A Review on Bacteriocin Extraction Techniques from Lactic Acid Bacteria.

Lactic acid bacteria (LAB) are widely known for the production of secondary metabolites such as organic acids and other bioactive compounds such as bacteriocins. Finding a broad application in food and healthcare, bacteriocins have received increased attention due to their inherent antimicrobial properties. However, the extraction of bacteriocins is often plagued with low yields due to the complexity of the extraction processes and the diversity of bacteriocins themselves. Here, we review the current knowledge related to bacteriocin extraction on the different extraction techniques for isolating bacteriocins from LAB. The advantages and disadvantages of each technique will also be critically appraised, taking into account factors such as extraction efficiency, scalability and cost-effectiveness. This review aims to guide researchers and professionals in selecting the most suitable approach for bacteriocin extraction from LAB by illuminating the respective advantages and limitations of various extraction techniques.

Enhancing early warning: A DNA biosensor with polyaniline/graphene nanocomposite for label-free voltammetric detection of saxitoxin-producing harmful algae.

Yearly reports of detrimental effects resulting from harmful algal blooms (HAB) are still received in Malaysia and other countries, particularly concerning fish mortality and seafood contamination, both of which bear consequences for the fisheries industry. The underlying reason is the absence of a dependable early warning system. Hence, this research aims to develop a single DNA biosensor that can detect a group of HAB species known for producing saxitoxin (SXT), which is commonly found in Malaysian waters. The screen-printed carbon electrode (SPCE)-based DNA biosensor was fabricated by covalent grafting of the 3' aminated DNA probe of the sxtA4 conserved domain in SXT-producing dinoflagellates on the reverse-phase polymerized polyaniline/graphene (PGN) nanocomposite electrode via carbodiimide linkage. The introduction of a carboxyphenyl layer to the PGN nanotransducing element was essential to augment the carboxylic groups on the graphene (RGO), facilitating attachment with the aminated DNA. The synergistic effect of the asynthesized nanocomposite of PANI and RGO, tremendously enhanced the electron transfer rate of the ferri/ferrocyanide redox probe at the SPCE transducer surface, allowing for the label-free bioanalytical assay of complementary DNA targets. The developed DNA biosensor featuring the capacity to detect a broad range of Alexandrium minutum (A. minutum) cell concentrations, ranging from 10 to 10,000,000 cells L-1. The quantification of A. minutum cells from pure algal culture by the electrochemical DNA biosensor has been well-validated with traditional microscopic techniques. Furthermore, Alexandrium tamiyavanichii, another toxigenic HAB species, exhibited a similar electrochemical characteristic signal to those observed with A. minutum, whilst the biosensor yielded appreciably distinctive results when subjected to a non-toxigenic microalgae species as a negative control, i.e. Isochrysis galbana. A compendium DNA biosensor design and electrochemical detection strategy at laboratory scale serves as a precursor to the potential development of portable device for on-site detection, thus expanding the utility and scope of biosensor technology.

Nutrient Deficiencies Impact on the Cellular and Metabolic Responses of Saxitoxin Producing Alexandrium minutum: A Transcriptomic Perspective.

Dinoflagellate Alexandrium minutum Halim is commonly associated with harmful algal blooms (HABs) in tropical marine waters due to its saxitoxin production. However, limited information is available regarding the cellular and metabolic changes of A. minutum in nutrient-deficient environments. To fill this gap, our study aimed to investigate the transcriptomic responses of A. minutum under nitrogen and phosphorus deficiency. The induction of nitrogen and phosphorus deficiency resulted in the identification of 1049 and 763 differently expressed genes (DEGs), respectively. Further analysis using gene set enrichment analysis (GSEA) revealed 702 and 1251 enriched gene ontology (GO) terms associated with nitrogen and phosphorus deficiency, respectively. Our results indicate that in laboratory cultures, nitrogen deficiency primarily affects meiosis, carbohydrate catabolism, ammonium assimilation, ion homeostasis, and protein kinase activity. On the other hand, phosphorus deficiency primarily affects the carbon metabolic response, cellular ion transfer, actin-dependent cell movement, signalling pathways, and protein recycling. Our study provides valuable insights into biological processes and genes regulating A. minutum's response to nutrient deficiencies, furthering our understanding of the ecophysiological response of HABs to environmental change.

Genome Sequencing and Analysis of Trichoderma (Hypocreaceae) Isolates Exhibiting Antagonistic Activity against the Papaya Dieback Pathogen, Erwinia mallotivora.

Erwinia mallotivora, the causal agent of papaya dieback disease, is a devastating pathogen that has caused a tremendous decrease in Malaysian papaya export and affected papaya crops in neighbouring countries. A few studies on bacterial species capable of suppressing E. mallotivora have been reported, but the availability of antagonistic fungi remains unknown. In this study, mycelial suspensions from five rhizospheric Trichoderma isolates of Malaysian origin were found to exhibit notable antagonisms against E. mallotivora during co-cultivation. We further characterised three isolates, Trichoderma koningiopsis UKM-M-UW RA5, UKM-M-UW RA6, and UKM-M-UW RA3a, that showed significant growth inhibition zones on plate-based inhibition assays. A study of the genomes of the three strains through a combination of Oxford nanopore and Illumina sequencing technologies highlighted potential secondary metabolite pathways that might underpin their antimicrobial properties. Based on these findings, the fungal isolates are proven to be useful as potential biological control agents against E. mallotivora, and the genomic data opens possibilities to further explore the underlying molecular mechanisms behind their antimicrobial activity, with potential synthetic biology applications.

Insights into Alexandrium minutum Nutrient Acquisition, Metabolism and Saxitoxin Biosynthesis through Comprehensive Transcriptome Survey.

The toxin-producing dinoflagellate Alexandrium minutum is responsible for the outbreaks of harmful algae bloom (HABs). It is a widely distributed species and is responsible for producing paralytic shellfish poisoning toxins. However, the information associated with the environmental adaptation pathway and toxin biosynthesis in this species is still lacking. Therefore, this study focuses on the functional characterization of A. minutum unigenes obtained from transcriptome sequencing using the Illumina Hiseq 4000 sequencing platform. A total of 58,802 (47.05%) unigenes were successfully annotated using public databases such as NCBI-Nr, UniprotKB, EggNOG, KEGG, InterPRO and Gene Ontology (GO). This study has successfully identified key features that enable A. minutum to adapt to the marine environment, including several carbon metabolic pathways, assimilation of various sources of nitrogen and phosphorus. A. minutum was found to encode homologues for several proteins involved in saxitoxin biosynthesis, including the first three proteins in the pathway of saxitoxin biosynthesis, namely sxtA, sxtG and sxtB. The comprehensive transcriptome analysis presented in this study represents a valuable resource for understanding the dinoflagellates molecular metabolic model regarding nutrient acquisition and biosynthesis of saxitoxin.

Pathogenic hitchhiker diversity on international ships' ballast water at West Malaysia port.

This study investigates bacterial diversity and potential pathogens in the international ships' ballast water at Tanjung Pelepas Port, Malaysia, using 16S rRNA amplicon sequencing. Thirty-four bacterial phylum, 305 families, 577 genera, and 941 species were detected in eight ballast water samples of different origins. The similarity of the bacterial composition between samples was found to be random and not tied to geographical locations. The bacterial abundance did not seem to be affected by related physicochemical except for temperature. Ballast water samples with a temperature lower than 25 °C showed a relatively lower bacterial abundance. A total of 33 potential pathogens were detected from all ballast water samples. Pseudomonas spp., Tenacibaculum spp., Flavobacteriaceae spp., Halomonas spp., and Acinetobacter junii are the potential pathogens with more than 10% OTU prevalence. This study would provide beneficial information for further enhancing ballast water microorganism guidelines in Malaysia.

Effects of Mullite, Maghemite, and Silver Nanoparticles Incorporated in ß-Wollastonite on Tensile Strength, Magnetism, Bioactivity, and Antimicrobial Activity.

ß-wollastonite (ßW) has sparked much interest in bone defect recovery and regeneration. Biomaterial-associated infections and reactions between implants with human cells have become a standard clinical concern. In this study, a green synthesized ßW, synthesized from rice husk ash and a calcined limestone precursor, was incorporated with mullite, maghemite, and silver to produce ß wollastonite composite (ßWMAF) to enhance the tensile strength and antibacterial properties. The addition of mullite to the ßWMAF increased the tensile strength compared to ßW. In vitro bioactivity, antibacterial efficacy, and physicochemical properties of the ß-wollastonite and ßWMAF were characterized. ßW and ßWMAF samples formed apatite spherules when immersed in simulated body fluid (SBF) for 1 day. In conclusion, ßWMAF, according to the tensile strength, bioactivity, and antibacterial activity, was observed in this research and appropriate for the reconstruction of cancellous bone defects.

Construction of Infectious Clones of Begomoviruses: Strategies, Techniques and Applications.

Begomovirus has become a potential threat to the agriculture sector. It causes significant losses to several economically important crops. Given this considerable loss, the development of tools to study viral genomes and function is needed. Infectious clones approaches and applications have allowed the direct exploitation of virus genomes. Infectious clones of DNA viruses are the critical instrument for functional characterization of the notable and newly discovered virus. Understanding of structure and composition of viruses has contributed to the evolution of molecular plant pathology. Therefore, this review provides extensive guidelines on the strategy to construct infectious clones of Begomovirus. Also, this technique's impacts and benefits in controlling and understanding the Begomovirus infection will be discussed.

Stingless Bee Honey: Evaluating Its Antibacterial Activity and Bacterial Diversity.

Stingless bee honey (SBH) is an astounding 'miracle liquid' with countless medicinal properties for various diseases such as gastroenteritis, cataracts, as well as for wound-healing. However, knowledge regarding it is still rather scarce. Henceforth, it is intriguing for us to contemplate on the less-studied stingless bee and its honey in particular. First and foremost, the antimicrobial ability of honey from eight different stingless bee species was tested to further proven its health benefit. Homotrigona fimbriata honey showed the highest antimicrobial activity with inhibition against five bacteria; Serratia marcescens, Escherichia coli, Bacillus subtilis, Alcaligenes faecalis and Staphylococcus aureus. The next aim of our study is to characterize their honey bacterial community via the use of 16S rRNA amplicon sequencing technology. A total of eight bacterial phyla, 71 families, 155 genera and 70 species were identified from our study and two of the stingless bee species honey were determined to have the highest bacterial diversity compared to other six stingless bee species, namely Heterotrigona erythrogastra and Tetrigona melanoleuca. Furthermost, Lactobacillus malefermentans was thought to be the native dominant bacteria of SBH due to its predominant presence throughout all studied species. The aforementioned SBH's antimicrobial results and characterization study of its bacterial diversity are hoped to carve the pathway towards extending its probiotic ability into our everyday lives.

Biosynthesis of Saxitoxin in Marine Dinoflagellates: An Omics Perspective.

Saxitoxin is an alkaloid neurotoxin originally isolated from the clam Saxidomus giganteus in 1957. This group of neurotoxins is produced by several species of freshwater cyanobacteria and marine dinoflagellates. The saxitoxin biosynthesis pathway was described for the first time in the 1980s and, since then, it was studied in more than seven cyanobacterial genera, comprising 26 genes that form a cluster ranging from 25.7 kb to 35 kb in sequence length. Due to the complexity of the genomic landscape, saxitoxin biosynthesis in dinoflagellates remains unknown. In order to reveal and understand the dynamics of the activity in such impressive unicellular organisms with a complex genome, a strategy that can carefully engage them in a systems view is necessary. Advances in omics technology (the collective tools of biological sciences) facilitated high-throughput studies of the genome, transcriptome, proteome, and metabolome of dinoflagellates. The omics approach was utilized to address saxitoxin-producing dinoflagellates in response to environmental stresses to improve understanding of dinoflagellates gene-environment interactions. Therefore, in this review, the progress in understanding dinoflagellate saxitoxin biosynthesis using an omics approach is emphasized. Further potential applications of metabolomics and genomics to unravel novel insights into saxitoxin biosynthesis in dinoflagellates are also reviewed.