Metagenomics analysis of bacterial structure communities within natural biofilm

Oral bacterial insights from a comparative study between healthy and comorbid diseased human individuals

The human oral cavity is colonized by a diverse microbial community, which includes both native and transient colonizers. The microbial composition is crucial for maintaining oral homeostasis, but due to overgrowth or imbalances of these microbial communities, dysbiosis can occur. There is a lack of understanding of the research of native and transient colonizers in the oral cavity of the Indian subpopulation Therefore, in our present study, we explored the role and prevalence of transient and native colonizers between healthy and comorbid oral diseased human individuals. Culture-dependent techniques and culture-independent 16S r DNA metagenomic analyses were employed to isolate and study the interactions of native and transient colonizers from human oral samples. Among the 66 human individuals of both healthy and comorbid individuals, the most abundant isolate was found to be Bacillus amyloliquefaciens MCC 4424. In addition, the more prevalent culturable isolate from the healthy samples was Streptococcus salivarius MTCC 13009, whereas in comorbid samples Staphylococcus pasteuri MTCC 13076, Rothia dentocariosa MTCC 13010 and Pseudomonas aeruginosa MTCC 13077 were prevalent to a greater extent. 16S rDNA metagenomic analyses revealed the prevalence and abundance of genera such as Bacteroidetes and Proteobacteria in healthy individuals; consequently, Fusobacteria and Firmicutes were observed mostly in comorbid individuals. The significant differences in bacterial population density were observed in terms of the Shannon index (p = 0.5145) and Simpson index (p = 0.9061) between the healthy and comorbid groups. B. amyloliquefaciens MCC 4424 exhibits antagonistic behavior when grown as a dual-species with native and transient colonizers. This result is very consistent with the findings of antibiofilm studies using confocal laser scanning microscopy, which revealed a significant reduction in biofilm biovolume (73 %) and maximum thickness (80 %) and an increase in the rough coefficient of biofilms (30 %). Our data suggested that B. amyloliquefaciens MCC 4424 can be a native colonizer of Indian sub-populations. It may act as a novel candidate for oral healthcare applications and greatly aids in the regulation of transient species in the oral cavity.

Hotspots and frontiers in Helicobacter pylori biofilm research: A bibliometric and visualization analysis from 1998 to 2023

Background

Helicobacterpylori (H. pylori) biofilm formation is a key factor in refractory H. pylori infection. The aim of this study was to understand research trends in H. pylori biofilms.

Methods

The Web of Science Core Collection database was used to retrieve publications published from 1998 to 2023. Different kinds of software, EXCEL, an online bibliometric analysis platform, and the VOS viewer were used to evaluate and visualize the bibliometric data.

Results

In total, 184 publications were identified, and the number of publications increased annually. The USA made the greatest contributions to this research field, while Helicobacter was the most productive journal. Grande rossella published the most papers, and the most productive institution was Gabriele D'Annunzio university. Co-occurrence network maps revealed that the keyword "Helicobacter pylori" ranked first in research field, and the keyword of "biofilm formation" and "in vitro" began to appear in the past three to five years. The majority of the five most-cited articles (60%) were published in USA and focused on the mechanism of H. pylori biofilm formation.

Conclusion

The annual number of publications on H. pylori biofilms has increased steadily over the past two decades and will continue to increase. Future studies should focus on evaluate the pharmacological effects, efficacy and safety of these anti-biofilm treatments in animal models and clinical trials.

New insights for tracking bacterial community structures in industrial wastewater from textile factories to surface water using phenotypic, 16S rRNA isolates identifications and high-throughput sequencing

Industrial wastewater can possibly change the microbial ecological environment. There are few studies that focus on the bacterial variety in textile wastewater effluents and after combination with domestic wastewater. Thus, this study aimed to determine dye degrading bacteria from textile wastewater and environmental water samples using cultural method followed by phenotypic using BIOLOG and genotypic identification (16S rRNA) for dye degrading isolates identifications. Moreover, the bacterial communities in three textile and four environmental samples using Illumina MiSeq high-throughput sequencing were investigated. The findings revealed that in textile water samples, the ratio of dye-degrading bacteria (DDB) to total bacterial counts (TBC) was 27%. The identified DDB genera by 16S rRNA based on the cultural approach were Citrobacter spp., Klebsiella spp., Enterobacter spp., Pseudomonas spp., and Aeromonas spp. Regarding to the metagenomics analyses, the environmental samples had 5,598 Operational Toxanomic Units (OTUs) more than textile wastewater samples (1,463 OTUs). Additionally, the most abundant phyla in the textile wastewater were Proteobacteria (24.45-94.83%), Bacteriodetes (0.5-44.84%) and Firmicutes (3.72-67.40%), while, Proteobacteria (30.8-76.3%), bacteroidetes (8.5-50%) and Acentobacteria (0.5-23.12%) were the most abundant phyla in the environmental samples. The maximum abundant bacteria at species level in environmental samples were Aquabacterium parvum (36.71%), Delftia tsuruhatensis (17.61%), Parabacteriodes chartae (15.39%) and Methylorubrum populi (7.51%) in El-Rahawy Drain water (RDW), River Nile water (RNW), wastewater (RWW) from WWTP in Zennin and El-Rahawy Drain sediment (RDS), respectively, whereas the maximum abundant bacteria at species level in textile wastewater were Alkalibacterium pelagium (34.11%), Enterobacter kobei (26.09%) and Chryseobacterium montanum (16.93%) in factory 1 (HBT) sample, SHB sample (before mixing with domestic wastewater) and SHB sample (after mixing with domestic wastewater), respectively. In conclusion, the microbial communities in textile wastewaters are similar to those in environmental samples at the phylum level but distinct at the genus and species levels because they are exposed to a wider range of environmental circumstances.

Bacterial community structure of electrogenic biofilm developed on modified graphite anode in microbial fuel cell

Formation of electrogenic microbial biofilm on the electrode is critical for harvesting electrical power from wastewater in microbial biofuel cells (MFCs). Although the knowledge of bacterial community structures in the biofilm is vital for the rational design of MFC electrodes, an in-depth study on the subject is still awaiting. Herein, we attempt to address this issue by creating electrogenic biofilm on modified graphite anodes assembled in an air-cathode MFC. The modification was performed with reduced graphene oxide (rGO), polyaniline (PANI), and carbon nanotube (CNTs) separately. To accelerate the growth of the biofilm, soybean-potato composite (plant) powder was blended with these conductive materials during the fabrication of the anodes. The MFC fabricated with PANI-based anode delivered the current density of 324.2 mA cm-2, followed by CNTs (248.75 mA cm-2), rGO (193 mA cm-2), and blank (without coating) (151 mA cm-2) graphite electrodes. Likewise, the PANI-based anode supported a robust biofilm growth containing maximum bacterial cell densities with diverse shapes and sizes of the cells and broad metabolic functionality. The alpha diversity of the biofilm developed over the anode coated with PANI was the loftiest operational taxonomic unit (2058 OUT) and Shannon index (7.56), as disclosed from the high-throughput 16S rRNA sequence analysis. Further, within these taxonomic units, exoelectrogenic phyla comprising Proteobacteria, Firmicutes, and Bacteroidetes were maximum with their corresponding level (%) 45.5, 36.2, and 9.8. The relative abundance of Gammaproteobacteria, Clostridia, and Bacilli at the class level, while Pseudomonas, Clostridium, Enterococcus, and Bifidobacterium at the genus level were comparatively higher in the PANI-based anode.

Effects of cinnamaldehyde against planktonic bacteria and biofilm formation of Shigella flexneri

Cinnamaldehyde (CA) has demonstrated anti-inflammatory, anti-tumor and anti-cancer activities; Its antimicrobial and antibiofilm actions against Shigella flexneri, on the other hand, have not been investigated. Sh. flexneri is a gram-negative foodborne pathogen that can be widely found in nature and some industrial production environments. In this current research, our aim was to examine the influences of CA on planktonic bacteria and biofilm formation. The minimum inhibitory concentration (MIC) of CA against Sh. flexneri strain was 100 μg/mL, while bacteria treated with CA showed a longer lag phase compared with the untreated control. CA effectively inactivated the Sh. flexneri in LB broth and fresh lettuce juice. CA treatment resulted in cell membrane permeability changes and dysfunction, as proven by cell membrane depolarization, decreased intracellular ATP concentration. In addition, CA was also discovered to increase the level of reactive oxygen species (ROS) in cells, and induce morphological changes in cells. Crystal violet staining showed that the biomass of biofilm was decreased significantly with CA in 24 h. Light microscopy and field emission scanning electron microscopy (FESEM) observations demonstrated decreased biofilm adhesion and destruction of biofilm architecture after treatment with CA. These findings indicated that CA acts as a natural bacteriostatic agent to control Sh. flexneri in food processing and production.

Emerging Bioanalytical Devices and Platforms for Rapid Detection of Pathogens in Environmental Samples

The development of robust bioanalytical devices and biosensors for infectious pathogens is progressing well with the advent of new materials, concepts, and technology. The progress is also stepping towards developing high throughput screening technologies that can quickly identify, differentiate, and determine the concentration of harmful pathogens, facilitating the decision-making process for their elimination and therapeutic interventions in large-scale operations. Recently, much effort has been focused on upgrading these analytical devices to an intelligent technological platform by integrating them with modern communication systems, such as the internet of things (IoT) and machine learning (ML), to expand their application horizon. This review outlines the recent development and applications of bioanalytical devices and biosensors to detect pathogenic microbes in environmental samples. First, the nature of the recent outbreaks of pathogenic microbes such as foodborne, waterborne, and airborne pathogens and microbial toxins are discussed to understand the severity of the problems. Next, the discussion focuses on the detection systems chronologically, starting with the conventional methods, advanced techniques, and emerging technologies, such as biosensors and other portable devices and detection platforms for pathogens. Finally, the progress on multiplex assays, wearable devices, and integration of smartphone technologies to facilitate pathogen detection systems for wider applications are highlighted.

Bioactive tri-component nanofibers from cellulose acetate/lignin//N-vanillidene-phenylthiazole copper-(II) complex for potential diaper dermatitis control

Current research targets innovative medical textiles of nanofibrous nature and antibacterial activity to prevent diaper dermatitis. The work is based on electrospun nanofibers from cellulose acetate (CA) and lignin (Lig) polymers. A series of new copper complexes were synthesized and loaded to the CA/Lig solution mix then subjected to electrospinning, giving rise to the tricomponent bioactive mats CA/Lig/Cu-complex. The surface morphology of electrospun nanofiber mats was smooth and homogenous as the concentration of lignin increased in the mixture. The incorporation of lignin improved the electrospinnability of the cellulose acetate; however, it increased the fiber diameter. The water contact angle, absorption underload were significantly improved as lignin content increased. The incorporation of Cu-complex in electrospun CA and CA/Lig fiber mats occurred without any substantial change in the surface morphology, indicating well encapsulation of the complex. The electrospun mats were active against Pseudomonas aeruginosa, Acinetobacter baumannii, Staphylococcus epidermidis, and Streptococcus faecalis. The cytotoxicity, protein leakage, and biological results, together with the above studies, would advocate copper complex loaded CA/Lig nanofibers as a potential candidate for hygienic applications.

Effects of pipe materials on the characteristic recognition, disinfection byproduct formation, and toxicity risk of pipe wall biofilms during chlorination in water supply pipelines

There are growing concerns over the contributions of biofilms to disinfection byproduct (DBP) formation in engineered water systems (EWSs). Three kinds of water supply pipes, ductile iron (DI), cement-lined stainless steel (SS) and polyethylene (PE) pipes, were selected for the experiment conducted in this study. Based on test results, the three pipe biofilms showed relatively obvious differences in growth, morphological characteristics, organic components and bacterial diversity. Secreted extracellular polymeric substance (EPS) accounted for more than 90% of the biofilm and had greater disinfection byproduct formation potential (DBPFP) than the cell phases. DI pipe wall biofilms had the highest DBPFP, which to a certain extent means that denser and richer organic matter can be produced as the precursor of different types of DBPs. UHPLC-Q Exactive was used to identify the types of DBPs generated from the chlorination of histidine (His), alanine (Ala) and tryptophan (Trp) shared by the three pipe materials and their formation pathways. Compared to carbonaceous disinfection by-products (C-DBPs), nitrogenous disinfection by-products (N-DBPs) had a significant advantage in toxicity generation potentials in the biofilms, especially dichloroacetonitrile (DCAN) and trichloronitromethane (TCNM). DCAN and haloacetic acids (HAAs) were the key to cytotoxicity in biofilms, while TCNM was dominant in biofilm genotoxicity.

Three-dimensional morphology of bacterial community developed on the index-matched materials

Herein, we demonstrate that the use of index-matching materials (IMMs) allows direct visualization of microbial cells maintained at a solid-liquid interface through confocal reflection microscopy (CRM). The refractive index mismatch induces a background reflection at the solid-liquid interface that dwarfs the reflection signals from the cells and results in low-contrast images. We found that the IMMs sufficiently suppressed the background reflection at the solid-liquid interface, facilitating the imaging of microbes at the solid surface using CRM. The use of IMMs allowed quantitative analysis of the morphology of the mesh-like structure of Pseudomonas aeruginosa biofilms formed under denitrifying conditions, which led us to propose a novel structural model of the highly porous biofilm structure. These results indicate that the use of CRM coupled with an IMM offers a unique and promising tool for probing the dynamics of biofilm formation, along with visualization of environmental organisms and newly isolated bacteria, for which transformation methods are difficult to establish.

Bacterial colonization dynamics and antibiotic resistance gene dissemination in the hospital environment after first patient occupancy: a longitudinal metagenetic study

BACKGROUND

Humans spend the bulk of their time in indoor environments. This space is shared with an indoor ecosystem of microorganisms, which are in continuous exchange with the human inhabitants. In the particular case of hospitals, the environmental microorganisms may influence patient recovery and outcome. An understanding of the bacterial community structure in the hospital environment is pivotal for the prevention of hospital-acquired infections and the dissemination of antibiotic resistance genes. In this study, we performed a longitudinal metagenetic approach in a newly opened ward at the Charité Hospital (Berlin) to characterize the dynamics of the bacterial colonization process in the hospital environment after first patient occupancy.

RESULTS

The sequencing data showed a site-specific taxonomic succession, which led to stable community structures after only a few weeks. This data was further supported by network analysis and beta-diversity metrics. Furthermore, the fast colonization process was characterized by a significant increase of the bacterial biomass and its alpha-diversity. The compositional dynamics could be linked to the exchange with the patient microbiota. Over a time course of 30 weeks, we did not detect a rise of pathogenic bacteria in the hospital environment, but a significant increase of antibiotic resistance determinants on the hospital floor.

CONCLUSIONS

The results presented in this study provide new insights into different aspects of the environmental microbiome in the clinical setting, and will help to adopt infection control strategies in hospitals and health care-related buildings. Video Abstract.

Faucet aerator design influences aerosol size distribution and microbial contamination level

Faucet aerators have been linked to multiple opportunistic pathogen outbreaks in hospital, especially Pseudomonas aeruginosa, their complex structure promoting biofilm development. The importance of bacteria aerosolization by faucet aerators and their incidence on the risk of infection remain to be established. In this study, ten different types of aerators varying in complexity, flow rates and type of flow were evaluated in a controlled experimental setup to determine the production of aerosols and the level of contamination. The aerosol particle number density and size distribution were assessed using a particle spectrometer. The bacterial load was quantified with a 14-stage cascade impactor, where aerosol particles were captured and separated by size, then analysed by culture and flow cytometry. The water was seeded with Pseudomonas fluorescens as a bacterial indicator. Aerosol particle size and mean mass distribution varied depending on the aerator model. Devices without aeration or with laminar flow produced the lowest number and mass of aerosol particles when measured with spectrometry. Models with aeration displayed wide differences in their potential production of aerosol particles. A new aerator with a low flow, no air inlet in its structure, and a spray stream produced 12 to 395 times fewer aerosol particles containing bacteria. However, the impact of low flow on biofilm development and incorporation of pathogens should be further investigated. Repeated use of aerators resulted in fouling which increased the quantity of bacteria released through aerosol particles. An in-depth mechanical cleaning including complete dismantling of the aerator was required to recover initial performances. Aerators should be selected to minimize aerosol production, considering the ease of maintenance and the main water usage at each sink. Low flow aerators produced a lower number of contaminated aerosol particles when new but may be more susceptible to fouling and quickly lose their initial advantage.

The role of biofilm in the development and dissemination of ubiquitous pathogens in drinking water distribution systems: an overview of surveillance, outbreaks, and prevention

A variety of pathogenic microorganisms can survive in the drinking water distribution systems (DWDS) by forming stable biofilms and, thus, continually disseminating their population through the system's dynamic water bodies. The ingestion of the pathogen-contaminated water could trigger a broad spectrum of illnesses and well-being-related obstacles. These waterborne diseases are a significant concern for babies, pregnant women, and significantly low-immune individuals. This review highlights the recent advances in understanding the microbiological aspects of drinking water quality, biofilm formation and its dynamics, health issues caused by the emerging microbes in biofilm, and approaches for biofilm investigation its prevention and suppression in DWDS.

The destruction of Escherichia coli adhered to pipe surfaces in a model drinking water distribution system via various antibiofilm agents

The aim of the study is to estimate the effectiveness of three antibiofilm agents against Escherichia coli biofilm that formed in six different types of pipelines. A laboratory-scale water system was built for this work to allow for the creation of biofilm in the pipelines studied. The level of the growth rate of E. coli biofilm cells was monitored over 90 days on those tested pipe materials. The results of bacterial cell densities displayed that the highest biofilm growth was observed in the biofilm formed on the iron (Fe) pipe. In contrast, the biofilm formation rate was significantly lower on copper (Cu) pipe compared to other materials. Three antibiofilm agents, including chlorine, silver ions (Ag⁺ ), and silver nanoparticles (AgNPs), were employed to eradicate the biofilm cells. E. coli counts indicated that AgNPs are more efficient in destructing any formed biofilm cells on all tested materials. At the same time, the chlorine was only useful in the case of biofilm developed on plastic and Cu. However, the antibiofilm efficiency of Ag⁺ performs similarly to chlorine against E. coli biofilm cells. Ultimately, AgNPs are considred the most powerful antibiofilm agent among the other agents toward the biofilm cells in their maturation stage, which offers an encouraging way for the long-term functioning of water systems. PRACTITIONER POINTS: The growth rate of E. coli biofilm cells was investigated on different materials. The count of biofilm cells developed on iron pipes was higher than other materials. The E. coli biofilm on iron pipe could resist chlorine and AgNPs to a large extent. The developed biofilm on copper pipe was more sensitive to chlorine, Ag⁺ . and AgNPs. The biofilm cells could be easily eradicated from plastic-based materials with all tested disinfectants.