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Chemosphere Mar 2024Zeolitic imidazolate framework (ZIF) is of wide interest in biomedical applications due to its extraordinary properties such as high storage capacity, functionality and...
Zeolitic imidazolate framework (ZIF) is of wide interest in biomedical applications due to its extraordinary properties such as high storage capacity, functionality and favorable biocompatibility. However, more comprehensive safety assessments are still essential before ZIF is broadly used in biomedicine. Using the characteristic that aldehyde groups on the surface of ZIF-90 can be modified with other functional groups, a series of ZIF-90s modified with different functional groups (oxime group, carboxyl group, amino group and sulfhydryl group) were synthesized to investigate the effect of functionalization on the toxicity of ZIF-90. ZIF-90 series showed concentration-dependent toxic effects on Photobacterium phosphoreum T3 and the functionalized ZIF-90s are more toxic than pristine ZIF-90, with the ZIF-90 modified with amino group (ZIF-90-NH) showing the strongest toxicity (IC = 23.06 mg/L). Based on the results of the cellular assay and stability exploration, we concluded that corresponding imidazole-ligand release and the property of positively charged are responsible for the elevated toxicity of ZIF-90-NH. Cell membrane damage, oxidative damage and luminescence damage are the main contributors to the toxic effects of ZIF-90 series. This study explored the effect of surface functionalization on the toxicity of ZIF and proposed mechanistic clues for the safety application of ZIF.
Topics: Zeolites; Metal-Organic Frameworks; Nanoparticles; Photobacterium
PubMed: 38215832
DOI: 10.1016/j.chemosphere.2024.141188 -
Vavilovskii Zhurnal Genetiki I Selektsii Dec 2023The light emitted by a luminescent bacterium serves as a unique native channel of information regarding the intracellular processes within the individual cell. In the...
The light emitted by a luminescent bacterium serves as a unique native channel of information regarding the intracellular processes within the individual cell. In the presence of highly sensitive equipment, it is possible to obtain the distribution of bacterial culture cells by the intensity of light emission, which correlates with the amount of luciferase in the cells. When growing on rich media, the luminescence intensity of individual cells of brightly luminous strains of the luminescent bacteria Photobacterium leiognathi and Ph. phosporeum reaches 104-105 quanta/s. The signal of such intensity can be registered using sensitive photometric equipment. All experiments were carried out with bacterial clones (genetically homogeneous populations). A typical dynamics of luminous bacterial cells distributions with respect to intensity of light emission at various stages of batch culture growth in a liquid medium was obtained. To describe experimental distributions, a phenomenological model that links the light of a bacterial cell with the history of events at the molecular level was constructed. The proposed phenomenological model with a minimum number of fitting parameters (1.5) provides a satisfactory description of the complex process of formation of cell distributions by luminescence intensity at different stages of bacterial culture growth. This may be an indication that the structure of the model describes some essential processes of the real system. Since in the process of division all cells go through the stage of release of all regulatory molecules from the DNA molecule, the resulting distributions can be attributed not only to luciferase, but also to other proteins of constitutive (and not only) synthesis.
PubMed: 38213711
DOI: 10.18699/VJGB-23-102 -
Foods (Basel, Switzerland) Dec 2023This study investigated the effect of sub-chilling whole gutted salmon and sub-chilled storage at -1 °C in modified-atmosphere packaging in two recyclable mono-material...
This study investigated the effect of sub-chilling whole gutted salmon and sub-chilled storage at -1 °C in modified-atmosphere packaging in two recyclable mono-material trays (CPET, HDPE). Quality parameters were measured, including water-holding properties, salt content, color, texture, lipid oxidation, and sensory and microbiological shelf life. The oxygen transmission rate was measured for the packages. Compared to traditional fish storage on ice, sub-chilling gave a 0.4% weight gain, better water-holding capacity, and higher salt content. The sub-chilled fish gave a significantly better sensory quality and microbiological shelf life of up to 49 days. Photobacterium was the dominating bacteria during storage. Salmon packaged in CPET trays had a higher drip loss than HDPE trays, but a lower rate of lipid oxidation (1-penten-3-ol). Our results showed the feasibility of significantly extending shelf life with sub-chilling, removing the need for ice. Moreover, using recyclable trays for packaging contributes to a circular economy without compromising food quality.
PubMed: 38201047
DOI: 10.3390/foods13010019 -
International Microbiology : the... Jan 2024Sun-drying is a traditional process for preparing dried shrimp in coastal area of South China, but its impacts on nutrition and the formation of flavor-contributory...
Sun-drying is a traditional process for preparing dried shrimp in coastal area of South China, but its impacts on nutrition and the formation of flavor-contributory substances in dried shrimp remain largely unknown. This study aimed to examine the effects of the production process on the microbiota and metabolites in dried shrimp. 16S rDNA amplicon sequencing was employed to identify 170 operational taxonomic units (OTUs), with Vibrio, Photobacterium, and Shewanella emerging as the primary pathogenic bacteria in shrimp samples. Lactococcus lactis was identified as the principal potential beneficial microorganism to accrue during the dried shrimp production process and found to contribute significantly to the development of desirable shrimp flavors. LC-MS-based analyses of dried shrimp sample metabolomes revealed a notable increase in compounds associated with unsaturated fatty acid biosynthesis, arachidonic acid metabolism, amino acid biosynthesis, and flavonoid and flavanol biosynthesis throughout the drying process. Subsequent exploration of the relationship between metabolites and bacterial communities highlighted the predominant coexistence of Bifidobacterium, Clostridium, and Photobacterium contributing heterocyclic compounds and metabolites of organic acids and their derivatives. Conversely, Arthrobacter and Staphylococcus were found to inhibit each other, primarily in the presence of heterocyclic compounds. This comprehensive investigation provides valuable insights into the dynamic changes in the microbiota and metabolites of dried shrimps spanning different drying periods, which we expect to contribute to enhancing production techniques and safety measures for dried shrimp processing.
PubMed: 38196020
DOI: 10.1007/s10123-023-00475-6 -
PeerJ 2024Nanoplastics (NPs) are an abundant, long-lasting, and widespread type of environmental pollution that is of increasing concern because of the serious threats they might...
Nanoplastics (NPs) are an abundant, long-lasting, and widespread type of environmental pollution that is of increasing concern because of the serious threats they might pose to ecosystems and species. Identifying the ecological effects of plastic pollution requires understanding the effects of NPs on aquatic organisms. Here, we used the Pacific white shrimp () as a model species to investigate whether ingestion of polystyrene NPs affects gut microbes and leads to metabolic changes in . The abundance of Proteobacteria increased and that of Bacteroidota decreased after NPs treatment. Specifically, spp., spp., spp., and spp. increased in abundance, whereas spp. and spp. decreased. Histological observations showed that exposed to NP displayed a significantly lower intestinal fold height and damaged intestinal structures compared with the control group. Exposure to NPs also stimulated alkaline phosphatase, lysozyme, and acid phosphatase activity, resulting in an immune response in . In addition, the content of triglycerides, total cholesterol, and glucose were significantly altered after NP exposure. These results provided significant ecotoxicological data that can be used to better understand the biological fate and effects of NPs in .
Topics: Animals; Gastrointestinal Microbiome; Ecosystem; Microplastics; Alkaline Phosphatase; Bacteroidetes; Penaeidae
PubMed: 38188162
DOI: 10.7717/peerj.16743 -
Brazilian Journal of Microbiology :... Mar 2024The frosty polar environment houses diverse habitats mostly driven by psychrophilic and psychrotolerant microbes. Along with traditional cultivation methods,...
The frosty polar environment houses diverse habitats mostly driven by psychrophilic and psychrotolerant microbes. Along with traditional cultivation methods, next-generation sequencing technologies have become common for exploring microbial communities from various extreme environments. Investigations on glaciers, ice sheets, ponds, lakes, etc. have revealed the existence of numerous microorganisms while details of microbial communities in the Arctic fjords remain incomplete. The current study focuses on understanding the bacterial diversity in two Arctic fjord sediments employing the 16S rRNA gene metabarcoding and its comparison with previous studies from various Arctic habitats. The study revealed that Proteobacteria was the dominant phylum from both the fjord samples followed by Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Chloroflexi and Chlamydiae. A significant proportion of unclassified reads derived from bacteria was also detected. Psychrobacter, Pseudomonas, Acinetobacter, Aeromonas, Photobacterium, Flavobacterium, Gramella and Shewanella were the major genera in both the fjord sediments. The above findings were confirmed by the comparative analysis of fjord metadata with the previously reported (secondary metadata) Arctic samples. This study demonstrated the potential of 16S rRNA gene metabarcoding in resolving bacterial composition and diversity thereby providing new in situ insights into Arctic fjord systems.
Topics: RNA, Ribosomal, 16S; Geologic Sediments; Estuaries; Bacteria; Microbiota; Arctic Regions
PubMed: 38175355
DOI: 10.1007/s42770-023-01217-6 -
Frontiers in Microbiology 2023Identification of enteric bacteria species by whole genome sequence (WGS) analysis requires a rapid and an easily standardized approach. We leveraged the principles of...
Identification of enteric bacteria species by whole genome sequence (WGS) analysis requires a rapid and an easily standardized approach. We leveraged the principles of average nucleotide identity using MUMmer (ANIm) software, which calculates the percent bases aligned between two bacterial genomes and their corresponding ANI values, to set threshold values for determining species consistent with the conventional identification methods of known species. The performance of species identification was evaluated using two datasets: the Reference Genome Dataset v2 (RGDv2), consisting of 43 enteric genome assemblies representing 32 species, and the Test Genome Dataset (TGDv1), comprising 454 genome assemblies which is designed to represent all species needed to query for identification, as well as rare and closely related species. The RGDv2 contains six spp., three spp., one , six spp., one , two spp., and thirteen spp., while the TGDv1 contains 454 enteric bacterial genomes representing 42 different species. The analysis showed that, when a standard minimum of 70% genome bases alignment existed, the ANI threshold values determined for these species were ≥95 for / and species, ≥93% for species, and ≥92% for and species. Using these metrics, the RGDv2 accurately classified all validation strains in TGDv1 at the species level, which is consistent with the classification based on previous gold standard methods.
PubMed: 38156000
DOI: 10.3389/fmicb.2023.1225207 -
Marine Pollution Bulletin Feb 2024In the recent study, we investigated the seasonal variations in root exudation and microbial community structure in the rhizosphere of seagrass Enhalus acoroides in the...
In the recent study, we investigated the seasonal variations in root exudation and microbial community structure in the rhizosphere of seagrass Enhalus acoroides in the South China Sea. We found that the quantity and quality of root exudates varied seasonally, with higher exudation rates and more bioavailable dissolved organic matter (DOM) during the seedling and vegetative stages in spring and summer. Using Illumina NovaSeq sequencing, we analyzed bacterial and fungal communities and discovered that microbial diversity and composition were influenced by root exudate characteristics s and seagrass biomass, which were strongly dependent on seagrass growth stages. Certain bacterial groups, such as Ruegeria, Sulfurovum, Photobacterium, and Ralstonia were closely associated with root exudation and may contribute to sulfur cycling, nitrogen fixation, and carbon remineralization, which were important for plant early development. Similarly, specific fungal taxa, including Astraeus, Alternaria, Rocella, and Tomentella, were enriched in spring and summer and showed growth-promoting abilities. Overall, our study suggests that seagrass secretes different compounds in its exudates at various developmental stages, shaping the rhizosphere microbial assemblages.
Topics: Microbiota; Carbon; Rhizosphere; Biomass; Growth and Development; Plant Roots; Soil Microbiology
PubMed: 38150979
DOI: 10.1016/j.marpolbul.2023.115940 -
Journal of the American Statistical... 2023Understanding how microbes interact with each other is key to revealing the underlying role that microorganisms play in the host or environment and to identifying...
Understanding how microbes interact with each other is key to revealing the underlying role that microorganisms play in the host or environment and to identifying microorganisms as an agent that can potentially alter the host or environment. For example, understanding how the microbial interactions associate with parasitic infection can help resolve potential drug or diagnostic test for parasitic infection. To unravel the microbial interactions, existing tools often rely on graphical models to infer the conditional dependence of microbial abundances to represent their interactions. However, current methods do not simultaneously account for the discreteness, compositionality, and heterogeneity inherent to microbiome data. Thus, we build a new approach called "compositional graphical lasso" upon existing tools by incorporating the above characteristics into the graphical model explicitly. We illustrate the advantage of compositional graphical lasso over current methods under a variety of simulation scenarios and on a benchmark study, the Tara Oceans Project. Moreover, we present our results from the analysis of a dataset from the Zebrafish Parasite Infection Study, which aims to gain insight into how the gut microbiome and parasite burden covary during infection, thus uncovering novel putative methods of disrupting parasite success. Our approach identifies changes in interaction degree between infected and uninfected individuals for three taxa, Photobacterium, Gemmobacter, and Paucibacter, which are inversely predicted by other methods. Further investigation of these method-specific taxa interaction changes reveals their biological plausibility. In particular, we speculate on the potential pathobiotic roles of Photobacterium and Gemmobacter in the zebrafish gut, and the potential probiotic role of Paucibacter. Collectively, our analyses demonstrate that compositional graphical lasso provides a powerful means of accurately resolving interactions between microbiota and can thus drive novel biological discovery.
PubMed: 38143789
DOI: 10.1080/01621459.2022.2164287 -
Microorganisms Nov 2023The upsurge in havoc being wreaked by antibiotic-resistant bacteria has led to an urgent need for efficacious alternatives to antibiotics. This study assessed the...
The upsurge in havoc being wreaked by antibiotic-resistant bacteria has led to an urgent need for efficacious alternatives to antibiotics. This study assessed the antibacterial efficacy of two isobutyl cyanoacrylate nanoparticles (iBCA-NPs), D6O and NP30, against major bacterial pathogens of fish. In vivo tests on rainbow trout were preceded by in vitro tests of minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). NP30 exhibited higher efficacy than D60, but both iBCA-NPs demonstrated dose-dependent and species-specific in vitro antibacterial properties against the bacterial isolates. Generally, Gram-negative bacteria were more resistant to the iBCA-NPs. , , and were particularly sensitive to both iBCA-NPs. Administered to rainbow trout at 3571.4 mg (iBCA-NP)/kg feed, the iBCA-NPs produced a relative gain rate and survival rates comparable to the control ( > 0.05). The condition factor and the hepatosomatic and viscerosomatic indices of fish were indifferentiable ( > 0.05) between the iBCA-NP groups and the control. The iBCA-NPs caused no alteration in stress, oxidative stress (superoxide dismutase, SOD), plasma complement titer, or lysozyme activity. This study presents the first report of antibacterial activity of iBCA-NPs against Gram-negative bacteria. The results of this study suggest that D60 and NP30 may contribute to reducing the amounts of antibiotics and chemotherapeutic agents used in aquaculture.
PubMed: 38138020
DOI: 10.3390/microorganisms11122877