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Correction for Lee et al., "Production and Characterization of Neutralizing Antibodies against Bungarus multicinctus Snake Venom".
Correction for Lee et al., "Production and Characterization of Neutralizing Antibodies against Bungarus multicinctus Snake Venom". Appl Environ Microbiol. 2017 Nov 15;83(22): Authors: Lee CH, Lee YC, Leu SJ, Lin LT, Chiang JR, Hsu WJ, Yang YY PMID: 29089362 [PubMed - in process] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - November 3, 2017 Category: Microbiology Authors: Lee CH, Lee YC, Leu SJ, Lin LT, Chiang JR, Hsu WJ, Yang YY Tags: Appl Environ Microbiol Source Type: research

Correction for Derntl et al., "Novel Strategies for Genomic Manipulation of Trichoderma reesei with the Purpose of Strain Engineering".
Correction for Derntl et al., "Novel Strategies for Genomic Manipulation of Trichoderma reesei with the Purpose of Strain Engineering". Appl Environ Microbiol. 2017 Nov 15;83(22): Authors: Derntl C, Kiesenhofer DP, Mach RL, Mach-Aigner AR PMID: 29089363 [PubMed - in process] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - November 3, 2017 Category: Microbiology Authors: Derntl C, Kiesenhofer DP, Mach RL, Mach-Aigner AR Tags: Appl Environ Microbiol Source Type: research

Hindgut mucosa-associated microbiome interacting with host regulating Escherichia coli O157:H7 shedding in cattle.
This study investigated the recto-anal junction (RAJ) mucosa associated microbiota and its relationship with host gene expression in SS and cattle where E. coli O157:H7 was not detected (NS), aiming to elucidate the mechanisms involved in super-shedding. In total, 14 phyla, 66 families and 101 genera of RAJ mucosa-associated bacteria were identified and Firmicutes (61.5 ± 7.5%), Bacteroidetes (27.9 ± 6.4%) and Proteobacteria (5.5 ± 2.1%) were the predominant phyla. Differential abundance analysis of operational taxonomic units (OTUs) identified 2 OTUs unique to SS which were members of Bacteroides and ...
Source: Applied and Environmental Microbiology - October 27, 2017 Category: Microbiology Authors: Wang O, McAllister TA, Plastow G, Stanford K, Selinger B, Guan LL Tags: Appl Environ Microbiol Source Type: research

Enterococcus faecalis responds to individual exogenous fatty acids independently of saturation or chain length.
We examined fatty acids commonly found in serum and those normally produced by E. faecalis to determine which fatty acids can induce protection from membrane damage. Supplementation with individual fatty acids produced a myriad of different effects on cellular growth, morphology, and stress response. However, only host-derived unsaturated fatty acids provided stress protection. Future studies are aimed to understand how these specific fatty acids induce protection from membrane damage. PMID: 29079613 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - October 27, 2017 Category: Microbiology Authors: Saito HE, Harp JR, Fozo EM Tags: Appl Environ Microbiol Source Type: research

Divergent responses of forest soil microbial communities under elevated CO2 in different depths of upper soil layers.
This study revealed a positive feedback of eCO2 in forest soils microbial communities which may provide a new insight for further understanding of forest ecosystem responses to global CO2 increases.IMPORTANCE The concentration of atmospheric carbon dioxide (CO2) is continuously increasing since the industrial revolution. Understanding the response of soil microbial communities to elevated atmospheric CO2 (eCO2) is important for predicting the contribution of forest ecosystem to global atmospheric change. This study analyzed the effect of eCO2 on microbial communities at two soil depths (0-5cm and 5-15cm) in a forest ecosys...
Source: Applied and Environmental Microbiology - October 27, 2017 Category: Microbiology Authors: Yu H, He Z, Wang A, Xie J, Wu L, Van Nostrand JD, Jin D, Shao Z, Schadt CW, Zhou J, Deng Y Tags: Appl Environ Microbiol Source Type: research

β-glucanase activity of the oral bacterium Tannerella forsythia contributes to the growth of a partner species, Fusobacterium nucleatum, in co-biofilms.
This study highlights the involvement of β-glucanase activity in the development of T. forsythia - F. nucleatum biofilms, and suggest that intake of dietary β-glucans might be a contributing risk factor in plaque development and periodontal disease pathogenesis. PMID: 29079615 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - October 27, 2017 Category: Microbiology Authors: Honma K, Ruscitto A, Sharma A Tags: Appl Environ Microbiol Source Type: research

Can interspecies hybrid Zygosaccharomyces rouxii produce allohaploid gamete?
Abstract In soy sauce manufacturing, Candida versatilis plays a role in the production of volatile flavor compounds, such as volatile phenols, but limited accessible information on its genome has prevented further investigation regarding aroma production and breeding. Although the draft genome sequence data of two strains of C. versatilis have recently been reported, these strains are not similar to each other. Here, we reassess the draft genome sequence data for strain t-1, which was originally reported to be C. versatilis, and conclude that strain t-1 is most probably not C. versatilis but a gamete of hybrid Zyg...
Source: Applied and Environmental Microbiology - October 27, 2017 Category: Microbiology Authors: Watanabe J, Uehara K, Tsukioka Y Tags: Appl Environ Microbiol Source Type: research

Staphylococcus edaphicus sp. nov., isolated in Antarctica, harbours mecC gene and genomic islands with suspected role in adaptation to extreme environment.
Krištofová L, Kekláková J, Petráš P, Doškař J Abstract Two Gram-stain-positive, coagulase-negative staphylococcal strains were isolated from abiotic sources, stone fragments and sandy soil in James Ross Island, Antarctica. Here we describe properties of novel species of the genus Staphylococcus that has near identical 16S rRNA gene sequence to Staphylococcus saprophyticus However, compared to S. saprophyticus and the next closest relatives, the new species demonstrates considerable phylogenetic distance at whole genome level, average nucleotide identity
Source: Applied and Environmental Microbiology - October 27, 2017 Category: Microbiology Authors: Pantůček R, Sedláček I, Indráková A, Vrbovská V, Mašlaňová I, Kovařovic V, Švec P, Králová S, Krištofová L, Kekláková J, Petráš P, Doškař J Tags: Appl Environ Microbiol Source Type: research

Harnessing the periplasm of bacteria to develop biocatalyst for biosynthesis of highly pure chemicals.
Abstract Although biocatalytic transformation has shown great promise in chemical synthesis, there remain significant challenges in controlling high selectivity without the formation of undesirable byproducts. For instance, few attempts have been successful in constructing biocatalyst for de novo synthesis of pure flavin mononucleotide (FMN) due to riboflavin (RF) accumulating inside the cytoplasm and being secreted with FMN. To address this problem, we show here a novel biosynthesis strategy, compartmentalizing the final FMN biosynthesis step in the periplasm of an engineered Escherichia coli strain. This constru...
Source: Applied and Environmental Microbiology - October 27, 2017 Category: Microbiology Authors: Yang Y, Wu Y, Hu Y, Wang H, Guo L, Fredrickson JK, Cao B Tags: Appl Environ Microbiol Source Type: research

Identification of heterotrophic zinc mobilization processes among bacterial strains isolated from wheat rhizosphere (Triticum aestivum L).
In this study, wheat rhizosphere soil serial dilutions were plated onto several solid microbiological media supplemented with scarcely soluble Zn oxide (ZnO) and 115 putative Zn solubilizing isolates were directly detected based on the formation of solubilization halo around the colonies. Eight strains were selected based on their Zn solubilization efficiency and siderophore production capacity. These included one Curtobacterium, two Plantibacter, three Pseudomonas, one Stenotrophomonas and one strain of Streptomyces In ZnO liquid solubilization assays, the presence of glucose clearly stimulated organic acid production, le...
Source: Applied and Environmental Microbiology - October 27, 2017 Category: Microbiology Authors: Costerousse B, Schönholzer-Mauclaire L, Frossard E, Thonar C Tags: Appl Environ Microbiol Source Type: research

Influence of cis element arrangement on promoter strength in Trichoderma reesei.
Abstract Trichoderma reesei can produce up to 100 g/l of extracellular proteins. The major and industrially relevant products are the cellobiohydrolase CBHI and the hemicellulase XYNI. Both encoding genes are transcriptionally activated by the regulatory protein Xyr1. The first 850 nucleotides of the cbh1 promoter contain fourteen Xyr1-binding sites (XBS), in the xyn1 promoter are eight XBS present. Some of these XBS are arranged in tandem, others as inverted repeats. One such cis element, an inverted repeat, plays a crucial role for the inducibility of the xyn1 promoter. We investigated the impact of the properti...
Source: Applied and Environmental Microbiology - October 27, 2017 Category: Microbiology Authors: Kiesenhofer DP, Mach RL, Mach-Aigner AR Tags: Appl Environ Microbiol Source Type: research

Genomes of novel microbial lineages assembled from the sub-ice waters of Lake Baikal.
We present a metagenomic study of Lake Baikal (East Siberia). Two samples obtained from the water column under the ice cover (5 and 20 m deep) in March have been deep sequenced and the reads assembled to generate metagenome assembled genomes (MAGs) that are representative of the microbes living in this special environment. Compared with freshwater bodies studied around the world, Lake Baikal had an unusually high fraction of Verrucomicrobia Other groups such as Actinobacteria or Proteobacteria were in similar proportions as those found in other lakes. Genomes (and probably cells) tended to be of small size presumably refle...
Source: Applied and Environmental Microbiology - October 27, 2017 Category: Microbiology Authors: Cabello-Yeves PJ, Zemskaya TI, Rosselli R, Coutinho FH, Zakharenko AS, Blinov VV, Rodriguez-Valera F Tags: Appl Environ Microbiol Source Type: research

Fate of Salmonella enterica and Enterohemorrhagic Escherichia coli cells, Artificially Internalized into Vegetable Seeds during Germination.
This study was undertaken to observe the physiological behavior of Salmonella enterica and enterohemorrhagic Escherichia coli (EHEC) cells, artificially internalized into vegetable seeds during the germination process. Surface-decontaminated seeds of alfalfa, fenugreek, lettuce, and tomato were vacuum-infiltrated with four individual strains of Salmonella or EHEC. Contaminated seeds were germinated at 25°C for 9 days and different sprout/seedling tissues were microbiologically analyzed every other day. Internalization of Salmonella and EHEC cells into vegetable seeds was confirmed by the absence of pathogens in seed-ri...
Source: Applied and Environmental Microbiology - October 27, 2017 Category: Microbiology Authors: Liu D, Cui Y, Walcott R, Chen J Tags: Appl Environ Microbiol Source Type: research

Abundance and multilocus sequence analysis of Vibrio associated with diseased elkhorn coral, Acropora palmata, of the Florida Keys.
This study examined the association of Vibrio bacteria with WPX occurrence from August 2012--2014 at Looe Key Reef in the Florida Keys, USA. The concentration of cultivable Vibrio was consistently greater in WPX samples compared to healthy samples. The relative abundance of Vibrio bacteria to total bacteria was four times higher in samples from WPX lesions compared to adjacent apparently healthy regions of diseased corals based on quantitative PCR (qPCR). Multilocus sequence analysis (MLSA) was used to assess the diversity of 69 Vibrio isolates collected from diseased and apparently healthy A. palmata colonies and the surr...
Source: Applied and Environmental Microbiology - October 27, 2017 Category: Microbiology Authors: Kemp KM, Westrich JR, Alabady MS, Edwards ML, Lipp EK Tags: Appl Environ Microbiol Source Type: research

Deciphering the origin, evolution and physiological function of the subtelomeric aryl-alcohol dehydrogenase gene family in the yeast Saccharomyces cerevisiae.
Abstract Homology searches indicate that Saccharomyces cerevisiae strain BY4741 contains seven redundant genes that encode putative aryl-alcohol dehydrogenases (AAD). Yeast AADs are located in subtelomeric regions of different chromosomes, and their functional role(s) remain enigmatic. Here, we show that two of these genes, AAD4 and AAD14, encode functional enzymes that reduce aliphatic and aryl-aldehydes concomitant with oxidation of cofactor NADPH, and that Aad4p and Aad14p exhibit different substrate preference patterns. Other yeast AADs are undergoing pseudogenization. The 5' sequence of AAD15 has been deleted...
Source: Applied and Environmental Microbiology - October 27, 2017 Category: Microbiology Authors: Yang DD, de Billerbeck GM, Zhang JJ, Rosenzweig F, Francois JM Tags: Appl Environ Microbiol Source Type: research

Bioinformatics analysis and characterization of highly efficient polyvinyl alcohol (PVA)-degrading enzymes from the novel PVA degrader Stenotrophomonas rhizophila QL-P4.
Abstract Polyvinyl alcohol (PVA) is used widely in industry, and associated environmental pollution is a serious problem. Herein, we report a novel, efficient PVA degrader, Stenotrophomonas rhizophila QL-P4, isolated from fallen leaves from virgin forest in the Qinling Mountains. The complete genome was obtained using single-molecule real-time (SMRT) technology and corrected using Illumina sequencing. Bioinformatics analysis revealed eight PVA/OVA (vinyl alcohol oligomer)-degrading genes. Of these, seven genes were predicted to be involved in the classical intracellular PVA/OVA degradation pathway, and one (BAY15_...
Source: Applied and Environmental Microbiology - October 27, 2017 Category: Microbiology Authors: Wei Y, Fu J, Wu J, Jia X, Zhou Y, Li C, Dong M, Wang S, Zhang J, Chen F Tags: Appl Environ Microbiol Source Type: research

Compartmentalization of Carbaryl Degradation Pathway: Molecular Characterization of Inducible Periplasmic Carbaryl Hydrolase from Pseudomonas spp.
This study highlights the significance of compartmentalization of metabolic pathway enzymes for efficient removal of toxic compounds. PMID: 29079626 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - October 27, 2017 Category: Microbiology Authors: Gautam K, Shetty D, Trivedi VD, Varunjikar M, Phale PS Tags: Appl Environ Microbiol Source Type: research

F-specific RNA bacteriophages, especially members of subgroup II, should be reconsidered as good indicators of viral pollution of oysters.
In this study, we investigated the potential of F-specific RNA bacteriophages (FRNAPH) as indicators of viral contamination in oysters, by focusing especially on the subgroup FRNAPH-II. These viral indicators have been neglected because of their sometimes different behavior from that of NoV in shellfish, especially during the depuration processes usually performed before marketing. However, a significant bias needs to be taken into account which is that, in the absence of routine culture methods, NoV is targeted by genome detection while FRNAPH presence is usually investigated by isolation of infectious particles. In this ...
Source: Applied and Environmental Microbiology - October 27, 2017 Category: Microbiology Authors: Hartard C, Leclerc M, Rivet R, Maul A, Loutreul J, Banas S, Boudaud N, Gantzer C Tags: Appl Environ Microbiol Source Type: research

Neutralizing anti-STa antibodies derived from enterotoxigenic Escherichia coli (ETEC) toxoid fusions with heat-stable toxin (STa) mutant STaN12S, STaL9A/N12S or STaN12S/A14T show little cross-reactivity with guanylin or uroguanylin.
In this study, we generated nontoxic fusion antigens that induced antibodies neutralizing STa enterotoxicity in vitro and not cross-reacting with guanylin or uroguanylin. These fusions become the preferred antigens for developing ETEC vaccines to potentially prevent the deaths of hundreds of thousands of young children and hundreds of millions of diarrheal cases each year. PMID: 29079628 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - October 27, 2017 Category: Microbiology Authors: Duan Q, Huang J, Xiao N, Seo H, Zhang W Tags: Appl Environ Microbiol Source Type: research

Plasticity of the pyruvate node modulates hydrogen peroxide production and acid tolerance in multiple oral streptococci.
Abstract Commensal Streptococcus sanguinis and Streptococcus gordonii are pioneer oral biofilm colonizers. Characteristic for both is the SpxB-dependent production of H2O2, which is crucial for inhibiting competing biofilm members, especially the cariogenic species Streptococcus mutans H2O2 production is strongly impacted by environmental conditions, yet few mechanisms are known. Dental plaque pH is one of the key parameters dictating dental plaque ecology, and ultimately oral health status. Therefore, the objective of the current study was to characterize the effect of environmental pH upon H2O2 production by S. ...
Source: Applied and Environmental Microbiology - October 27, 2017 Category: Microbiology Authors: Cheng X, Redanz S, Cullin N, Zhou X, Xu X, Joshi V, Koley D, Merritt J, Kreth J Tags: Appl Environ Microbiol Source Type: research

Conditional Function of Autoaggregative Protein Cah and Common cah Mutations in Shiga Toxin-Producing Escherichia coli.
We examined the function of Cah in biofilm formation and host colonization to better understand selective pressures for cah mutations. EDL933-Cah played a conditional role in biofilm formation in vitro: it enhanced E. coli DH5α biofilm formation on glass surfaces under agitated culture conditions that prevented autoaggregation, but inhibited biofilm formation under hydrostatic conditions that facilitated autoaggregation. This function appeared to be strain-dependent since Cah-mediated biofilm formation was diminished when an EDL933-cah was expressed in SS17. Deletion of cah in EDL933 enhanced bacterial attachment to ...
Source: Applied and Environmental Microbiology - October 20, 2017 Category: Microbiology Authors: Carter MQ, Brandl MT, Kudva IT, Katani R, Moreau MR, Kapur V Tags: Appl Environ Microbiol Source Type: research

Estimating population turnover rates from relative quantification methods reveals microbial dynamics in marine sediment.
Abstract Difficulty quantifying biogeochemically significant microbes in marine sediments limits our ability to assess interspecific interactions, population turnover times, and niches of uncultured taxa. We incubated surface sediments from Cape Lookout Bight, North Carolina USA, anoxically at 21°C for 122 days. Sulfate decreased until day 68, after which methane increased, with hydrogen concentration consistent with predicted values of an electron donor exerting thermodynamic control. We measured turnover times using two relative quantification methods, quantitative PCR (qPCR) and the product of 16S gene read...
Source: Applied and Environmental Microbiology - October 20, 2017 Category: Microbiology Authors: Kevorkian R, Bird JT, Shumaker A, Lloyd KG Tags: Appl Environ Microbiol Source Type: research

Synthesis of heterologous mevalonic acid pathway enzymes in Clostridium ljungdahlii for the conversion of fructose and of syngas to mevalonate and isoprene.
This study demonstrates the ability to synthesize a heterologous metabolic pathway in C. ljungdahlii, an organism capable of metabolizing either simple sugars or syngas or both together (mixotrophy). Syngas is an inexpensive source of carbon and reducing equivalents and is produced as a major component of some industrial waste gas, and can be generated by gasification of cellulosic biowaste, and of municipal solid waste. Its conversion to useful products therefore offers potential cost and environmental benefits. The ability of C. ljungdahlii to grow mixotrophically also enables the recapture, should there be sufficient re...
Source: Applied and Environmental Microbiology - October 20, 2017 Category: Microbiology Authors: Diner BA, Fan J, Scotcher MC, Wells DH, Whited GM Tags: Appl Environ Microbiol Source Type: research

Engineering the enantioselectivity and thermostability of a (+)- γ-lactamase from Microbacterium hydrocarbonoxydans for the kinetic resolution of Vince lactam.
In this study, the enantioselectivity and thermostability of a (+)-γ-lactamase from Microbacterium hydrocarbonoxydans as the catalyst in the kinetic resolution of Vince lactam were improved. Enantiomerically pure (-)-Vince lactam is the key synthon in the synthesis of antiviral drugs such as carbovir and abacavir, which are used to fight against human HIV and hepatitis B viruses. The work was initialized by using the combinatorial active-site saturation test strategy to engineer the enantioselectivity of the enzyme. The approach resulted in two mutants, Val54Ser and Val54Leu, which catalyzed the hydrolysis of Vince l...
Source: Applied and Environmental Microbiology - October 20, 2017 Category: Microbiology Authors: Gao S, Zhu S, Huang R, Li H, Wang H, Zheng G Tags: Appl Environ Microbiol Source Type: research

Transcriptional activities of the microbial consortium living with the marine nitrogen-fixing cyanobacterium Trichodesmium reveal potential roles in community-level nitrogen cycling.
Abstract Trichodesmium are globally distributed cyanobacteria whose nitrogen-fixing capabilities fuel primary production in warm, oligotrophic oceans. Like many photoautotrophs, Trichodesmium serve as hosts to various other microorganisms, yet little is known about how this associated community modulates fluxes of environmentally relevant chemical species into and out of the supraorganismal structure. Here we utilized metatranscriptomics to examine gene-expression activities of microbial communities associated with Trichodesmium erythraeum (strain IMS101) using laboratory-maintained enrichment cultures that have p...
Source: Applied and Environmental Microbiology - October 20, 2017 Category: Microbiology Authors: Lee MD, Webb EA, Walworth NG, Fu FX, Held NA, Saito MA, Hutchins DA Tags: Appl Environ Microbiol Source Type: research

The enigmatic genome of an obligate ancient Spiroplasma symbiont in a hadal holothurian.
This study presents the genome of endosymbiotic spiroplasmas in the gut of sea cucumber captured in the Mariana trench. The extreme reduction of the genome and loss of essential metabolic pathways strongly support its endosymbiotic life mode. Moreover, a considerable part of the genome was occupied by CRISPR/Cas system to provide immunity against viruses and antimicrobial toxin-coding genes for degradation of microbes. This novel species of Spiroplasma is probably an important protective symbiont for the sea cucumbers in the hadal zone. PMID: 29054873 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - October 20, 2017 Category: Microbiology Authors: He LS, Zhang PW, Huang JM, Zhu FC, Danchin A, Wang Y Tags: Appl Environ Microbiol Source Type: research

Extracellular Polymeric Matrix Production and Relaxation under Fluid Shear and Mechanical Pressure in Staphylococcus aureus Biofilms.
Abstract The viscoelasticity of a biofilm's EPS (extracellular-polymeric-substance) matrix conveys protection against mechanical challenges, but adaptive responses of biofilm inhabitants to produce EPS are not well known. Here, we compare the response of a biofilm of an EPS producing (ATCC 12600) and non-EPS producing (5298) Staphylococcus aureus strain to fluid shear and mechanical challenge. Confocal-Laser-Scanning-Microscopy confirmed absence of calcofluorwhite-stainable EPS in biofilms of S. aureus 5298. ATR-FTIR spectroscopy combined with tribometry indicated that the polysaccharide production per bacterium i...
Source: Applied and Environmental Microbiology - October 20, 2017 Category: Microbiology Authors: Hou J, Veeregowda DH, van de Belt-Gritter B, Busscher HJ, van der Mei HC Tags: Appl Environ Microbiol Source Type: research

A novel steroid-coenzyme A ligase from Novosphingobium sp. strain Chol11 is essential for an alternative degradation pathway for bile salts.
This study provides further evidence of the diversity of metabolic pathways for the degradation of steroid compounds in environmental bacteria. The knowledge about these pathways contributes to the understanding of the CO2-releasing part of the global C-cycle. Furthermore, it is useful for investigating the fate of pharmaceutical steroids in the environment, some of which may act as endocrine disruptors. PMID: 29054875 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - October 20, 2017 Category: Microbiology Authors: Yücel O, Holert J, Ludwig KC, Thierbach S, Philipp B Tags: Appl Environ Microbiol Source Type: research

The Canonical Biotin Synthesis Enzyme, 8-Amino-7-Oxononanoate Synthase (BioF), Utilizes Different Acyl Chain Donors in Bacillus subtilis and Escherichia coli.
Abstract BioF (8-amino-7-oxononanoate synthase) is a strictly conserved enzyme that catalyzes the first step in assembly of the fused heterocyclic rings of biotin. The BioF acyl chain donor has long been thought to be pimeloyl-CoA. Indeed, in vitro the Escherichia coli and Bacillus sphaericus enzymes have been shown to condense pimeloyl-CoA with L-alanine in a pyridoxal 5' -phosphate-dependent reaction with concomitant CoA release and decarboxylation of L-alanine. However, recent in vivo studies of E. coli and Bacillus subtilis suggested that the BioF proteins of the two bacteria could have different specificities...
Source: Applied and Environmental Microbiology - October 20, 2017 Category: Microbiology Authors: Manandhar M, Cronan JE Tags: Appl Environ Microbiol Source Type: research

A mutator phenotype promoting the emergence of spontaneous oxidative stress resistant mutants in Campylobacter jejuni.
Abstract Campylobacter jejuni is a leading cause of foodborne illnesses worldwide. As a microaerophilic organism, C. jejuni must be able to defend against oxidative stress encountered both in the host and in the environment. How Campylobacter utilizes a mutation-based mechanism for adaptation to oxidative stress is still unknown. Here we present a previously undescribed phenotypic and genetic mechanism that promotes the emergence of oxidative stress resistant mutants. Specifically, we showed that a naturally occurring mutator phenotype, resulting from a loss of function mutation in the DNA repair enzyme MutY, incr...
Source: Applied and Environmental Microbiology - October 13, 2017 Category: Microbiology Authors: Dai L, Sahin O, Tang Y, Zhang Q Tags: Appl Environ Microbiol Source Type: research

Formation of Staphylococcus aureus biofilm in the presence of sub-lethal concentrations of disinfectants: a transcriptomic analysis using RNA-seq.
Abstract Staphylococcus aureus is a common biofilm-forming pathogen. Low doses of disinfectants have previously been reported to promote biofilm formation and to increase virulence. The aim of this study was to use RNA-seq analysis to investigate global transcriptional changes in S. aureus in response to sub-lethal concentrations of commonly used food industry disinfectants (ethanol, Et; chloramine T, ChT; and their combination, Et_ChT), in order to better understand the effects of these agents on biofilm formation.Treatment with Et and Et_ChT resulted in more significantly altered expression profiles, compared to...
Source: Applied and Environmental Microbiology - October 13, 2017 Category: Microbiology Authors: Slany M, Oppelt J, Cincarova L Tags: Appl Environ Microbiol Source Type: research

Role of wall shear stress on Cryptosporidium parvum oocyst attachment to environmental biofilms.
This study investigated Cryptosporidium parvum oocyst deposition onto biofilms as a function of shear stress under laminar or turbulent flow. Annular rotating bioreactors were used to grow stabilized stream biofilms at shear stresses ranging from 0.038 to 0.46 Pa. These steady-state biofilms were then used to assess the impact of hydrodynamic condition on C. parvum oocyst attachment. C. parvum deposition onto biofilms followed a pseudo-second-order model under both laminar (after a lag phase) and turbulent flows. The total number of oocysts attached to the biofilm at steady state decreased as the hydrodynamic wall shear st...
Source: Applied and Environmental Microbiology - October 13, 2017 Category: Microbiology Authors: Luo X, Jedlicka SS, Jellison KL Tags: Appl Environ Microbiol Source Type: research

Conjugation-mediated horizontal gene transfer of Clostridium perfringens plasmids in the chicken gastrointestinal tract results in the formation of new virulent strains.
This study has investigated the effect of plasmid transfer on disease pathogenesis, with two genetically distinct transconjugants constructed under in vitro conditions, within the intestinal tract of chickens. This study also demonstrates that plasmid transfer can occur naturally in the host gut environment, without the need for antibiotic selective pressure to be applied. The demonstration of plasmid transfer within the chicken host may have implications for disease progression and pathogenesis of C. perfringens-mediated disease. Such horizontal gene transfer events are likely to be common in the clostridia and may be a k...
Source: Applied and Environmental Microbiology - October 13, 2017 Category: Microbiology Authors: Lacey JA, Keyburn AL, Ford ME, Portela RW, Johanesen PA, Lyras D, Moore RJ Tags: Appl Environ Microbiol Source Type: research

Multiple roles of two efflux pumps in a polycyclic aromatic hydrocarbon-degrading Pseudomonas putida strain B6-2 (DSM 28064).
This study provides insights into the versatile physiological functions of the widely distributed efflux pumps in the biodegradation of PAHs.IMPORTANCE PAHs are notorious for their recalcitrance to degradation in environment. The high frequency of the occurrence of the efflux pump genes was observed in the genomes of effective PAH-degraders; however, their specific roles in the degradation of PAHs are still obscure. The significance of our study is identifying the function and mechanism of the efflux pump SrpABC of Pseudomonas putida strain B6-2 (DSM 28064) in the biphenyl degradation process. SrpABC is crucial in releasin...
Source: Applied and Environmental Microbiology - October 13, 2017 Category: Microbiology Authors: Yao X, Tao F, Zhang K, Tang H, Xu P Tags: Appl Environ Microbiol Source Type: research

Methanogenic paraffin biodegradation: alkylsuccinate synthase gene quantification and dicarboxylic acid production.
Abstract Paraffinic n-alkanes (> C17) that are solid at ambient temperature comprise a large fraction of many crude oils. The comparatively low water solubility and reactivity of these long-chain alkanes can lead to their persistence in the environment following fuel spills, and pose serious problems for crude oil recovery operations by clogging oil production wells. However, the degradation of waxy paraffins under the anoxic conditions characterizing contaminated groundwater environments and deep subsurface energy reservoirs is poorly understood. Here, we assessed the ability for a methanogenic culture enriche...
Source: Applied and Environmental Microbiology - October 13, 2017 Category: Microbiology Authors: Oberding LK, Gieg LM Tags: Appl Environ Microbiol Source Type: research

An A/U-rich enhancer region is required for high-level protein secretion through the HlyA Type I secretion system.
Abstract Efficient protein secretion is often a valuable alternative to classic cellular expression. Early on, bacterial Type I secretion systems (T1SS) were employed to allow heterologous secretion of fusion proteins. However, this approach was not fully exploited, as many proteins could not be secreted at all or only at low levels. Here, we present an engineered microbial secretion system, which allows the effective production of proteins up to a molecular weight above 88 kDa. This system is based on the hemolysin A (HlyA) T1SS of the Gram-negative bacterium Escherichia coli, which exports polypeptides when fuse...
Source: Applied and Environmental Microbiology - October 13, 2017 Category: Microbiology Authors: Khosa S, Scholz R, Schwarz C, Trilling M, Hengel H, Jaeger KE, Smits SHJ, Schmitt L Tags: Appl Environ Microbiol Source Type: research

A novel metabolic pathway for N-Methylpyrrolidone degradation in Alicycliphilus sp. BQ1.
, Lozano L, Cruz-Gómez MJ, Loza-Tavera H Abstract The molecular mechanisms underlying the biodegradation of N-Methylpyrrolidone (NMP), a widely used industrial solvent that produces skin irritation in humans, and is teratogenic in rats, are unknown. Alicycliphilus sp. BQ1 degrades NMP. By studying a transposon-tagged mutant unable to degrade NMP, we identified a six-gene cluster (nmpABCDEF), transcribed as a polycistronic mRNA, encoding enzymes involved in NMP biodegradation. nmpA and the transposon-affected gene nmpB encode a N-methylhydantoin amidohydrolase that would transform NMP to γ-N-methylamin...
Source: Applied and Environmental Microbiology - October 13, 2017 Category: Microbiology Authors: Solís-González CJ, Domínguez-Malfavón L, Vargas-Suárez M, Gaytán I, Cevallos MÁ, Lozano L, Cruz-Gómez MJ, Loza-Tavera H Tags: Appl Environ Microbiol Source Type: research

Common presence of aerobic anoxygenic photosynthesis within the genus Limnohabitans.
In this study, we detected photosynthesis genes pufLM and bchY in 28 out of 46 strains from three Limnohabitans lineages. The obtained pufM sequences are very closely related to environmental pufM sequences detected in various freshwater habitats, indicating ubiquity and potential importance of photoheterotrophic Limnohabitans in nature.Additionally, we sequenced and analyzed the genomes of 5 potentially photoheterotrophic Limnohabitans strains to gain further insights into their phototrophic capacity. The structure of the photosynthesis gene cluster turned out to be highly conserved within the genus Limnohabitans and also...
Source: Applied and Environmental Microbiology - October 13, 2017 Category: Microbiology Authors: Kasalický V, Zeng Y, Piwosz K, Šimek K, Kratochvilová H, Koblížek M Tags: Appl Environ Microbiol Source Type: research

Microhomology Mediated High-throughput Gene Inactivation Strategy for Hyperthermophilic Crenarchaeon Sulfolobus islandicus.
Abstract Sulfolobus islandicus is rapidly emerging as a model system for studying the biology and evolution within the TACK lineage of the Archaeal domain. As the tree of life grows, identifying the cellular function of genes within this lineage will have significant impacts on our understanding of the evolution of Last Archaeal Eukaryote Common Ancestor (LEACA) and the differentiation of Archaea from Eukaryotes during the evolution of the modernday cell. To progress our understanding of this key Archaeal organism, we report a novel high-throughput method for targeted gene inactivation in S. islandicus through one...
Source: Applied and Environmental Microbiology - October 13, 2017 Category: Microbiology Authors: Zhang C, Whitaker RJ Tags: Appl Environ Microbiol Source Type: research

Comparative genomics-based markers: discrimination of host-specificity in Fusarium oxysporum.
Abstract The polyphyletic nature of many formae speciales of Fusarium oxysporum (Fo) prevents molecular identification of newly encountered strains based on conserved, vertically inherited genes. Alternative molecular detection methods that could replace labour- and time-intensive disease assays are therefore highly desired. Effectors are functional elements in the pathogen-host interaction and have been found to show very limited sequence diversity between strains of the same forma specialis, which makes them potential markers for host-specific pathogenicty. We therefore compared candidate effector genes extracte...
Source: Applied and Environmental Microbiology - October 13, 2017 Category: Microbiology Authors: van Dam P, de Sain M, Ter Horst A, van der Gragt M, Rep M Tags: Appl Environ Microbiol Source Type: research

Housefly (Musca domestica) and blow fly (Protophormia terraenovae) as vectors of colistin resistance genes-carrying bacteria.
This study reports mcr-1 carriage in Providencia spp. and detection of mcr-2 and mcr-3 after their initial identification in Belgium and China, respectively. This study suggests flies might contribute significantly to the dissemination of bacteria carrying these genes into a large variety of ecological niches. Further studies are warranted to explore the roles that flies might play in the spread of colistin resistance genes.Importance Antimicrobial resistance is recognized as one of the most serious global threats to human health. An option for treatment of the Gram-negative ESKAPE bacteria with multiple drug resistance wa...
Source: Applied and Environmental Microbiology - October 13, 2017 Category: Microbiology Authors: Zhang J, Wang J, Chen L, Yassin AK, Kelly P, Butaye P, Li J, Gong J, Cattley R, Qi K, Wang C Tags: Appl Environ Microbiol Source Type: research

Prevalence and Antimicrobial Resistance of Enterococci Isolated from Retail Meats in the United States, 2002-2014.
Abstract Bacteria of the genus Enterococcus are important human pathogens that are frequently resistant to a number of clinically important antibiotics. They are also used as a marker of animal fecal contamination of human foods, and are employed as sentinel organisms for tracking trends in resistance to antimicrobials with gram-positive activity. As part of the National Antimicrobial Resistance Monitoring System (NARMS), we evaluated several retail meat commodities for the presence of enterococci from 2002-2014, finding 92.0% to be contaminated. The majority of isolates were either E. faecalis (64.0%) or E. faeci...
Source: Applied and Environmental Microbiology - October 13, 2017 Category: Microbiology Authors: Tyson GH, Nyirabahizi E, Crarey E, Kabera C, Lam C, Rice-Trujillo C, McDermott PF, Tate H Tags: Appl Environ Microbiol Source Type: research

Purification, characterization and heterologous production of plantaricyclin A, a novel circular bacteriocin produced by Lactobacillus plantarum NI326.
Abstract Bacteriocins from lactic acid bacteria (LAB) are of increasing interest in recent years due to their potential as natural preservatives against food and beverage spoilage microorganisms. In a screening study for LAB, we isolated a strain, Lactobacillus plantarum NI326, from olives with activity against a strain belonging to the beverage-spoilage bacterium Alicyclobacillus acidoterrestris spp. Genome sequencing of the strain enabled the identification of a gene cluster encoding a putative circular bacteriocin and proteins involved in its modification, transport and immunity. This novel bacteriocin, named p...
Source: Applied and Environmental Microbiology - October 13, 2017 Category: Microbiology Authors: Borrero J, Kelly E, O'Connor PM, Kelleher P, Scully C, Cotter PD, Mahony J, van Sinderen D Tags: Appl Environ Microbiol Source Type: research

Genotypic and phenotypic characteristics in association with biofilm formation in different pathotypes of human clinical Escherichia coli isolates.
In this study, we genotypically and phenotypically characterized 187 human clinical E. coli isolates representing various pathotypes (e.g., uropathogenic, enteropathogenic and enteroaggregative E. coli). We investigated the presence of biofilm-associated genes ("genotype") and phenotypically analyzed the isolates for motility, curli and cellulose production ("phenotype"). We developed a new screening method to examine the in vitro biofilm formation ability. In summary, we found a high prevalence of biofilm-associated genes. However, we could not detect a biofilm-associated gene or specific phenotype cor...
Source: Applied and Environmental Microbiology - October 6, 2017 Category: Microbiology Authors: Schiebel J, Böhm A, Nitschke J, Burdukiewicz M, Weinreich J, Ali A, Roggenbuck D, Rödiger S, Schierack P Tags: Appl Environ Microbiol Source Type: research

Phylogenetic Background and Virulence-Associated Traits of Escherichia coli Obtained from Surface Waters and Diverse Animals in Minnesota and Wisconsin.
Abstract Possible external reservoirs for extraintestinal pathogenic Escherichia coli (ExPEC) strains that cause infections in humans are poorly defined. Because of the tremendous human health importance of ExPEC infections, we assessed surface waters and domesticated and wild animals in Minnesota and Wisconsin as potential reservoirs of ExPEC of human health relevance. We characterized 595 E. coli isolates (obtained from 1999-2002; 280 from seven surface water sites, 315 from feces of 13 wild and domesticated animal species) for phylogroup and virulence genotype, including inferred ExPEC status, by using multiple...
Source: Applied and Environmental Microbiology - October 6, 2017 Category: Microbiology Authors: Johnson JR, Johnston BD, Delavari P, Thuras P, Clabots C, Sadowsky MJ Tags: Appl Environ Microbiol Source Type: research

The murein hydrolase LytF of Streptococcus sanguinis and the ecological consequences of competence development.
Abstract The overall health of the oral cavity is dependent upon a proper homeostasis between health-associated bacterial colonizers and bacteria known to promote dental caries. Streptococcus sanguinis is a health-associated commensal, a known early colonizer of the acquired tooth pellicle, and is naturally competent. We have shown that LytF, a competence-controlled murein hydrolase, is capable of inducing the release of extracellular DNA (eDNA) from oral bacteria. Precipitated and purified LytF were used as treatments against planktonic cultures and biofilms. Higher amounts of eDNA were released from cultures tre...
Source: Applied and Environmental Microbiology - October 6, 2017 Category: Microbiology Authors: Cullin N, Redanz S, Lampi KJ, Merritt J, Kreth J Tags: Appl Environ Microbiol Source Type: research

Chromosomal aneuploidy improves brewing characteristics of sake yeast.
Abstract The effect of chromosomal aneuploidy on the brewing characteristics in brewery yeasts has not been studied. Here, we report that chromosomal aneuploidy in sake brewery yeast (Saccharomyces cerevisiae) leads to the development of favorable brewing characteristics. We found that pyruvate-underproducing sake yeast, which produces less off-flavor diacetyl, is aneuploid and trisomic for chromosomes XI and XIV. To confirm that this phenotype is due to aneuploidy, we obtained 45 haploids with various chromosomal additions and investigated their brewing profiles. A greater number of chromosomes correlated with a ...
Source: Applied and Environmental Microbiology - October 6, 2017 Category: Microbiology Authors: Kadowaki M, Fujimaru Y, Taguchi S, Ferdouse J, Sawada K, Kimura Y, Terasawa Y, Agrimi G, Anai T, Noguchi H, Toyoda A, Fujiyama A, Akao T, Kitagaki H Tags: Appl Environ Microbiol Source Type: research

Stringent Response Regulators Contribute to the Recovery from Glucose-Phosphate Stress in Escherichia coli.
Abstract In enteric bacteria like Escherichia coli, the transcription factor SgrR and the small RNA SgrS regulate the response to glucose-phosphate stress, a metabolic dysfunction that results in growth inhibition and stems from the intracellular accumulation of sugar-phosphates. SgrR activates transcription of sgrS, and SgrS helps to rescue cells from stress in part by inhibiting uptake of stressor sugar-phosphates. While the regulatory targets of this stress response are well described, less is known about how the SgrR-SgrS response itself is regulated. To further characterize regulation of the glucose-phosphate...
Source: Applied and Environmental Microbiology - October 6, 2017 Category: Microbiology Authors: Kessler JR, Cobe BL, Richards GR Tags: Appl Environ Microbiol Source Type: research

Differential MS2 Interaction with Food Contact Surfaces Determined by Atomic Force Microscopy and Virus Recovery.
Abstract Enteric viruses are recognized as a major etiology for U.S. foodborne infections. These viruses are easily transmitted via food contact surfaces. Understanding virus interactions with surfaces may facilitate developing improved means for their removal thus reducing transmission. Using MS2 coliphage as a virus surrogate, the strength of virus adhesion onto common food processing and preparation surfaces of polyvinyl chloride (PVC) and glass were assessed by atomic force microscopy (AFM) and virus recovery assays. The interaction forces of MS2 to various surfaces were measured from adhesion peaks in force-d...
Source: Applied and Environmental Microbiology - October 6, 2017 Category: Microbiology Authors: Shim J, Stewart DS, Nikolov AD, Wasan DT, Wang R, Yan R, Shieh YC Tags: Appl Environ Microbiol Source Type: research

Stenotrophomonas-like bacteria are widespread symbionts in cone snail venom ducts.
Abstract Cone snails are biomedically important sources of peptide drugs, but it is not known whether snail-associated bacteria affect venom chemistry. To begin to answer this question, we performed 16S rRNA gene amplicon sequencing of eight cone snail species, comparing their microbiomes with each other and with those from a variety of other marine invertebrates. We show that the cone snail microbiome is distinct from those in other marine invertebrates and conserved in specimens from around the world, including the Philippines, Guam, California, and Florida. We found that all venom ducts examined contain diverse...
Source: Applied and Environmental Microbiology - October 6, 2017 Category: Microbiology Authors: Torres JP, Tianero MD, Robes JMD, Kwan JC, Biggs JS, Concepcion GP, Olivera BM, Haygood MG, Schmidt EW Tags: Appl Environ Microbiol Source Type: research