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Oncogenesis Apr 2024Change within the intratumoral microbiome is a common feature in lung and other cancers and may influence inflammation and immunity in the tumor microenvironment,...
Change within the intratumoral microbiome is a common feature in lung and other cancers and may influence inflammation and immunity in the tumor microenvironment, affecting growth and metastases. We previously characterized the lung cancer microbiome in patients and identified Acidovorax temperans as enriched in tumors. Here, we instilled A. temperans in an animal model driven by mutant K-ras and Tp53. This revealed A. temperans accelerates tumor development and burden through infiltration of proinflammatory cells. Neutrophils exposed to A. temperans displayed a mature, pro-tumorigenic phenotype with increased cytokine signaling, with a global shift away from IL-1β signaling. Neutrophil to monocyte and macrophage signaling upregulated MHC II to activate CD4 T cells, polarizing them to an IL-17A phenotype detectable in CD4 and γδ populations (T17). These T17 cells shared a common gene expression program predictive of poor survival in human LUAD. These data indicate bacterial exposure promotes tumor growth by modulating inflammation.
PubMed: 38570533
DOI: 10.1038/s41389-024-00513-6 -
Plant Biotechnology Journal Oct 2023The photosynthetic light reaction in cyanobacteria constitutes a highly attractive tool for productive biocatalysis, as it can provide redox reactions with high-energy...
The photosynthetic light reaction in cyanobacteria constitutes a highly attractive tool for productive biocatalysis, as it can provide redox reactions with high-energy reduction equivalents using sunlight and water as sources of energy and electrons, respectively. Here, we describe the first artificial light-driven redox cascade in Synechocystis sp. PCC 6803 to convert cyclohexanone to the polymer building block 6-hydroxyhexanoic acid (6-HA). Co-expression of a Baeyer-Villiger monooxygenase (BVMO) and a lactonase, both from Acidovorax sp. CHX100, enabled this two-step conversion with an activity of up to 63.1 ± 1.0 U/g without accumulating inhibitory ε-caprolactone. Thereby, one of the key limitations of biocatalytic reactions, that is, reactant inhibition or toxicity, was overcome. In 2 L stirred-tank-photobioreactors, the process could be stabilized for 48 h, forming 23.50 ± 0.84 mm (3.11 ± 0.12 g/L) 6-HA. The high specificity enabling a product yield (Y ) of 0.96 ± 0.01 mol/mol and the remarkable biocatalyst-related yield of 3.71 ± 0.21 g /g illustrate the potential of producing this non-toxic product in a synthetic cascade. The fine-tuning of the energy burden on the catalyst was found to be crucial, which indicates a limitation by the metabolic capacity of the cells possibly being compromised by biocatalysis-related reductant withdrawal. Intriguingly, energy balancing revealed that the biotransformation could tap surplus electrons derived from the photosynthetic light reaction and thereby relieve photosynthetic sink limitation. This study shows the feasibility of light-driven biocatalytic cascade operation in cyanobacteria and highlights respective metabolic limitations and engineering targets to unleash the full potential of photosynthesis.
Topics: Synechocystis; Biocatalysis; Oxidation-Reduction; Mixed Function Oxygenases; Photosynthesis
PubMed: 37439151
DOI: 10.1111/pbi.14113 -
PloS One 2023In practical production, cane stems with buds are generally used as seed for propagation. However, long-terms cane stems only easily lead to some problems such as...
In practical production, cane stems with buds are generally used as seed for propagation. However, long-terms cane stems only easily lead to some problems such as disease sensitivity, quality loss, etc. Recently, cane seedings, which are produced by tissue culture were used in sugarcane production, but few studies on cane health related to tissue culture seedings. Therefore, to evaluate the immunity and health of sugarcanes growing from different reproduction modes, the endophytic microbial compositions in cane roots between stem and tissue culture seedlings were analyzed using high-throughput techniques. The results showed that the endophytic microbial compositions in cane roots were significant differences between stem and tissue culture seedlings. At the genus level, Pantoea, Bacillus, Streptomyces, Lechevalieria, Pseudomonas, Nocardioides, unclassified_f__Comamonadaceae enriched as the dominant endophytic bacterial genera, and Rhizoctonia, Sarocladium, Scytalidium, Wongia, Fusarium, unclassified_f__Phaeosphaer, unclassified_c__Sordariom, unclassified_f__Stachybot, Poaceascoma, Microdochium, Arnium, Echria, Mycena and Exophiala enriched as the dominant endophytic fungal genera in cane roots growing from the tissue culture seedlings. In contrast, Mycobacterium, Massilia, Ralstonia, unclassified_f__Pseudonocardiacea, norank_f__Micropepsaceae, Leptothrix and Bryobacter were the dominant endophytic bacterial genera, and unclassified_k__Fungi, unclassified_f__Marasmiaceae, Talaromyces, unclassified_c__Sordariomycetes and Trichocladium were the dominant endophytic fungal genera in cane roots growing from stem seedlings. Additionally, the numbers of bacterial and fungal operational taxonomic units (OTUs) in cane roots growing from tissue culture seedlings were significantly higher than those of stem seedlings. It indicates that not only the endophytic microbial compositions in cane roots can be shaped by different propagation methods, but also the stress resistance of sugarcanes can be improved by the tissue culture propagation method.
Topics: Canes; Ascomycota; Fusarium; Actinomycetales; Plant Roots; Streptomyces; Agaricales; Fungi, Unclassified; Sordariales; Endophytes
PubMed: 37582116
DOI: 10.1371/journal.pone.0290167 -
Frontiers in Cellular and Infection... 2023is a seed-borne bacterial pathogen that causes bacterial fruit blotch in cucurbits and severely affects the production of cucumbers and watermelons globally. In this...
is a seed-borne bacterial pathogen that causes bacterial fruit blotch in cucurbits and severely affects the production of cucumbers and watermelons globally. In this study, we investigated the effects of di-(2-ethylhexyl) phthalate (DEHP) on the growth, metabolism, and virulence of . Bacterial population was not affected by DEHP exposure; moreover, significant changes were not observed in lipid peroxidation, membrane permeability, and nucleic acid leakage. However, palmitoleic acid content was increased in the cell membrane of DEHP-exposed . Further, DEHP exposure increased the activity of TCA cycle-related enzymes, including α-ketoglutarate dehydrogenase and succinyl-CoA synthetase, along with increase in the content of glutamate, succinate, fumarate, and malate in TCA cycle. Additionally, total 270 genes were differentially expressed by the treatment, of which 28 genes were upregulated and 242 genes, including those related to translation, flagellum-dependent cell motility, and flagellum assembly, were downregulated. Regarding virulence traits, swimming activity was decreased in DEHP-exposed ; however, biofilm formation was not affected in assay. Moreover, relative expression of pathogenicity genes, including and , were decreased in DEHP-exposed compared to that of unexposed . Therefore, these results suggest that DEHP accumulation in soil could potentially influence the metabolism and virulence traits of .
Topics: Virulence; Diethylhexyl Phthalate; Comamonadaceae
PubMed: 37692166
DOI: 10.3389/fcimb.2023.1228713 -
Journal, Genetic Engineering &... Nov 2023The health index of any population is directly correlated with the water quality, which in turn depends upon physicochemical characteristics and the microbiome of that...
BACKGROUND
The health index of any population is directly correlated with the water quality, which in turn depends upon physicochemical characteristics and the microbiome of that aquatic source. For maintaining the water quality, knowledge of microbial diversity is a must. The present investigation attempts to evaluate the microflora of Baner. Metagenomics has been proven to be the technique for examining the genetic diversity of unculturable microbiota without using traditional culturing techniques. The microbial profile of Baner is analyzed using metagenomics for the first time to the best of our knowledge.
RESULTS
To explore the microbial diversity of Baner, metagenomics analysis from 3 different sites was done. Data analysis identified 29 phyla, 62 classes, 131 orders, 268 families, and 741 genera. Proteobacteria was found to be the most abundant phylum in all the sampling sites, with the highest abundance at S sampling site (94%). Bacteroidetes phylum was found to be second abundant in S and S site, whereas Actinobacteria was second dominant in sampling site S. Enterobacteriaceae family was dominant in site S1, whereas Comamonadaceae and Pseudomonadaceae was abundant in sites S and S respectively. The Baner possesses an abundant bacterial profile that holds great promise for developing bioremediation tactics against a variety of harmful substances.
CONCLUSION
Baner river's metagenomic analysis offers the first insight into the microbial profile of this hilly stream. Proteobacteria was found to be the most abundant phylum in all the sampling sites indicating anthropogenic interference and sewage contamination. The highest abundance of proteobacteria at S reveals it to be the most polluted site, as it is the last sampling site downstream of the area under investigation, and falls after crossing the main city, so more human intervention and pollution were observed. Despite some pathogens, a rich profile of bacteria involved in bioremediation, xenobiotic degradation, and beneficial fish probiotics was observed, reflecting their potential applications for improving water quality and establishing a healthy aquaculture and fishery section.
PubMed: 38015339
DOI: 10.1186/s43141-023-00601-x -
Frontiers in Microbiology 2023Auxin response factor (ARF) is a critical regulator in the auxin signaling pathway, involved in a variety of plant biological processes. Here, gene members of 24 and 39...
Auxin response factor (ARF) is a critical regulator in the auxin signaling pathway, involved in a variety of plant biological processes. Here, gene members of 24 and 39 were identified in two genomes of clones AP85-441 and Np-X, respectively. Phylogenetic analysis showed that all genes were clustered into four clades, which is identical to those genes in maize () and sorghum (). The gene structure and domain composition of this ARF family are conserved to a large degree across plant species. The and genes were unevenly distributed on chromosomes 1-8 and 1-10 in the two genomes of AP85-441 and Np-X, respectively. Segmental duplication events may also contribute to this gene family expansion in . The post-transcriptional regulation of genes likely involves sugarcane against various stressors through a miRNA-medicated pathway. Expression levels of six representative genes were analyzed by qRT-PCR assays on two sugarcane cultivars [LCP85-384 (resistant to leaf scald) and ROC20 (susceptible to leaf scald)] triggered by subsp. () and () infections and salicylic acid (SA) treatment. functioned as a positive regulator under and stress, whereas it was a negative regulator under SA treatment. genes played positive roles against both pathogenic bacteria and SA stresses. Additionally, was negatively modulated by and stimuli in both cultivars, particularly LCP85-384. These findings imply that sugarcane exhibit functional redundancy and divergence against stressful conditions. This work lays the foundation for further research on gene functions in sugarcane against diverse environmental stressors.
PubMed: 37744907
DOI: 10.3389/fmicb.2023.1257355 -
Microbiology Spectrum Dec 2023Bacterial fruit blotch (BFB), which is caused by the seed-borne bacterium , is a devastating disease affecting cucurbit crops throughout the world. Although seed...
Bacterial fruit blotch (BFB), which is caused by the seed-borne bacterium , is a devastating disease affecting cucurbit crops throughout the world. Although seed fermentation and treatment with disinfectants can provide effective management of BFB, they cannot completely guarantee pathogen-free seedstock, which suggests that is a highly stress-resistant pathogen. Toxin-antitoxin (TA) systems are common among a diverse range of bacteria and have been reported to play a role in bacterial stress response. However, there is currently much debate about the relationship between TA systems and stress response in bacteria. The current study characterized a novel TA system (Aave_1720-Aave_1719) from that affects both biofilm formation and survival in response to sodium hypochlorite stress. The mechanism of neutralization differed from typical TA systems as two separate mechanisms were associated with the antitoxin, which exhibited characteristics of both type II and type V TA systems. The Aave_1720-Aave_1719 system described here also constitutes the first known report of a double-ribonuclease TA system in bacteria, which expands our understanding of the range of regulatory mechanisms utilized by bacterial TA systems, providing new insight into the survival of in response to stress.
Topics: Toxin-Antitoxin Systems; Fruit; Seeds; Antitoxins
PubMed: 37819152
DOI: 10.1128/spectrum.02169-23 -
Frontiers in Plant Science 2023() is a causal agent of watermelon bacterial fruit blotch (BFB) disease. Because resistance cultivars/lines have not yet been developed, it is imperative to elucidate...
() is a causal agent of watermelon bacterial fruit blotch (BFB) disease. Because resistance cultivars/lines have not yet been developed, it is imperative to elucidate 's virulence factors and their mechanisms to develop resistant cultivars/lines in different crops, including watermelon. The glucose-6-phosphate isomerase (GPI) is a reversible enzyme in both glycolysis and gluconeogenesis pathways in living organisms. However, the functions of GPI are not characterized in . In this study, we determined the roles of GpiAc (GPI in ) by proteomic and phenotypic analyses of the mutant lacking GPI. The mutant displayed significantly reduced virulence to watermelon in two different virulence assays. The mutant's growth patterns were comparable to the wild-type strain in rich medium and M9 with glucose but not with fructose. The comparative proteome analysis markedly identified proteins related to virulence, motility, and cell wall/membrane/envelope. In the mutant, biofilm formation and twitching halo production were reduced. We further demonstrated that the mutant was less tolerant to osmotic stress and lysozyme treatment than the wild-type strain. Interestingly, the tolerance to alkali conditions was remarkably enhanced in the mutant. These results reveal that GpiAc is involved not only in virulence and glycolysis/gluconeogenesis but also in biofilm formation, twitching motility, and tolerance to diverse external stresses suggesting the pleiotropic roles of GpiAc in . Our study provides fundamental and valuable information on the functions of previously uncharacterized glucose 6-phosphate isomerase and its virulence mechanism in .
PubMed: 38023913
DOI: 10.3389/fpls.2023.1275438 -
Microorganisms Jul 2023, the causative agent of bacterial fruit blotch, can be divided into two main groups based on factors such as pathogenicity and host species preference. PilA is an...
, the causative agent of bacterial fruit blotch, can be divided into two main groups based on factors such as pathogenicity and host species preference. PilA is an important structural and functional component of type IV pili (T4P). Previous studies have found significant differences in DNA sequences between group I and group II strains of . In this study, we characterized in the group I strain pslb65 and the group II strain Aac5. mutants, complementation strains, and cross-complementation strains were generated, and their biological phenotypes were analyzed to identify functional differences between in the two groups. deletion mutants (pslb65Δ and Aac5Δ) showed significantly reduced pathogenicity compared with the wild-type (WT) strains; pslb65-Δ also completely lost twitching motility, whereas Aac5-Δ only partially lost motility. In King's B medium, there were no significant differences in biofilm formation between pslb65-Δ and WT pslb65, but Aac5-Δ showed significantly reduced biofilm formation compared to WT Aac5. In M9 minimal medium, both mutants showed significantly lower biofilm formation compared to the corresponding WT strains, although biofilm formation was recovered in the complementation strains. The biofilm formation capacity was somewhat recovered in the cross-complementation strains but remained significantly lower than in the WT strains. The interspecies competitive abilities of pslb65-Δ and Aac5-Δ were significantly lower than in the WT strains; Aac5-Δ was more strongly competitive than pslb65-Δ, and the complementation strains recovered competitiveness to WT levels. Furthermore, the cross-complementation strains showed stronger competitive abilities than the corresponding WT strains. The relative expression levels of genes related to T4P and the type VI secretion system were then assessed in the mutants via quantitative PCR. The results showed significant differences in the relative expression levels of multiple genes in pslb65-Δ and Aac5-Δ compared to the corresponding WT stains. This indicated the presence of specific differences in function between the two groups, but the regulatory mechanisms involved require further study.
PubMed: 37512977
DOI: 10.3390/microorganisms11071806 -
Microorganisms Jun 2024Waste Water Treatment Plants (WWTP) aim to reduce contamination in effluent water; however, studies indicate antimicrobial resistance genes (ARGs) persist...
Metagenomic Investigation of the Short-Term Temporal and Spatial Dynamics of the Bacterial Microbiome and the Resistome Downstream of a Wastewater Treatment Plant in the Iskar River in Bulgaria.
Waste Water Treatment Plants (WWTP) aim to reduce contamination in effluent water; however, studies indicate antimicrobial resistance genes (ARGs) persist post-treatment, potentially leading to their spread from human populated areas into the environment. This study evaluated the impact of a large WWTP serving 125,000 people on the Iskar River in Bulgaria, by characterizing the spatial and short-term temporal dynamics in bacterial community dynamics and resistance profiles of the surface water. Pairs of samples were collected biweekly on four dates from two different locations, one about 800 m after the WWTP effluents and the other 10 km downstream. Taxonomic classification revealed the dominance of and , notably the genera , , , , and . The taxonomic structure corresponded with both lentic and lotic freshwater habitats, with exhibiting a significant decrease over the study period. Principal Coordinate Analysis revealed statistically significant differences in bacterial community composition between samples collected on different dates. Differential abundance analysis identified notable enrichment of and There were shifts within the enriched or depleted bacterial taxa between early and late sampling dates. High relative abundance of the genes , , , (macrolides); , , , and (tetracyclines); and (sulphonamides); and , (beta-lactams) were detected, with trends of increased presence in the latest sampling dates and in the location closer to the WWTP. Of note, genes conferring resistance to carbapenems OXA-58 and IMP-33-like were identified. Co-occurrence analysis of ARGs and mobile genetic elements on putative plasmids showed few instances, and the estimated human health risk score (0.19) according to MetaCompare2.0 was low. In total, 29 metagenome-assembled genomes were recovered, with only a few harbouring ARGs. This study enhances our understanding of freshwater microbial community dynamics and antibiotic resistance profiles, highlighting the need for continued ARGs monitoring.
PubMed: 38930632
DOI: 10.3390/microorganisms12061250