Cell immobilization for production of lactic acid biofilms do it naturally

Biofilm application in the microbial biochemicals production process

Biofilms can be naturally formed through the attachment of microorganisms on the supporting materials. However, natural biofilms formed in the environment may cause some detrimental effects, such as the equipment contamination and food safety issues et al. On the contrary, biofilms mediated microbial fermentation provides a promising approach for the efficient biochemicals production owing to the properties of self-immobilization, high resistance to toxic reactants and maintenance of long-term cells activity. While few reviews have specifically addressed the biological application of biofilms in the microbial fermentation process. Accordingly, this review will comprehensively summarize the biofilms formation mechanism and potential functions in the microbial fermentation process. Furthermore, the construction strategies for the formation of stable biofilms through synthetic biology technology or the modification of suitable supporting materials will be also discussed. The application of biofilms mediated fermentation will provide an outlook for the biorefinery platform in the future.

Functional and transcriptional profiling of non-coding RNAs in yeast reveal context-dependent phenotypes and in trans effects on the protein regulatory network

Non-coding RNAs (ncRNAs), including the more recently identified Stable Unannotated Transcripts (SUTs) and Cryptic Unstable Transcripts (CUTs), are increasingly being shown to play pivotal roles in the transcriptional and post-transcriptional regulation of genes in eukaryotes. Here, we carried out a large-scale screening of ncRNAs in Saccharomyces cerevisiae, and provide evidence for SUT and CUT function. Phenotypic data on 372 ncRNA deletion strains in 23 different growth conditions were collected, identifying ncRNAs responsible for significant cellular fitness changes. Transcriptome profiles were assembled for 18 haploid ncRNA deletion mutants and 2 essential ncRNA heterozygous deletants. Guided by the resulting RNA-seq data we analysed the genome-wide dysregulation of protein coding genes and non-coding transcripts. Novel functional ncRNAs, SUT125, SUT126, SUT035 and SUT532 that act in trans by modulating transcription factors were identified. Furthermore, we described the impact of SUTs and CUTs in modulating coding gene expression in response to different environmental conditions, regulating important biological process such as respiration (SUT125, SUT126, SUT035, SUT432), steroid biosynthesis (CUT494, SUT053, SUT468) or rRNA processing (SUT075 and snR30). Overall, these data capture and integrate the regulatory and phenotypic network of ncRNAs and protein-coding genes, providing genome-wide evidence of the impact of ncRNAs on cellular homeostasis.

A quarter of the yeast genome comprises non-coding RNA molecules (ncRNAs), which do not translate into proteins but are involved in the regulation of gene expression. ncRNAs can affect nearby genes by physically interfering with their transcription (cis mode of action), or they interact with DNA, proteins or other RNAs to regulate the expression of distant genes (trans mode of action). Examples of cis-acting ncRNAs have been broadly described, however, genome-wide studies to identify functional trans-acting ncRNAs involved in global gene regulation are still lacking. Here, we used a ncRNA yeast deletion collection to score ncRNA impact on cellular function in different environmental conditions. A group of 20 ncRNA deletion mutants with broad fitness diversity were selected to investigate the ncRNA effect on the protein and ncRNA expression network. We showed a high correlation between altered phenotypes and global transcriptional changes, in an environmental dependent manner. We confirmed the trans acting regulation of ncRNAs in the genome and their role in altering the expression of transcription factors. These findings support the notion of the involvement of ncRNAs in fine tuning cellular expression via regulation of transcription factors, as an advantageous RNA-mediated mechanism that can be fast and cost-effective for the cells.

Probiotics Biofilm-Integrated Electrospun Nanofiber Membranes: A New Starter Culture for Fermented Milk Production

Electrospun nanofiber membranes are widely investigated in the past few decades as candidates for tissue engineering, which can mimic natural extracellular matrix (ECM) and improve cell adhesion, proliferation, and expression on nanofiber membranes. However, the formation of bacterial biofilms on nanofiber membranes and application of the biofilm-integrated nanofiber membranes remain largely unknown. Here, electrospun cellulose acetate nanofiber membranes are first utilized as scaffold materials for Lactobacillus plantarum ( L. plantarum) biofilm formation. Nanofiber membranes proved to be an excellent scaffold for bacteria biofilm with high stability, where biofilms were interlocked with nanofibers forming a cohesive structure. In comparison with planktonic bacteria, L. plantarum biofilms on nanofiber membranes show excellent gastrointestinal resistance. Instead of decreasing, the number of viable cells increased after 3 h digestion in vitro. The L. plantarum biofilm-integrated nanofiber membranes were used as reusable starter cultures for fermented milk production showing excellent fermentative ability and higher survival of L. plantarum during shelf life. The viable cells in fermented milk remained at 11 log CFU/g throughout the reusable batches, which is far above the required value of 7 log CFU/g in commercial products. In addition, the produced fermented milk possesses shorter fermentation time and higher survival of probiotics during shelf life. The results suggest electrospun nanofiber membranes are ideal scaffold materials for bacteria biofilms immobilization in biotechnology and fermentation engineering, which broaden the potential use of electrospun nanofiber membranes in microbiology and strengthen the application of biofilms in fermentation engineering.

Recent advances on biogranules formation in dark hydrogen fermentation system: Mechanism of formation and microbial characteristics

Hydrogen producing granules (HPGs) are most promising biological methods used to treat organic rich wastes and generate clean hydrogen energy. This review provides information regarding types of immobilization, supporting materials and microbiome involved on HPG formation and its performances. In this review, importance has been given to three kinds of immobilization techniques such as adsorption, encapsulation, and entrapment. The HPG, characteristics and types of organic and inorganic supporting materials followed for enhancing hydrogen yield were also discussed. This review also considers the applications of HPG for sustainable and high rate hydrogen production. A detailed discussion on insight of key mechanism for HPGs formation and its performances for stable operation of high rate hydrogen production system are also provided.

Analyzing the influence of microstructured surfaces on the lactic acid production of Lactobacillus delbrueckii lactis in a flow-through cell system

Microorganisms growing in biofilms might be possible biocatalysts for future biotechnological production processes. Attached to a surface and embedded in an extracellular polymeric matrix, they create their preferred environment and form robust cultures for continuous systems. With the objective of implementing highly efficient processes, productive biofilms need to be understood comprehensively. In this study, the influence of microstructured metallic surfaces on biofilm productivity was researched. To conduct this study, titanium and stainless steel sheets were polished, micromilled, as well as coated with particles. Subsequently, the metal sheets were exposed to the lactic acid producing Lactobacillus delbrueckii subsp. lactis under laminar and homogeneous flow conditions in a custom-built flow cell. A proof-of-concept showed that biofilm formation in the system only occurred on the designated substratum. Following a 24-h batch cultivation for primary biofilm development, the culture was continuously provided with glucose containing medium. As different experimental series have indicated, the process resulted to be stable for up to eleven days. Primary metabolite productivity averaged around 6-7 g/(L h). Interestingly, the productivity was shown to be affected neither by the type of metal, nor by the applied microstructures. Nevertheless, a higher dry biomass weight determined on micro-milled substratum indicates a complementary differentiation of biofilm components in future experiments.

Progress in biocatalysis with immobilized viable whole cells: systems development, reaction engineering and applications

Viable microbial cells are important biocatalysts in the production of fine chemicals and biofuels, in environmental applications and also in emerging applications such as biosensors or medicine. Their increasing significance is driven mainly by the intensive development of high performance recombinant strains supplying multienzyme cascade reaction pathways, and by advances in preservation of the native state and stability of whole-cell biocatalysts throughout their application. In many cases, the stability and performance of whole-cell biocatalysts can be highly improved by controlled immobilization techniques. This review summarizes the current progress in the development of immobilized whole-cell biocatalysts, the immobilization methods as well as in the bioreaction engineering aspects and economical aspects of their biocatalytic applications.

Biofilm evolution and viability during in situ preparation of a graphene/exoelectrogen composite biofilm electrode for a high-performance microbial fuel cell

Effect of microbial reduction of graphene oxide on evolution and viability of biofilm during preparation of graphene/exoelectrogen biofilm anode in microbial fuel cell (MFC) were studied by sampling the biofilm at different stages of MFC operation.

Multi-Fixed-Bed Bioreactor System Applied for Bioprocess Development of Immobilized Lactic Acid Bacteria

The multi-fixed-bed bioreactor“Multiferm”provides a downscaled system for the development of fixed-bed processes with immobilized microorganisms or cells. It consists of twelve single fixed-bed units that can be operated independently. Different bacterial strains, carriers used for immobilization, media or flow rates can be studied in one compact experimental set-up. Experiments can be run in parallel to allow for determination of experimental errors. In these studies several continuous cultivations were carried out withLactobacillus delbrueckiissp.bulgaricususing different dilution rates and culture durations as proof-of-concept for theMultiferm. Parameters relevant for process design such as reproducibility of simultaneously performed cultures, optimal dilution rate and long-term performance were determined by means of volume specific lactate and biomass productivity. First indications on a reduced growth rate of the cells due to immobilization were found.

The influence of shear on the metabolite yield of Lactobacillus rhamnosus biofilms

A tubular recycle bioreactor was employed to ensure homogeneous shear conditions on the biofilm surface. Superficial liquid velocities of 0.19 ms(-1), 0.37 ms(-1), 0.55 ms(-1) and 3.65 ms(-1) were used. The highest velocity resulted in negligible cell attachment (chemostat) while the ratio of attached-to-total cell mass escalated as the superficial velocity decreased. The lactic acid yield on glucose increased from 0.75 g g(-1) to 0.90 g g(-1) with declining shear while the corresponding acetoin yield on glucose decreased from 0.074 g g(-1) to 0.017 g g(-1). Redox analysis of the catabolites revealed a net consumption of NADH in the anabolism, while the extent of NADH consumption decreased when shear was reduced. This was attributed to the formation of more extracellular polymeric substance (EPS) at low shear conditions. A simplified metabolic flux model was used to estimate the EPS content of the biomass as a function of the shear velocity. Rate data supported the notion of increased EPS at lower shear.

Attachment and biofilm formation by foodborne bacteria in meat processing environments: causes, implications, role of bacterial interactions and control by alternative novel methods

Attachment of potential spoilage and pathogenic bacteria to food contact surfaces and the subsequent biofilm formation represent serious challenges to the meat industry, since these may lead to cross-contamination of the products, resulting in lowered-shelf life and transmission of diseases. In meat processing environments, microorganisms are sometimes associated to surfaces in complex multispecies communities, while bacterial interactions have been shown to play a key role in cell attachment and detachment from biofilms, as well as in the resistance of biofilm community members against antimicrobial treatments. Disinfection of food contact surfaces in such environments is a challenging task, aggravated by the great antimicrobial resistance of biofilm associated bacteria. In recent years, several alternative novel methods, such as essential oils and bacteriophages, have been successfully tested as an alternative means for the disinfection of microbial-contaminated food contact surfaces. In this review, all these aspects of biofilm formation in meat processing environments are discussed from a microbial meat-quality and safety perspective.

The intestinal microbiota, gastrointestinal environment and colorectal cancer: a putative role for probiotics in prevention of colorectal cancer?

Colorectal cancer (CRC) is the third most commonly diagnosed cancer in the United States, and, even though 5-15% of the total CRC cases can be attributed to individual genetic predisposition, environmental factors could be considered major factors in susceptibility to CRC. Lifestyle factors increasing the risks of CRC include elevated body mass index, obesity, and reduced physical activity. Additionally, a number of dietary elements have been associated with higher or lower incidence of CRC. In this context, it has been suggested that diets high in fruit and low in meat might have a protective effect, reducing the incidence of colorectal adenomas by modulating the composition of the normal nonpathogenic commensal microbiota. In addition, it has been demonstrated that changes in abundance of taxonomic groups have a profound impact on the gastrointestinal physiology, and an increasing number of studies are proposing that the microbiota mediates the generation of dietary factors triggering colon cancer. High-throughput sequencing and molecular taxonomic technologies are rapidly filling the knowledge gaps left by conventional microbiology techniques to obtain a comprehensive catalog of the human intestinal microbiota and their associated metabolic repertoire. The information provided by these studies will be essential to identify agents capable of modulating the massive amount of gut bacteria in safe noninvasive manners to prevent CRC. Probiotics, defined as "live microorganisms which, when administered in adequate amounts, confer a health benefit on the host" (219), are capable of transient modulation of the microbiota, and their beneficial effects include reinforcement of the natural defense mechanisms and protection against gastrointestinal disorders. Probiotics have been successfully used to manage infant diarrhea, food allergies, and inflammatory bowel disease; hence, the purpose of this review was to examine probiotic metabolic activities that may have an effect on the prevention of CRC by scavenging toxic compounds or preventing their generation in situ. Additionally, a brief consideration is given to safety evaluation and production methods in the context of probiotics efficacy.