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pubmed: 0099-2240



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Oral administration of a select mixture of Bacillus probiotics affects the gut microbiota and goblet cell function in newly weaned MUC4 resistant pigs following Escherichia coli challenge.

Oral administration of a select mixture of Bacillus probiotics affects the gut microbiota and goblet cell function in newly weaned MUC4 resistant pigs following Escherichia coli challenge.

Appl Environ Microbiol. 2016 Nov 23;:

Authors: Zhang W, Zhu YH, Zhou D, Wu Q, Song D, Dicksved J, Wang JF

Abstract
Structural disruption of the gut microbiota and impaired goblet cell function are collateral etiologic factors in enteric diseases. Low, moderate, or high doses of a Bacillus licheniformis-B. subtilis mixture (BLS-mix) were orally administered to MUC4 resistant piglets for 1 week before the F4-expressing ETEC strain (F4(+) ETEC) challenge. The luminal contents were collected from the mucosa of colon on day 8 after F4(+) ETEC challenge. BLS-mix attenuated E. coli-induced expansion of Bacteroides uniformis, Eubacterium eligens, Acetanaerobacterium and Sporobacter populations. Clostridium and Turicibacter populations increased following F4(+) ETEC challenge in pigs pretreated with low-dose BLS-mix. Lactobacillus gasseri and L. salivarius populations increased after administering BLS-mix during E. coli infection. The beneficial effects of BLS-mix were due in part to expansion of certain Clostridium, Lactobacillus, and Turicibacter populations, with a corresponding increase in the number of goblet cells in the ileum via upregulated Atoh1 expression, in turn increasing MUC2 production, thus preserving the mucus barrier and enhancing host defenses against enteropathogenic bacteria. However, excessive BLS-mix consumption may increase the risk for enteritis, partly through disruption of colonic microbial ecology, characterized by expansion of Proteobacteria and impaired goblet cell function in the ileum. Our findings suggest that oral administration of BLS-mix reprograms the gut microbiota and enhances goblet cell function to ameliorate enteritis.
IMPORTANCE: The present study is important for improving our understanding the protective role of probitics against the infection of Escherichia coli in piglets. Structural disruption of the gut microbiota and impaired goblet cell function are collateral etiologic factors in enteric diseases. In this study, low, moderate, or high doses of a Bacillus licheniformis-B. subtilis mixture (BLS-mix) were orally administered to MUC4 resistant piglets for 1 week before the F4-expressing ETEC strain (F4(+) ETEC) challenge. Our findings suggest that oral administration of BLS-mix reprograms the gut microbiota and enhances goblet cell function to ameliorate enteritis.

PMID: 27881419 [PubMed - as supplied by publisher]




Environmental pseudomonads inhibit cystic fibrosis patient-derived Pseudomonas aeruginosa.

Environmental pseudomonads inhibit cystic fibrosis patient-derived Pseudomonas aeruginosa.

Appl Environ Microbiol. 2016 Nov 23;:

Authors: Chatterjee P, Davis E, Yu F, James S, Wildschutte JH, Wiegmann DD, Sherman DH, McKay RM, LiPuma JJ, Wildschutte H

Abstract
Pseudomonas aeruginosa is an opportunistic pathogen which is evolving resistance to many currently used antibiotics. While much research has been devoted to the roles of pathogenic P. aeruginosa in cystic fibrosis (CF) patients, less is known of its ecological properties. P. aeruginosa dominate the lungs during chronic infection in CF patients, yet its abundance in some environments is less compared to other diverse groups of pseudomonads. Here, we sought to determine if clinical isolates of P. aeruginosa are vulnerable to environmental pseudomonads that dominate soil and water habitats in one-to-one competitions which may provide a source of inhibitory factors. We isolated a total of 330 pseudomonads from diverse habitats of soil and freshwater ecosystems and competed these strains against one another to determine their capacity of antagonistic activity. Over 900 individual inhibitory events were observed. Extending the analysis to P. aeruginosa isolates revealed that clinical isolates, including ones with increased alginate production, were susceptible to competition by multiple environmental strains. We performed transposon mutagenesis on one isolate and identified a ∼14.8 kb locus involved in antagonistic activity. Only two other environmental isolates were observed to encode the locus, suggesting the presence of additional unique compounds or interactions among other isolates involved in outcompeting P. aeruginosa This collection of strains represent a source of compounds that are active against multiple pathogenic strains. With the evolution of P. aeruginosa to currently used antibiotics, these environmental strains provide opportunities for novel compound discovery against drug resistant clinical strains.
IMPORTANCE: We demonstrate that clinical CF-derived isolates of P. aeruginosa are susceptible to competition in the presence of environmental pseudomonads. We observe that many diverse environmental strains exhibit variable antagonistic profiles against a panel of clinical P. aeruginosa isolates, suggesting the presence of distinct mechanisms of inhibition among these ecological strains. Understanding the properties of these antagonistic events offers the potential for discoveries of antimicrobial compounds or metabolic pathways important to the development of novel treatments for P. aeruginosa infections.

PMID: 27881418 [PubMed - as supplied by publisher]




Analysis of germination capacity and inventarisation of germinant receptor (sub)clusters of genome sequenced Bacillus cereus environmental isolates and model strains.

Analysis of germination capacity and inventarisation of germinant receptor (sub)clusters of genome sequenced Bacillus cereus environmental isolates and model strains.

Appl Environ Microbiol. 2016 Nov 23;:

Authors: Warda AK, Xiao Y, Boekhorst J, Wells-Bennik MH, Nierop Groot MN, Abee T

Abstract
Spore germination of 17 Bacillus cereus food isolates and reference strains was evaluated using flow cytometry analysis in combination with fluorescent staining at a single spore level. This approach allowed for rapid collection of germination data in more than 20 conditions including heat activation of spores, germination in complex media (BHI and TSB), and exposure to saturating concentrations of single amino acids and the combination of alanine and inosine. Whole genome sequence comparison revealed a total of eleven clusters of operons encoded germinant receptors (GRs); GerK, GerI and GerL were present in all strains, whereas GerR, GerS, GerG, GerQ, GerX, GerF, GerW and GerZ (sub)clusters showed a more diverse presence/absence in different strains. The spores of tested strains displayed high diversity with regard to their sensitivity and responsiveness to selected germinants and heat activation. The two laboratory strains, ATCC 14579 and ATCC 10987, and 11 food isolates showed a good germination response in a range of conditions, whereas four other strains (B4085, B4086, B4116 and B4153) belonging to phylogenetic group IIIA showed a very weak germination response even in BHI and TSB media. Germination responses could not be linked to specific (combinations of) GRs, but is was noted that the four group IIIA strains contained pseudogenes or variants of subunit C in their gerL cluster. Additionally, two of those strains (B4086, B4153) carried pseudogenes in the gerK and gerRI (sub-)clusters, that possibly affected functionality of these GRs.
IMPORTANCE: Germination of bacterial spores is a critical step before vegetative growth can resume. Food products may contain nutrient germinants that trigger germination and outgrowth of Bacillus spp. spores possibly leading to food spoilage or foodborne illness. Prediction of spore germination behaviour is however very challenging, especially for spores of natural isolates that tend to show more diverse germination responses than laboratory strains. This study provided information on the genetic diversity in GRs and corresponding sub-clusters encoded by B cereus strains as well as their germination behaviour and possible associations with GRs. The approach used has provided information on the genetic diversity in GRs and corresponding sub-clusters encoded by B cereus strains as well as their germination behaviour and possible associations with GRs, and provides a basis for further extension of the knowledge on the role of GRs in B. cereus (group member) ecology and transmission to the host.

PMID: 27881417 [PubMed - as supplied by publisher]




Metagenomics of two severe foodborne outbreaks provides diagnostic signatures and signs of co-infection not attainable by traditional methods.

Metagenomics of two severe foodborne outbreaks provides diagnostic signatures and signs of co-infection not attainable by traditional methods.

Appl Environ Microbiol. 2016 Nov 23;:

Authors: Huang AD, Luo C, Pena-Gonzalez A, Weigand MR, Tarr C, Konstantinidis KT

Abstract
Diagnostic testing for foodborne pathogens relies on culture-based techniques that are not rapid enough for real-time disease surveillance and do not give a quantitative picture of pathogen abundance or the response of the natural microbiome. Powerful sequence-based, culture-independent approaches such as shotgun metagenomics could sidestep these limitations, and potentially reveal a pathogen-specific signature on the microbiome that would have implications not only for diagnostics but also for better understanding disease progression and pathogen ecology. However, metagenomics have not yet been validated for foodborne pathogen detection. Toward closing these gaps, we applied shotgun metagenomics to stool samples collected from two geographically isolated (Alabama and Colorado) foodborne outbreaks, where the etiologic agents were identified as distinct strains of Salmonella enterica serovar Heidelberg by culture-dependent methods. Metagenomic investigations were consistent with the culture-based findings and revealed, in addition, the in-situ abundance and level of intra-population diversity of the pathogen, the possibility for co-infections with Staphylococcus aureus, and significant shifts in the gut microbiome during infection relative to reference healthy samples. Additionally, we designed our bioinformatics pipeline to deal with several challenges associated with analysis of clinical samples such as the high frequency of co-eluting human DNA sequences and assessment of the virulence potential of pathogens. Comparisons of these results to those of other studies revealed that in several cases of diarrheal outbreaks -but not all- the disease and healthy states of the gut microbial community might be distinguishable, opening new possibilities for diagnostics.
IMPORTANCE STATEMENT: Diagnostic testing for enteric pathogens has relied for decades on culture-based techniques but a total of 38.4 million cases of foodborne illness per year cannot be attributed to specific causes. This study describes new culture-independent metagenomic approaches and the associated bioinformatics approaches to detect and type the causative agents of microbial disease with unprecedented accuracy, opening new possibilities for future development of health technologies and diagnostics. Our tools and approaches should be applicable to other microbial diseases in addition to foodborne diarrhea.

PMID: 27881416 [PubMed - as supplied by publisher]




Whole genome relationships among Francisella bacteria of diverse origin define new species and provide specific regions for detection.

Whole genome relationships among Francisella bacteria of diverse origin define new species and provide specific regions for detection.

Appl Environ Microbiol. 2016 Nov 23;:

Authors: Challacombe JF, Petersen JM, Gallegos-Graves V, Hodge D, Pillai S, Kuske CR

Abstract
Francisella tularensis (Ft) is a highly virulent zoonotic pathogen that causes tularemia, and because of weaponization efforts in past world wars, is considered a Tier 1 biothreat agent. Detection and surveillance of Ft may be confounded by the presence of uncharacterized, closely related organisms. Through DNA-based diagnostics and environmental surveys, novel clinical and environmental Francisella isolates have been obtained in recent years. Here we present 17 new Francisella genomes and a comparison of their characteristics to each other and to 14 publicly available genomes as well as a comparative analysis of 16S rRNA and sdhA genes from over 90 Francisella strains. Delineation of new species in bacteria is challenging, especially when isolates having very close genomic characteristics exhibit different physiological features - for example, when some are virulent pathogens in humans and animals, while others are non-pathogenic or are opportunistic pathogens. Species resolution within Francisella varies with analyses of single genes, multiple gene or protein sets, or whole genome comparisons of nucleic acid and amino acid sequences. Analyses focusing on single genes (16S rRNA, sdhA), multiple gene sets (virulence genes, LPS biosynthesis, pathogenicity island) and whole genome comparisons (nucleotide and protein) gave congruent results, but with different discrimination confidence. We designate four new species within the genus; Francisella opportunistica sp. nov. (MA06-7296), Francisella salina sp. nov. (TX07-7308), Francisella uliginis sp. nov. (TX07-7310), and Francisella frigiditurris sp. nov. (CA97-1460). This study provides a robust comparative framework to discern species and virulence features of newly detected Francisellas IMPORTANCE: DNA-based detection and sequencing methods have identified thousands of new bacteria in the human body and the environment. In most cases, there are no cultured isolates that correspond to these sequences. While DNA-based approaches are highly sensitive, accurately assigning species is difficult without known near-relatives for comparison. This ambiguity poses challenges for clinical cases, disease epidemics and environmental surveillance, where response times must be short. Many new Francisella isolates have been identified globally. However, their species designations and potential for causing human disease remain ambiguous. Through detailed genome comparisons, we identified features that differentiate F. tularensis from clinical and environmental Francisella isolates and provide a knowledge base for future comparison of Francisellas identified in clinical samples or environmental surveys.

PMID: 27881415 [PubMed - as supplied by publisher]




Enhanced glucose consumption and organic acid production by engineered Corynebacterium glutamicum based on analysis of a pfkB1 deletion mutant.

Enhanced glucose consumption and organic acid production by engineered Corynebacterium glutamicum based on analysis of a pfkB1 deletion mutant.

Appl Environ Microbiol. 2016 Nov 23;:

Authors: Hasegawa S, Tanaka Y, Suda M, Jojima T, Inui M

Abstract
In the analysis of a carbohydrate metabolite pathway, we found interesting phenotypes in a mutant strain of Corynebacterium glutamicum deficient in pfkB1, which encodes fructose-1-phosphate kinase. After aerobically cultivated with fructose as a carbon source, this mutant consumed glucose and produced organic acid, predominantly L-lactate, more than 2-fold as compared with the wild-type grown with glucose under conditions of oxygen deprivation. This considerably higher fermentation capacity was unique for the combination of the pfkB1 deletion and fructose cultivation. In the metabolome and transcriptome analyses of this strain, marked intracellular accumulation of fructose-1-phosphate, and significant upregulation of several genes related to the phosphoenolpyruvate:carbohydrate phosphotransferase system, glycolysis, and organic acid synthesis were identified. We then examined strains overexpressing several of these identified genes, and demonstrated enhanced glucose consumption and organic acid production by these engineered strains, which values are comparable with those of the model pfkB1 deletion mutant grown with fructose. L-Lactate production by the ppc deletion mutant of the engineered strain was 2,390 mM (i.e., 215 g/L) after 48 h under oxygen deprivation, which was 2.7-fold increased over that of the ppc-deleted wild-type.
IMPORTANCE: Enhancement of glycolytic flux is important for improving microbiological production of chemicals, but overexpression of glycolytic enzymes has often resulted in little positive effect. That is presumably because central carbon metabolism is under the complex and strict regulation not only transcriptionally but also post-transcriptionally, such as by the ATP/ADP ratio. In contrast, we studied a mutant strain of Corynebacterium glutamicum that showed markedly enhanced glucose consumption and organic acid production, and based on the findings, identified several genes whose overexpression were effective to enhance glycolytic flux under conditions of oxygen deprivation. These results will help to understand the regulatory mechanisms of glycolytic flux, and can be widely applied to improvement of microbial production of useful chemicals.

PMID: 27881414 [PubMed - as supplied by publisher]