Project description:Early detection of spoilage microorganisms and food pathogens is of major importance in preventing food recalls and foodborne outbreaks. Although constant effort is invested in developing sensitive methods for rapid microbial detection, none of the current methods enables the detection of food pathogens within a few hours; therefore, development of innovative early-warning food-testing strategies are needed. Herein, we assessed a novel strategy that harnesses the microbiome signature of a food product to determine deviations in the abundance of particular community members and detect production defects. Employing the production process of barbecued (BarBQ) pastrami as a model, we characterized the microbiome profiles of the product along the production line using next-generation sequencing of the 16S rRNA gene, concentrating on the live microbiota. Following the establishment of a microbiome dataset representing a properly produced product, we were able to identify shifts in the microbiome profile of a defective batch produced under potassium lactate deficiency. With the identification of Vibrio and Lactobacillus as potential indicator bacteria for potassium lactate deficiency, rapid qPCR assays were designed for their quantification. Aligned with the microbiome profiling results, these qPCR assays were effective for rapid identification of a defective production event. This implies the use of rapid quantification targeting microbiome profile-derived indicator bacteria for in-house detection of defective batches and identification of food-safety and quality events with results obtained on the same day. The suggested strategy should pave the way toward safer and more efficient food-production systems.
Project description:This project reports the characterization of the lactate racemase system in Lactobacillus plantarum. The lactate racemase (LarA) is a nickel-dependent enzyme. The apo-enzyme (apoLarA) is activated by a single nickel-containing maturation protein (LarE) that requires preactivation by two other accessory proteins (LarC which is a fusion between LarC1 and LarcC2 and LarB). Data submitted here identify the purified forms of Lar proteins.
Project description:Indole is an intercellular and interkingdom signaling molecule, which is widespread in diverse ecological niches. Caenorhabditis elegans is a bacterivorous nematode living in soil and compost environments and a useful model host for the study of host-microbe interactions. While various bacteria and some plants produce a large quantity of extracellular indole, little is known about the effects of indole, its derivatives, and indole-producing bacteria on behaviors in C. elegans and animals. Here, we show that C. elegans senses and moves toward indole and indole-producing bacteria, such as Escherichia coli, Shigella boydii, Providencia stuartii, and Klebsiella oxytoca, while avoids non-indole producing pathogenic bacteria. It was also found that indole-producing bacteria and non-indole-producing bacteria exert divergent effects on egg-laying behavior of C. elegans via indole. In addition, various indole derivatives also modulate chemotaxis, egg-laying behavior, and survival of C. elegans. In contrast, indole at a high concentration to kill C. elegans that has the ability to detoxify indole via oxidation and glucosylation, indicating predator-prey interactions via a double-edged molecule indole. Transcriptional analysis showed that indole markedly up-regulated gene expression of cytochrome P450 family, UDP-glucuronosyltransferase, glutathione S-transferase, which explained well the modification of indole in C. elegans, while down-regulated expression of collagen genes and F-box genes. Our findings suggest that indole and its derivatives are important interkingdom signaling molecules in bacteria-nematode interactions.
Project description:Sodium oligomannate (GV-971), an oligosaccharide drug approved in China for treating mild-to-moderate Alzheimer's disease (AD), was previously found to recondition the gut microbiota and limit altered peripheral Th1 immunity in AD transgenic mice. As a follow-up study, we here provide advances by pinpointing a Lactobacillus murinus strain that highly expressed a gene encoding a putative adhesin containing Rib repeats (Ribhigh-L.m.) that was particularly enriched in 5XFAD transgenic mice. Mechanistically, Ribhigh-L.m. adherence to the gut epithelia upregulated fecal metabolites, among which lactate ranked as the top candidate. Lactate stimulated the epithelial production of serum amyloid A (SAA) in gut via GPR81-NFκB axis, contributing to peripheral Th1 activation. Moreover, GV-971 disrupted the adherence of Ribhigh-L.m. to gut epithelia via directly binding to Rib, leading to the reduced SAA and alleviated Th1-skewed inflammation. These findings were replicated in early-staged AD patients. Together, we gained further insights between gut bacteria and AD progression and the mechanism of GV-971 in treating AD.
Project description:Transcriptional profiling of Salmonella Typhimurium SL1344 wild type grown to OD600=1 in LB alone or in LB supplemented with 2mM Indole, or with 2mM indole for 15 min (called shock). The goal is to determine Salmonella response to indole at different time points. Different conditions were tested. The reference on each hybridisation is the chromosome DNA of the wild type strain. 4 replicates each for LB and LB + Indole, 6 replicates for indole shock.
Project description:Indole-3-carbinol is used as a dietary supplement and has potential use as a therapeutic agent for the prevention of various types of cancer. While substantial evidence exists that indole-3-carbinol can reduce the risk of cancers induced by several known carcinogens when administered to animals, indole-3-carbinol can also function as an initiator and tumor promoter in certain models. The carcinogenic potential of indole-3-carbinol has not been studied in a 2-year bioassay. The objective of the microarray study was to evaluate the transcriptional changes in liver from rats exposed to 0 or 300 mg/kg indole-3-carbinol. At 3 months, livers were analyzed from female Harlan Sprague Dawley rats in the 2-year gavage study of indole-3-carbinol.
Project description:Indole is ubiquitously synthesized by plants and bacteria and functions as an inter species signaling molecule to modulate a wide variety of cellular activities. However, it is not clear how the indole signal is perceived and responded by plant growth promoting rhizobacteria (PGPR) at the rhizosphere. Here, we demonstrated that indole enhanced antibiotic tolerance of Pseudomonas fluorescens 2P24, a PGPR well known for its biocontrol capacity. By conducting quantitative proteomic analysis, we showed that indole influences the expression of multiple genes including the emhABC operon encoding the major multidrug efflux pump in P. fluorescens 2P24. The indole-induced antibiotic tolerance was not related to bacterial dormancy or slow growth, but depended on the emhABC operon and the divergently transcribed TetR-like regulator emhR. By binding to the semi-palindromic operator sequence, EmhR repressed the expression of emhABC. It was further revealed that indole bound to EmhR and weakened the interaction between EmhR and the operator. This is consistent with our finding that indole-induced expression of the EmhABC efflux pump is dependent on EmhR. Using homology modeling and molecular dynamics simulation, we found that indole binding resulted in significantly decreased distance between the two DNA-recognizing α3 helices within the EmhR dimer, which would possibly account for its compromised DNA binding capacity. EmhR was further shown to globally influence protein expressions, especially transporters and proteins involved in the denitrification pathway. This EmhR-dependent, indole-induced antibiotic tolerance is likely to be prevalent in the Pseudomonas species, as the EmhR homologue in Pseudomonas syringae was also shown to be responsible for the indole-induced antibiotic tolerance. Taken together, our results revealed an indole-sensing transcription factor EmhR responsible for indole-induced antibiotic tolerance in Pseudomonas species and have important implications on the general mechanism for the indole sensing and responses in rhizobacteria.