A Bibliographic Exploration of Bacterial Houses: Biofilm Matrix Research and Future Frontiers

Abstract

This paper explores the intriguing parallels between bacterial behavior and human actions, specifically the tendency of bacteria to adhere to surfaces, construct bacterial “houses” known as a biofilm matrix, nurture growth and reproduction within the biofilm matrix, and disperse upon maturity. Termed as the bacterial “houses”, biofilm matrices exert significant influence on various aspects of human life. A well-structured biofilm matrix serves as the foundation for establishing biofilm reactors capable of efficiently removing heavy metal pollutants from water. Conversely, a dysfunctional biofilm matrix can lead to infections and subsequent illnesses in the human body. Therefore, the study of the biofilm matrix emerges as pivotal. Employing a bibliographic study methodology, this paper analyzes 1000 web of science articles in the field, investigating key keywords, influential countries/regions, organizations, and their interconnections. The findings illuminate the primary themes in biofilm matrix research and offer insights into future directions for this critical field of study.

1. Introduction

Bacteria, microscopic architects of their own environments, exhibit behavioral parallels with human societies [1]. They adhere to surfaces, construct intricate “houses”, nurture within these habitats, and ultimately disperse [2]. These bacterial abodes, referred to as biofilm matrices, constitute a fascinating microcosm with far-reaching implications for various facets of human life [3]. The quality of these matrices can either be a boon or a bane—a well-structured biofilm matrix holds the potential to establish biofilm reactors capable of efficiently removing heavy metal pollutants from water [4], while a compromised matrix can pave the way for infections and subsequent illnesses in the human body [5]. Therefore, the study of biofilm matrix stands at the nexus of environmental sustainability and public health [6].

Biofilm matrices, as the architectural marvels of bacterial communities, represent a microcosm of self-sustaining life [7]. Similar to human societies, bacteria engage in communal living, constructing intricate matrix that serve as protective shelters and facilitators of growth [8]. The matrix, composed of a complex amalgamation of extracellular polymeric substances (EPSs) secreted by bacteria, create a microenvironment conducive to bacterial survival and proliferation [9].

The significance of a biofilm matrix extends beyond the microbial realm, influencing various aspects of human life [9]. A well-formed biofilm matrix acts as a promising resource for environmental remediation. Specifically, it provides a platform for the development of biofilm reactors capable of efficiently removing heavy metal pollutants from water sources [4]. This eco-friendly approach not only addresses environmental challenges but also holds immense potential for sustainable water management.

Conversely, when biofilm matrices deviate from their optimal state, they become potential sources of harm to human health [5]. Compromised, the matrices serve as breeding grounds for pathogenic bacteria, leading to infections and diseases in the human body. Understanding the delicate balance of biofilm matrix dynamics becomes crucial for developing strategies to mitigate the risks associated with bacterial infections.

To unravel the multifaceted nature of biofilm matrices, this paper employs a bibliographic study methodology [10]. By analyzing a diverse selection of 1000 articles from reputable journals and databases, we aim to distill the core themes and advancements within the biofilm matrix research domain. Our focus extends beyond individual studies, encompassing the broader landscape of research to identify trends, gaps, and potential areas for future exploration.

Our bibliographic study delves into the key elements shaping the biofilm matrix research landscape. By identifying prevalent keywords, we aim to discern the core themes that have garnered scholarly attention. Additionally, analyzing the geographical distribution of research efforts allows us to recognize the global footprint of biofilm matrix studies, highlighting regions at the forefront of scientific inquiry. Simultaneously, we explore the contributions of various organizations, shedding light on the collaborative networks and influential entities driving advancements in this field.

This paper presents a comprehensive overview of the current state of biofilm matrix research and identifies potential future directions through a bibliographic study. By analyzing keywords, geographic concentrations, and influential organizations, we aim to anticipate emerging trends and challenges. Our review of publications from the most influential universities and research institutes uncovers and interprets cutting-edge advancements in the biofilm matrix domain.

2. Materials and Methods

In November 2023, a comprehensive data collection was conducted using Web of Science, a reputable bibliographic database with various sub-databases [11]. The search focused on the term “biofilm matrix”, and the author selected the top 1000 papers from this database to ensure reliability and broad applicability.

For visualizing the bibliographic analysis, the powerful data visualization tool VOSviewer (Version: 1.6.17) was used [12,13]. The data files downloaded from Web of Science were imported into VOSviewer, which allowed for the adjustment of parameters according to the specific goals of the analysis and the diverse sources of data [14,15]. It is important to note that creating maps from web data often requires data cleaning to ensure accuracy and reliability. VOSviewer facilitated this data-cleaning process, helping to produce robust and meaningful visualizations.

Unless stated otherwise, the mapping performed with VOSviewer followed the default settings as outlined in previous studies [10]. In the keyword analysis, a minimum occurrence of “40” for keywords was set. For the country analysis, at least “10” documents from each country were required for inclusion. Similarly, the organization analysis included only those organizations with a minimum of “7” documents.

3. Results

Figure 1 serves as an enlightening visual representation, offering a comprehensive analysis of the most crucial keywords associated with the term “biofilm matrix”. This meticulous examination not only provides valuable insights into the field but also brings to the forefront prominent species names integral to biofilm matrix research. Noteworthy among these are “Pseudomonas aeruginosa”, “Staphylococcus aureus”, and “Escherichia coli”, recognized as primary model organisms contributing significantly to advancing our comprehension of biofilm matrices.

Simultaneously, the keyword analysis delves into the constituents of biofilm matrices, revealing terms such as “protein”, “polysaccharide”, and “extracellular DNA”. These components reflect the fundamental materials required by bacteria to construct their “houses” or biofilm matrices. This nuanced exploration not only enriches our understanding of the structural elements but also underscores the intricate processes involved in the formation of biofilm matrices.

Furthermore, the analysis illuminates key process-related terms including “adhesion”, “expression”, “growth”, “infections”, and “resistance”. These terms highlight the fundamental processes intricately linked to biofilm matrices, providing a deeper understanding of the dynamic interactions within these microbial communities. Unraveling the significance of both the identified species and the underlying processes is not only central to grasping the nuances of biofilm matrix studies but also crucial for appreciating their profound implications across diverse applications and industries.

This holistic understanding serves as a foundation for future research endeavors and innovations in the dynamic field of biofilm matrices. By deciphering the intricate interplay between species, constituents, and processes, researchers can pave the way for advancements that extend beyond fundamental studies, influencing practical applications in fields ranging from medicine to industry. The revelations from this analysis contribute not only to the academic understanding of biofilm matrices but also hold the potential to drive innovation and breakthroughs in the broader scientific community.

Figure 2 illustrates the primary countries involved in biofilm matrix research. It is evident that the United States and China occupy central positions, underscoring their significant contributions to recent research in the field of biofilm matrices. Additionally, other countries and regions such as Canada, England, France, Denmark, Germany, Ireland, the Netherlands, Belgium, Switzerland, Iran, Brazil, Portugal, Poland, Japan, India, Turkey, and Russia have also played crucial roles in advancing biofilm matrix studies.

This global distribution of research efforts emphasizes that biofilm matrix research is not confined to the contributions of a single country; rather, it necessitates collaborative efforts and active participation from various nations. The synergy of diverse perspectives and expertise from around the world is essential for achieving more impactful and comprehensive scientific outcomes in the realm of biofilm matrix research. This collaborative approach reflects the interconnected nature of scientific endeavors, where international cooperation enhances the collective understanding and advancement of knowledge in this crucial field.

Figure 3 depicts the key organizations involved in biofilm matrix research. It is evident that Nanyang Technological University, Ohio State University, Stanford University, and the University of Copenhagen occupy central positions, signifying their pivotal roles in advancing research in the field of biofilm matrices. Additionally, other prominent institutions such as the University of Wisconsin, the University of Pennsylvania, Montana State University, Harvard University, the National University of Singapore, Aarhus University, the Technical University of Munich, the Technical University of Denmark, the University of Zurich, and the University of Dundee are recognized as the main players in the biofilm matrix research field.

The research landscape in biofilm matrix studies is characterized by a diverse and collaborative network of institutions. While certain universities play central roles, the field is not dominated by a few top-tier institutions but thrives on international collaborations involving numerous universities. This highlights the importance of global cooperative efforts, demonstrating that advancements in biofilm matrix research are a collective achievement supported by contributions from various academic institutions worldwide. Therefore, fostering international collaborations is crucial for advancing progress and knowledge in this field. For industrial sectors, such as pharmaceutical companies, seeking to collaborate on biofilm matrix-related projects, the mentioned research institutions and their regions are valuable reference points.

4. Discussion

4.1. Bacterial Architects: Crafting Biofilm Habitats for Life’s Processes

To facilitate our understanding, we can compare the relationship between bacteria and the biofilm matrix to that of humans and their houses. Bacteria, akin to ingenious architects, function as master builders, intricately crafting their “houses” in the form of a biofilm matrix (Table 1). This matrix provides a multifaceted environment for their initial attachment, maturation, and eventual dispersion [16]. Within the complex architecture of the biofilm matrix, numerous integral components converge, including proteins, polysaccharides, extracellular DNA, lipids, and other elements essential to the structural integrity and functionality of this microbial habitat [17] (Figure 4).

Proteins take center stage as the foundational bricks within the intricate construction of the biofilm matrix [18,19,20]. Their prominence lies not only in sheer abundance but also in their pivotal role, constituting a substantial and indispensable aspect of the entire biofilm structure. Much like the bricks that form the essential groundwork for a physical house, these proteins contribute significantly to the biofilm’s structural framework, providing the necessary support and foundation for the intricate three-dimensional matrix that defines microbial habitats. Their multifaceted functions extend beyond mere abundance, acting as key players in orchestrating the stability and coherence of the biofilm, akin to the foundational bricks that uphold the structural integrity of a well-built edifice.

Polysaccharides assume a function comparable to reinforcing steel in the intricate architecture of the biofilm matrix [21,22,23]. Acting as a structural backbone, polysaccharides contribute crucial support and stability to the overall framework, mirroring the way reinforcing steel fortifies the structural integrity of buildings. Their involvement goes beyond mere composition; these polysaccharides play an instrumental role in fortifying the biofilm matrix, ensuring its resilience and longevity as a microbial dwelling. This reinforcement mechanism not only bolsters the structural integrity of the biofilm but also enhances its ability to withstand external pressures, environmental fluctuations, and other challenges, creating a robust and enduring habitat for microbial life processes.

Extracellular DNA, another vital component, can be metaphorically compared to cement [24,25]. This genetic material acts as the binding agent, intricately connecting the protein “bricks” and polysaccharide “steel”, solidifying the entire matrix. The intricate interplay of these components highlights the cohesive nature of the biofilm, sustained by the presence of extracellular DNA.

Lipids, functioning as additives in this microbial construction, play a dual role as lubricants and fixatives [26]. They facilitate the smooth transport of various components within the matrix while simultaneously securing them in designated areas. This lipid-driven process ensures the optimal arrangement and functionality of the diverse elements within the biofilm matrix.

In essence, the organic amalgamation of proteins, polysaccharides, extracellular DNA, lipids, and other elements transforms bacteria into skilled architects, enabling them to construct resilient and efficient “houses” in the form of biofilm matrices, each uniquely tailored to their specific ecological needs and challenges.

Table 1. Components of biofilm matrix and their functions.

Components	Key Findings	Reference
Protein	Microorganisms primarily exist as biofilms, surface-attached microbial communities with diverse compositions, where proteinaceous elements, including adhesins and flagella subunits, are crucial.	[18]
Protein	Protein involvement varies in different stages of Staphylococci biofilm formation.	[19]
Protein	This study explores Staphylococcus aureus biofilm dynamics on clinically relevant materials, revealing surface-dependent variations in formation efficiency and the evolving roles of poly-N-acetyl-β-(1-6)-glucosamine (PNAG) and proteins in early and later stages, respectively.	[20]
Polysaccharide	The study unveils the crucial role of the Psl exopolysaccharide in biofilm formation by mucoid Pseudomonas aeruginosa, indicating that Psl is a vital matrix component for both nonmucoid and mucoid biofilms, with potential implications for designing therapies for Pseudomonas aeruginosa infections in cystic fibrosis patients.	[21]
Polysaccharide	Pel, one of the extracellular polysaccharides produced by Pseudomonas aeruginosa, serves a dual function in biofilms by acting as a crucial structural scaffold for cell-to-cell interactions and enhancing resistance to aminoglycoside antibiotics, with its impact being strain-specific in biofilm development.	[22]
Polysaccharide	Extracellular polysaccharides, including alginate, Pel, and Psl in Pseudomonas aeruginosa, contribute to biofilm matrix formation, with strain-specific variations in Pel and Psl functions, suggesting redundancy as a mechanism for biofilm stability and adaptability.	[23]
Extracellular DNA	The research developed a novel approach with mass spectrometry, identifying previously unrecognized DNA-binding lipoproteins in Staphylococcus aureus biofilms that enhance biofilm formation, contribute to structure, and are linked to nuclease production, extending the electrostatic net model to include these proteins as anchor points between extracellular DNA and the bacterial cell surface.	[24]
Extracellular DNA	Extracellular DNA in biofilms, initially overlooked but now recognized for its pivotal role, influences bacterial adhesion, biofilm structure, and antimicrobial resistance through active secretion or controlled cell lysis, acid–base interactions, the chelation of cations, and triggering genetic responses, highlighting its potential as a target for biofilm sensitization and novel antimicrobial strategies.	[25]
Lipid	This paper highlights that while rhamnolipids have been previously considered crucial for hydrocarbon uptake in bacterial cells, recent evidence indicates their primary role in surface-associated motility and biofilm development, providing insights into their environmental impact in microbial ecosystems.	[26]

Table 1. Components of biofilm matrix and their functions.

Components	Key Findings	Reference
Protein	Microorganisms primarily exist as biofilms, surface-attached microbial communities with diverse compositions, where proteinaceous elements, including adhesins and flagella subunits, are crucial.	[18]
Protein	Protein involvement varies in different stages of Staphylococci biofilm formation.	[19]
Protein	This study explores Staphylococcus aureus biofilm dynamics on clinically relevant materials, revealing surface-dependent variations in formation efficiency and the evolving roles of poly-N-acetyl-β-(1-6)-glucosamine (PNAG) and proteins in early and later stages, respectively.	[20]
Polysaccharide	The study unveils the crucial role of the Psl exopolysaccharide in biofilm formation by mucoid Pseudomonas aeruginosa, indicating that Psl is a vital matrix component for both nonmucoid and mucoid biofilms, with potential implications for designing therapies for Pseudomonas aeruginosa infections in cystic fibrosis patients.	[21]
Polysaccharide	Pel, one of the extracellular polysaccharides produced by Pseudomonas aeruginosa, serves a dual function in biofilms by acting as a crucial structural scaffold for cell-to-cell interactions and enhancing resistance to aminoglycoside antibiotics, with its impact being strain-specific in biofilm development.	[22]
Polysaccharide	Extracellular polysaccharides, including alginate, Pel, and Psl in Pseudomonas aeruginosa, contribute to biofilm matrix formation, with strain-specific variations in Pel and Psl functions, suggesting redundancy as a mechanism for biofilm stability and adaptability.	[23]
Extracellular DNA	The research developed a novel approach with mass spectrometry, identifying previously unrecognized DNA-binding lipoproteins in Staphylococcus aureus biofilms that enhance biofilm formation, contribute to structure, and are linked to nuclease production, extending the electrostatic net model to include these proteins as anchor points between extracellular DNA and the bacterial cell surface.	[24]
Extracellular DNA	Extracellular DNA in biofilms, initially overlooked but now recognized for its pivotal role, influences bacterial adhesion, biofilm structure, and antimicrobial resistance through active secretion or controlled cell lysis, acid–base interactions, the chelation of cations, and triggering genetic responses, highlighting its potential as a target for biofilm sensitization and novel antimicrobial strategies.	[25]
Lipid	This paper highlights that while rhamnolipids have been previously considered crucial for hydrocarbon uptake in bacterial cells, recent evidence indicates their primary role in surface-associated motility and biofilm development, providing insights into their environmental impact in microbial ecosystems.	[26]

4.2. Exploring the Biofilm Matrix Landscape

Over the past few years, there has been a notable surge in research papers dedicated to exploring the diverse facets of the biofilm matrix. This upswing can be attributed to the increasing awareness among scientists about the profound impact of the biofilm matrix on various aspects of human daily life. Table 2 thoughtfully compiles a range of key research papers published during this period, providing insights into the significant growth in this field.

Upon a closer examination of Table 2, the varied spectrum of microorganisms utilized by researchers to investigate the intricacies of the biofilm matrix becomes apparent. These microorganisms encompass Escherichia coli, Shewanella oneidensis, Comamonas testosterone, Bacillus halodurans, and Pseudomonas aeruginosa, highlighting the diversity of species harnessed in the pursuit of knowledge about the biofilm matrix. Moreover, the research areas within biofilm matrix studies exhibit the same diversity as the microorganisms themselves.

In the field of engineering, the biofilm matrix has emerged as a powerful tool for addressing environmental challenges. Many developing countries face water pollution due to heavy metals. The biofilm matrix can play a crucial role in removing pollutants and purifying water sources [27,28]. Concurrently, it has found applications in the development of microbial fuel cells that generate energy, opening new avenues for sustainable power generation [29]. Additionally, the biofilm matrix has played a transformative role in civil engineering, contributing to the advancement of self-healing concrete, which holds the potential to revolutionize infrastructure durability [30].

In the medical sphere, the biofilm matrix poses a unique challenge in the context of lung infections [31,32,33]. Techniques for preventing and treating such infections have become a focal point of intense research efforts, given their critical importance to public health and well-being. Simultaneously, the field of chemical characterization has witnessed significant endeavors aimed at unraveling the chemical mapping and obtaining higher-resolution fluorescence images of the biofilm matrix [34]. The study highlighted that various environmental factors, including temperature, pH, salt, glucose concentration, and oxygen levels, significantly influence the biofilm formation of Staphylococcus [35]. These endeavors have deepened our understanding of the intricate composition of biofilm matrices and their potential applications.

In summary, the growing interest in the biofilm matrix and its multifaceted roles underscore the pivotal position this field occupies in contemporary research, offering innovative solutions to some of the most pressing challenges in environmental engineering, healthcare, and materials science.

Table 2. Prominent research in the biofilm matrix field over the past 15 years.

Category	Model Species	Main Findings	Reference
Engineering	Shewanella sp. HRCR-1	U(VI) was immobilized by the Shewanella sp. HRCR-1 biofilms	[27]
Engineering	Shewanella oneidensis	Cr(VI) was immobilized by the Shewanella oneidensis MR-1 biofilm	[4]
Engineering	Comamonas testosteroni	Biodegradation of 3-chloroaniline by Comamonas testosteroni biofilm and c-di-GMP	[28]
Engineering	Shewanella oneidensis/Escherichia coli	Electricity genernation and high-performance microbial fuel cells by biofilm matrix	[29]
Engineering	Bacillus halodurans	Biofilm matrix enhanced the self-repairing process in concrete	[30]
Engineering	Pseudomonas	Biofilm matrix formed a ba permeable reactive barrier (PRB) working with zerovalent iron to stop the organic pollutant	[36,37,38]
Medicine	Pseudomonas aeruginosa	Biofilm matrix led to infection in a patient with COVID-19	[31]
Medicine	Pseudomonas aeruginosa	Biofilm matrix led to chronic lung infection	[32]
Medicine	Staphylococcus aureus	Staphylococcus aureus biofilm formation causing infection can be reduced by linezolid or vancomycin	[33]
Medicine	Staphylococcus	The study found that various environmental factors, including temperature, pH, salt, glucose concentration, and oxygen levels, significantly influence the biofilm formation of Staphylococcus	[35]
Chemical characterization	Shewanella oneidensis	Molecular ion signal intensity for in situ biofilm matrix SIMS analysis was improved	[34]
Chemical characterization	Shewanella oneidensis	In situ molecular imaging of the biofilm matrix was achieved by SIMS	[39,40]
Chemical characterization	Pseudomonas aeruginosa	The biofilm matrix is identified by MALDI-TOF MS	[41]

Table 2. Prominent research in the biofilm matrix field over the past 15 years.

Category	Model Species	Main Findings	Reference
Engineering	Shewanella sp. HRCR-1	U(VI) was immobilized by the Shewanella sp. HRCR-1 biofilms	[27]
Engineering	Shewanella oneidensis	Cr(VI) was immobilized by the Shewanella oneidensis MR-1 biofilm	[4]
Engineering	Comamonas testosteroni	Biodegradation of 3-chloroaniline by Comamonas testosteroni biofilm and c-di-GMP	[28]
Engineering	Shewanella oneidensis/Escherichia coli	Electricity genernation and high-performance microbial fuel cells by biofilm matrix	[29]
Engineering	Bacillus halodurans	Biofilm matrix enhanced the self-repairing process in concrete	[30]
Engineering	Pseudomonas	Biofilm matrix formed a ba permeable reactive barrier (PRB) working with zerovalent iron to stop the organic pollutant	[36,37,38]
Medicine	Pseudomonas aeruginosa	Biofilm matrix led to infection in a patient with COVID-19	[31]
Medicine	Pseudomonas aeruginosa	Biofilm matrix led to chronic lung infection	[32]
Medicine	Staphylococcus aureus	Staphylococcus aureus biofilm formation causing infection can be reduced by linezolid or vancomycin	[33]
Medicine	Staphylococcus	The study found that various environmental factors, including temperature, pH, salt, glucose concentration, and oxygen levels, significantly influence the biofilm formation of Staphylococcus	[35]
Chemical characterization	Shewanella oneidensis	Molecular ion signal intensity for in situ biofilm matrix SIMS analysis was improved	[34]
Chemical characterization	Shewanella oneidensis	In situ molecular imaging of the biofilm matrix was achieved by SIMS	[39,40]
Chemical characterization	Pseudomonas aeruginosa	The biofilm matrix is identified by MALDI-TOF MS	[41]

4.3. Biofilm Matrix in the Era of Big Data and Machine Learning

In the ever-evolving landscape of the present era, the rapid evolution of various innovative technologies, notably big data and machine learning, has left an indelible mark across a spectrum of fields. These technological marvels have seamlessly integrated into diverse domains, from ecological predictions [42] and facial detection [43] to the cutting-edge realm of self-driving technology [44]. As we stand at the cusp of a technological renaissance, one can envision an exciting future where the transformative potential of these technologies extends to the intricate world of biofilm matrix research [45].

In this visionary future, biofilm matrix data, enriched with invaluable information like chemical mapping data, stands poised for systematic collection and compilation. Imagine a scenario where this wealth of data is sourced from a multitude of studies, coalescing into a monumental database housing more than a thousand records. This envisioned database emerges as a colossal and comprehensive resource, representing a veritable treasure trove for scientists embarking on the profound exploration of biofilm matrix intricacies. With such an extensive dataset at their fingertips, scientists are primed to leverage the formidable power of machine learning models, unlocking deeper insights into the multifaceted dimensions of biofilm matrix dynamics [46].

The implications of this convergence between advanced technologies and biofilm matrix research are monumental. The envisioned insights, drawn from the extensive dataset, have the potential to transcend the boundaries of biofilm studies, permeating various realms of scientific inquiry. In the realm of medical sciences, these revelations could become instrumental in shaping informed medical decision making, revolutionizing drug design methodologies, and fortifying infection control strategies. As we peer into this technological crystal ball, we witness the emergence of a new epoch—an era where knowledge-driven approaches take center stage in the relentless pursuit of combatting biofilm-related health threats.

This collaborative synergy between cutting-edge technologies and the intricate realm of biofilm matrices opens a gateway to innovation and transformative possibilities. It not only underscores the remarkable potential of amalgamating advanced technologies with biofilm matrix research but also signifies a paradigm shift toward more informed, efficacious, and personalized strategies in our ongoing battle against the myriad health challenges posed by biofilm-related issues. The envisioned future, painted with the strokes of technological prowess and scientific exploration, beckons us toward a horizon where our understanding of biofilm matrix intricacies propels us into a new era of groundbreaking solutions and improved healthcare outcomes.

5. Conclusions

Using a bibliographic study methodology, this research systematically analyzed articles to identify core themes and advancements in the biofilm matrix domain. The findings offer a comprehensive overview of current research and insights into potential future directions, setting the stage for further exploration and innovation in this dynamic field. Understanding the balance and dynamics of biofilm matrix is essential for tackling environmental sustainability challenges and mitigating public health risks.