Search

In recent years, much attention has been directed towards the integration of dark fermentation process into a biorefinery concept to enhance the energetic gains, thereby improving the competitiveness of this process. The volatile fatty acids (VFAs) from dark fermentative H2-producing processes serve as precursors for the microbial synthesis of a broad spectrum of biotechnologically-important products such as biofuels and biocommodities. These products are desirable substrates for secondary bioprocesses due to their biodegradable nature and affordability. This short review discusses the use of acidogenic-derived VFAs in the production of value-added compounds such as polyhydroxyalkanoates (PHAs) alongside the microbial-based fuels (hydrogen, biogas, and electricity), and other valuable compounds (succinic acid, citric acid, and butanol). The review also highlights the strategies that have been used to enhance the extraction of VFAs from acidogenic effluents and other related waste streams. The application of novel enhancement techniques such as nanoparticles during VFAs recovery is also discussed in this work. Furthermore, the work highlights some of the recent advances in dark fermentation-based biorefinery, particularly the development of pilot-scale processes. Finally, the review provides some suggestions on the advancement of dark fermentation-based biorefineries using VFAs that are derived from acidogenic processes.

Insertion sequences (ISs) are mobile pieces of DNA that are widespread in bacterial genomes. IS movements typically involve (i) excision of the IS element, (ii) cutting of target site DNA, and (iii) IS element insertion. This process generates a new copy of the IS element and a short duplication at the target site. It has been noted that, for some extant IS copies, no target site duplications (TSDs) are readily identifiable. TSD absence has been attributed to degeneration of the TSD after the insertion event, recombination between identical ISs, or adjacent deletions. Indeed, the latter two-recombination between ISs and adjacent deletions-are frequent causes for the absence of TSDs, which we demonstrate here in an analysis of genome sequence data from the Lenski long-term evolution experiment. Furthermore, we propose that some IS movements-namely, those that occur in association with large-scale genomic rearrangements-do not generate TSDs, and occur without evidence for recombination between ISs or adjacent deletions. In support of this hypothesis, we provide two direct, empirical observations of such IS transposition events: an IS 5 movement plus a large deletion in Escherichia coli C, and an IS 481 movement occurring with a large duplication in Pseudomonas fluorescens SBW25. Although unlikely, it is possible that the observed deletion and associated IS movement occurred in two successive events in one overnight culture. However, an IS at the center of a large-scale duplication is not readily explained, suggesting that IS element activity may promote both large-scale deletions and duplications., Importance: Insertion sequences are the most common mobile genetic elements found in bacterial genomes, and hence they significantly impact bacterial evolution. We observe insertion sequence movement at the center of large-scale deletions and duplications that occurred during laboratory evolution experiments with Escherichia coli and Pseudomonas fluorescens , involving three distinct types of transposase. We raise the possibility that the transposase does not mediate DNA cleavage but instead inserts into existing DNA breaks. Our research highlights the importance of insertion sequences for the generation of large-scale genomic rearrangements and raises questions concerning the mechanistic basis of these mutations., Competing Interests: The authors declare no conflict of interest.

The complement of tRNA genes within a genome is typically considered to be a (relatively) stable characteristic of an organism. Here, we demonstrate that bacterial tRNA gene set composition can be more flexible than previously appreciated, particularly regarding tRNA gene copy number. We report the high-rate occurrence of spontaneous, large-scale, tandem duplication events in laboratory populations of the bacterium Pseudomonas fluorescens SBW25. The identified duplications are up to ∼1 Mb in size (∼15% of the wildtype genome) and are predicted to change the copy number of up to 917 genes, including several tRNA genes. The observed duplications are inherently unstable: they occur, and are subsequently lost, at extremely high rates. We propose that this unusually plastic type of mutation provides a mechanism by which tRNA gene set diversity can be rapidly generated, while simultaneously preserving the underlying tRNA gene set in the absence of continued selection. That is, if a tRNA set variant provides no fitness advantage, then high-rate segregation of the duplication ensures the maintenance of the original tRNA gene set. However, if a tRNA gene set variant is beneficial, the underlying duplication fragment(s) may persist for longer and provide raw material for further, more stable, evolutionary change., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

The rate and accuracy of translation hinges upon multiple components - including transfer RNA (tRNA) pools, tRNA modifying enzymes, and rRNA molecules - many of which are redundant in terms of gene copy number or function. It has been hypothesized that the redundancy evolves under selection, driven by its impacts on growth rate. However, we lack empirical measurements of the fitness costs and benefits of redundancy, and we have poor a understanding of how this redundancy is organized across components. We manipulated redundancy in multiple translation components of Escherichia coli by deleting 28 tRNA genes, 3 tRNA modifying systems, and 4 rRNA operons in various combinations. We find that redundancy in tRNA pools is beneficial when nutrients are plentiful and costly under nutrient limitation. This nutrient-dependent cost of redundant tRNA genes stems from upper limits to translation capacity and growth rate, and therefore varies as a function of the maximum growth rate attainable in a given nutrient niche. The loss of redundancy in rRNA genes and tRNA modifying enzymes had similar nutrient-dependent fitness consequences. Importantly, these effects are also contingent upon interactions across translation components, indicating a layered hierarchy from copy number of tRNA and rRNA genes to their expression and downstream processing. Overall, our results indicate both positive and negative selection on redundancy in translation components, depending on a species' evolutionary history with feasts and famines., Competing Interests: PR, WN, JG, DA No competing interests declared, (© 2023, Raval et al.)

Brain tumor represents the most lethal form of cancer with the highest mortality and morbidity rates irrespective of age and sex. Advancements in macromolecule-based therapy (such as nucleic acids and peptides) have shown promising roles in the treatment of brain tumor where the phenomenon of severe toxicities due to the conventional chemotherapeutic agents can be circumvented. Despite its preclinical progress, successful targeting of these macromolecules across the blood-brain barrier without altering their physical and chemical characteristics is of great challenge. With the advent of nanotechnology, nowadays targeted delivery of therapeutics is being explored extensively and these macromolecules, including peptides and nucleic acids, have shown initial success in the treatment, where dendrimer has shown its potential for optimal delivery. Dendrimers are being favored as a mode of drug delivery due to their nano-spherical size and structure, high solubilization potential, multivalent surface, and high loading capacity, where biomolecule resembling characteristics of dendritic 3D structures has shown effective delivery of various therapeutic agents to the brain. Armed with targeting ligands to these dendrimers further expedite the transportation of these multifunctional shuttles specifically to the glioblastoma cells. Thus, a focus has been made in this review on therapeutic applications of dendrimer platforms in brain tumor treatment. The future development of dendrimers as a potential platform for nucleic acid and peptide delivery and its promising clinical application could provide effective and target-specific treatment against brain tumors., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

The possibility of breaking down cellulose-rich food waste through biofilm engineering was investigated. Six previously isolated strains from naturally degrading fruits and vegetables, screened for biofilm-forming ability and cellulolytic activity, were selected to enrich a biocarrier seeding microbial consortium. The food waste model used in this study was cabbage which was aerobically digested under repeated water rinsing and regular effluent drainage. The engineered biocarrier biofilm's functionality was evaluated by tracing microbial succession following metagenomic sequencing, quantitative PCR, scanning electron microscopy, and cellulolytic activity before and after the digestion processes. The engineered microbial consortium demonstrated superior biofilm-forming ability on biocarriers than the original microbial consortium and generally displayed a higher cellulolytic activity. The presented study provides one of the few studies of food waste aerobic digestion using engineered biofilms. Insights presented in this study could help further optimize aerobic food waste digestion., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

In this study, a phylogenic analysis was performed on pathogens previously identified in Hong Kong wet markets' cutting boards. Phylogenetic comparisons were made between phylotypes obtained in this study and environmental and clinical phylotypes for establishing the possible origin of selected bacterial species isolated from wet market cutting board ecosystems. The results reveal a strong relationship between wet market bacterial assemblages and environmental and clinically relevant phylotypes. However, our poor knowledge of potential cross-contamination sources within these wet markets is further exacerbated by failing to determine the exact or presumed origin of its identified pathogens. In this study, several clinically relevant bacterial pathogens such as Klebsiella pneumoniae , Streptococcus suis and Streptococcus porcinus were linked to cutting boards associated with pork; Campylobacter fetus , Staphylococcus aureus , Escherichia coli , and A. caviae in those associated with poultry; and Streptococcus varanii , A. caviae , Vibrio fluvialis , and Vibrio parahaemolyticus in those associated with seafood. Identifying non-foodborne clinically relevant pathogens in wet market cutting boards in this study confirms the need for safety approaches for wet market meat, including cold storage. The presented study justifies the need for future systematic epidemiological studies to determine identified microbial pathogens. Such studies should bring about significant improvements in the management of hygienic practices in Hong Kong's wet markets and work towards a One Health goal by recognizing the importance of wet markets as areas interconnecting food processing with animal and clinical environments., Competing Interests: The authors declare no conflict of interest., (© 2021 The Authors.)

The presence of antibiotics such as erythromycin, even in trace amounts, has long been acknowledged for negatively impacting ecosystems in freshwater environments. Although many studies have focused on the impact of antibiotic pollution at a macroecological level, the impact of erythromycin on microecosystems, such as freshwater biofilms, is still not fully understood. This knowledge gap may be attributed to the lack of robust multispecies biofilm models for fundamental investigations. Here, we used a lab-cultured multispecies biofilm model to elucidate the holistic response of a microbial community to erythromycin exposure using metagenomic and metabolomic approaches. Metagenomic analyses revealed that biofilm microbial diversity did not alter following erythromycin exposure. Notably, certain predicted metabolic pathways such as cell-cell communication pathways, amino acid metabolism, and peptidoglycan biosynthesis, mainly by the phyla Actinobacteria, Alpha/Beta-proteobacteria, Bacteroidetes, and Verrucomicrobia, were found to be involved in the maintenance of homeostasis-like balance in the freshwater biofilm. Further untargeted metabolomics data highlighted changes in lipid metabolism and linoleic acid metabolism and their related molecules as a direct consequence of erythromycin exposure. Overall, the study presented a unique picture of how multispecies biofilms respond to single environmental stress exposures. Moreover, the study demonstrated the feasibility of using lab simulated multispecies biofilms for investigating their interaction and reactivity of specific bioactive compounds or pollutants at a fundamental level., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Accessing food through wet markets is a common global daily occurrence, where fresh meat can be purchased to support an urbanizing world population. Similar to the wet markets in many other metropolitan cities in Asia, Hong Kong wet markets vary and are characterized by differing hygiene routines and access to essential modern technologies. The lack of risk assessments of food contact surfaces in these markets has led to substantial gaps in food safety knowledge and information that could help improve and maintain public health. Microbial profiling analyses were conducted on cutting boards that had been used to process pork, poultry, and seafood at 11 different wet markets. The markets differed in hygiene protocols and access to modern facilities. Irrespective of whether wet markets have access of modern infrastructure, the hygiene practices were largely found to be inefficient based on the prevalence of bacterial species typically associated with foodborne pathogens such as Campylobacter fetus , Clostridium perfringens , Staphylococcus aureus , and Vibrio parahaemolyticus ; indicator organisms such as Escherichia coli ; as well as nonfoodborne pathogenic bacterial species potentially associated with nosocomial infections, such as Klebsiella pneumoniae and Enterobacter cloacae . Other Vibrio species, V. parahaemolyticus and V. vulnificus , typically associated with contaminated raw or undercooked seafood with the potential to cause illness in humans, were also found on wooden cutting boards. This study indicated that the hygienic practices used in Hong Kong wet markets are not sufficient for preventing the establishment of spoilage or pathogenic organisms. This study serves as a basis to review current hygiene practices in wet markets and provides a framework to reassess existing safety protocols.

In recent years, most biofilm studies have focused on fundamental investigations using multispecies biofilm models developed preferentially in simulated naturally occurring low-nutrient medium than in artificial nutrient-rich medium. Because biofilm development under low-nutrient growth media is slow, natural media are often supplemented with an additional carbon source to increase the rate of biofilm formation. However, there are knowledge gaps in interpreting the effects of such supplementation on the resulting biofilm in terms of structure and microbial community composition. We investigated the effects of supplementation of a simulated freshwater medium with sodium citrate on the resulting structure, bacterial community composition, and microbial network interactions of an early-stage multispecies biofilm model. Qualitative and quantitative analyses of acquired confocal laser scanning microscopy data confirmed that sodium citrate supplementation distinctly increased biofilm biomass. Sequencing data revealed that the microbial community structure of biofilms grown in sodium citrate-supplemented conditions was characterized with increased relative abundance and dominance of Proteobacteria compared with that of biofilms grown in sodium citrate-free conditions. Our findings suggest that the supplementation of a low-nutrient medium with a carbon source in experiments involving multispecies biofilms may lead to structural and compositional biases of the microbial community, causing changes in biofilm phenotype.

Hong Kong's wet markets play a crucial role in the country's supply of safe, fresh meat to satisfy the dietary needs of its population. Whilst food safety regulations have been introduced over the past few years to maintain the microbial safety of foods sold from these wet markets, it remains unclear whether the hygiene maintenance that is performed on the wooden cutting boards used for meat-processing is effective. In fact, hygiene maintenance may often be overlooked, and hygiene standards may be insufficient. If so, this may lead to the spread of harmful pathogens through cross-contamination, thereby causing severe risks to public health. The aim of this study was to determine the level of microbial transfer between wooden cutting boards and swine meat of various qualities, using 16S metagenomic sequencing, strain identification and biofilm screening of isolated strains. The results established that: (a) the traditional hygiene practices used for cleaning wooden cutting boards in Hong Kong's wet markets expose the surfaces to potentially harmful microorganisms; (b) the processing of microbially contaminated meat on cutting boards cleaned using traditional practices leads to cross-contamination; and (c) several potentially pathogenic microorganisms found on the cutting boards have good biofilm-forming abilities. These results reinforce the need to review the traditional methods used to clean wooden cutting boards after the processing of raw meat in Hong Kong' wet markets so as to prevent cross-contamination events. The establishment of proper hygiene protocols may reduce the spread of disease-causing microorganisms (including antibiotic-resistant microorganisms) in food-processing environments.

Contaminants in freshwater environments, as well as the associated negative impacts on agricultural produce, have emerged as a critical theme of the water-energy-food nexus affecting food safety and irrigation management. Agricultural produce exposed to irrigation with questionable freshwater can internalize and concentrate pollutants. However, the potential risks posed by the ubiquitous presence of biofilms within irrigation water distribution systems (IWDS) remains overlooked, even though such biofilms may harbor and spread pathogenic, chemical, and other environmental pollutants. Our limited knowledge about the role and functional attributes of IWDS biofilms can be blamed mostly to experimental challenges encountered during attempted studies of these biofilms in their natural environments. Hence, a laboratory-based experimental system designed to simulate a freshwater environment was combined with a biofilm reactor capable of recreating the piping environments in water distribution systems. This experimental system was then tested to assess the robustness and repeatability of experimental early-stage biofilms with respect to physical structure and microbial community, using state-of-the-art confocal microscopy and next-generation sequencing, respectively. The results demonstrated the suitability of this laboratory-based experimental system for studying the impacts of selected pollutants on irrigation water distribution systems., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Millions every day purchase their raw meat in wet markets around the globe, especially in Hong Kong city, where modern and a traditional way of living is made possible. While food hygiene standards in Hong Kong have more recently focused on the safety of meat sold in these wet markets, the hygienic surface level of wooden cutting boards used for processing meats is seldom observed. This original study performed microbial community profiling, as well as isolating and identifying various strains multiple wooden cutting boards from nine wet markets located on Hong Kong Island. Our study also investigated the efficiency of scraping the surface of cutting boards as a traditional cleaning technique in Hong Kong. Results indicate that these hygienic practices are inefficient for guarantying proper surface hygiene as some most tested cutting boards were found to harbor microbial species typically associated with hospital nosocomial infections, such as Klebsiella pneumoni ae. Further analysis also led to discovering the presence of antibiotic-resistant genes (ARGs) among isolated strains. Our results showcase the significance and effects of cross-contamination in Hong Kong wet markets, especially with regards to the potential spreading of clinically-relevant strains and ARGs on food processing surfaces. This study should, therefore, serve as a basis to review current hygienic practices in Hong Kong's wet market on a larger scale, thereby improving food safety and ultimately, public health., (Copyright © 2019 Lo, Ngan, Tsun, Hsing, Lau, Hung, Chan, Lai, Yao, Pu and Habimana.)

The quality of freshwater undoubtedly reflects the health of our surrounding environment, society, and economy, as these are supported by various freshwater ecosystems. Monitoring efforts have therefore been considered a vital means of ensuring the ecological health of freshwater environments. Nevertheless, most aquatic environmental monitoring strategies largely focus on bulk water sampling for analysis of physicochemical and key biological indicators, which for the most part do not consider pollution events that occur at any time between sampling events. Because benthic biofilms are ubiquitous in aquatic environments, pollution released during sporadic events may be absorbed by these biofilms, which can act as repositories of pollutants. The aim of this study was to assess whether benthic biofilm monitoring could provide an efficient way of properly characterizing the extent of pollution in aquatic environments. Here, bulk water and benthic biofilms were sampled from three Hong Kong streams having various pollution profiles, and subsequently compared via high-resolution microscopy, metagenomic analysis, and analytical chemistry. The results indicated that biofilms were, indeed, reservoirs of environmental pollutants, having different profiles compared with that of the corresponding bulk water samples. Moreover, the results also suggested that biofilms sampled in polluted areas were characterized by a higher species richness. While the analytical testing of benthic biofilms still needs further development, the integration of chemical-pollutant profiles and biofilm sequencing data in future studies may provide unique perspectives for understanding and identifying pollution-related biofilm biomarkers., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Endomyces fibuliger is a yeast used in the production of Chinese rice wine. It secretes enzymes such as glucoamylase, alpha-amylase and acid protease. Very little is known of the genetics of E. fibuliger. In order to develop a transformation system for this yeast, orotidine-5'-phosphate decarboxylase mutant strains were obtained and characterized. Transformation of the E. fibuliger ura3 mutant F1 with an integrative plasmid that carried the wild-type URA3 gene of E. fibuliger gave complementation of this mutation. The E. fibuliger gene encodes the orotidine-5'-phosphate decarboxylase enzyme consisting of 266 amino acid residues with a 69.4% sequence identity with orotidine-5'-phosphate decarboxylase of Saccharomyces cerevisiae. Our finding that E. fibuliger URA3 complements the ura3 mutation in S. cerevisiae confirms that the URA3 gene of E. fibuliger encodes a protein that exerts a similar function.