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Polymers
  • Review
  • Open Access

18 August 2023

From Nature to Lab: Sustainable Bacterial Cellulose Production and Modification with Synthetic Biology

,
and
1
Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, 2000 Maribor, Slovenia
2
Faculty of Mechanical Engineering, Institute of Engineering Materials and Design, University of Maribor, 2000 Maribor, Slovenia
3
Faculty of Chemistry and Chemical Engineering, University of Maribor, 2000 Maribor, Slovenia
*
Author to whom correspondence should be addressed.
This article belongs to the Special Issue Advanced Cellulose-Based Materials: From Nanoparticles to Complex Structures and Composites

Abstract

Bacterial cellulose (BC) is a macromolecule with versatile applications in medicine, pharmacy, biotechnology, cosmetology, food and food packaging, ecology, and electronics. Although many bacteria synthesize BC, the most efficient BC producers are certain species of the genera Komagataeibacter and Novacetimonas. These are also food-grade bacteria, simplifying their utilization at industrial facilities. The basic principles of BC synthesis are known from studies of Komagataeibacter xylinus, which became a model species for studying BC at genetic and molecular levels. Cellulose can also be of plant origin, but BC surpasses its purity. Moreover, the laboratory production of BC enables in situ modification into functionalized material with incorporated molecules during its synthesis. The possibility of growing Komagataeibacter and Novacetimonas species on various organic substrates and agricultural and food waste compounds also follows the green and sustainable economy principles. Further intervention into BC synthesis was enabled by genetic engineering tools, subsequently directing it into the field of synthetic biology. This review paper presents the development of the fascinating field of BC synthesis at the molecular level, seeking sustainable ways for its production and its applications towards genetic modifications of bacterial strains for producing novel types of living biomaterials using the flexible metabolic machinery of bacteria.

1. Review Contents

The Scheme 1 gives an overview of the sections covered in this review.
Scheme 1. An overview of the sections covered in this review.

3. Strategies for Improvement of Bacterial Cellulose Production and Modification

3.1. Conventional Methods for Improvements of Bacterial Cellulose Production and Modification

Applications and commercialization of BC were initially significantly limited by low yields in laboratory fermenters and inefficient scale-up of the production process to an industrial scale, as economically justified yields were not achievable in industrial bioreactors []. Consequently, researchers dedicated several years of studies to optimizing bioprocess factors by modifying culturing strategies and conditions. They investigated the influence of essential medium components, carbon sources, various additives, temperature, pH, dissolved oxygen concentration, dimensions of laboratory vessels, and different fermentation techniques, focusing on static and agitated cultures (Figure 8) and bioreactors [,,,,,].
Figure 8. BC’s final appearance depends on the fermentation technique, with static culture (top) resulting in BC membranes (pellicles) that form at the liquid–air interface and assume the shape of the laboratory vessel, and agitated culture (bottom) leading to the submerged formation of irregular BC pellets (adapted from de Amorim et al. [] (CC BY)).
Static culture—the most popular strategy for producing BC, in which microorganisms form a cellulose pellicle at the liquid–air interface—is limited by long cultivation times. This drawback can be overcome by the agitation fermentation technique, where bacteria are incubated on a shaker, resulting in BC with a similar chemical structure. Although bacterial growth in agitated culture is higher than in static culture, shaking can lead to the occurrence of mutants in cellulose operons, which do not contribute to the final BC yield [].
Researchers have attempted to improve the original medium to optimize cellulose production by adding a cheaper nitrogen source, such as corn steep liquor, incorporating various sulfates and phosphates, and removing organic acids [,]. The carbon source is one the most extensively studied components of the growth medium, as it significantly affects the BC yield. BC-producing bacteria vary in their ability to assimilate and utilize different carbon sources []. To enhance the BC yield, a wide range of primary metabolites have been tested, including various types of carbohydrates such as monosaccharides (e.g., D-xylose, D-xylulose, fructose, galactose, glucose), disaccharides (e.g., lactose, maltose, sucrose), oligosaccharides, organic acids, and sugar alcohols (e.g., ethanol, mannitol) [,,,,,,,].
Before the introduction of genetic engineering techniques in BC production, the artificial selection of strains was considered a relatively simple genetic intervention capable of influencing the production process. Various species of bacteria used in industrial BC production exhibit different yields depending on the growth medium and culturing conditions. They also differ in the properties of the final product, particularly in its purity and crystallinity. Artificial selection, combined with naturally occurring mutations, allowed researchers to identify the most successful strains with the highest product yield and quality for each species [,,]. While such a non-targeted approach can be successful, it cannot gain the speed and precision of genetic engineering. Furthermore, it is unsuitable for introducing new functionalities into microorganisms since the necessary genes are commonly missing [].
Like any natural or synthetic material, BC has limited usability, which can be expanded through various conventional functionalization methods. Based on the approach of modifying the material, three types of cellulose are distinguished: bacterial nanocellulose (BNC), cellulose nanocrystals (CNCs), and cellulose nanofibrils (CNFs). BNC is produced through a bottom-up approach by bacteria metabolizing low molecular weight carbohydrates []. Applying the top-down approach to BNC enables the production of CNCs and CNFs. CNCs are formed through treatment with chemicals, such as ionic liquids, lithium hydroxide, N,N dimethylacetamide/lithium chloride, N-methylmorpholine-N-oxides, and NaOH-urea/thiourea [,,,,]. CNFs are obtained through mechanical processes, such as high-pressure homogenization and grinding combined with enzymatic pretreatments [,]. Particular challenges accompany the production of cellulose nanomaterials. The limited selection of suitable solvents leads to the use of toxic and hazardous chemicals, which pollute the environment and limit the recyclability and disposal of products. Meanwhile, mechanical processing methods may compromise the physical properties of the biopolymer.
Conventionally, without using genetic engineering methods, numerous composites can be produced where BC is combined with other materials. In principle, we can distinguish two different strategies. In the first strategy, the in situ strategy, various reinforcement materials are added directly into the growth medium and incorporated by microorganisms during the biosynthesis of BC. Commonly added substances capable of improving the functional properties of BC include agar [], aloe vera [], carboxymethyl cellulose [], conductive polymers (polyaniline, PEDOT:PSS, polypyrrole) [], graphene oxide [], metal nanoparticles [], multiwalled carbon nanotubes [], poly-3-butyrate [], and sodium alginate []. Some issues associated with this kind of strategy include the precipitation of added substances and the unsuccessful incorporation of reinforcement materials into the pellicle. In the second strategy, the ex situ strategy, physical absorption or hydrogen bond formation is employed to establish connections between additives and the cellulose matrix. Such nanocomposites are often developed by combining BC with carbon nanotubes, chitosan [], collagen [], conductive polymers [], hyaluronic acid [], hydroxyapatite [], metal nanoparticles [], metal oxides [], and montmorillonite []. The use of these reinforcement materials enhances the mechanical, electrical, and antimicrobial properties of BC. The utility of this strategy is mainly restricted by the non-uniform size of additives and cellulose pores, as well as the hydrophilic nature of BC, which hinders interactions with hydrophobic reinforcement materials [].
Gao et al. [] showed the production of functional BC by K. sucrofermentans where instead of genetically engineering the microorganisms, they modified glucose into synthetic 6-carboxyfluorescein glucose (6-CF-Glc). The bacteria grown in the modified glucose medium synthesized a cellulose pellicle with unnatural green fluorescing capabilities (Figure 9). The fluorescence intensity was controlled by varying the concentration of 6-CF-Glc in the growth medium.
Figure 9. The fluorescence intensity of functional BC grown in the presence of 6-carboxyfluorescein glucose (6-CF-Glc) depends on the substrate concentration; a high concentration of 6-CF-Glc (top) and low concentration of 6-CF-Glc (bottom) with average fluorescence intensities of 1492 a.u. and 612 a.u., respectively (adapted from Gao et al. [] (CC BY)).

3.2. Co-Culturing Bacteria for Improvements of Bacterial Cellulose Production and Functionality

Several examples exist of using the co-culture approach for BC production (Figure 10). In one of the early studies, K. xylinus and Lactobacillus mali were co-cultured in corn- steep liquor supplemented with sucrose []. The authors noted a 3-fold improvement in BC production compared to the monoculture of K. xylinus, due to cell–cell interactions and the exopolysaccharide produced by L. mali. BC made in N. hansenii and E. coli ATCC 700728 co-culture displayed superior mechanical properties []. In the co-culture of N. hansenii ATCC 23769 and Lactococcus lactis APJ3, a copolymer of BC and hyaluronic acid was successfully produced, showing improved water-holding capacity compared to regular cellulose pellicles []. Similarly, in the co-culture of K. xylinus and Ralstonia eutropha, a mechanically superior nanocomposite of BC and polyhydroxybutyrate was developed []. Gunduz et al. [] expanded this approach by co-culturing N. hansenii ATCC 23769 with a consortium of microorganisms (e.g., Lactobacillus casei, L. lactis, Rhodopseudomonas palustris, and S. cerevisiae) that assists the display of multiple functionalities. They achieved a 40-fold increase in water-holding abilities compared to the monoculture of K. xylinus.
Figure 10. Schematic representation of co-culture approach for obtaining BC and hyaluronic acid (HA) composite (adapted from Brugnoli et al. [] (CC BY)).
Taking a slightly different approach inspired by the symbiotic culture of bacteria and yeast (SCOBY) used for fermenting kombucha tea, Gilbert et al. [] produced BC in a co-culture of genetically modified yeast and a wild-type strain of K. rhaeticus. They focused on genetically modifying the yeast S. cerevisiae, a well-known model organism that can be genetically manipulated in ways not possible with the Komagataeibacter genus. The authors initially aimed to genetically engineer the yeast, known for its excellent protein secretion capabilities, to secrete proteins that would functionalize the developing cellulose pellicle. They tested this concept using β-lactam hydrolyzing enzyme TEM1 β-lactamase, and apparent enzymatic activity was detected in the pellicles produced in the co-culture containing both BC-producing bacteria and genetically modified yeast. This activity was preserved even after the functionalized BC was dried and rehydrated. Furthermore, they designed a yeast strain that modifies pellicles’ physical properties. The microorganisms simultaneously secreted different cellulose-degrading enzymes, including β-glucosidase, cellobiohydrolases, endoglucanase, and lytic polysaccharide monooxygenases. They found that the BC production was not significantly reduced, but some of the pellicle’s physical properties, especially its tensile strength and Young’s modulus, were weakened. Co-culturing acetic acid bacteria and yeast was also used to investigate whether the living BC-based hybrid materials can sense and react. They designed a yeast biosensor system based on the synthetic transcription factor Z3EV and the reporter gene encoding the green fluorescent protein (GFP), whose transcription could be induced by the estrogen steroid hormone β-estradiol (BED). Since the cellulose pellicle grown in such co-culture displayed intense green fluorescence when exposed to externally applied BED, the authors concluded that the living BC-based hybrid materials can sense environmental stimuli and react correspondingly.

3.3. Genetic Engineering of Bacterial Cellulose Producing Strains

Although genetic engineering has been one of the critical tools in biotechnological research and industrial biotechnology since the 1980s, until recently, it was not extensively used for improving the production or modification of BC. This may be attributed to numerous non-genetic interventions that researchers and manufacturers employed effectively to enhance production, increase yield, modify the properties of the biopolymer, and introduce new functionalities to the resulting material. However, in the last two decades (Table 1), several examples proved that using genetic engineering of Komagataeibacter species can render additional improvements to BC production.
Table 1. Timeline of key examples intending to improve BC production and modification.

3.3.1. Conventional Gene Targeted Approaches for Modification of Bacterial Cellulose Production

Initially, genetic modifications of Komagataeibacter spp. were confined to plasmid vector backbones, such as pSA and pBBR122, and focused on adding or removing genes to enhance BC production []. The first more significant demonstration of genetic engineering in cellulose-producing bacteria was reported in a study from 1999, where a DNA sequence encoding the sucrose synthase of mung bean (Vigna radiata) was introduced into K. sucrofermentans []. The genetically modified bacteria produced more BC than the wild-type strain when sucrose was present in the growth medium. Among the positive effects of the described genetic manipulation, which enabled acetic acid bacteria to metabolize sucrose, was increased BC yield and the possibility of using cheaper sucrose-based growth media.
An alternative method to improve BC yield using an inexpensive growth medium was developed by Battad-Bernardo et al. []. Their genetically modified bacteria could metabolize a low-cost lactose-based medium derived from whey. By inserting the E. coli β-galactosidase-encoding gene (lacZ) into K. xylinus, researchers achieved a 28-fold increase in BC production.
On the other hand, Chien et al. [] aimed to enhance BC production by improving cells’ oxygen utilization. They induced the expression of the vhb gene, which encodes Vitreoscilla hemoglobin, in K. xylinus BCRC 12334. As a result, the genetically engineered strain showed better oxygen regulation than the wild-type strain. The expression of the vhb gene led to 50% higher cell growth and 20% higher BC production when the bacteria were incubated on a shaker.
During BC production, the cell oxidizes glucose to gluconic acid, leading to acidification of the growth medium, which in turn slows down BC production. Shigematsu et al. [] attempted to address this issue by knocking out the gdh gene, which encodes glucose dehydrogenase, the enzyme responsible for converting glucose to gluconic acid. The authors reported a 1.7-fold improvement in BC production in the genetically modified strain compared to its wild-type counterpart.
As part of an extensive study to improve BC production, Jang et al. [] used data from the sequenced genome and metabolome analysis of K. xylinus to construct a genome-scale metabolic model. Initially, they overexpressed two carbon metabolism-connected genes, pgi (coding for glucose-6-phosphate isomerase), and gnd (coding for phosphogluconate dehydrogenase), originating from E. coli or Corynebacterium glutamicum, resulting in a 2-fold increase in BC yield. In their model, they discovered that the intracellular level of adenosine triphosphate (ATP) plays a critical role in determining the BC yield. The enzyme glucose-6-phosphate dehydrogenase, encoded by the zwf gene, acts as a branching point where the cellular mechanism decides whether to metabolize glucose or use it for biosynthetic reactions. Since the activity of this enzyme is significantly inhibited by high levels of intracellular ATP, an increase in intracellular ATP concentration redirects more glucose molecules toward cellulose synthesis reactions. To maximize the intracellular ATP level, Gwon et al. [] used a plasmid containing the pfkA gene, which encodes phosphofructokinase, an enzyme critical for glycolysis absent in the genus Komagataeibacter. Heterologous expression of the E. coli pfkA gene established the glycolytic pathway in K. xylinus (where glucose is usually metabolized via the alternative pentose phosphate pathway), resulting in a four-fold increase in intracellular ATP concentration, higher growth, and improved BC production.
In another significant study, Yadav et al. [] introduced a bla promoter-controlled operon consisting of three genes from Candida albicans into K. xylinus, thereby altering the flow of cellular metabolites during the BC biosynthesis. This genetic intervention enabled the incorporation of the chitin monomer, activated cytoplasmic UDP-N-acetylglucosamine (UDP-GlcNAc), into the glucan chains alongside UDP-Glc. When both glucose and N-acetylglucosamine were available in the growth medium, the cellulose synthase of the genetically modified strain used UDP-Glc and UDP-GlcNAc to synthesize a copolymer of cellulose and chitin (Figure 11). The resulting cellulose/chitin copolymer exhibited improved in vivo degradability due to the susceptibility of chitin to degradation by enzymes in animal lysosomes. The authors also found that partial or complete glucose replacement with GlcNAc significantly reduced the final cellulose production.
Figure 11. Schematic representation of cellulose/chitin copolymer production in genetically modified strain of K. xylinus expressing operon of three genes from C. albicans (GlcNAc—N-acetylglucosamine, UDP-GlcNAc–UDP-N-acetylglucosamine) (adapted from Singh et al. [] (CC BY)).
The properties of produced BC were also investigated by Jacek et al. [], who studied how the motility genes motA and motB influence the morphology of the cellulose pellicle in N. hansenii. Overexpression of the two genes resulted in a loosening of the intramembrane structure and fiber thickening. In contrast, disrupting the same genes, causing reduced mobility, led to a denser and more compact BC with improved mechanical properties.
Liu et al. [] focused on improving another fundamental physicochemical property of BC, which is its water-holding capacity. Working on Enterobacter sp. FY-07, they induced the expression of the wca operon, carrying the genetic code for colanic acid, a water-soluble polysaccharide. By varying the concentration of the inducer, cellulose hydrogels differing in crystallinity, rheological properties, and water-holding capacity were developed. Their water-holding capacity was 1.7 times higher than that of the pellicle produced by the wild-type strain.

3.3.2. Standardized Genetic Tools for Bacterial Cellulose Production with Advanced Characteristics

Florea et al. [] were the first to develop a standardized genetic toolkit (Figure 12) for BC-producing bacteria, specifically for the K. rhaeticus iGEM strain isolated from a kombucha tea pellicle. Their study selected five replicative plasmid backbones, including pSEVA321, pSEVA331, pSEVA351, pBAV1K-T5-sfGFP, and pBla-Vhb-122. Their genetic toolkit also included reporter genes encoding various fluorescent proteins, terminator sequences, synthetic promoters of different strengths, and two types of regulated promoters. The inducible promoters were regulated by transcription factors, chemically inducible with anhydrotetracycline, which is an antibiotic analog, or N-acyl-homoserine lactone (AHL), a quorum sensing molecule involved in intercellular communication. They designed their genetic toolkit to a standardized cloning format named BioBricks, which allows for quick assembly of variously combined modular DNA parts in E. coli plasmids and subsequent introduction into K. rhaeticus. To demonstrate the usefulness of the new standardized genetic toolkit, the authors genetically engineered bacteria to respond to different concentrations of AHL. Afterward, they induced the production of red fluorescence only on one side of the developing pellicle or only in its newest layers, thus illustrating that spatial patterning is achievable with their tools. Furthermore, they replaced the module for red fluorescence with another one that expressed a synthetic RNA-based silencing system designed to repress the chromosomal gene for the enzyme UDP-glucose pyrophosphorylase, which is crucial for BC synthesis. As a result of this genetic intervention, they obtained a genetically modified bacterium that stopped producing a BC pellicle when a sufficient concentration of AHL was added to the growth medium.
Figure 12. Overview of standard synthetic biology methods that are utilized for the development of living and functional BC-based hybrid materials; (a) synthetic libraries comprise modular DNA parts (including promoters, ribosome-binding sites (RBSs), coding sequences (CDSs), and terminators) which can be joined together into gene constructs for transformation into a host microorganism, such as yeast (circles) or Komagataeibacter (rods); (b) genetically modified cells secrete cellulose nanofibers into their surroundings and gradually form a BC pellicle within which they are contained; (c) BC pellicle encompasses living genetically modified cells that can sense and react as a response to selected externally applied signals, such as light, chemicals, and diffusible signaling molecules (adapted from Singh et al. [] (CC BY)).
In the following study [], the same group of researchers successfully demonstrated, through an innovative experiment, that the induction of gene expression in plasmids of the aforementioned bacterial cells can be controlled by other genetically modified cells grown in the same co-culture. The genetically engineered strain producing a red fluorescent protein (RFP) when induced with AHL, was combined with another recombinant strain capable of constitutively expressing the gene for the AHL-synthesizing LuxI enzyme. The new strain, consisting of the so-called sender cells, secreted AHL molecules into the medium where co-culture was grown. When these molecules reached a sufficient concentration and were near the so-called receiver cells, controlled by AHL, they initiated the production of RFP (Figure 13). Through this experiment, the researchers illustrated that the two genetically modified cells coexisted in co-culture while producing BC capable of creating red fluorescence. Perhaps more significantly, this study revealed that it is possible to grow materials that autonomously detect borders between different populations of genetically modified cells and induce gene expression only at those specific locations.
Figure 13. Comparison of red fluorescence response in the co-culture of sender and receiver cells (left) and monoculture of receiver cells (right) (adapted from Walker et al. [] (CC BY)).
Teh et al. [] extended the existing genetic toolkit by introducing several additional modular parts, such as new constitutive promoters and terminator sequences. They incorporated an arabinose-inducible promoter (PBAD) that reacts to high sugar concentrations (4%). Through different experiments, they demonstrated that the standardized genetic toolkit was efficient not only for K. rhaeticus but also for various strains of K. xylinus and N. hansenii. They also described programmable regulation of gene expression using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) approach. By employing CRISPR-mediated inhibition of two genes involved in BC synthesis, namely acsAB and acsD, they successfully reduced the BC yield by 15% in the first case and 5% in the second case.
In a similar experiment, another group used CRISPR-mediated inhibition to regulate the UGPase-encoding galU gene expression in K. xylinus CGMCC 2955. They found that changing the gene’s expression could influence the crystallinity and porosity of the BC pellicle. When repressing this gene, the porosity of BC increased by 0.5-fold. In contrast, the crystallinity of the cellulose network only increased to a certain extent with increasing expression (when the galU expression was 30 times higher than in the control group, the crystallinity started to decrease) [].
The promising opportunities of genetic toolkits extend to BC-composite production where bacteria synthesize another polymer alongside cellulose. Fang et al. [] demonstrated the biosynthesis of such composites by inserting the curdlan-synthesizing gene (crdS) from Agrobacterium into K. xylinus AY201. The genetically modified bacteria co-produced cellulose and curdlan with minimal changes in the crystallinity of the resulting composite. However, due to the variable pore size, the surface properties of the composite were slightly altered.
To accelerate BC production and make it more cost-effective, researchers came up with the idea of transferring the ability to biosynthesize the cellulose pellicle, which is characteristic of the Komagataeibacer genus, to better-studied model organisms with advanced genetic toolkits []. Although successful reconstitution of cellulose synthase in E. coli was achieved through the heterologous co-expression of genes for proteins BcsA, BcsB, and diguanylate cyclase, the genetically modified bacteria produced amorphous cellulose, highlighting the significance of genes responsible for export and crystallization, namely genes for proteins BcsC and BcsD []. Buldum et al. [] took it further by introducing the entire bcsABCD operon into E. coli, resulting in the recombinant biosynthesis of cellulose with an exceptional fiber structure measuring from 10 to 20 μm in diameter.

4. Conclusions and Perspectives

This review highlights the remarkable potential of BC as an ultrafine nanomaterial comprised of versatile macromolecules with wide-ranging applications. The promising trajectory of BC research offers exciting perspectives for numerous industries and scientific domains. BC’s versatile properties are poised to revolutionize medicine, with potential applications in tissue engineering, wound dressings, and targeted drug-delivery systems. Pharmaceutical advancements may harness BC’s encapsulation capabilities to improve drug stability and bioavailability. Additionally, BC shows great potential in cosmetology, offering opportunities for enhanced skincare products, hair treatments, and wound-healing materials. In electronics and biotechnology, the integration of BC promises the development of flexible and biocompatible materials, facilitating the creation of innovative electronic devices, biosensors, and bioelectronics.
Using synthetic biology tools to genetically engineer BC-producing bacteria introduces a new era of living biomaterials with tailored functionalities, unlocking further possibilities for advanced bioproducts. While these prospects are promising, scaling up BC production remains a challenge that requires continued research to optimize fermentation processes, refine production techniques, and explore sustainable substrates.
By embracing sustainable approaches and employing synthetic biology, BC’s transformative potential can be harnessed across various applications, paving the way for groundbreaking developments in biomaterials and biotechnology. Collaborative efforts across disciplines will be crucial in fully realizing the applications of BC and shaping a more sustainable and innovative future.

Author Contributions

Conceptualization, V.P., S.G. and J.T.; writing—original draft preparation, V.P.; writing—review and editing, V.P., S.G. and J.T.; funding acquisition, S.G. and J.T. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Slovenian Research and Innovation Agency through research programs P2-0006, P2-0118 and research project J2-2487.

Institutional Review Board Statement

Not applicable.

Data Availability Statement

Data sharing not applicable.

Acknowledgments

We acknowledge Urška Jančič, Bernarda Karničnik, Kim Fijok, and Eva Cepec from the University of Maribor for providing Figure 1b,c, Figure 3 and Figure 4 (left panel), and Figure 6a, respectively.

Conflicts of Interest

The authors declare no conflict of interest.

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