Genomic island-encoded regulatory proteins in enterohemorrhagic Escherichia coli O157:H7

Enterohemorrhagic Escherichia coli (EHEC) is an important zoonotic pathogen that is a major cause of foodborne diseases in most developed and developing countries and can cause uncomplicated diarrhoea, haemorrhagic colitis, and haemolytic uraemic syndrome. O islands (OIs), which are unique genomic islands in EHEC O157:H7, are composed of 177 isolated genomic features and harbour 26% of the total genes that are absent in the non-pathogenic E. coli K-12 genome. In the last twenty years, many OI-encoded proteins have been characterized, including proteins regulating virulence, motility, and acid resistance. Given the critical role of regulatory proteins in the systematic and hierarchical regulation of bacterial biological processes, this review summarizes the OI-encoded regulatory proteins in EHEC O157:H7 characterized to date, emphasizing OI-encoded regulatory proteins for bacterial virulence, motility, and acid resistance. This summary will be significant for further exploration and understanding of the virulence and pathogenesis of EHEC O157:H7.

Motility-activating mutations upstream of flhDC reduce acid shock survival of Escherichia coli

Many neutralophilic bacterial species try to evade acid stress with an escape strategy, which is reflected in the increased expression of genes coding for flagellar components. Extremely acid-tolerant bacteria, such as Escherichia coli, survive the strong acid stress, e.g., in the stomach of vertebrates. Recently, we were able to show that the induction of motility genes in E. coli is strictly dependent on the degree of acid stress, i.e., they are induced under mild acid stress but not under severe acid stress. However, it was not known to what extent fine-tuned expression of motility genes is related to fitness and the ability to survive periods of acid shock. In this study, we demonstrate that the expression of FlhDC, the master regulator of flagellation, is inversely correlated with the acid shock survival of E. coli. We encountered this phenomenon when analyzing mutants from the Keio collection, in which the expression of flhDC was altered by an insertion sequence element. These results suggest a fitness trade-off between acid tolerance and motility.IMPORTANCEEscherichia coli is extremely acid-resistant, which is crucial for survival in the gastrointestinal tract of vertebrates. Recently, we systematically studied the response of E. coli to mild and severe acidic conditions using Ribo-Seq and RNA-Seq. We found that motility genes are induced at pH 5.8 but not at pH 4.4, indicating stress-dependent synthesis of flagellar components. In this study, we demonstrate that motility-activating mutations upstream of flhDC, encoding the master regulator of flagella genes, reduce the ability of E. coli to survive periods of acid shock. Furthermore, we show an inverse correlation between motility and acid survival using a chromosomal isopropyl β-D-thio-galactopyranoside (IPTG)-inducible flhDC promoter and by sampling differentially motile subpopulations from swim agar plates. These results reveal a previously undiscovered trade-off between motility and acid tolerance and suggest a differentiation of E. coli into motile and acid-tolerant subpopulations, driven by the integration of insertion sequence elements.

Functionalization of a zirconia surface by covalently immobilized fibronectin and its effects on resistance to thermal, acid, and mechanical exposure

Silane chemistry has emerged as a powerful tool for surface modification, offering a versatile means to enhance the properties of various substrates, such as dental implant abutment materials. In this study, we investigated the stability of the 3-aminopropyldiisopropylethoxysilane (APDS) layer on yttria-partially stabilized zirconia (Y-TZP) surfaces after mechanical, acid, and thermal treatment in order to simulate fluctuations within the oral cavity. To accomplish that, the viability of human gingival fibroblasts on APDS-modified surfaces after applied treatment strategies was assessed by live/dead staining. Moreover, the hydrolysis stability and enzymatic degradation resistance of crosslinked fibronectin to the APDS layer was examined by immunostaining and western blot. The results revealed that the applied modifications were not affected by the different treatment conditions and could withstand the fluctuations in the oral cavity. Furthermore, crosslinked fibronectin on silanized Y-TZP was stable against hydrolysis over 21 days and enzymatic degradation. We thus can conclude that the proposed functionalization method has high potential to tolerate harmful effects within the oral cavity and remains unchanged on the surface.

lactis Bb12 and the improvement of acid resistance by purine and pyrimidine compounds

AIMS

During fermentation, the accumulation of acidic products can induce media acidification, which restrains the growth of Bifidobacterium animalis subsp. lactis Bb12 (Bb12). This study investigated the nutrient consumption patterns of Bb12 under acid stress and effects of specific nutrients on the acid resistance of Bb12.

METHODS AND RESULTS

Bb12 was cultured in chemically defined medium (CDM) at different initial pH values. Nutrient consumption patterns were analyzed in CDM at pH 5.3, 5.7, and 6.7. The patterns varied with pH: Asp + Asn had the highest consumption rate at pH 5.3 and 5.7, while Ala was predominant at pH 6.7. Regardless of the pH levels (5.3, 5.7, or 6.7), ascorbic acid, adenine, and Fe2+ were vitamins, nucleobases, and metal ions with the highest consumption rates, respectively. Nutrients whose consumption rates exceeded 50% were added individually in CDM at pH 5.3, 5.7, and 6.7. It was demonstrated that only some of them could promote the growth of Bb12. Mixed nutrients that could promote the growth of Bb12 were added to three different CDM. In CDM at pH 5.3, 5.7, and 6.7, it was found that the viable cell count of Bb12 was the highest after adding mixed nutrients, which were 8.87, 9.02, and 9.10 log CFU ml-1, respectively.

CONCLUSIONS

The findings suggest that the initial pH of the culture medium affects the nutrient consumption patterns of Bb12. Specific nutrients can enhance the growth of Bb12 under acidic conditions and increase its acid resistance.

Ribosome profiling reveals the fine-tuned response of Escherichia coli to mild and severe acid stress

IMPORTANCE

Bacteria react very differently to survive in acidic environments, such as the human gastrointestinal tract. Escherichia coli is one of the extremely acid-resistant bacteria and has a variety of acid-defense mechanisms. Here, we provide the first genome-wide overview of the adaptations of E. coli K-12 to mild and severe acid stress at both the transcriptional and translational levels. Using ribosome profiling and RNA sequencing, we uncover novel adaptations to different degrees of acidity, including previously hidden stress-induced small proteins and novel key transcription factors for acid defense, and report mRNAs with pH-dependent differential translation efficiency. In addition, we distinguish between acid-specific adaptations and general stress response mechanisms using denoising autoencoders. This workflow represents a powerful approach that takes advantage of next-generation sequencing techniques and machine learning to systematically analyze bacterial stress responses.

EvgS/EvgA, the unorthodox two-component system regulating bacterial multiple resistance

IMPORTANCE

EvgS/EvgA, one of the five unorthodox two-component systems in Escherichia coli, plays an essential role in adjusting bacterial behaviors to adapt to the changing environment. Multiple resistance regulated by EvgS/EvgA endows bacteria to survive in adverse conditions such as acidic pH, multidrug, and heat. In this minireview, we summarize the specific structures and regulation mechanisms of EvgS/EvgA and its multiple resistance. By discussing several unresolved issues and proposing our speculations, this review will be helpful and enlightening for future directions about EvgS/EvgA.

Development of Mortars That Use Recycled Aggregates from a Sodium Silicate Process and the Influence of Graphene Oxide as a Nano-Addition

This research analyses how different cement mortars behave in terms of their physical and mechanical properties. Several components were necessary to make seven mixes of mortars, such as Portland cement, standard sand, and solid waste from a factory of sodium silicate, in addition to graphene oxide. Furthermore, graphene oxide (GO) was selected to reduce the micropores and increase the nanopores in the cement mortar. Hence, some tests were carried out to determine their density, humidity content, water absorption capacity, open void porosity, the alkali-silica reaction, as well as flexural and mechanical strength and acid resistance. Thus, standard-sand-manufactured mortars' mechanical properties were proved to be slightly better than those manufactured with recycled waste; the mortars with this recycled aggregate presented problems of alkali-silica reaction. In addition, GO (in a ratio GO/cement = 0.0003) performed as a filler, improving the mechanical properties (30%), alkali-silica (80%), and acid resistance.

Genome sequencing of 15 acid-tolerant yeasts

We report draft genome sequences for 15 non-conventional Saccharomycotina yeast strains obtained from public culture repositories. Included in our collection are eight strains of Pichia with broad tolerance to dicarboxylic acids. The genome sequences of these strains will enable comparative genomics of acid-tolerant phenotypes and strain engineering of non-conventional hosts.

Enhancement of the Acid Resistance of Silty Clay Using Nano-Magnesium Oxide

Hydrochloric acid is prevalent in numerous industries; leakage of this acid may cause persistent problems in the soil. The study aims to prevent any adverse impact of acid on the strength characteristics of silty clay soil by modifying the soil's acid resistance. In this study, unconfined compression tests are performed to investigate the strength of contaminated silty clay soil with concentrations of 4%, 8%, and 12% of HCl solution and the strength of treated soil with 0.4%, 0.5%, 0.6%, and 0.8% of nano-magnesium oxide. In addition, the strength of the soil enhanced with nano-MgO contaminated with different concentrations of hydrochloric acid was investigated to assess the effect of nano-MgO on modifying the acid resistance of clay soil. Moreover, the FE-SEM test was performed to analyze the microstructure of the soil under different circumstances. Based on the results, the strength of clay soil decreased due to contamination with the hydrochloric acid solutions; the reduction in strength was more noticeable when the acid solution became more acidic. Adding 0.6% of nano-magnesium oxide enhances the strength by about 114%. Findings show that adding 0.6% nano-MgO to the soil before exposing it to hydrochloric acid can enhance its acid resistance; the strength of the treated soil with nano-MgO was better at resisting the acid than the untreated soil.

Insight into the acid tolerance mechanism of Acetilactobacillus jinshanensis subsp. aerogenes Z-1

Several lactic acid bacteria (LAB) are double-edged swords in the production of Sichuan bran vinegar; on the one hand, they are important for the flavour of the vinegar, but on the other hand, they result in vinegar deterioration because of their gas-producing features and their acid resistance. These characteristics intensify the difficulty in managing the safe production of vinegar using strains such as Acetilactobacillus jinshanensis subsp. aerogenes Z-1. Therefore, it is necessary to characterize the mechanisms underlying their acid tolerance. The results of this study showed a survival rate of 77.2% for Z-1 when exposed to pH 3.0 stress for 1 h. This strain could survive for approximately 15 days in a vinegar solution with 4% or 6% total acid content, and its growth was effectively enhanced by the addition of 10 mM of arginine (Arg). Under acidic stress, the relative content of the unsaturated fatty acid C18:1 (n-11) increased, and eight amino acids accumulated in the cells. Meanwhile, based on a transcriptome analysis, the genes glnA, carA/B, arcA, murE/F/G, fabD/H/G, DnaK, uvrA, opuA/C, fliy, ecfA2, dnaA and LuxS, mainly enriched in amino acid transport and metabolism, protein folding, DNA repair, and cell wall/membrane metabolism processes, were hypothesized to be acid resistance-related genes in Z-1. This work paves the way for further clarifying the acid tolerance mechanism of Z-1 and shares applicable perspectives for vinegar brewing.

Expanded roles of lactate-sensing LldR in transcription regulation of the Escherichia coli K-12 genome: lactate utilisation and acid resistance

LldR is a lactate-responsive transcription factor (TF) that transcriptionally regulates the lldPRD operon consisting of lactate permease and lactate dehydrogenase. The lldPRD operon facilitates the utilisation of lactic acid in bacteria. However, the role of LldR in whole genomic transcriptional regulation, and the mechanism involved in adaptation to lactate remains unclear. We used genomic SELEX (gSELEX) to comprehensively analyse the genomic regulatory network of LldR to understand the overall regulatory mechanism of lactic acid adaptation of the model intestinal bacterium Escherichia coli. In addition to the involvement of the lldPRD operon in utilising lactate as a carbon source, genes related to glutamate-dependent acid resistance and altering the composition of membrane lipids were identified as novel targets of LldR. A series of in vitro and in vivo regulatory analyses led to the identification of LldR as an activator of these genes. Furthermore, the results of lactic acid tolerance tests and co-culture experiments with lactic acid bacteria suggested that LldR plays a significant role in adapting to the acid stress induced by lactic acid. Therefore, we propose that LldR is an l-/d-lactate sensing TF for utilising lactate as a carbon source and for resistance to lactate-induced acid stress in intestinal bacteria.

ClC Chloride Channels in Gram-Negative Bacteria and Its Role in the Acid Resistance Systems

Pathogenic bacteria that colonize the human intestinal tract have evolved strategies to overcome acidic conditions when they pass through the gastrointestinal tract. Amino acid-mediated acid resistance systems are effective survival strategies in a stomach that is full of amino acid substrate. The amino acid antiporter, amino acid decarboxylase, and ClC chloride antiporter are all engaged in these systems, and each one plays a role in protecting against or adapting to the acidic environment. The ClC chloride antiporter, a member of the ClC channel family, eliminates negatively charged intracellular chloride ions to avoid inner membrane hyperpolarization as an electrical shunt of the acid resistance system. In this review, we will discuss the structure and function of the prokaryotic ClC chloride antiporter of amino acid-mediated acid resistance system.

Influencing Factors of Sulfuric Acid Resistance of Ca-Rich Alkali-Activated Materials

In this paper, we distinguished the degradation of alkali-activated material (AAM) exposed to sulfuric acid as physical (scaling, spalling, cracking, breaking, etc.) and chemical degradation (neutralization), because the mechanisms of these two types of degradation are different. Then, the effects of curing method, raw materials, and their mixing proportions on the two kinds of degradation of AAMs containing GGBFS were investigated in detail, including liquid-filler ratio, component of alkali activator, chemical admixture, inactive filler alternative to fly ash (FA), addition of municipal waste incineration bottom ash (BA), etc. The experimental results show that (a) small liquid-filler ratio, heat-curing, and the use of blended alkali activator solution of sodium silicate and NaOH can reduce both physical and chemical degradation of AAMs; (b) large GGBFS content or AE agent addition decreases the physical degradation, but increases the chemical degradation; (c) using crushed stone powder to replace FA and adding BA or a retarder would increase the physical and chemical degradation; but (d) the use of drying shrinkage reducer composed of polyether derivatives does not affect acid resistance. We also discussed the applicability and limitation of XRD and SEM-EDS in analyzing the chemical compositions of Ca-rich AAMs exposed to sulfuric acid, and found that (e) XRD analysis can identify the gypsum formation, and the gypsum peak intensity is related to the physical degradation of the Ca-rich AAMs; (f) by SEM-EDS analysis, the decalcification and dealkalization of C-A-S-H gels can be judged from the decrease in the average Ca/Si atomic ratio and the average Na atomic percentage in the acid corrosion area, but dealumination can be only determined from the dissimilarity of Al and Si elemental maps; and (g) if the CaO/SO₃ molar ratio ranges from 0.8 to 1.0, gypsum formation can be estimated.

Disruption of the sensor kinase phoQ gene decreases acid resistance in plant growth-promoting rhizobacterium Rahnella aquatilis HX2

AIMS

Rahnella aquatilis HX2, a promising plant growth-promoting rhizobacterium (PGPR) in the field, contains genes homologous to the PhoP/PhoQ two-component regulatory system. Although this system regulates stress response in numerous pathogens, PhoP/PhoQ characterization in a PGPR has not received in-depth exploration.

METHODS AND RESULTS

The phoQ gene was mutated in strain HX2 using an in-frame deletion strategy. Compared to the wild type, the phoQ mutant exhibited increased sensitivity to acidic conditions (pH 4.0) in a chemically defined medium and in mild acidic natural soil (pH 5.7). The phoQ mutant also exhibited increased swimming motility under acidic conditions. Acid resistance was restored in the mutant by introducing the phoQ gene on a plasmid. Three acid resistance genes, add, cfa, and fur were downregulated significantly, whereas the chaperone encoding gene, dnak, was upregulated when the phoQ mutant was exposed to acid stress.

CONCLUSIONS

This study suggested that the PhoP/PhoQ system positively regulates the acid resistance of R. aquatilis HX2.

Corrigendum: Compositional quality and potential gastrointestinal behavior of probiotic products commercialized in Italy

[This corrects the article DOI: 10.3389/fmed.2018.00059.].

Improvement in Acid Resistance of Polyimide Membranes: A Sustainable Cross-Linking Approach via Green-Solvent-Based Fenton Reaction

In this study, we present a facile surface modification method using green solvents for a commercial polyimide (PI) nanofiltration membrane to exhibit good acid stability. To enhance acid stability, the PI organic solvent nanofiltration membrane was modified using Fenton's reaction, an oxidative cross-linking process, using environmentally friendly solvents: water and ethanol. The surface properties of the pristine and modified PI membranes were investigated and compared using various analytical tools. We studied the surface morphology using scanning electron microscopy, performed elemental analysis using X-ray photoelectron spectroscopy, investigated chemical bonds using attenuated total reflectance-Fourier transform infrared spectroscopy, and studied thermal stability using thermogravimetric analysis. The acid resistances of the pristine and modified membranes were confirmed through performance tests. The pristine PI nanofiltration membrane exposed to a 50 w/v% sulfuric acid for 4 h showed an increase in the normalized water flux to 205% and a decrease in the MgSO₄ normalized rejection to 44%, revealing damage to the membrane. The membrane modified by the Fenton reaction exhibited a decline in flux and improved rejection, which are typical performance changes after surface modification. However, the Fenton-modified membrane exposed to 50 w/v% sulfuric acid for 4 h showed a flux increase of 7% and a rejection increase of 4%, indicating improved acid resistance. Furthermore, the Fenton post-treatment enhanced the thermal stability and organic solvent resistance of the PI membrane. This study shows that the acid resistance of PI membranes can be successfully improved by a novel and facile Fenton reaction using green solvents.

Synthesis, Photochemistry, Computational Study and Potential Application of New Styryl-Thiophene and Naphtho-Thiophene Benzylamines

In this research, the synthesis, photochemistry, and computational study of new cis- and trans-isomers of amino-thienostilbenes is performed to test the efficiency of their production and acid resistance, and to investigate their electronic structure, photoreactivity, photophysical characteristics, and potential biological activity. The electronic structure and conformations of synthesized thienostilbene amines and their photocyclization products are examined computationally, along with molecular modeling of amines possessing two thiophene rings that showed inhibitory potential toward cholinesterases. New amino-styryl thiophenes, with favorable photophysical properties and proven acid resistance, represent model compounds for their water-soluble ammonium salts as potential styryl optical dyes. The comparison with organic dyes possessing a trans-aminostilbene subunit as the scaffold shows that the newly synthesized trans-aminostilbenes have very similar absorbance wavelengths. Furthermore, their functionalized cis-isomers and photocyclization products are good candidates for cholinesterase inhibitors because of the structural similarity of the molecular skeleton to some already proven bioactive derivatives.

Engineering of Acid-Resistant d-Allulose 3-Epimerase for Functional Juice Production

d-Allulose, a rare sugar and functional sweetener, can be biosynthesized by d-allulose 3-isomerase (DAE). However, most of the reported DAEs exhibit poor resistance under acidic conditions, which severely limited their application. Here, surface charge engineering and random mutagenesis were used to construct a mutant library of CcDAE from Clostridium cellulolyticum H10, combined with high-throughput screening to identify mutants with high activity and resistance under acidic conditions. The mutant M3 (I114R/K123E/H209R) exhibited high activity (3.36-fold of wild-type) and acid resistance (10.6-fold of wild-type) at pH 4.5. The structure-function relationship was further analyzed by molecular dynamics (MD) simulations, which indicated that M3 had a higher number of hydrogen bonds and negative surface charges than the wild type. A multienzyme cascade system including M3 was used to convert high-calorie sugars in acidic juices, and functional juices containing 7.8-15.4 g/L d-allulose were obtained. Our study broadens the manufacture of functional foods containing d-allulose.

Heterogeneity and Evolutionary Tunability of Escherichia coli Resistance against Extreme Acid Stress

Since acidic environments often serve as an important line of defense against bacterial pathogens, it is important to fully understand how the latter manage to mount and evolve acid resistance mechanisms. Escherichia coli, a species harboring many pathovars, is typically equipped with the acid fitness island (AFI), a genomic region encoding the GadE master regulator together with several GadE-controlled functions to counter acid stress. This study reveals that gadE and consequently AFI functions are heterogeneously expressed even in the absence of any prior acid stress, thereby preemptively creating acid-resistant subpopulations within a clonal E. coli population. Directed evolution efforts selecting for modulated gadE expression confirm that a gain-of-function mutation in the EvgS sensor kinase can constitutively upregulate gadE expression and concomitant acid resistance. However, we reveal that such upregulation of EvgS also causes cross-resistance to heat stress because of SafA-mediated cross-activation of the PhoPQ regulon. Surprisingly, loss of function of the serC gene (encoding phosphoserine/phosphohydroxythreonine aminotransferase) can also significantly upregulate gadE expression, acid resistance, and heat cross-resistance, although via a currently cryptic mechanism. As such, our data reveal a noisy expression of gadE in E. coli that is functional for the survival of sudden acid stress and that can readily be genetically tuned. IMPORTANCE Acidic environments constitute one of the most important stresses for enteric bacteria and can be encountered in both natural (e.g., host gastrointestinal tract) and manmade (e.g., food processing) environments. The enteric species Escherichia coli harbors many pathovars and is well known for its ability to cope with acid stress. In this study, we uncover that E. coli's acid fitness island (AFI), a genomic region that encodes important functions to deal with acid stress, is by default expressed in a heterogeneous manner. In fact, using microfluidics-based single-cell approaches, we further demonstrate that this heterogeneity preemptively creates a clonal subpopulation that is much better equipped to survive a sudden acid shock. In addition, we reveal that environments with recurring acid stress can readily select for mutants displaying a higher fraction of AFI-expressing cells. These new insights are important to properly understand and anticipate the survival characteristics of E. coli.

The Role of Regulator Catabolite Control Protein A (CcpA) in Streptococcus agalactiae Physiology and Stress Response

Streptococcus agalactiae is a leading cause of infections in neonates. This opportunistic pathogen colonizes the vagina, where it has to cope with acidic pH and hydrogen peroxide produced by lactobacilli. Thus, in the host, this bacterium possesses numerous adaptation mechanisms in which the pleiotropic regulators play a major role. The transcriptional regulator CcpA (catabolite control protein A) has previously been shown to be the major regulator involved in carbon catabolite repression in Gram-positive bacteria but is also involved in other functions. By transcriptomic analysis, we characterized the CcpA-dependent gene regulation in S. agalactiae. Approximately 13.5% of the genome of S. agalactiae depends on CcpA for regulation and comprises genes involved in sugar uptake and fermentation, confirming the role of CcpA in carbon metabolism. We confirmed by electrophoretic mobility shift assays (EMSAs) that the DNA binding site called cis-acting catabolite responsive element (cre) determined for other streptococci was effective in S. agalactiae. We also showed that CcpA is of capital importance for survival under acidic and oxidative stresses and is implicated in macrophage survival by regulating several genes putatively or already described as involved in stress response. Among them, we focused our study on SAK_1689, which codes a putative UspA protein. We demonstrated that SAK_1689, highly downregulated by CcpA, is overexpressed under oxidative stress conditions, this overexpression being harmful for the bacterium in a ΔccpA mutant. IMPORTANCE Streptococcus agalactiae is a major cause of disease burden leading to morbidity and mortality in neonates worldwide. Deciphering its adaptation mechanisms is essential to understand how this bacterium manages to colonize its host. Here, we determined the regulon of the pleiotropic regulator CcpA in S. agalactiae. Our findings reveal that CcpA is not only involved in carbon catabolite repression, but is also important for acidic and oxidative stress resistance and survival in macrophages.

Commercially Available Enteric Empty Hard Capsules, Production Technology and Application

Currently, there is a growing need to prepare small batches of enteric capsules for individual therapy or clinical evaluation since many acidic-sensitive substances should be protected from the stomach's acidic environment, including probiotics or fecal material, in the fecal microbiota transplantation (FMT) process. A suitable method seems to be the encapsulation of drugs or lyophilized alternatively frozen biological suspensions in commercial hard enteric capsules prepared by so-called Enteric Capsule Drug Delivery Technology (ECDDT). Manufacturers supply these types of capsules, made from pH-soluble polymers, in products such as AR Caps®, EnTRinsicTM, and Vcaps® Enteric, or capsules made of gelling polymers that release their content as the gel erodes over time when passing through the digestive tract. These include DRcaps®, EMBO CAPS® AP, BioVXR®, or ACGcaps™ HD. Although not all capsules in all formulations meet pharmaceutical requirements for delayed-release dosage forms in disintegration and dissolution tests, they usually find practical application. This literature review presents their composition and properties. Since ECDDT is a new technology, this article is based on a limited number of references.

Lactic Acid Resistance and Population Structure of Escherichia coli from Meat Processing Environment

To explore the effect of beef processing on Escherichia coli populations in relation to lactic acid resistance, this study investigated the links among acid response, phylogenetic structure, genome diversity, and genotypes associated with acid resistance of meat plant E. coli. Generic E. coli isolates (n = 700) were from carcasses, fabrication equipment, and beef products. Acid treatment was carried out in Luria-Bertani broth containing 5.5% lactic acid (pH 2.9). Log reductions of E. coli ranged from <0.5 to >5 log CFU/mL (median: 1.37 log). No difference in lactic acid resistance was observed between E. coli populations recovered before and after a processing step or antimicrobial interventions. E. coli from the preintervention carcasses were slightly more resistant than E. coli isolated from equipment, differing by <0.5 log unit. Acid-resistant E. coli (log reduction <1, n = 45) had a higher prevalence of genes related to energy metabolism (ydj, xap, ato) and oxidative stress (fec, ymjC) than the less resistant E. coli (log reduction >1, n = 133). The ydj and ato operons were abundant in E. coli from preintervention carcasses. In contrast, fec genes were abundant in E. coli from equipment surfaces. The preintervention E. coli contained phylogroups A and B1 in relatively equal proportions. Phylogroup B1 predominated (95%) in the population from equipment. Of note, E. coli collected after sanitation shared either the antigens of O8 or H21. Additionally, genome diversity decreased after chilling and equipment sanitation. Overall, beef processing did not select for E. coli resistant to lactic acid but shaped the population structure. IMPORTANCE Antimicrobial interventions have significantly reduced the microbial loads on carcasses/meat products; however, the wide use of chemical and physical biocides has raised concerns over their potential for selecting resistant populations in the beef processing environment. Phenotyping of acid resistance and whole-genome analysis described in this study demonstrated beef processing practices led to differences in acid resistance, genotype, and population structure between carcass- and equipment-associated E. coli but did not select for the acid-resistant population. Results indicate that genes coding for the metabolism of long-chain sugar acids (ydj) and short-chain fatty acids (ato) were more prevalent in carcass-associated than equipment-associated E. coli. These results suggest E. coli from carcasses and equipment surfaces have been exposed to different selective pressures. The findings improve our understanding of the microbial ecology of E. coli in food processing environments and in general.

Review of Escherichia coli O157:H7 Prevalence, Pathogenicity, Heavy Metal and Antimicrobial Resistance, African Perspective

Escherichia coli O157:H7 is an important food-borne and water-borne pathogen that causes hemorrhagic colitis and the hemolytic-uremic syndrome in humans and may cause serious morbidity and large outbreaks worldwide. People with bloody diarrhea have an increased risk of developing serious complications such as acute renal failure and neurological damage. The hemolytic-uremic syndrome (HUS) is a serious condition, and up to 50% of HUS patients can develop long-term renal dysfunction or blood pressure-related complications. Children aged two to six years have an increased risk of developing HUS. Clinical enteropathogenic Escherichia coli (EPEC) infections show fever, vomiting, and diarrhea. The EPEC reservoir is unknown but is suggested to be an asymptomatic or symptomatic child or an asymptomatic adult carrier. Spreading is often through the fecal-oral route. The prevalence of EPEC in infants is low, and EPEC is highly contagious in children. EPEC disease in children tends to be clinically more severe than other diarrheal infections. Some children experience persistent diarrhea that lasts for more than 14 days. Enterotoxigenic Escherichia coli (ETEC) strains are a compelling cause of the problem of diarrheal disease. ETEC strains are a global concern as the bacteria are the leading cause of acute watery diarrhea in children and the leading cause of traveler’s diarrhea. It is contagious to children and can cause chronic diarrhea that can affect the development and well-being of children. Infections with diarrheagenic E. coli are more common in African countries. Antimicrobial agents should be avoided in the acute phase of the disease since studies showed that antimicrobial agents may increase the risk of HUS in children. The South African National Veterinary Surveillance and Monitoring Programme for Resistance to Antimicrobial Drugs has reported increased antimicrobial resistance in E. coli. Pathogenic bacterial strains have developed resistance to a variety of antimicrobial agents due to antimicrobial misuse. The induced heavy metal tolerance may also enhance antimicrobial resistance. The prevalence of antimicrobial resistance depends on the type of the antimicrobial agent, bacterial strain, dose, time, and mode of administration. Developing countries are severely affected by increased resistance to antimicrobial agents due to poverty, lack of proper hygiene, and clean water, which can lead to bacterial infections with limited treatment options due to resistance.

Integrated AlphaFold2 and DEER investigation of the conformational dynamics of a pH-dependent APC antiporter

The Amino Acid-Polyamine-Organocation (APC) transporter GadC contributes to the survival of pathogenic bacteria under extreme acid stress by exchanging extracellular glutamate for intracellular γ-aminobutyric acid (GABA). Its structure, determined in an inward-facing conformation at alkaline pH, consists of the canonical LeuT-fold with a conserved five-helix inverted repeat, thereby resembling functionally divergent transporters such as the serotonin transporter SERT and the glucose-sodium symporter SGLT1. However, despite this structural similarity, it is unclear if the conformational dynamics of antiporters such as GadC follow the blueprint of these or other LeuT-fold transporters. Here, we used double electron-electron resonance (DEER) spectroscopy to monitor the conformational dynamics of GadC in lipid bilayers in response to acidification and substrate binding. To guide experimental design and facilitate the interpretation of the DEER data, we generated an ensemble of structural models in multiple conformations using a recently introduced modification of AlphaFold2 . Our experimental results reveal acid-induced conformational changes that dislodge the Cterminus from the permeation pathway coupled with rearrangement of helices that enables isomerization between inward- and outward-facing states. The substrate glutamate, but not GABA, modulates the dynamics of an extracellular thin gate without shifting the equilibrium between inward- and outward-facing conformations. In addition to introducing an integrated methodology for probing transporter conformational dynamics, the congruence of the DEER data with patterns of structural rearrangements deduced from ensembles of AlphaFold2 models illuminates the conformational cycle of GadC underpinning transport and exposes yet another example of the divergence between the dynamics of different families in the LeuT-fold.

Mycobacterial Response to Acidic Environment: Protective Mechanisms

Given the emergence and spread of multidrug-resistant and extensively drug-resistant strains of Mycobacterium tuberculosis (Mtb), the world faces the urgency of new drugs to combat tuberculosis (TB). Understanding the biochemical/physiological processes enabling Mtb to survive the stressful environment within macrophages and acquire tolerance, resistance and persistence against the stresses are the key to developing new approaches to tackle this health problem. As Mtb gains entry into the respiratory tract and is engulfed by macrophages, lowering pH acts as a primary defence of phagosomes within macrophages and also in the centres of caseating granulomas. It becomes essential for the pathogen to maintain pH homeostasis for survival in these conditions. Acid resistance mechanisms are well known and extensively studied in other bacteria such as Escherichia coli, Lactobacillus spp., Brucella spp., Helicobacter pylori and Listeria monocytogenes. However, in the case of Mtb, acid tolerance and resistance mechanisms still need to be explored in detail. This review targets to provide the current understanding of underlying mechanisms involved in countering low pH faced by Mtb as the acid resistance/tolerance mechanisms contribute to the pathogenesis of the disease.

Cooperative Interaction between Acid and Copper Resistance in Escherichia coli

The persistence of pathogenic Escherichia coli under acidic conditions poses a serious risk to food safety, especially in acidic foods such as kimchi. To identify the bacterial factors required for acid resistance, transcriptomic analysis was conducted on an acid-resistant enterotoxigenic E. coli strain and the genes with significant changes in their expression under acidic pH were selected as putative resistance factors against acid stress. These genes included those associated with a glutamatedependent acid resistance (GDAR) system and copper resistance. E. coli strains lacking GadA, GadB, or YbaST, the components of the GDAR system, exhibited significantly attenuated growth and survival under acidic stress conditions. Accordantly, the inhibition of the GDAR system by 3-mercaptopropionic acid and aminooxyacetic acid abolished bacterial adaptation and survival under acidic conditions, indicating the indispensable role of a GDAR system in acid resistance. Intriguingly, the lack of cueR encoding a transcriptional regulator for copper resistance genes markedly impaired bacterial resistance to acid stress as well as copper. Conversely, the absence of YbaST severely compromised bacterial resistance against copper, suggesting an interplay between acid and copper resistance. These results suggest that a GDAR system can be a promising target for developing control measures to prevent E. coli resistance to acid and copper treatments.

Mechanical and Durability Analysis of Fly Ash Based Geopolymer with Various Compositions for Rigid Pavement Applications

Ordinary Portland cement (OPC) is a conventional material used to construct rigid pavement that emits large amounts of carbon dioxide (CO₂) during its manufacturing process, which is bad for the environment. It is also claimed that OPC is susceptible to acid attack, which increases the maintenance cost of rigid pavement. Therefore, a fly ash based geopolymer is proposed as a material for rigid pavement application as it releases lesser amounts of CO₂ during the synthesis process and has higher acid resistance compared to OPC. This current study optimizes the formulation to produce fly ash based geopolymer with the highest compressive strength. In addition, the durability of fly ash based geopolymer concrete and OPC concrete in an acidic environment is also determined and compared. The results show that the optimum value of sodium hydroxide concentration, the ratio of sodium silicate to sodium hydroxide, and the ratio of solid-to-liquid for fly ash based geopolymer are 10 M, 2.0, and 2.5, respectively, with a maximum compressive strength of 47 MPa. The results also highlight that the durability of fly ash based geopolymer is higher than that of OPC concrete, indicating that fly ash based geopolymer is a better material for rigid pavement applications, with a percentage of compressive strength loss of 7.38% to 21.94% for OPC concrete. This current study contributes to the field of knowledge by providing a reference for future development of fly ash based geopolymer for rigid pavement applications.

The Identity of the Constriction Region of the Ribosomal Exit Tunnel Is Important to Maintain Gene Expression in Escherichia coli

Mutational changes in bacterial ribosomes often affect gene expression and consequently cellular fitness. Understanding how mutant ribosomes disrupt global gene expression is critical to determining key genetic factors that affect bacterial survival. Here, we describe gene expression and phenotypic changes presented in Escherichia coli cells carrying an uL22(K90D) mutant ribosomal protein, which displayed alterations during growth. Ribosome profiling analyses revealed reduced expression of operons involved in catabolism, indole production, and lysine-dependent acid resistance. In general, translation initiation of proximal genes in several of these affected operons was substantially reduced. These reductions in expression were accompanied by increases in the expression of acid-induced membrane proteins and chaperones, the glutamate-decarboxylase regulon, and the autoinducer-2 metabolic regulon. In agreement with these changes, uL22(K90D) mutant cells had higher glutamate decarboxylase activity, survived better in extremely acidic conditions, and generated more biofilm in static cultures compared to their parental strain. Our work demonstrates that a single mutation in a non-conserved residue of a ribosomal protein affects a substantial number of genes to alter pH resistance and the formation of biofilms. IMPORTANCE All newly synthesized proteins must pass through a channel in the ribosome named the exit tunnel before emerging into the cytoplasm, membrane, and other compartments. The structural characteristics of the tunnel could govern protein folding and gene expression in a species-specific manner but how the identity of tunnel elements influences gene expression is less well-understood. Our global transcriptomics and translatome profiling demonstrate that a single substitution in a non-conserved amino acid of the E. coli tunnel protein uL22 has a profound impact on catabolism, cellular signaling, and acid resistance systems. Consequently, cells bearing the uL22 mutant ribosomes had an increased ability to survive acidic conditions and form biofilms. This work reveals a previously unrecognized link between tunnel identity and bacterial stress adaptation involving pH response and biofilm formation.

Durability of Cellulosic-Fiber-Reinforced Geopolymers: A Review

Geopolymers have high early strength, fast hardening speed and wide sources of raw materials, and have good durability properties such as high temperature resistance and corrosion resistance. On the other hand, there are abundant sources of plant or cellulose fibers, and it has the advantages of having a low cost, a light weight, strong adhesion and biodegradability. In this context, the geopolymer sector is considering cellulose fibers as a sustainable reinforcement for developing composites. Cellulosic-fiber-reinforced geopolymer composites have broad development prospects. This paper presents a review of the literature research on the durability of cellulosic-fiber-reinforced geopolymer composites in recent years. In this paper, the typical properties of cellulose fibers are summarized, and the polymerization mechanism of geopolymers is briefly discussed. The factors influencing the durability of cellulosic-fiber-reinforced geopolymer composites were summarized and analyzed, including the degradation of fibers in a geopolymer matrix, the toughness of fiber against matrix cracking, the acid resistance, and resistance to chloride ion penetration, high temperature resistance, etc. Finally, the influence of nanomaterials on the properties of geopolymer composites and the chemical modification of fibers are analyzed, and the research on cellulosic-fiber-reinforced geopolymer composites is summarized.

Transcriptomic and Metabolomic Profiling Reveals That KguR Broadly Impacts the Physiology of Uropathogenic Escherichia coli Under in vivo Relevant Conditions

Urinary tract infections are primarily caused by uropathogenic Escherichia coli (UPEC). In contrast to the intestinal E. coli strains that reside in nutrient-rich gut environment, UPEC encounter distinct niches, for instance human urine, which is an oxygen- and nutrient-limited environment. Alpha-ketoglutarate (KG) is an abundant metabolite in renal proximal tubule cells; and previously we showed that two-component signaling system (TCS) KguS/KguR contributes to UPEC colonization of murine urinary tract by promoting the utilization of KG as a carbon source under anaerobic conditions. However, knowledge about the KguR regulon and its impact on UPEC fitness is lacking. In this work, we analyzed transcriptomic and metabolomic changes caused by kguR deletion under anaerobiosis when KG is present. Our results indicated that 620 genes were differentially expressed in the ΔkguR mutant, as compared to the wild type; of these genes, 513 genes were downregulated and 107 genes were upregulated. Genes with substantial changes in expression involve KG utilization, acid resistance, iron uptake, amino acid metabolism, capsule biosynthesis, sulfur metabolism, among others. In line with the transcriptomics data, several amino acids (glutamate, lysine, etc.) and uridine 5′-diphosphogalactose (involved in capsule biosynthesis) were significantly less abundant in the ΔkguR mutant. We then confirmed that the ΔkguR mutant, indeed, was more sensitive to acid stress than the wild type, presumably due to downregulation of genes belonging to the glutamate-dependent acid resistance system. Furthermore, using gene expression and electrophoretic mobility shift assays (EMSAs), we demonstrate that KguR autoregulates its own expression by binding to the kguSR promoter region. Lastly, we performed a genome-wide search of KguR binding sites, and this search yielded an output of at least 22 potential binding sites. Taken together, our data establish that in the presence of KG, KguR broadly impacts the physiology of UPEC under anaerobiosis. These findings greatly further our understanding of KguS/KguR system as well as UPEC pathobiology.

Solar-to-Pharmaceutical Raw Material Production: Photoelectrochemical Naphthoquinone Formation Using Stabilized BiVO4 Photoanodes in Acid Media

In the quest for efficient use of solar energy to produce high-value-added chemicals, we first achieved the photoelectrochemical (PEC) diketonization of naphthalene, using a BiVO₄/WO₃ photoanode, to obtain naphthoquinone, an important pharmaceutical raw material with excellent efficiency by solar energy conversion. In the electrochemical (EC) reaction using F-doped SnO₂ (FTO) substrates and a 0.5 M H₂SO₄ H₂O-acetone (60 vol %) mixed solution containing 5 mM naphthalene, we produced a small amount of naphthoquinone evolution in the dark. However, naphthoquinone (η_NQ)'s Faradic efficiency and its evolution rate at 1.7 V_Ag/AgCl were only 28.5% and 0.48 μmol·cm^-2·h^-1, respectively. The PEC reaction using a WO₃ photoanode had very low efficiency for naphthalene diketonization, with low η_NQ and evolution rate values at 1.1 V_Ag/AgCl of 0.3% and 0.039 μmol·cm^-2·h^-1, respectively. In contrast, the BiVO₄/WO₃ photoanode strongly enhanced the PEC reaction, and the η_NQ and evolution rates at 1.1 V_Ag/AgCl were boosted up to 37.5% and 4.7 μmol·cm^-2·h^-1, respectively. The evolution rate of the PEC reaction in the BiVO₄/WO₃ photoanode was 10 times higher than that of the EC reaction with the FTO substrate regardless of the very low bias voltage. This result suggests that the BiVO₄-based photoanode was very efficient for the selective oxidation of naphthalene even in acid media because of the acetone-mixed electrolyte's anti-photocorrosion effect and the multilayering of WO₃ and BiVO₄. At a naphthalene concentration of 20 mM, the naphthoquinone evolution rate reached its maximum value of 7.1 μmol·cm^-2·h^-1. Although η_NQ tended to decrease with the increase in the electric charge, it reached 100% at a low bias voltage of 0.7 V_Ag/AgCl. An intensity-modulated photocurrent spectroscopy analysis indicated the rate constant of charge transfer at the photoanode surface to the naphthalene molecules was strongly enhanced at a low bias voltage of 0.7-1.1 V_Ag/AgCl, resulting in the high η_NQ value. The acid-resistant BiVO₄/WO₃ photoanode functioned in acetone-mixed electrolytes enabled the realization of a new PEC oxidation reaction driven by solar energy to produce high-value-added pharmaceutical raw materials.

Effects of Steel Fibers (SF) and Ground Granulated Blast Furnace Slag (GGBS) on Recycled Aggregate Concrete

Recycled aggregate is a good option to be used in concrete production as a coarse aggregate that results in environmental benefits as well as sustainable development. However, recycled aggregate causes a reduction in the mechanical and durability performance of concrete. On the other hand, the removal of industrial waste would be considerably decreased if it could be incorporated into concrete production. One of these possibilities is the substitution of the cement by slag, which enhances the concrete poor properties of recycled aggregate concrete as well as provides a decrease in cement consumption, reducing carbon dioxide production, while resolving a waste management challenge. Furthermore, steel fiber was also added to enhance the tensile capacity of recycled aggregate concrete. The main goal of this study was to investigate the characteristics of concrete using ground granulated blast-furnace slag (GGBS) as a binding material on recycled aggregate fibers reinforced concrete (RAFRC). Mechanical performance was assessed through compressive strength and split tensile strength, while durability aspects were studied through water absorption, acid resistance, and dry shrinkage. The results detected from the different experiments depict that, at an optimum dose (40% RCA, 20%GGBS, and 2.0%), compressive and split tensile strength were 39% and 120% more than the reference concrete, respectively. Furthermore, acid resistance at the optimum dose was 36% more than the reference concrete. Furthermore, decreased water absorption and dry shrinkage cracks were observed with the substitution of GGBS into RAFRC.

Acid-Tolerant Sulfate Tetrahedral Cages from Anion-Coordination-Driven Assembly

Supramolecular cages have been constructed by anion-coordination-driven assembly (ACDA) in recent years and have shown unique host-guest interactions. However, most of the reported cages are made of the phosphate ion (PO₄ ^3- ); other anions have rarely been explored. Here we show for the first time that the sulfate ion (SO₄ ^2- ) is also able to form the A₄ L₄ tetrahedral motif with tris-bis(urea) ligands, but this is dependent on the stoichiometry of the sulfate ion (in solution). Notably, the sulfate cages display enhanced resistance for both Brønsted (pH as low as 4.3 in acetone containing 15 % water) and Lewis acids (metal complexes) compared to the corresponding phosphate cages, and thus could find applications where an acidic (proton or metals) environment is required.

Characterization of a Novel Glutamine Synthetase From Trichinella spiralis and Its Participation in Larval Acid Resistance, Molting, and Development

Trichinella spiralis is a major foodborne parasite worldwide. After the encapsulated muscle larvae (ML) in meat are ingested, the ML are liberated in the stomach of the host and activated into intestinal infectious larvae (IIL), which develop into adult worm after molting four times. A novel glutamine synthetase (TsGS) was identified from T. spiralis IIL at 10 h post-infection, but its biological role in T. spiralis life cycle is not clear. The aim of this study was to investigate the biological characteristics of TsGS and its functions in larval acid resistance, molting, and development. TsGS has a glutamine synthetase (GS) catalytic domain. Complete TsGS sequence was cloned and expressed in Escherichia coli BL21. rTsGS has good immunogenicity. qPCR and Western blotting showed that TsGS was highly expressed at IIL stage, and immunofluorescence revealed that TsGS was principally localized at the cuticle and intrauterine embryos of this nematode. rTsGS has enzymatic activity of natural GS to hydrolyze the substrate (Glu, ATP, and NH₄⁺). Silencing of TsGS gene significantly reduced the IIL survival at pH 2.5, decreased the IIL burden, and impeded larval molting and development. The results demonstrated that TsGS participates in T. spiralis larval acid resistance, molting and development, and it might be a candidate vaccine target against Trichinella molting and development.

Durability Properties of Ultra-High Performance Lightweight Concrete (UHPLC) with Expanded Glass

It is important to ensure the durability and safety of structures. In the case of newly developed materials that are outside the current rules, it is important to investigate all aspects of structural safety. The material studied in the following is a structural lightweight concrete with an ultra-high-performance matrix and expanded glass as a lightweight aggregate. The material, with a compressive strength of 60-100 MPa and a bulk density of 1.5-1.9 kg/dm³, showed high capillary porosities of 12 vol% (ultra-high-performance concretes (UHPC) < 5 vol%). Since the capillary porosity basically enables transport processes into the concrete, the material had to be examined more closely from the aspect of durability. Freeze-thaw resistance (68 g/m²) and chemical attack with sulfate at pH 3.5 for 12 weeks (16 g/m²) showed no increase in concrete corrosion. Targeted carbonation (0.53 mm/year^0.5) and chloride penetration resistance (6.0 × 10^-13 to 12.6 × 10^-13 m²/s) also showed good results against reinforcement corrosion. The results show that most of the measured capillary pores resulted from the lightweight aggregate and were not all present as a pore system. Thus, the durability was only slightly affected and the concrete can be compared to an UHPC. Only the abrasion resistance showed an increased value (22,000 mm³/5000 mm²), which, however, only matters if the material is used as a screed.

Transcriptome Analysis of Komagataeibacter europaeus CGMCC 20445 Responses to Different Acidity Levels During Acetic Acid Fermentation

In the industrial production of high-acidity vinegar, the initial ethanol and acetic acid concentrations are limiting factors that will affect acetic acid fermentation. In this study, Komagataeibacter europaeus CGMCC 20445 was used for acetic acid shake flask fermentation at an initial ethanol concentration of 4.3% (v/v). We conducted transcriptome analysis of K. europaeus CGMCC 20445 samples under different acidity conditions to elucidate the changes in differentially expressed genes throughout the fermentation process. We also analyzed the expression of genes associated with acid-resistance mechanisms. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that the differentially expressed genes were enriched in ribosomes, citrate cycle, butanoate metabolism, oxidative phosphorylation, pentose phosphate, and the fatty acid biosynthetic pathways. In addition, this study found that K. europaeus CGMCC 20445 regulates the gene expression levels of cell envelope proteins and stress-responsive proteins to adapt to the gradual increase in acidity during acetic acid fermentation. This study improved the understanding of the acid resistance mechanism of K. europaeus and provided relevant reference information for the further genetic engineering of this bacterium.

Acid resistance system CadBA is implicated in acid tolerance and biofilm formation and is identified as a new virulence factor of Edwardsiella tarda

Edwardsiella tarda is a facultative intracellular pathogen in humans and animals. The Gram-negative bacterium is widely considered a potentially important bacterial pathogen. Adaptation to acid stress is important for the transmission of intestinal microbes, so the acid-resistance (AR) system is essential. However, the AR systems of E. tarda are totally unknown. In this study, a lysine-dependent acid resistance (LDAR) system in E. tarda, CadBA, was characterized and identified. CadB is a membrane protein and shares high homology with the lysine/cadaverine antiporter. CadA contains a PLP-binding core domain and a pyridoxal phosphate-binding motif. It shares high homology with lysine decarboxylase. cadB and cadA are co-transcribed under one operon. To study the function of the cadBA operon, isogenic cadA, cadB and cadBA deletion mutant strains TX01ΔcadA, TX01ΔcadB and TX01ΔcadBA were constructed. When cultured under normal conditions, the wild type strain and three mutants exhibited the same growth performance. However, when cultured under acid conditions, the growth of three mutants, especially TX01ΔcadA, were obviously retarded, compared to the wild strain TX01, which indicates the important involvement of the cadBA operon in acid resistance. The deletion of cadB or cadA, especially cadBA, significantly attenuated bacterial activity of lysine decarboxylase, suggesting the vital participation of cadBA operon in lysine metabolism, which is closely related to acid resistance. The mutations of cadBA operon enhanced bacterial biofilm formation, especially under acid conditions. The deletions of the cadBA operon reduced bacterial adhesion and invasion to Hela cells. Consistently, the deficiency of cadBA operon abated bacterial survival and replication in macrophages, and decreased bacterial dissemination in fish tissues. Our results also show that the expression of cadBA operon and regulator cadC were up-regulated upon acid stress, and CadC rigorously regulated the expression of cadBA operon, especially under acid conditions. These findings demonstrate that the AR CadBA system was a requisite for the resistance of E. tarda against acid stress, and played a critical role in bacterial infection of host cells and in host tissues. This is the first study about the acid resistance system of E. tarda and provides new insights into the acid-resistance mechanism and pathogenesis of E. tarda.

Organic Acid Exposure Enhances Virulence in Some Listeria monocytogenes Strains Using the Galleria mellonella Infection Model

Prior research has suggested that the use of organic acids in the food industry may unintentionally enhance pathogenicity of Listeria monocytogenes strain N1-227 and R2-499. This study explored the connection between habituation to L-lactic acid or acetic acid and virulence in L. monocytogenes strains N1-227 and R2-499 using selected gene expression analysis and the in vivo Galleria mellonella wax worm model for infection. Expression of transcription factors (sigB and prfA) and genes related to acid resistance (gadD2, gadD3, and arcA) and bile resistance (bsh and bilE) or to virulence (inlA, inlB, hly, plcA, plcB, uhpT, and actA) was investigated by quantitative real-time PCR (qRT-PCR), while in vivo virulence was assessed by following the lethal time to 50% population mortality (LT₅₀) of G. mellonella larvae after injection of untreated and habituated L. monocytogenes. Twenty minutes of habituation to the organic acids at pH 6.0 significantly increased expression of key acid and bile stress response genes in both strains, while expression of virulence genes was strain-dependent. The expression of transcription factor sigB was strain-dependent and there was no significant change in the expression of transcription factor prfA in both strains. Habituation to acid increased virulence of both strains as evidenced by decreased LT₅₀ of G. mellonella larvae injected with Listeria habituated to either acid. In summary, habituation of both L. monocytogenes strains to organic acids up-regulated expression of several stress and virulence genes and concurrently increased virulence as measured using the G. mellonella model.

Acid-Resistance Enhancement of Thin-Film Composite Membrane Using Barrier Effect of Graphene Oxide Nanosheets

In this study, the effect of graphene oxide nanosheets (GONs) embedded in a thin-film composite (TFC) polyamide (PA) membrane on the acid resistance of the membrane was investigated by comparison with the effect of oxidized single-walled carbon nanotubes (o-SWNTs). Both GONs and o-SWNTs increased the hydrophilicity of the membranes and caused the formation of ridges and clustered bumps on the surfaces, resulting in slightly improved water permeability. However, the o-SWNTs-embedded membrane did not show a difference in acid resistance depending on the concentration of embedded material, but the acid resistance of the GONs-embedded membrane increased with increasing concentration. The acid resistance of the GONs-embedded membranes appears to be mainly due to the barrier effect caused by the nanosheet shape of the GONs along with a sacrificial role of the PA layer protruded by the addition of GONs and the decrease of acid reaction sites by the hydrogen bonding between GONs and PA. When the TFC PA membrane was prepared with a high amount (300 ppm) of the GONs without considering aggregation of GONs, membrane selectivity exceeding 95% was maintained 4.7 times longer than the control TFC membrane. This study shows that the acid resistance can be enhanced by the use of GONs, which give a barrier effect to the membrane.

TiO2 Decorated Low-Molecular Chitosan a Microsized Adsorbent for a 68Ge/68Ga Generator System

We report column material for a ⁶⁸Ge/⁶⁸Ga generator with acid resistance and excellent adsorption and desorption capacity of ⁶⁸Ge and ⁶⁸Ga, respectively. Despite being a core element of the ⁶⁸Ge/⁶⁸Ga generator system, research on this has been insufficient. Therefore, we synthesized a low molecular chitosan-based TiO₂ (LC-TiO₂) adsorbent via a physical trapping method as a durable ⁶⁸Ge/⁶⁸Ga generator column material. The adsorption/desorption studies exhibited a higher separation factor of ⁶⁸Ge/⁶⁸Ga in the concentration range of HCl examined (0.01 M to 1.0 M). The prepared LC-TiO₂ adsorbent showed acid resistance capabilities with >93% of ⁶⁸Ga elution yield and 1.6 × 10^-4% of ⁶⁸Ge breakthrough. In particular, the labeling efficiency of DOTA and NOTA, by using the generator eluted ⁶⁸Ga, was quite encouraging and confirmed to be 99.65 and 99.69%, respectively. Accordingly, the resulting behavior of LC-TiO₂ towards ⁶⁸Ge/⁶⁸Ga adsorption/desorption capacity and stability with aqueous HCl exhibited a high potential for ion-exchange solid-phase extraction for the ⁶⁸Ge/⁶⁸Ga generator column material.

Genome-Wide Identification of Genes Involved in Acid Stress Resistance of Salmonella Derby

Resistance to and survival under acidic conditions are critical for Salmonella to infect the host. As one of the most prevalent serotypes identified in pigs and humans, how S. Derby overcomes acid stress remains unclear. Here, we de novo sequenced the genome of a representative S. Derby strain 14T from our S. Derby strain stock and identified its acid resistance-associated genes using Tn-seq analysis. A total of 35 genes, including those belonging to two-component systems (TCS) (cpxAR), the CRISPR-Cas system (casCE), and other systems, were identified as essential for 14T to survive under acid stress. The results demonstrated that the growth curve and survival ability of ΔcpxA and ΔcpxR were decreased under acid stress, and the adhesion and invasion abilities to the mouse colon cancer epithelial cells (MC38) of ΔcpxR were also decreased compared with the wild type strain, suggesting that the TCS CpxAR plays an essential role in the acid resistance and virulence of S. Derby. Also, CasC and CasE were found to be responsible for acid resistance in S. Derby. Our results indicate that acid stress induces multiple genes’ expression to mediate the acid resistance of S. Derby and enhance its pathogenesis during an infection.

Acid-Resistant BiVO4 Photoanodes: Insolubility Control by Solvents and Weak W Diffusion in the Lattice

We have revealed for the first time that BiVO₄ photoanodes can be used even in strong acid media by mixing organic solvents into the electrolyte and depositing multilayers with a WO₃ bottom layer. In general, the BiVO₄ photoanodes are photocorrosive, especially in acid solutions. However, this shortcoming has been overcome using a combination of the two aforementioned modifications. We deduced that the contribution of each mixing organic solvent for the anti-photocorrosion of BiVO₄ in sulfuric acid solutions can be evaluated on the basis of a new empirical indicator that incorporates molecular density, the Hansen solubility parameter, and molecular polarizability. Acetone and tert-butyl alcohol were especially promising solvents for stabilizing BiVO₄ in acid media. We confirmed that the mixed organic solvents stabilized surface-emergent Bi oxide species as a passivation layer, which was generated via multilayering with a WO₃ bottom layer. During heat treatment in the fabrication process, W weakly diffused into the BiVO₄ layer and a Bi oxide layer was formed on the outermost surface because of the Bi segregation that arose from the charge compensation between W⁶⁺ and V⁵⁺ in the BiVO₄ lattice. The surface Bi oxide layer, which was protected by the mixed organic solvents, steadily served as a passivation layer for anti-photocorrosion of the underlying BiVO₄ layer. We have confirmed that the BiVO₄/WO₃ photoanodes in acetone-mixed aqueous sulfuric acid solution reliably functioned for a photoelectrochemical reaction under simulated sunlight illumination, and photoelectrochemical production of S₂O₈^2- ions was confirmed under light irradiation at λ > 480 nm. These results suggest that the BiVO₄-based photoanodes have significant potential for use in acid media in conjunction with very straightforward modifications.

The lipoprotein NlpD in Cronobacter sakazakii responds to acid stress and regulates macrophage resistance and virulence by maintaining membrane integrity

Cronobacter sakazakii, an emerging opportunistic pathogen, is implicated in severe foodborne outbreak infections in premature and full-term infants. Generally, acid tolerance is vital for the pathogenesis of foodborne pathogens; however, its role in C. sakazakii virulence remains largely unknown. To screen out acid-tolerance determinants from transposon mutants, anovel counterselection method using gentamicin and acid was developed. Using the counterselection method and growth assay, we screened several acid-sensitive mutants and found that nlpD encodes an acid-resistance factor in C. sakazakii. 

Compared to the wild-type strain, the nlpD mutant exhibited attenuated virulence in a rat model. Using macrophage THP-1 cells and a pH probe, we verified that nlpD enables bacteria to resist macrophages by resisting acidification. Finally, we confirmed that nlpD maintains C. sakazakii membrane integrity in acid using propidium iodide permeabilization assays via flow cytometry. Our results confirm that nlpD is a novel virulence factor that permits C. sakazakii to survive under acid stress conditions. Considering that NlpD is a conserved lipoprotein located in the bacterial outer membrane, NlpD could be used as a target for drug development.

The Salmonella LysR Family Regulator RipR Activates the SPI-13-Encoded Itaconate Degradation Cluster

Itaconate is a dicarboxylic acid that inhibits the isocitrate lyase enzyme of the bacterial glyoxylate shunt. Activated macrophages have been shown to produce itaconate, suggesting that these immune cells may employ this metabolite as a weapon against invading bacteria. Here, we demonstrate that in vitro, itaconate can exhibit bactericidal effects under acidic conditions similar to the pH of a macrophage phagosome. In parallel, successful pathogens, including Salmonella, have acquired a genetic operon encoding itaconate degradation proteins, which are induced heavily in macrophages. We characterized the regulation of this operon by the neighboring gene ripR in specific response to itaconate. Moreover, we developed an itaconate biosensor based on the operon promoter that can detect itaconate in a semiquantitative manner and, when combined with the ripR gene, is sufficient for itaconate-regulated expression in Escherichia coli Using this biosensor with fluorescence microscopy, we observed bacteria responding to itaconate in the phagosomes of macrophages and provide additional evidence that gamma interferon stimulates macrophage itaconate synthesis and that J774 mouse macrophages produce substantially more itaconate than the human THP-1 monocyte cell line. In summary, we examined the role of itaconate as an antibacterial metabolite in mouse and human macrophages, characterized the regulation of Salmonella's defense against it, and developed it as a convenient itaconate biosensor and inducible promoter system.

Escherichia Coli Increases its ATP Concentration in Weakly Acidic Environments Principally through the Glycolytic Pathway

Acid resistance is an intrinsic characteristic of intestinal bacteria in order to survive passage through the stomach. Adenosine triphosphate (ATP), the ubiquitous chemical used to power metabolic reactions, activate signaling cascades, and form precursors of nucleic acids, was also found to be associated with the survival of Escherichia coli (E. coli) in acidic environments. The metabolic pathway responsible for elevating the level of ATP inside these bacteria during acid adaptation has been unclear. E. coli uses several mechanisms of ATP production, including oxidative phosphorylation, glycolysis and the oxidation of organic compounds. To uncover which is primarily used during adaptation to acidic conditions, we broadly analyzed the levels of gene transcription of multiple E. coli metabolic pathway components. Our findings confirmed that the primary producers of ATP in E. coli undergoing mild acidic stress are the glycolytic enzymes Glk, PykF and Pgk, which are also essential for survival under markedly acidic conditions. By contrast, the transcription of genes related to oxidative phosphorylation was downregulated, despite it being the major producer of ATP in neutral pH environments.

Enhanced Viability of Probiotics against Gastric Acid by One-Step Coating Process with Poly-L-Lysine: In Vitro and In Vivo Evaluation

Due to their low acid tolerance, a majority of probiotics face difficulties with regard to surviving in the gastric environment long enough to reach the intestinal surfaces where they colonize and provide health benefits. We prepared a probiotic delivery system that can enhance their viability in acidic conditions by developing a one-step poly-L-lysine (PLL) coating process. We determined whether the coating process was successful by measuring the zeta potential and observing it with confocal scanning microscopy. PLL-coated L. plantarum (PLL-LP), incubated in a solution of pH 2 for 2 h, exhibited a higher viability (6.86 ± 0.12 log CFU/mL of viable cells) than non-coated L. plantarum (non-coated LP), which exhibited only 2.7 ± 1.23 log CFU/mL of viable cells. In addition, a higher amount of L. plantarum was detected in the feces of mice orally administered PLL-LP (6.2 ± 0.4 log CFU/g of feces) than in the feces of the control groups. In addition to enhancing probiotic viability in pH 2 solution, the PLL coating showed no effect on the probiotic growth pattern and the viability of either freeze-dried L. plantarum or L. plantarum, stored at −20 °C and 4 °C, respectively. Overall, these results indicated that the PLL coating is a promising potential probiotic delivery system.

Metabolic Traits of Bovine Shiga Toxin-Producing Escherichia Coli (STEC) Strains with Different Colonization Properties

Cattle harbor Shiga toxin-producing Escherichia coli (STEC) in their intestinal tract, thereby providing these microorganisms with an ecological niche, but without this colonization leading to any clinical signs. In a preceding study, genotypic characterization of bovine STEC isolates unveiled that their ability to colonize cattle persistently (STEC^per) or only sporadically (STEC^spo) is more closely associated with the overall composition of the accessory rather than the core genome. However, the colonization pattern could not be unequivocally linked to the possession of classical virulence genes. This study aimed at assessing, therefore, if the presence of certain phenotypic traits in the strains determines their colonization pattern and if these can be traced back to distinctive genetic features. STEC^spo strains produced significantly more biofilm than STEC^per when incubated at lower temperatures. Key substrates, the metabolism of which showed a significant association with colonization type, were glyoxylic acid and L-rhamnose, which were utilized by STEC^spo, but not or only by some STEC^per. Genomic sequences of the respective glc and rha operons contained mutations and frameshifts in uptake and/or regulatory genes, particularly in STEC^per. These findings suggest that STEC^spo conserved features leveraging survival in the environment, whereas the acquisition of a persistent colonization phenotype in the cattle reservoir was accompanied by the loss of metabolic properties and genomic mutations in the underlying genetic pathways.

Turning the Screw: Engineering Extreme pH Resistance in Escherichia coli through Combinatorial Synthetic Operons

Adoption of microorganisms as platforms for sustainable biobased production requires host cells to be able to withstand harsh conditions, usually very distant from those in which these organisms are naturally adapted to thrive. However, novel survival mechanisms unearthed by the study of microbiomes from extreme habitats may be exploited to enhance microbial robustness under the strict conditions needed for different industrial appplications. In this work, synthetic biology approaches were used to engineer enhanced acidic resistance in Escherichia coli through the characterization of a collection of unique operons composed of combinatorial assemblies of three novel genes from an extreme environment and three synthetic ribosome binding sites. The results here presented illustrate the efficacy of combining different metagenomic genes for resistance in synthetic operons, as expression of these gene clusters increased hundred-fold the survival percentage of cells exposed to an acidic shock in minimal media at pH 1.9 under aerobic conditions.

Molecular design of a signaling system influences noise in protein abundance under acid stress in different γ-Proteobacteria

Bacteria have evolved different signaling systems to sense and adapt to acid stress. One of these systems, the CadABC-system, responds to a combination of low pH and lysine availability. In Escherichia coli, the two signals are sensed by the pH sensor and transcription activator CadC and the co-sensor LysP, a lysine-specific transporter. Activated CadC promotes the transcription of the cadBA operon, which codes for the lysine decarboxylase CadA and the lysine/cadaverine antiporter CadB. The copy number of CadC is controlled translationally. Using a bioinformatics approach, we identified the presence of CadC with ribosomal stalling motifs together with LysP in species of the Enterobacteriaceae family. In contrast, we identified CadC without stalling motifs in species of the Vibrionaceae family, but the LysP co-sensor was not identified. Therefore, we compared the output of the Cad system in single cells of the distantly related organisms E. coli and V. campbellii using fluorescently-tagged CadB as the reporter. We observed a heterogeneous output in E. coli, and all the V. campbellii cells produced CadB. The copy number of the pH sensor CadC in E. coli was extremely low (≤4 molecules per cell), but it was 10-fold higher in V. campbellii An increase in the CadC copy number in E. coli correlated with a decrease in heterogeneous behavior. This study demonstrated how small changes in the design of a signaling system allow a homogeneous output and, thus, adaptation of Vibrio species that rely on the CadABC-system as the only acid resistance system.Importance Acid resistance is an important property of bacteria, such as Escherichia coli, to survive acidic environments like the human gastrointestinal tract. E. coli possess both passive and inducible acid resistance systems to counteract acidic environments. Thus, E. coli evolved sophisticated signaling systems to sense and appropriately respond to environmental acidic stress by regulating the activity of its three inducible acid resistance systems. One of these systems is the Cad system that is only induced under moderate acidic stress in a lysine-rich environment by the pH-responsive transcriptional regulator CadC. The significance of our research is in identifying the molecular design of the Cad systems in different Proteobacteria and their target expression noise at single cell level during acid stress conditions.