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Frontiers in Microbiology 2024Bacterial degradation mechanism for high chlorinated pentachlorobiphenyl (PentaCB) with worse biodegradability has not been fully elucidated, which could limit the full...
Bacterial degradation mechanism for high chlorinated pentachlorobiphenyl (PentaCB) with worse biodegradability has not been fully elucidated, which could limit the full remediation of environments afflicted by the complex pollution of polychlorinated biphenyls (PCBs). In this research, a new PentaCB-degrading bacterium that has not been reported was obtained using enzymatic screening method. The characteristics of its intracellular enzymes, proteome and metabolome variation during PentaCB degradation were investigated systematically compared to non-PentaCB conditions. The findings indicate that the degradation rate of PentaCB (1 mg/L) could reach 23.9% within 4 hours and achieve complete degradation within 12 hours, with the mixture of intracellular enzymes being most effective at a pH of 6.0. During the biodegradation of PentaCB, the 12 up-regulated proteins characterized included ABC transporter PentaCB-binding protein, translocase protein TatA, and signal peptidase I (SPase I), indicating the presence of functional proteins for PentaCB degradation in both the cytoplasm and the outer surface of the cytoplasmic membrane. Furthermore, five differentially enriched metabolites were strongly associated with the aforementioned proteins, especially the up-regulated 1, 2, 4-benzenetriol which feeds into multiple degradation pathways of benzoate, chlorocyclohexane, chlorobenzene and aminobenzoate. These relevant results help to understand and speculate the complex mechanisms regarding PentaCB degradation by , which have both theoretical and practical implications for PCB bioremediation.
PubMed: 38933025
DOI: 10.3389/fmicb.2024.1389805 -
Molecules (Basel, Switzerland) Jun 2024Due to the intricate complexity of the original microbiota, residual heat-resistant enzymes, and chemical components, identifying the essential factors that affect dairy...
Due to the intricate complexity of the original microbiota, residual heat-resistant enzymes, and chemical components, identifying the essential factors that affect dairy quality using traditional methods is challenging. In this study, raw milk, pasteurized milk, and ultra-heat-treated (UHT) milk samples were collectively analyzed using metagenomic next-generation sequencing (mNGS), high-throughput liquid chromatography-mass spectrometry (LC-MS), and gas chromatography-mass spectrometry (GC-MS). The results revealed that raw milk and its corresponding heated dairy products exhibited different trends in terms of microbiota shifts and metabolite changes during storage. Via the analysis of differences in microbiota and correlation analysis of the microorganisms present in differential metabolites in refrigerated pasteurized milk, the top three differential microorganisms with increased abundance, ( 0.01), unclassified class ( 0.05), and ( 0.01), were detected; these were highly correlated with certain metabolites in pasteurized milk ( > 0.8). This indicated that these genera were the main proliferating microorganisms and were the primary genera involved in the metabolism of pasteurized milk during refrigeration-based storage. Microorganisms with decreased abundance were classified into two categories based on correlation analysis with certain metabolites. It was speculated that the heat-resistant enzyme system of a group of microorganisms with high correlation ( > 0.8), such as and , was the main factor causing milk spoilage and that the group with lower correlation ( < 0.3) had a lower impact on the storage process of pasteurized dairy products. By comparing the metabolic pathway results based on metagenomic and metabolite annotation, it was proposed that protein degradation may be associated with microbial growth, whereas lipid degradation may be linked to raw milk's initial heat-resistant enzymes. By leveraging the synergy of metagenomics and metabolomics, the interacting factors determining the quality evolution of dairy products were systematically investigated, providing a novel perspective for controlling dairy processing and storage effectively.
Topics: Microbiota; Animals; Milk; Food Storage; Pasteurization; High-Throughput Nucleotide Sequencing; Dairy Products; Metagenomics; Gas Chromatography-Mass Spectrometry; Food Handling; Bacteria; Metabolome
PubMed: 38930811
DOI: 10.3390/molecules29122745 -
Marine Drugs Jun 2024Deep-sea environments, as relatively unexplored extremes within the Earth's biosphere, exhibit notable distinctions from terrestrial habitats. To thrive in these extreme...
Deep-sea environments, as relatively unexplored extremes within the Earth's biosphere, exhibit notable distinctions from terrestrial habitats. To thrive in these extreme conditions, deep-sea actinomycetes have evolved unique biochemical metabolisms and physiological capabilities to ensure their survival in this niche. In this study, five actinomycetes strains were isolated and identified from the Mariana Trench via the culture-dependent method and 16S rRNA sequencing approach. The antimicrobial activity of sp. B1075 was found to be the most potent, and therefore, it was selected as the target strain. Molecular networking analysis via the Global Natural Products Social Molecular Networking (GNPS) platform identified 25 flavonoid compounds as flavonoid secondary metabolites. Among these, genistein was purified and identified as a bioactive compound with significant antibacterial activity. The complete synthesis pathway for genistein was proposed within strain B1075 based on whole-genome sequencing data, with the key gene being (encoding chalcone synthase). The expression of the gene was significantly regulated by high hydrostatic pressure, with a consequent impact on the production of flavonoid compounds in strain B1075, revealing the relationship between actinomycetes' synthesis of flavonoid-like secondary metabolites and their adaptation to high-pressure environments at the molecular level. These results not only expand our understanding of deep-sea microorganisms but also hold promise for providing valuable insights into the development of novel pharmaceuticals in the field of biopharmaceuticals.
Topics: Genistein; Anti-Bacterial Agents; Microbacterium; RNA, Ribosomal, 16S; Actinobacteria; Secondary Metabolism; Phylogeny; Acyltransferases
PubMed: 38921587
DOI: 10.3390/md22060276 -
Insects Jun 2024Microorganisms within insects play a vital role in maintaining the basal physiological functions of the insects, with olfactory signals as critical components of insect...
Microorganisms within insects play a vital role in maintaining the basal physiological functions of the insects, with olfactory signals as critical components of insect survival strategies. (), an invasive alien pest inflicting significant damage to eucalyptus trees, harbors a rich and varied bacterial community within its body. However, the impact of its endogenous bacteria and their microbial Volatile Organic Compounds (mVOCs) on the behavioral preferences of remains unexplored to date. This study focused on nine cultivable and dominant endogenous bacterial strains within . Using a Y-tube olfactometer, we investigated the behavioral responses of female to the mVOCs emitted by these bacteria. Concurrently, gas chromatography-mass spectrometry (GC-MS) was employed to quantify the mVOCs produced by these endogenous bacteria. Our findings revealed that sp. exhibited the highest attractiveness of , whereas sp. and exerted the most significant avoidance effects. The analysis of the mVOCs further highlighted the significance of aldehyde compounds, notably 2,3,6-trichlorobenzaldehyde, and alkane compounds, such as eicosane, in mediating the repellency and attraction effects. These results contribute to a deeper understanding of the invasion mechanism of and provide a scientific basis for developing novel biopesticides or elicitors.
PubMed: 38921169
DOI: 10.3390/insects15060455 -
The Science of the Total Environment Jun 2024Root-associated microbiota provide great fitness to hosts under environmental stress. However, the underlying microecological mechanisms controlling the interaction...
Root-associated microbiota provide great fitness to hosts under environmental stress. However, the underlying microecological mechanisms controlling the interaction between heavy metal-stressed plants and the microbiota are poorly understood. In this study, we screened and isolated representative amplicon sequence variants (strain M4) from rhizosphere soil samples of Trifolium repens L. growing in areas with high concentrations of heavy metals. To investigate the microecological mechanisms by which T. repens adapts to heavy metal stress in abandoned mining areas, we conducted potting experiments, bacterial growth promotion experiments, biofilm formation experiments, and chemotaxis experiments. The results showed that high concentrations of heavy metals significantly altered the rhizosphere bacterial community structure of T. repens and significantly enriched Microbacterium sp. Strain M4 was demonstrated to significantly increased the biomass and root length of T. repens under heavy metal stress. Additionally, L-proline and stigmasterol could promote bacterial growth and biofilm formation and induce chemotaxis for strain M4, suggesting that they are key rhizosphere secretions of T. repens for Microbacterium sp. recruitment. Our results suggested that T. repens adapted the heavy metal stress by reshaping rhizosphere secretions to modify the rhizosphere microbiota.
PubMed: 38914340
DOI: 10.1016/j.scitotenv.2024.174057 -
Food Chemistry: X Jun 2024In this study, the metabolic profiles of traditional craftsmanship (TC) Liupao tea presented great changes at different processing stages. The contents of flavonoids and...
In this study, the metabolic profiles of traditional craftsmanship (TC) Liupao tea presented great changes at different processing stages. The contents of flavonoids and their glycosides generally exhibited a continuing downward trend, resulting in the sensory quality of TC-Liupao tea gradually improved. However, the taste of TC-Liupao tea faded when piling exceeded 12 h, as a result of the excessive degradation of some key flavor substances. Therefore, it could be deduced that piling for 10 h might be optimum for the quality formation of TC-Liupao tea. , , , and were the dominant bacteria during piling. The correlation analysis between differential metabolites and bacteria showed that only and were significantly correlated to metabolites, demonstrating that the bacteria had less effect on the transformation of metabolites. Thus, the metabolic structure change during the process of TC-Liupao tea might be mainly attributed to the high temperature and humidity environment.
PubMed: 38911914
DOI: 10.1016/j.fochx.2024.101516 -
Chemosphere Jun 2024Leaf microbiota have been extensively applied in the biological control of plant diseases, but their crucial roles in mitigating atmospheric heavy metal (HM) deposition...
Leaf microbiota have been extensively applied in the biological control of plant diseases, but their crucial roles in mitigating atmospheric heavy metal (HM) deposition and promoting plant growth remain poorly understood. This study demonstrates that elevated atmospheric HM deposition on rice leaves significantly shapes distinct epiphytic and endophytic microbiota across all growth stages. HM stress consistently leads to the dominance of epiphytic Pantoea and endophytic Microbacterium in rice leaves, particularly during the booting and filling stages. Leaf-bound HMs stimulate the differentiation of specialized microbial communities in both endophytic and epiphytic compartments, thereby regulating leaf microbial interactions. Metagenomic binning retrieved high-quality genomes of keystone leaf microorganisms, indicating their potential for essential metabolic functions. Notably, Pantoea and Microbacterium show significant HM resistance, plant growth-promoting capabilities, and diverse element cycling functions. They possess genes associated with metal(loid) resistance, such as ars and czc, suggesting their ability to detoxify arsenic(As) and cadmium(Cd). They also support carbon, nitrogen, and sulfur cycling, with genes linked to carbon fixation, nitrogen fixation, and sulfur reduction. Additionally, these bacteria may enhance plant stress resistance and growth by producing antioxidants, phytohormones, and other beneficial compounds, potentially improving HM stress tolerance and nutrient availability in rice plants. This study shows that atmospheric HMs affect rice leaf microbial communities, prompting plants to seek microbial help to combat stress. The unique composition and metabolic potential of rice leaf microbiota offer a novel perspective for mitigating adverse stress induced by atmospheric HM deposition. This contributes to the utilization of leaf microbiota to alleviate the negative impact of heavy metal deposition on rice development and food security.
PubMed: 38908447
DOI: 10.1016/j.chemosphere.2024.142680 -
IScience Jun 2024remains one of the deadliest infectious agents globally. Amidst efforts to control TB, long treatment duration, drug toxicity, and resistance underscore the need for...
remains one of the deadliest infectious agents globally. Amidst efforts to control TB, long treatment duration, drug toxicity, and resistance underscore the need for novel therapeutic strategies. Despite advances in understanding the interplay between microbiome and disease in humans, the specific role of the microbiome in predicting disease susceptibility and discriminating infection status in tuberculosis still needs to be fully investigated. We investigated the impact of infection and -specific IFNγ immune responses on airway microbiome diversity by performing TB GeneXpert and QuantiFERON-GOLD assays during the follow-up phase of a longitudinal HIV-Lung Microbiome cohort of individuals recruited from two large independent cohorts in rural Uganda. rather than IFNγ immune response mainly drove a significant reduction in airway microbiome diversity. A microbiome signature comprising , , , and accurately discriminated active TB from Latent TB and uninfected individuals.
PubMed: 38904070
DOI: 10.1016/j.isci.2024.110142 -
Bioscience, Biotechnology, and... Jun 2024Hydrazidase from Microbacterium hydrocarbonoxydans was revealed to catalyze synthetic hydrazide compounds, enabling the bacteria to grow with them as sole carbon source,...
Hydrazidase from Microbacterium hydrocarbonoxydans was revealed to catalyze synthetic hydrazide compounds, enabling the bacteria to grow with them as sole carbon source, but natural substrates have remained unknown. In this study, kinetic analyses of hydrazidase with parabens showed that the compounds can be substrates. Then, methylparaben induced gene expressions of the operon containing hydrazidase and ABC transporter, and the compound as sole carbon source was able to grow the bacteria. Furthermore, homology search was carried out revealing that several actinomycetes possess hydrazidase-homolog in the operon. Among those bacteria, an amidase from Pseudonocardia acaciae was subjected to a kinetic analysis and a structure determination revealing similar but not identical to those of hydrazidase. Since parabens are reported to exist in plants and soil, and several actinomycetes codes the homologous operon, the enzymes with those operons may play a physiologically important role for bacterial survival with use of parabens.
PubMed: 38886122
DOI: 10.1093/bbb/zbae083 -
Bioresources and Bioprocessing Jun 2024Esterases are crucial biocatalysts in chiral compound synthesis. Herein, a novel esterase EstSIT01 belonging to family V was identified from Microbacterium chocolatum...
Esterases are crucial biocatalysts in chiral compound synthesis. Herein, a novel esterase EstSIT01 belonging to family V was identified from Microbacterium chocolatum SIT101 through genome mining and phylogenetic analysis. EstSIT01 demonstrated remarkable efficiency in asymmetrically hydrolyzing meso-dimethyl ester [Dimethyl cis-1,3-Dibenzyl-2-imidazolidine-4,5-dicarboxyate], producing over 99% yield and 99% enantiomeric excess (e.e.) for (4S, 5R)-monomethyl ester, a crucial chiral intermediate during the synthesis of d-biotin. Notably, the recombinant E. coli expressing EstSIT01 exhibited over 40-fold higher activity than that of the wild strain. EstSIT01 displays a preference for short-chain p-NP esters. The optimal temperature and pH were 45 °C and 10.0, with K and k values of 0.147 mmol/L and 5.808 s, respectively. Molecular docking and MD simulations suggest that the high stereoselectivity for meso-diester may attribute to the narrow entrance tunnel and unique binding pocket structure. Collectively, EstSIT01 holds great potential for preparing chiral carboxylic acids and esters.
PubMed: 38879848
DOI: 10.1186/s40643-024-00776-2