Bacterial proteomics of freeze-dried bacterial powder
Ontology highlight
ABSTRACT:
ORGANISM(S): Lactobacillus Delbrueckii Subsp. Bulgaricus
SUBMITTER: 
Pimin Gong
PROVIDER: PXD076427 | iProX | Tue Mar 31 00:00:00 BST 2026
REPOSITORIES: iProX
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Project description:we employed high-throughput scRNA-seq to systematically profile bacterial populations throughout the freeze-drying and storage processes. Through unsupervised clustering, we delineated functional clusters with distinct physiological characteristics and fitness advantages.
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Project description:Purpose: Lactococcus lactis is the primary constituent of many industrial starter cultures used in food fermentations. However, this bacterium is exposed to several stressful conditions during the industrial process. L. lactis TOMSC161 has been shown to resist better to freeze-drying and storage when cells are harvested at the late stationary compared to the early stationary phase. Methods: In this work, the physiological changes that occur during growth (early and late stationary phases) were studied using transcriptomic, proteomic and cytometric approaches in order to elucidate the cell mechanisms involved in the stress tolerance of L. lactis TOMSC161 to freeze-drying and storage processes. Results: The majority of altered abundances for genes determined by transcriptomic analysis indicated a slowdown at the late stationary phase in general metabolism and in the incomplete reduction of O2 leading to reactive oxygen species (ROS), in comparison to the early stationary phase. Furthermore, the expression of genes involved in general and oxidative stress responses was over-expressed at the late stationary phase when compared to the early stationary phase, thus explaining the better resistance to freeze-drying and the storage of cells harvested after six hours of stationary phase. Superoxide anion detection was performed by flow cytometry and related to the ROS production of starters. Superoxide anion concentration was lower for cells harvested at the late stationary phase when compared to cells harvested at the early stationary phase. Conclusions: L. lactis TOMSC161 was thus able to develop an oxidative stress “pre-adaptation” during the stationary phase making it possible to better resist freeze-drying and storage stresses and especially oxidative stress.
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Project description:In vitro systems involving microbial fermentation such as the Hohenheim gas test (HGT) typically need freshly obtained inocula such as rumen fluid or faeces. The objective of this study was to test the possibility of becoming independent of fresh faeces by using preserved faeces. Fresh faeces from sheep (control, C) was compared with seven differently preserved faeces in the HGT by using nine feeds and studying in vitro gas production (GP). Preservation involved freezing at -20°C (FR), shock-freezing with liquid nitrogen (N) and additional freezing at -20°C (FRN), FRN followed by defrosting (FRNdef), shock-freezing with liquid N and freeze-drying (FDN), freeze-drying (FD), freeze-drying and storage for three weeks (FD3W) and six months (FD6M). MA metaproteomics workflow was used to analyse the effects of treatments C, FR, FRN, FD, and FDN on to study changes in microbial community composition and functionactivity.
2026-03-27 | PXD060439 | Pride
Project description:To determine the transcriptomic (mRNA and microRNA) content present in fresh apheresis platelets and freeze dried platelets (Thrombosomes) we used RNA-Seq approach. The goal was to determine if the freeze drying process maintained the transcriptomic cargo of the fresh platelets.
2026-02-23 | GSE262835 | GEO
Project description:This study reports on the influence of lactic acid fermentation on the proteomic and peptidomic profiles of spirulina protein isolate (SPI)-fortified, freeze-dried powders containing living Lacticaseibacillus rhamnosus GG (LGG) cells during in vitro digestion. For comparison, powders fortified with whey protein isolate (WPI) and pea protein isolate (PPI) were also evaluated. Prior to freeze-drying, the powder precursors were either non-treated or fermented. Capillary SDS–PAGE electropherograms revealed a mild proteolytic effect due to fermentation. C-phycocyanin (SPI) and β-lactoglobulin (WPI) showed the highest resistance to pepsinolysis. All samples were responsive to pancreases, with fermented WPI showing the lowest responsiveness. Fermentation enhanced the degree of hydrolysis (DH) in gastric chymes, whereas in intestinal chymes, DH followed the order SPI > PPI > WPI, with fermentation showing no significant impact. A total of 6, 11, and 52 potential bioactive peptide sequences, associated with various beneficial activities, were identified in the SPI, PPI, and WPI digesta, respectively. The highest amino acid bioaccessibilities were observed for cysteine and methionine in SPI, isoleucine and arginine in PPI, and glycine in WPI. In conclusion, fortifying probiotic formulations with protein isolates offers secondary health benefits, stemming from the release of bioactive peptides and bioaccessible essential amino acids.
2025-02-05 | PXD052301 | Pride
Project description:Here we found Rosa roxburghii fruit extracts effectively increase TERT expression and telomerase activity in cultured human mesenchymal stem cells. Both Rosa roxburghii fruit extracts by freeze drying and spray drying methods increase the activity of telomerase. Rosa roxburghii fruit freeze drying extracts is able to reduce reactive oxygen species levels, enhance SOD activity and resistance to oxidative stress, and reduce DNA damage caused by oxidative stress or radiation. Rosa roxburghii fruit extracts promoted cell proliferation, improved senescent cell morphology, delayed replicative cellular senescence, attenuated cell cycle supressors and alleviated the senescence-associated secretory phenotype. Transcriptome and metabolic profilings found that Rosa roxburghii fruit extract promote cell proliferation and DNA repair pathways, decreased triglycerides as well. Overall, we provided a theoretical basis for the application of Rosa roxburghii fruit as an anti-aging natural product.
2024-04-01 | GSE261987 | GEO
Project description:This study took the advantage of the availability of a methylated mutant (ΔpglX ) of Lacticaseibacillus (L.) paracasei Zhang to test our hypothesis that DNA methylation could protect lactic acid bacteria from freeze-drying and post-freeze-drying storage stresses. Active cultures of the wild-type and mutant were freeze-dried and stored at 30 ℃ for different duration (30, 60, and 90 days) before reactivation. Proteomic analyses was implemented to identify differentially expressed proteins (DEPs) of the bacteria.
| PXD043736 |
Project description:This study took the advantage of the availability of a methylated mutant (ΔpglX ) of Lacticaseibacillus (L.) paracasei Zhang to test our hypothesis that DNA methylation could protect lactic acid bacteria from freeze-drying and post-freeze-drying storage stresses. Active cultures of the wild-type and mutant were freeze-dried and stored at 30 ℃ for different duration (30, 60, and 90 days) before reactivation. Proteomic analyses was implemented to identify differentially expressed proteins (DEPs) of the bacteria.The confidence of proteomic results was assessed by PRM validation.
| PXD043735 |
Project description:Purpose: The goal of this study was to determine the microRNA (miRNA) content of extracellular vesicles (EVs) derived from murine mesenchymal stem cells (mMSC), and evaluate reproducibility among distinct EV productions. We also aimed at assessing the effect of freeze-drying on EV miRNA content, by performing sequencing on freeze-dried EVs and calculating statistical difference between unmodified and freeze-dried EVs. Methods: mMSC-derived EVs were obtained from mMSC in culture in reduced serum medium Opti-MEM by differential centrifugation, with a final step at 100,000 g for 110 min at 4°C. EV pellets (freeze-dried (n=3) or not (n=2)) were resuspended in Qiazol lysis buffer and RNA was extracted following RNeasy Micro kit. cDNA libraries for sequencing were prepared using the TruSeq Small RNA Sample Preparation Kit. Amplified cDNA constructs were purified on 6 % PAGE gel and DNA molecules corresponding to 15–50 nucleotide transcripts were excised, eluted from gel, and concentrated. Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component (Illumina). Before statistical analysis, genes with less than 15 reads (cumulating all the analysed samples) were filtered out. Differentially expressed miRNA were identified using three Bioconductor packages: edgeR, DESeq and DESeq2. Results: Considering miRNAs detected with at least 5 counts (in terms of normalised counts), 339 miRNAs were identified and miRNA content was highly conserved among the two batches tested, with 237 miRNAs out of the 339 present in both batches (70%). Statistical analysis did not evidence statistical difference between unmodified EVs (n=2) and freeze-dried EVs (n=3) (DESeq2, p<0.05). No statistical difference was found using other Bioconductor packages DESeq and edgeR. These results indicated conservation of miRNA content following freeze-drying. Conclusion: mMSC-EV miRNA content was comparable between the two EV productions analysed, indicating reproducibility. Some of the miRNAs identified were consistent with previously published results on MSC-derived EVs. Freeze-drying conserved miRNA content.
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