabricated by in situ cultivation method have the advantages of both high loading capacity of encapsulated viable cells and good protection during gastrointestinal digestion. Full article

Free anammox bacteria are superior in growth rate, but poor sedimentation performance limits their application in sewage treatment. In this study, we investigated how to form aggregates of free anammox bacteria to improve sedimentation performance. Calcium addition tests proved that free anammox bacteria could aggregate and form a larger entirety with better sedimentation performance through calcium cross-linking with alginate-like exopolysaccharides (ALEs). This was indicated by the particle size increasing by 411.45% and sedimentation performance (measured with supernatant transmittance) increasing by 195.35% after adding calcium for 12 h. Soluble extracellular polymeric substance (S-EPS) extraction and freeze–thaw testing elucidated that providing more cross-linking sites can strengthen the cross-linking, as indicated by the sedimentation performance increasing by 158.57% and 394.80%, respectively. Static experiments showed that cross-linking time was equally important. The sedimentation performance improved with longer static times under no severe external disturbances, with a 324.61% improvement after 84 h. However, the bacteria burst and the anammox activity disappeared after freeze–thaw treatment. Based on the above test results, a potential method for forming aggregates of free anammox bacteria to improve sedimentation performance was proposed: extract S-EPS with centrifugation first, add calcium, and keep the sludge free from external hydraulic interference. Full article

A disturbed balance within the dental biofilm can result in the dominance of cariogenic and periodontopathogenic species and disease development. Due to the failure of pharmacological treatment of biofilm infection, a preventive approach to promoting healthy oral microbiota is necessary. This study analyzed the influence of Streptococcus salivarius K12 on the development of a multispecies biofilm composed of Streptococcus mutans, S. oralis and Aggregatibacter actinomycetemcomitans. Four different materials were used: hydroxyapatite, dentin and two dense polytetrafluoroethylene (d-PTFE) membranes. Total bacteria, individual species and their proportions in the mixed biofilm were quantified. A qualitative analysis of the mixed biofilm was performed using scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). The results showed that in the presence of S. salivarius K 12 in the initial stage of biofilm development, the proportion of S. mutans was reduced, which resulted in the inhibition of microcolony development and the complex three-dimensional structure of the biofilm. In the mature biofilm, a significantly lower proportion of the periodontopathogenic species A. actinomycetemcomitans was found in the salivarius biofilm. Our results show that S. salivarius K 12 can inhibit the growth of pathogens in the dental biofilm and help maintain the physiological balance in the oral microbiome. Full article