Review Article | Published:

The biofilm matrix

Nature Reviews Microbiology volume 8, pages 623633 (2010) | Download Citation



The microorganisms in biofilms live in a self-produced matrix of hydrated extracellular polymeric substances (EPS) that form their immediate environment. EPS are mainly polysaccharides, proteins, nucleic acids and lipids; they provide the mechanical stability of biofilms, mediate their adhesion to surfaces and form a cohesive, three-dimensional polymer network that interconnects and transiently immobilizes biofilm cells. In addition, the biofilm matrix acts as an external digestive system by keeping extracellular enzymes close to the cells, enabling them to metabolize dissolved, colloidal and solid biopolymers. Here we describe the functions, properties and constituents of the EPS matrix that make biofilms the most successful forms of life on earth.

Key points

  • Formation of the biofilm matrix induces a unique environment for bacteria that allows the dynamic biofilm mode of life. Biofilms, and the resulting lifestyle, are built in specific, defined steps, producing a bacterial community that is heterogeneous in space and time.

  • Extracellular polymeric substances (EPS) immobilize biofilm cells, keeping them in long-term close proximity and, thus, allowing intense interactions to occur, including cell–cell communication, horizontal gene transfer and the formation of synergistic microconsortia.

  • Owing to the retention of extracellular enzymes in the matrix, a versatile external digestive system is generated: dissolved and particulate nutrients imported through the water phase of the matrix can be sequestered, accumulated and utilized. The matrix acts as an ultimate recycling yard, keeping all the components of lysed cells available, including DNA, and possibly therefore serving as a large genetic archive. Gradient formation creates a wide range of very different habitats, contributing to biodiversity in biofilms.

  • The matrix protects organisms in the biofilm from desiccation, biocides, antibiotics, heavy metals, ultraviolet radiation, host immune defences and many protozoan grazers.

  • Eventually, EPS can serve as a nutrient source, but — as for many other structural polymers in biology — some EPS components are only slowly biodegradable. The vast variety of EPS components means that their complete degradation requires a wide range of enzymes.

  • Ecologically, competition and cooperation in the confined space of the EPS matrix, and competition for the limited nutrients in particular, lead to constant adaptation of population fitness.

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We are grateful for the inspiring cooperation with partners in the research group on 'Physico-chemistry of Biofilms': W. Borchard, K.-E. Jaeger, H. Kuhn, C. Mayer and W. Veeman. We also acknowledge financial support by the German Research Foundation to various EPS research projects. Furthermore, constructive, critical and stimulating comments and discussions with I. Sutherland are highly appreciated.

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  1. Biofilm Centre, University of Duisburg-Essen, Geibelstrasse 41, D-47057 Duisburg, Germany.

    • Hans-Curt Flemming
    •  & Jost Wingender


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Correspondence to Hans-Curt Flemming.



A loose definition for microbial aggregates that usually accumulate at a solid–liquid interface and are encased in a matrix of highly hydrated EPS. Included in this definition are cell aggregates such as flocs (floating biofilms) and sludge, which are not attached to an interface but which share the characteristics of biofilms. Multispecies biofilms can form stable microconsortia, develop physiochemical gradients, and undergo horizontal gene transfer and intense cell–cell communication, and these consortia therefore represent highly competitive environments.

Extracellular polymeric substances

Hydrated biopolymers (including polysaccharides, proteins, nucleic acids and lipids) that are secreted by biofilm cells to encase and immobilize microbial aggregates. These biopolymers are responsible for the macroscopic appearance of biofilms, which are frequently referred to as 'slime'.

Humic substance

A component of the natural organic matter in soil and water enviroments. Humic substances are mixtures of compounds that are formed by limited degradation and transformation of dead organic matter and that are resistant to complete biodegradation. They can be divided into three main fractions: humic acids, fulvic acids and humin. They usually include phenolic and polyaromatic compounds (containing peptide and carbohydrate moieties with carboxylic substituents), providing the acidic character.


A long, thin, helically shaped bacterial appendage that provides motility. A flagellum consists of several components and moves by rotation, much like a propeller. The motor is anchored in the cytoplasmic membrane and the cell wall.


A bacterial surface structure that is similar to a fimbria but is typically a longer structure, and that is present on the cell surface in one or two copies. Pili can be receptors for bacteriophages and also facilitate genetic exchange between bacterial cells during conjugation. Type IV pili mediate twitching motility, which is a flagella-independent form of bacterial translocation over surfaces, and can be involved in biofilm development.


A filamentous structure composed of one or a few proteins that extends from the surface of a cell and can have diverse functions. Fimbriae are involved in attachment to both animate and inanimate surfaces and in the formation of pellicles and biofilms. They assist in the disease process of some pathogens, such as S. enterica, Neisseria gonorrhoea and Bordetella pertussis.

Membrane vesicle

A vesicle that is formed from the outer membrane of Gram-negative bacteria, is secreted from the cell surface and contains extracellular enzymes and nucleic acids. These vesicles may represent mobile elements in the EPS matrix.


A discrete polysaccharide (sometimes also protein) layer that is firmly attached to the surface of a bacterial cell, closely surrounding it, in contrast to less compact, amorphous slime that is shed into the more distant extracellular environment.


A protein or glycoprotein of plant, animal or microbial origin that binds to carbohydrates with a characteristic specificity. Fluorescently labelled lectins can be used as probes to investigate EPS composition, enabling the microscopic in situ detection of EPS and their distribution in biofilms.

Raman microscopy

A spectroscopic technique based on inelastic light scattering (Raman scattering) of monochromatic laser light in the near-ultraviolet range, revealing vibrational, rotational and other low-frequency modes in a system. The technique is used for the analysis of chemical bonds and is suitable for very small volumes, allowing spectra and chemical information to be obtained for the molecules present in that volume.

Matrix void

A pore or channel in the biofilm matrix that contains liquid water and is not filled with hydrated EPS molecules.


A laminated microbial mat that is typically built from layers of filamentous cyanobacteria and other microorganisms that become fossilized. Stromatolites are the oldest records of life on Earth, dating back 3.5 billion years.

Surface-active property

The ability of a molecule to alter the interface of two different phases. Substances with surface-active properties (surfactants) are amphipatic molecules with both hydrophilic and hydrophobic (generally hydrocarbon) moieties. They partition preferentially at the interface between fluid phases with different degrees of polarity and hydrogen bonding, such as oil–water interfaces.


A substance that is synthesized by living cells (mostly bacteria and yeasts) and that is surface active. Biosurfactants reduce surface tension, stabilize emulsions, promote foaming and are generally non-toxic and biodegradable. When grown on hydrocarbon substrates as a carbon source, microorganisms can synthesize a wide range of biosurfactants, such as glycolipids and phospholipids. These chemicals are apparently synthesized to emulsify the hydrocarbon substrate and facilitate its transport into the cells. In some bacterial species, such as P. aeruginosa, biosurfactants are also involved in a group movement behaviour called swarming motility.

Hydraulic decoupling

The formation of areas that have virtually no exchange of water content with their environment. An example is a desiccated EPS layer that covers an area with a high water content but has very low water transport through the layer, retaining the water underneath.

Elasticity modulus

The tendency of an object or material to reversibly develop an elastic force in response to deformation. Mathematically, the elasticity modulus is the proportionality factor between the force and the deformation, or, in other words, the slope on a plot of stress versus strain in the elastic deformation region. Stiff materials have a higher elasticity modulus, whereas soft materials have a lower one.

Stress relaxation

A deviation from the ideal elastic behaviour of a material due to an internal relief of stress under constant strain. Some materials, when put under mechanical tension, undergo internal flow processes (termed 'creep') that are at least partially irreversible and lead to a constant deformation of the test specimen.

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