Soil metagenome
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Project description:The phenomenon of viable but non-culturable (VBNC) referred as a dormant state of non-sporulating bacteria enhancing the survival in adverse environments. To our knowledge, only few studies have been performed on whole genomic expression of V. parahaemolyticus in VBNC state compared with cells in exponential and early stationary phases. Since many VBNC state studies found DNA, RNA and protein degradation, we hypothesise that gene regulation of VBNC cells is highly reduced, down-regulation of gene expression is dominant and only metabolic functions crucial for survival are kept on a sustained basis. In the VBNC state we found 509 significantly induced genes and 309 significantly repressed by more than twofold compared with unstressed phases among 4820 investigated genes (adjusted P-value < 0.05). Furthermore, up-regulation was dominant in most of the non-metabolism functional categories, while five metabolism-related functional categories revealed down-regulation in the VBNC state. To our knowledge, this is the first study of comprehensive transcriptomic analyses of three phases of V. parahaemolyticus RIMD2210633. Although the mechanism of VBNC state is not yet clear, massive regulation of gene expression occurs in the VBNC state compared with expression in unstressed phases and thus, VBNC cells are active cells. VBNC state gene expression was detected in total bacterial RNA of V. parahaemolyticus. Three phases (exponential phase, early stationary phase, and VBNC state) were used in 8 biological replicates. Gene expression in exponential phase and early stationary phase was used for normalization, respectively.
2015-01-28 | E-GEOD-65340 | biostudies-arrayexpress
Project description:Bacteria have developed multiple strategies, such as sporulation, to cope with environmental stress. Non-sporulating bacteria, however, may “hibernate” into a so-called viable but non-culturable (VBNC) state, where they are no longer able to grow in standard culture media and thus become undetectable by conventional growth-based methods. VBNC pathogens pose a significant risk for human and animal health as they can “wake up” back into a vegetative and virulent state. Although hundreds of bacterial species have been reported to enter a VBNC state in response to various stresses (e.g. thermal, osmotic, starvation, antibiotics), the molecular mechanisms governing this phenotypic switch remains largely elusive. Here, we report an in-depth characterization of the VBNC state transition process in the bacterial pathogen Listeria monocytogenes in response to nutritional deprivation. We found that starvation in mineral water drives L.monocytogenes into a VBNC state via a unique mechanism of cell wall shedding that generates cellwall-deficient coccoid forms. Transcriptomic and gene-targeted approaches revealed the stress response regulator SigB and the autolysin NamA as major mediators of cell wall loss and VBNC state transition.
2024-08-01 | GSE246157 | GEO
Project description:The phenomenon of viable but non-culturable (VBNC) referred as a dormant state of non-sporulating bacteria enhancing the survival in adverse environments. To our knowledge, only few studies have been performed on whole genomic expression of V. parahaemolyticus in VBNC state compared with cells in exponential and early stationary phases. Since many VBNC state studies found DNA, RNA and protein degradation, we hypothesise that gene regulation of VBNC cells is highly reduced, down-regulation of gene expression is dominant and only metabolic functions crucial for survival are kept on a sustained basis. In the VBNC state we found 509 significantly induced genes and 309 significantly repressed by more than twofold compared with unstressed phases among 4820 investigated genes (adjusted P-value < 0.05). Furthermore, up-regulation was dominant in most of the non-metabolism functional categories, while five metabolism-related functional categories revealed down-regulation in the VBNC state. To our knowledge, this is the first study of comprehensive transcriptomic analyses of three phases of V. parahaemolyticus RIMD2210633. Although the mechanism of VBNC state is not yet clear, massive regulation of gene expression occurs in the VBNC state compared with expression in unstressed phases and thus, VBNC cells are active cells.
2015-01-28 | GSE65340 | GEO
Project description:Copper-based materials are actively explored for their potential as antimicrobial agents. However, recent studies show that sublethal concentrations of Cu ions can induce the viable-but-non-culturable (VBNC) cell state in certain bacteria, hampering with contamination control and monitoring. Despite the growing number of omics studies investigating the VBNC state, the underlying molecular mechanisms remain largely enigmatic. Here, we determine variations in protein expression of Cupriavidus metallidurans CH34 in different phases of the Cu-induced VBNC state via quantitative LC-MS/MS analysis at multiple sample time points. With this approach, we aimed to reveal cellular adaptations triggering VBNC formation and the characteristic spontaneous recovery of culturability (resuscitation). This submission contains controls and is part of the other pride submission PXD056297.
2025-05-07 | PXD056326 | Pride
Project description:Viable but nonculturable (VBNC) organisms have been underestimated and neglected when studying dormant phenotypes. In clinical settings, VBNC cells may contribute to non-apparent infections capable of being reactivated after months or even years, as for the case of Mycobacterium tuberculosis. The lack of specific and reliable methodology prevents the proper characterization of the VBNC state. Ultimately, these organisms pose a public health risk with potential implications in several industries ranging from pharmaceuticals to food industry. Research regarding their induction and resuscitation is of major importance. Bacteria are able to respond to several environmental and physiological oscillations in part via two-component systems (TCSs). BtsS/BtsR and YpdA/YpdB are two TCSs of Escherichia coli that form a pyruvate sensing network. Their role in the VBNC state is explored in this study.
2018-11-23 | PXD009463 | Pride
Project description:Characterization of the putative genetic determinants of the VBNC state in a known spore-forming Gram-positive organism Bacillus subtilis 168. The VBNC state was induced under osmotic stress and aminoglycoside treatment. The transcriptome landscape of VBNC cells was compared to the viable, antibiotic sensitive B. subtilis cells and to the viable cells with no antibiotic treatment.
2022-07-02 | GSE207180 | GEO
Project description:Here, we report 17 metagenome-assembled genomes (MAGs) recovered from microbial consortia of forest and pasture soils in the Brazilian Eastern Amazon. The bacterial MAGs have the potential to act in important ecological processes, including carbohydrate degradation and sulfur and nitrogen cycling.
| S-EPMC9670897 | biostudies-literature
Project description:The metagenomes of complex microbial communities are rich sources of novel biocatalysts. We exploited the metagenome of a mixed microbial population for isolation of more than 15 different genes encoding novel biocatalysts by using a combined cultivation and direct cloning strategy. A 16S rRNA sequence analysis revealed the presence of hitherto uncultured microbes closely related to the genera Pseudomonas, Agrobacterium, Xanthomonas, Microbulbifer, and Janthinobacterium. Total genomic DNA from this bacterial community was used to construct cosmid DNA libraries, which were functionally searched for novel enzymes of biotechnological value. Our searches in combination with cosmid sequencing resulted in identification of four clones encoding 12 putative agarase genes, most of which were organized in clusters consisting of two or three genes. Interestingly, nine of these agarase genes probably originated from gene duplications. Furthermore, we identified by DNA sequencing several other biocatalyst-encoding genes, including genes encoding a putative stereoselective amidase (amiA), two cellulases (gnuB and uvs080), an alpha-amylase (amyA), a 1,4-alpha-glucan branching enzyme (amyB), and two pectate lyases (pelA and uvs119). Also, a conserved cluster of two lipase genes was identified, which was linked to genes encoding a type I secretion system. The novel gene aguB was overexpressed in Escherichia coli, and the enzyme activities were determined. Finally, we describe more than 162 kb of DNA sequence that provides a strong platform for further characterization of this microbial consortium.
| S-EPMC201203 | biostudies-literature
Project description:Escherichia coli O157:H7 can cause haemorrhagic colitis and haemolytic uremic syndrome (HUS) in humans. This pathogen has been implicated in large food-borne outbreaks all over the world. By investigating the implicated salted salmon roe, Makino et al. (2000) suggested that E. coli O157:H7 in the viable but nonculturable (VBNC) state should be the culprit of the outbreak in Japan. High pressure CO2 (HPCD), one of the non-thermal pasteurization techniques, is an effective means to inactivate microorganisms. But in the previous study, we have demonstrated for the first time that HPCD could induce E. coli O157:H7 into the VBNC state, which poses a potential health risk to HPCD-treated products. In order to explore the potential formation mechanisms of VBNC E. coli O157:H7 induced by HPCD, the high-throughput Illumina RNA-seq transcriptomic analysis was conducted for E. coli O157:H7 cells treated at 5 MPa and 25 ℃ for 40 min (VBNC cells) and exponential-phase cells (the control). Finally, 97 genes that differentially transcribed between VBNC state and the control were obtained, with 22 genes up-regulated and 75 genes down-regulated in VBNC cells. These differentially expressed genes were classified in a variety of functional categories, including central metabolic processes, gene replication and expression, cell division, general stress response, respiration, membrane biosynthesis and transport and pathogenicity. Based on these differentially expressed genes, we suggest putative formation mechanisms of VBNC cells induced by HPCD. The finding will provide theoretical foundation for restraining the VBNC state formation under HPCD processing.
2016-06-19 | GSE62394 | GEO
Project description:Copper-based materials are actively explored for their potential as antimicrobial agents. However, recent studies show that sublethal concentrations of Cu ions can induce the viable-but-non-culturable (VBNC) cell state in certain bacteria, hampering with contamination control and monitoring. Despite the growing number of omics studies investigating the VBNC state, the underlying molecular mechanisms remain largely enigmatic. Here, we determine variations in protein expression of Cupriavidus metallidurans CH34 in different phases of the Cu-induced VBNC state via quantitative LC-MS/MS analysis at multiple sample time points. With this approach, we aimed to reveal cellular adaptations triggering VBNC formation and the characteristic spontaneous recovery of culturability (resuscitation). Entry into the VBNC state correlated with a widespread response to oxidative stress as well as restricted pyruvate metabolism. The expression of specific metal resistance determinants changed with Cu exposure time and culminated in strong upregulation of proteins linked to periplasmic Cu ion detoxification during the resuscitation phase. We suggest that this delayed induction of Cu resistance proteins is caused by the gradual reconstitution of cellular energy reserves through degradation of polyhydroxybutyrate granules. Furthermore, Cu-treated cells showed upregulation of several chemotaxis proteins, and increased cell motility was observed phenotypically. Our results reveal highly dynamic proteomic response patterns and contribute fundamental insights into the VBNC state, while also emphasizing the advantages of time-resolved proteomic analysis.
2025-05-07 | PXD056297 | Pride