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ABSTRACT: Salmonella is a relevant pathogen, which causes foodborne outbreaks associated with both high and low moisture foods (LMF). This study evaluated the effect of previous desiccation stress on the acid resistance of S. Typhimurium ATCC 14028 using blanched peanut kernels as an LMF model. Salmonella was recovered from the peanut samples throughout 180 days of blanched peanut kernels storage at 28 ºC. During this period two death rates were verified, 0.04 log cfu/g/day in the first 30 days and 0.007 log cfu/g/day between 30 and180 days.Regarding acid resistance, there was no difference (P > 0.05) in the Salmonella growth/death kinetics between the undesiccated sample (TSB)and the cells recovered from peanut samples over 180 days of storage after 4 h at pHs 3.0, 3.5, 4.5 and 7.2. The average growth rate observed for pH 7.2 was 0.44 log cfu/ml/h. At pH 4.5, the Salmonella counts did not change significantly over 4 h. In contrast, Salmonella populations declined by 0.14 to 0.29 log cfu/ml/h at pH 3.5. At pH 3.0 declines were estimated to be 0.65 log cfu/ml/h for the undesiccated sample and 2.07 log cfu/ml/h for Salmonella recovered from peanuts stored for 120 days. Therefore, our data indicated that desiccation stress caused during the peanut storagedid not influence the Salmonella acid resistance.

RESUMO: Em alimentos de baixa umidade (LMF), o primeiro desafio encontrado por patógenos como a Salmonella é o estresse de dessecação. Neste estudo, o efeito prévio do estresse de dessecação sobre a resistência ácida de S. Typhimurium ATCC 14028 foi avaliado utilizando amendoim blancheado como um modelo de LMF. Salmonella foi recuperada das amostras de amendoim após 180 dias de estocagem a 28 ºC. Durante este período foram verificadas duas taxas de mortalidade, 0,04 log ufc/g/dia nos primeiros 30 dias e 0,007 log ufc/g/dia entre 30 e 180 dias. Com relação à resistência ácida, não houve diferença (P > 0,05) na cinética de crescimento/morte de Salmonella entre a amostra sem estresse dessecativo (TSB) e as amostras de amendoim após 4 h em pHs 3,0, 3,5, 4,5 e 7,2. A taxa média de crescimento observada para o pH 7,2 foi de 0,44 log cfu/ml/h. No pH 4,5, a contagem de Salmonella não mudou significativamente durante 4 h. Em contraste, a população de Salmonella diminuiu de 0,14 a 0,29 log cfu/ml/h no pH 3,5. No pH 3,0, a queda foi estimada em 0,65 log cfu/ml/h para a amostra sem estresse dessecativo e 2,07 log cfu/ml/h para a Salmonella recuperada das amostras de amendoim estocadas por 120 dias. Portanto, nossos dados indicaram que o estresse dessecativo causado durante a estocagem do amendoim não influenciou a resistência ácida de Salmonella.

RESUMO

Salmonella is a relevant pathogen, which causes foodborne outbreaks associated with both high and low moisture foods (LMF). This study evaluated the effect of previous desiccation stress on the acid resistance of S. Typhimurium ATCC 14028 using blanched peanut kernels as an LMF model. Salmonella was recovered from the peanut samples throughout 180 days of blanched peanut kernels storage at 28 ºC. During this period two death rates were verified, 0.04 log cfu/g/day in the first 30 days and 0.007 log cfu/g/day between 30 and180 days.Regarding acid resistance, there was no difference (P > 0.05) in the Salmonella growth/death kinetics between the undesiccated sample (TSB)and the cells recovered from peanut samples over 180 days of storage after 4 h at pHs 3.0, 3.5, 4.5 and 7.2. The average growth rate observed for pH 7.2 was 0.44 log cfu/ml/h. At pH 4.5, the Salmonella counts did not change significantly over 4 h. In contrast, Salmonella populations declined by 0.14 to 0.29 log cfu/ml/h at pH 3.5. At pH 3.0 declines were estimated to be 0.65 log cfu/ml/h for the undesiccated sample and 2.07 log cfu/ml/h for Salmonella recovered from peanuts stored for 120 days. Therefore, our data indicated that desiccation stress caused during the peanut storagedid not influence the Salmonella acid resistance.

Em alimentos de baixa umidade (LMF), o primeiro desafio encontrado por patógenos como a Salmonella é o estresse de dessecação. Neste estudo, o efeito prévio do estresse de dessecação sobre a resistência ácida de S. Typhimurium ATCC 14028 foi avaliado utilizando amendoim blancheado como um modelo de LMF. Salmonella foi recuperada das amostras de amendoim após 180 dias de estocagem a 28 ºC. Durante este período foram verificadas duas taxas de mortalidade, 0,04 log ufc/g/dia nos primeiros 30 dias e 0,007 log ufc/g/dia entre 30 e 180 dias. Com relação à resistência ácida, não houve diferença (P > 0,05) na cinética de crescimento/morte de Salmonella entre a amostra sem estresse dessecativo (TSB) e as amostras de amendoim após 4 h em pHs 3,0, 3,5, 4,5 e 7,2. A taxa média de crescimento observada para o pH 7,2 foi de 0,44 log cfu/ml/h. No pH 4,5, a contagem de Salmonella não mudou significativamente durante 4 h. Em contraste, a população de Salmonella diminuiu de 0,14 a 0,29 log cfu/ml/h no pH 3,5. No pH 3,0, a queda foi estimada em 0,65 log cfu/ml/h para a amostra sem estresse dessecativo e 2,07 log cfu/ml/h para a Salmonella recuperada das amostras de amendoim estocadas por 120 dias. Portanto, nossos dados indicaram que o estresse dessecativo causado durante a estocagem do amendoim não influenciou a resistência ácida de Salmonella.

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Verrucomicrobia are a group of microorganisms that have been proposed to be deeply rooted in the Tree of Life. Some are methanotrophs that oxidize the potent greenhouse gas methane and are thus important in decreasing atmospheric concentrations of the gas, potentially ameliorating climate change. They are widespread in various environments including soil and fresh or marine waters. Recently, a clade of extremely acidophilic Verrucomicrobia, flourishing at pH < 3, were described from high-temperature geothermal ecosystems. This novel group could be of interest for studies about the emergence of life on Earth and to astrobiologists as homologs for possible extraterrestrial life. In this paper, we describe predicted mechanisms for survival of this clade at low pH and suggest its possible evolutionary trajectory from an inferred neutrophilic ancestor. Extreme acidophiles are defined as organisms that thrive in extremely low pH environments (≤ pH 3). Many are polyextremophiles facing high temperatures and high salt as well as low pH. They are important to study for both providing fundamental insights into biological mechanisms of survival and evolution in such extreme environments and for understanding their roles in biotechnological applications such as industrial mineral recovery (bioleaching) and mitigation of acid mine drainage. They are also, potentially, a rich source of novel genes and pathways for the genetic engineering of microbial strains. Acidophiles of the Verrucomicrobia phylum are unique as they are the only known aerobic methanotrophs that can grow optimally under acidic (pH 2-3) and moderately thermophilic conditions (50-60°C). Three moderately thermophilic genera, namely Methylacidiphilum, Methylacidimicrobium, and Ca. Methylacidithermus, have been described in geothermal environments. Most of the investigations of these organisms have focused on their methane oxidizing capabilities (methanotrophy) and use of lanthanides as a protein cofactor, with no extensive study that sheds light on the mechanisms that they use to flourish at extremely low pH. In this paper, we extend the phylogenetic description of this group of acidophiles using whole genome information and we identify several mechanisms, potentially involved in acid resistance, including "first line of defense" mechanisms that impede the entry of protons into the cell. These include the presence of membrane-associated hopanoids, multiple copies of the outer membrane protein (Slp), and inner membrane potassium channels (kup, kdp) that generate a reversed membrane potential repelling the intrusion of protons. Acidophilic Verrucomicrobia also display a wide array of proteins potentially involved in the "second line of defense" where protons that evaded the first line of defense and entered the cell are expelled or neutralized, such as the glutamate decarboxylation (gadAB) and phosphate-uptake systems. An exclusive N-type ATPase F0-F1 was identified only in acidophiles of Verrucomicrobia and is predicted to be a specific adaptation in these organisms. Phylogenetic analyses suggest that many predicted mechanisms are evolutionarily conserved and most likely entered the acidophilic lineage of Verrucomicrobia by vertical descent from a common ancestor. However, it is likely that some defense mechanisms such as gadA and kup entered the acidophilic Verrucomicrobia lineage by horizontal gene transfer.

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The genome streamlining theory suggests that reduction of microbial genome size optimizes energy utilization in stressful environments. Although this hypothesis has been explored in several cases of low-nutrient (oligotrophic) and high-temperature environments, little work has been carried out on microorganisms from low-pH environments, and what has been reported is inconclusive. In this study, we performed a large-scale comparative genomics investigation of more than 260 bacterial high-quality genome sequences of acidophiles, together with genomes of their closest phylogenetic relatives that live at circum-neutral pH. A statistically supported correlation is reported between reduction of genome size and decreasing pH that we demonstrate is due to gene loss and reduced gene sizes. This trend is independent from other genome size constraints such as temperature and G + C content. Genome streamlining in the evolution of acidophilic bacteria is thus supported by our results. The analyses of predicted Clusters of Orthologous Genes (COG) categories and subcellular location predictions indicate that acidophiles have a lower representation of genes encoding extracellular proteins, signal transduction mechanisms, and proteins with unknown function but are enriched in inner membrane proteins, chaperones, basic metabolism, and core cellular functions. Contrary to other reports for genome streamlining, there was no significant change in paralog frequencies across pH. However, a detailed analysis of COG categories revealed a higher proportion of genes in acidophiles in the following categories: "replication and repair," "amino acid transport," and "intracellular trafficking". This study brings increasing clarity regarding the genomic adaptations of acidophiles to life at low pH while putting elements, such as the reduction of average gene size, under the spotlight of streamlining theory.

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The microorganisms that constitute the oral microbiome can cause oral diseases, including dental caries and endodontic infections. The use of natural products could help to overcome bacterial resistance to the antimicrobials that are currently employed in clinical therapy. This study assessed the antimicrobial activity of the Copaifera pubiflora oleoresin and of the compounds isolated from this resin against oral bacteria. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) assays provided values ranging from 6.25 to > 400 µg/mL for the C. pubiflora oleoresin and its isolated compounds. The fractional inhibitory concentration index (FICI) assay showed that the oleoresin and chlorhexidine did not act synergistically. All the tested bacterial strains formed biofilms. MICB50 determination revealed inhibitory action: values varied from 3.12-25 µg/mL for the oleoresin, and from 0.78 to 25 µg/mL for the ent-hardwickiic acid. Concerning biofilm eradication, the C. pubiflora oleoresin and hardwickiic acid eradicated 99.9 % of some bacterial biofilms. Acid resistance determination showed that S. mutans was resistant to acid in the presence of the oleoresin and ent-hardwickiic acid at pH 4.0, 4.5, and 5.0 at all the tested concentrations. Analysis of DNA/RNA and protein release by the cell membrane demonstrated that the oleoresin and hardwiickic acid damaged the bacterial membrane irreversibly, which affected membrane integrity. Therefore, the C. pubiflora oleoresin and ent-hardwickiic acid have potential antibacterial effect and can be used as new therapeutic alternatives to treat oral diseases such as dental caries and endodontic infections.

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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.

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Organisms that thrive in extremely acidic environments (≤pH 3.5) are of widespread importance in industrial applications, environmental issues, and evolutionary studies. Leptospirillum spp. constitute the only extremely acidophilic microbes in the phylogenetically deep-rooted bacterial phylum Nitrospirae. Leptospirilli are Gram-negative, obligatory chemolithoautotrophic, aerobic, ferrous iron oxidizers. This paper predicts genes that Leptospirilli use to survive at low pH and infers their evolutionary trajectory. Phylogenetic and other bioinformatic approaches suggest that these genes can be classified into (i) "first line of defense", involved in the prevention of the entry of protons into the cell, and (ii) neutralization or expulsion of protons that enter the cell. The first line of defense includes potassium transporters, predicted to form an inside positive membrane potential, spermidines, hopanoids, and Slps (starvation-inducible outer membrane proteins). The "second line of defense" includes proton pumps and enzymes that consume protons. Maximum parsimony, clustering methods, and gene alignments are used to infer the evolutionary trajectory that potentially enabled the ancestral Leptospirillum to transition from a postulated circum-neutral pH environment to an extremely acidic one. The hypothesized trajectory includes gene gains/loss events driven extensively by horizontal gene transfer, gene duplications, gene mutations, and genomic rearrangements.

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BACKGROUND: It has been reported that lasers can increase resistance to enamel acids, and when it is associated with fluoride, both are reported to work in synergy, achieving a reduction of the solubility of enamel. Currently, other remineralizing agents have been shown to effectively inhibit enamel demineralization. OBJECTIVES: The aim of the study was to evaluate acid resistance in the occlusal surface of permanent teeth, treated with remineralizing agents, erbium-doped yttrium aluminum garnet (Er:YAG) laser and combined treatments. MATERIAL AND METHODS: Eighty samples of enamel were randomly assigned to 8 groups (n = 10): a control group, and groups treated with sodium fluoride (NaF), casein phosphopeptide-amorphous calcium phosphate with NaF (CPP-ACPF), hydroxyapatite-NaF-xylitol (HA-NaF-X), Er:YAG laser (L), L+NaF, L+CPP-ACPF, and L+HA-NaF-X. The samples were placed in an acid solution and the released calcium (Ca) was quantified by atomic absorption spectrometry. RESULTS: In the groups treated with NaF and L+NaF, a lower loss of Ca was observed - 15.27 ±5.17 mg/L and 15.20 ±3.85 mg/L, respectively - compared to the control group, which had the highest Ca loss: 21.93 ±13.24 mg/L. CONCLUSIONS: Although the combination of Er:YAG laser plus NaF and the single application of NaF showed values suggesting superior resistance to demineralization of dental enamel compared to all the other groups in the study, no statistically significant differences were found to support this assertion.

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ABSTRACT: The objective of this study was to evaluate the acid resistance of Salmonella enterica serovar Enteritidis (S. Enteritidis) in stored pork and in simulated gastric fluid (SGF). A culture of S. Enteritidis was subjected to acid treatment prior to inoculation into pork, stored under refrigeration at frozen temperatures and exposed to SGF. The S. Enteritidis CCS3 and ATCC 13076 strains previously subjected to acid treatment (at pH 4.0-5.0) were inoculated in pork and stored at 4°C and -18°C. Storage at 4ºC did not affect the populations of both S. Enteritidis strains. After 84 days at -18°C, the mean population of both CCS3 and ATCC strains were reduced by 0.8 and 1.5 log cycles, respectively. Prior acid treatment did not enhance the survival of both strains at low temperatures. After acid treatment and low temperature storage, S. Enteritidis ATCC 13076 lost culturability after being exposed to SGF for 10 minutes. In contrast, S. Enteritidis CCS3 was tolerant until three hours of SGF exposure. S. Enteritidis CCS3 submitted to pH 4.0 was more tolerant to SGF exposure than when submitted to pH 4.5, 5.0 and without acid treatment. Therefore, this study indicates that exposure to an acidic and cold environment during processing enhanced the ability of S. Enteritidis to survive in the gastric environment of the human stomach, possibly increasing the risk of a Salmonella infection after consumption of pork.

RESUMO: O objetivo deste estudo foi avaliar a resistência ao ácido de Salmonella enterica serovar Enteritidis (S. Enteritidis) previamente submetidas a tratamento ácido e inoculadas em carne suína armazenada em temperaturas de refrigeração e congelamento ao fluido gástrico simulado (FGS). As linhagens de S. Enteritidis CCS3 and ATCC 13076 previamente submetidas a tratamento ácido variando de pH 4.0 a 5.0 foram inoculadas em carne de porco e armazenadas a 4 e −18°C. A estocagem por sete dias a 4°C não afetou as populações das duas linhagens de S. Enteritidis. Após 84 dias a -18°C, as reduções médias das populações das linhagens foram de 0,8 e 1,5 ciclos logarítmicos, respectivamente. O tratamento ácido prévio não aumentou a sobrevivência das duas culturas sob baixas temperaturas. Após tratamento ácido e estocagem em temperaturas baixas, S. Enteritidis ATCC 13076 perdeu a culturabilidade após 10 minutos de desafio ao FGS. Contrariamente, S. Enteritidis CCS3 mostrou-se tolerante à exposição por três horas ao FGS. S. Enteritidis CCS3 submetidas a tratamento ácido prévio em pH 4,0 mostraram-se mais tolerantes à exposição por 180 minutos ao FGS que células submetidas aos tratamentos ácidos em pH 4,5 e 5,0 e células sem tratamento. Portanto, este estudo indica que S. Enteritidis submetida a um ambiente ácido e frio durante o processamento pode melhorar a sua capacidade de sobreviver à barreira gástrica em humanos, possivelmente, aumentando o risco de surto por Salmonella após consumo de carne de porco.

RESUMO

The objective of this study was to evaluate the acid resistance of Salmonella enterica serovar Enteritidis (S. Enteritidis) in stored pork and in simulated gastric fluid (SGF). A culture of S. Enteritidis was subjected to acid treatment prior to inoculation into pork, stored under refrigeration at frozen temperatures and exposed to SGF. The S. Enteritidis CCS3 and ATCC 13076 strains previously subjected to acid treatment (at pH 4.0-5.0) were inoculated in pork and stored at 4°C and -18°C. Storage at 4ºC did not affect the populations of both S. Enteritidis strains. After 84 days at -18°C, the mean population of both CCS3 and ATCC strains were reduced by 0.8 and 1.5 log cycles, respectively. Prior acid treatment did not enhance the survival of both strains at low temperatures. After acid treatment and low temperature storage, S. Enteritidis ATCC 13076 lost culturability after being exposed to SGF for 10 minutes. In contrast, S. Enteritidis CCS3 was tolerant until three hours of SGF exposure. S. Enteritidis CCS3 submitted to pH 4.0 was more tolerant to SGF exposure than when submitted to pH 4.5, 5.0 and without acid treatment. Therefore, this study indicates that exposure to an acidic and cold environment during processing enhanced the ability of S. Enteritidis to survive in the gastric environment of the human stomach, possibly increasing the risk of a Salmonella infection after consumption of pork.(AU)

O objetivo deste estudo foi avaliar a resistência ao ácido de Salmonella enterica serovar Enteritidis (S. Enteritidis) previamente submetidas a tratamento ácido e inoculadas em carne suína armazenada em temperaturas de refrigeração e congelamento ao fluido gástrico simulado (FGS). As linhagens de S. Enteritidis CCS3 and ATCC 13076 previamente submetidas a tratamento ácido variando de pH 4.0 a 5.0 foram inoculadas em carne de porco e armazenadas a 4 e 18°C. A estocagem por sete dias a 4°C não afetou as populações das duas linhagens de S. Enteritidis. Após 84 dias a -18°C, as reduções médias das populações das linhagens foram de 0,8 e 1,5 ciclos logarítmicos, respectivamente. O tratamento ácido prévio não aumentou a sobrevivência das duas culturas sob baixas temperaturas. Após tratamento ácido e estocagem em temperaturas baixas, S. Enteritidis ATCC 13076 perdeu a culturabilidade após 10 minutos de desafio ao FGS. Contrariamente, S. Enteritidis CCS3 mostrou-se tolerante à exposição por três horas ao FGS. S. Enteritidis CCS3 submetidas a tratamento ácido prévio em pH 4,0 mostraram-se mais tolerantes à exposição por 180 minutos ao FGS que células submetidas aos tratamentos ácidos em pH 4,5 e 5,0 e células sem tratamento. Portanto, este estudo indica que S. Enteritidis submetida a um ambiente ácido e frio durante o processamento pode melhorar a sua capacidade de sobreviver à barreira gástrica em humanos, possivelmente, aumentando o risco de surto por Salmonella após consumo de carne de porco.(AU)

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Using phylogenomic and gene compositional analyses, five highly conserved gene families have been detected in the core genome of the phylogenetically coherent genus Acidithiobacillus of the class Acidithiobacillia. These core gene families are absent in the closest extant genus Thermithiobacillus tepidarius that subtends the Acidithiobacillus genus and roots the deepest in this class. The predicted proteins encoded by these core gene families are not detected by a BLAST search in the NCBI non-redundant database of more than 90 million proteins using a relaxed cut-off of 1.0e-5. None of the five families has a clear functional prediction. However, bioinformatic scrutiny, using pI prediction, motif/domain searches, cellular location predictions, genomic context analyses, and chromosome topology studies together with previously published transcriptomic and proteomic data, suggests that some may have functions associated with membrane remodeling during cell division perhaps in response to pH stress. Despite the high level of amino acid sequence conservation within each family, there is sufficient nucleotide variation of the respective genes to permit the use of the DNA sequences to distinguish different species of Acidithiobacillus, making them useful additions to the armamentarium of tools for phylogenetic analysis. Since the protein families are unique to the Acidithiobacillus genus, they can also be leveraged as probes to detect the genus in environmental metagenomes and metatranscriptomes, including industrial biomining operations, and acid mine drainage (AMD).