Growth promotion and gut microbiota: insights from antibiotic use.

abstract：:Molecular approaches have revealed considerable diversity and uncultured novelty in natural prokaryotic populations, but not direct links between the new genotypes detected and ecosystem processes. Here we describe the influence of the structure of communities of ammonia-oxidizing bacteria on nitrogen cycling in micro...

journal_title：Environmental microbiology

authors： Webster G,Embley TM,Freitag TE,Smith Z,Prosser JI

更新日期：2005-05-01 00:00:00

abstract：:Xeromyces bisporus can grow on sugary substrates down to 0.61, an extremely low water activity. Its genome size is approximately 22 Mb. Gene clusters encoding for secondary metabolites were conspicuously absent; secondary metabolites were not detected experimentally. Thus, in its 'dry' but nutrient-rich environment, X...

journal_title：Environmental microbiology

authors： Leong SL,Lantz H,Pettersson OV,Frisvad JC,Thrane U,Heipieper HJ,Dijksterhuis J,Grabherr M,Pettersson M,Tellgren-Roth C,Schnürer J

更新日期：2015-02-01 00:00:00

abstract：:Mas5, a yeast heat shock protein classified to the Hsp40 group, is homologous to bacterial archetype DnaJ but functionally unexplored in filamentous fungi. Here we identify a Mas5 homologue (46.86 kDa) in Beauveria bassiana and show its indispensability for host infection and environmental adaptation of the fungal ins...

journal_title：Environmental microbiology

authors： Wang J,Ying SH,Hu Y,Feng MG

更新日期：2016-03-01 00:00:00

abstract：:A common bacterial strategy for monitoring environmental challenges is to use two-component systems, which consist of a sensor histidine kinase (HK) and a response regulator (RR). In the food-borne pathogen Bacillus cereus, the alternative sigma factor sigma(B) is activated by the RR RsbY. Here we present strong indic...

journal_title：Environmental microbiology

authors： de Been M,Tempelaars MH,van Schaik W,Moezelaar R,Siezen RJ,Abee T

更新日期：2010-03-01 00:00:00

abstract：:Although the roles of introns have been much debated in eukaryotic organisms, none of them have been functionally characterized in Fusarium graminearum. In this study, we characterized the roles of introns in regulation of fungicide-sensitivity of F. graminearum. β2 tub, cyp51A and myosin-5 are important target genes ...

journal_title：Environmental microbiology

authors： Li Y,Luo S,Jia X,Zhu Y,Chen D,Duan Y,Hou Y,Zhou M

更新日期：2017-10-01 00:00:00

abstract：:The bacterial diversity of an industrial biofilter used for waste gas abatement in an animal-rendering plant was investigated. A 16S rDNA clone library was generated and 444 clones were screened using computer-aided amplified ribosomal DNA restriction analysis (ARDRA). Of the screened clones, 60.8% showed unique ARDRA...

journal_title：Environmental microbiology

authors： Friedrich U,Prior K,Altendorf K,Lipski A

更新日期：2002-11-01 00:00:00

abstract：:Cultivation-independent surveys of ribosomal RNA genes have revealed the existence of novel microbial lineages, many with no known cultivated representatives. Ribosomal RNA-based analyses, however, often do not provide significant information beyond phylogenetic affiliation. Analysis of large genome fragments recovere...

journal_title：Environmental microbiology

authors： Béjà O,Suzuki MT,Koonin EV,Aravind L,Hadd A,Nguyen LP,Villacorta R,Amjadi M,Garrigues C,Jovanovich SB,Feldman RA,DeLong EF

更新日期：2000-10-01 00:00:00

abstract：:Although plants introduced for site restoration are pre-selected for specific traits (e.g. trace element bioaccumulation, rapid growth in poor soils), the in situ success of these plants likely depends on the recruitment of appropriate rhizosphere microorganisms from their new environment. We introduced three willow (...

journal_title：Environmental microbiology

authors： Bell TH,Cloutier-Hurteau B,Al-Otaibi F,Turmel MC,Yergeau E,Courchesne F,St-Arnaud M

更新日期：2015-08-01 00:00:00

abstract：:In this paper we present the in silico assessment of the diversity of variable regions of the small subunit ribosomal RNA (SSU rRNA) gene based on an ecosystem-specific curated database, describe a probe design procedure based on two hypervariable regions with minimal redundancy and test the potential of such probe de...

journal_title：Environmental microbiology

authors： Rajilić-Stojanović M,Heilig HG,Molenaar D,Kajander K,Surakka A,Smidt H,de Vos WM

更新日期：2009-07-01 00:00:00

abstract：:Studies assessing the effects of anthropogenic inputs on the taxonomic and functional diversity of bacterioplankton communities in lotic ecosystems are limited. Here, we applied 16S rRNA gene amplicon and whole-genome shotgun sequencing to examine the microbial diversity in samples from the Kalamas River (Northwest Gr...

journal_title：Environmental microbiology

authors： Meziti A,Tsementzi D,Ar Kormas K,Karayanni H,Konstantinidis KT

更新日期：2016-12-01 00:00:00

abstract：:The bacterial degradation of polysaccharides is central to marine carbon cycling, but little is known about the bacterial taxa that degrade specific marine polysaccharides. Here, bacterial growth and community dynamics were studied during the degradation of the polysaccharides chitin, alginate and agarose in microcosm...

journal_title：Environmental microbiology

authors： Wietz M,Wemheuer B,Simon H,Giebel HA,Seibt MA,Daniel R,Brinkhoff T,Simon M

更新日期：2015-10-01 00:00:00

abstract：:In recent years, the importance of the Gram-negative bacterium Stenotrophomonas as an opportunistic pathogen as well as in biotechnology has increased. The aim of the present study was to develop new methods for distinguishing between strains closely related to the potentially human pathogenic Stenotrophomonas maltoph...

journal_title：Environmental microbiology

authors： Ribbeck-Busch K,Roder A,Hasse D,de Boer W,Martínez JL,Hagemann M,Berg G

更新日期：2005-11-01 00:00:00

abstract：:Marine myoviruses (i.e. bacteriophages with a contractile tail sheath) are numerically abundant and genetically diverse. We developed a terminal restriction fragment length polymorphism assay (TRFLP) for g23, the conserved gene encoding the major capsid protein, to investigate T4-like myovirus communities at USC's Mic...

journal_title：Environmental microbiology

authors： Chow CE,Fuhrman JA

更新日期：2012-08-01 00:00:00

abstract：:Methanogenesis was characterized in hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico both in situ and after long-term manipulation in a greenhouse environment. Substrate addition experiments indicate methanogenesis to occur primarily through the catabolic demethylation of non-competitive sub...

journal_title：Environmental microbiology

authors： Smith JM,Green SJ,Kelley CA,Prufert-Bebout L,Bebout BM

更新日期：2008-02-01 00:00:00

abstract：:Pseudomonas aeruginosa is a widely distributed environmental bacterium but is also an opportunistic pathogen that represents an important health hazard due to its high intrinsic antibiotic resistance and its production of virulence factors. The genetic structure of P. aeruginosa populations using whole genome sequence...

journal_title：Environmental microbiology

authors： García-Ulloa M 2nd,Ponce-Soto GY,González-Valdez A,González-Pedrajo B,Díaz-Guerrero M,Souza V,Soberón-Chávez G

更新日期：2019-08-01 00:00:00

abstract：:Many bacterial pathogens rely on quorum sensing to control virulence gene expression. Based on numerous experiments conducted under well-defined conditions, quorum sensing interference is considered as a promising strategy to tackle infections and thus might have the potential to (partially) replace antibiotics. Despi...

journal_title：Environmental microbiology

authors： Liu Y,Qin Q,Defoirdt T

更新日期：2018-11-01 00:00:00

abstract：:The d- and l-forms of lactate are important fermentation metabolites produced by intestinal bacteria but are found to negatively affect mucosal barrier function and human health. Both enantiomers of lactate can be converted with acetate into the presumed beneficial butyrate by a phylogenetically related group of anaer...

journal_title：Environmental microbiology

authors： Shetty SA,Boeren S,Bui TPN,Smidt H,de Vos WM

更新日期：2020-11-01 00:00:00

abstract：:Eco-physiological variation and local adaptation are key issues in microbial ecology. Here, we investigated the thermal adaptation of 19 strains of the same Spumella morphospecies (Chrysophyceae, Heterokonta). In order to test for local adaptation and the existence of specific ecotypes we analysed growth rates of thes...

journal_title：Environmental microbiology

authors： Boenigk J,Jost S,Stoeck T,Garstecki T

更新日期：2007-03-01 00:00:00

abstract：:Food security depends on enhancing production and reducing loss to pests and pathogens. A promising alternative to agrochemicals is the use of plant growth-promoting rhizobacteria (PGPR), which are commonly associated with many, if not all, plant species. However, exploiting the benefits of PGPRs requires knowledge of...

journal_title：Environmental microbiology

authors： Alsohim AS,Taylor TB,Barrett GA,Gallie J,Zhang XX,Altamirano-Junqueira AE,Johnson LJ,Rainey PB,Jackson RW

更新日期：2014-07-01 00:00:00

abstract：:Despite recognition of the importance of soil bacteria to terrestrial ecosystem functioning there is little consensus on the factors regulating belowground biodiversity. Here we present a multi-scale spatial assessment of soil bacterial community profiles across Great Britain (> 1000 soil cores), and show the first la...

journal_title：Environmental microbiology

authors： Griffiths RI,Thomson BC,James P,Bell T,Bailey M,Whiteley AS

更新日期：2011-06-01 00:00:00

abstract：:Nutrient scarcity is a common condition in nature, but the resulting extremely low growth rates (below 0.025 h(-1) ) are an unexplored research area in Bacillus subtilis. To understand microbial life in natural environments, studying the adaptation of B. subtilis to near-zero growth conditions is relevant. To this end...

journal_title：Environmental microbiology

authors： Overkamp W,Ercan O,Herber M,van Maris AJ,Kleerebezem M,Kuipers OP

更新日期：2015-02-01 00:00:00

abstract：:Biofilms are dynamic players in biogeochemical cycling in running waters and are subjected to environmental stressors like those provoked by climate change. We investigated whether a 2°C increase in flowing water would affect prokaryotic community composition and heterotrophic metabolic activities of biofilms grown un...

journal_title：Environmental microbiology

authors： Romaní AM,Borrego CM,Díaz-Villanueva V,Freixa A,Gich F,Ylla I

更新日期：2014-08-01 00:00:00

abstract：:Soda lakes are an environment with an unusually high pH and often high salinity. To identify the active methanotrophs in the Soda lake sediments, sediment slurries were incubated with a 10% (v/v) (13)CH(4) headspace and the (13)C-labelled DNA was subsequently extracted from these sediments following CsCl density gradi...

journal_title：Environmental microbiology

authors： Lin JL,Radajewski S,Eshinimaev BT,Trotsenko YA,McDonald IR,Murrell JC

更新日期：2004-10-01 00:00:00

abstract：:An enriched sulphidogenic consortium capable of mineralizing benzene was used to study the metabolic pathway of anaerobic benzene degradation. Benzoate was detected in active cultures and benzene was confirmed to be the source of this benzoate by the addition of deuterated benzene (D6) and subsequent detection of deut...

journal_title：Environmental microbiology

authors： Phelps CD,Zhang X,Young LY

更新日期：2001-09-01 00:00:00

abstract：:The mqsRA operon encodes a toxin-antitoxin pair that was characterized to participate in biofilm and persister cell formation in Escherichia coli. Notably, the antitoxin MqsA possesses a C-terminal DNA-binding domain that recognizes the [5'-AACCT(N)2-4 AGGTT-3'] motif and acts as a transcriptional regulator controllin...

journal_title：Environmental microbiology

authors： Wang Y,Zhang SP,Zhang MY,Kempher ML,Guo DD,Han JT,Tao X,Wu Y,Zhang LQ,He YX

更新日期：2019-05-01 00:00:00

abstract：:Trichodesmium spp. play key roles in global carbon and nitrogen budgets and thus defining what controls their productivity is important for understanding climate change. While iron availability has been shown to be an important chemical factor for controlling both growth and nitrogen fixation rates in Trichodesmium, a...

journal_title：Environmental microbiology

authors： Chappell PD,Webb EA

更新日期：2010-01-01 00:00:00

abstract：:Environmental SSU rDNA-based surveys are contributing to the dramatic revision of eukaryotic high-level diversity and phylogeny as the number of sequence data increases. This ongoing revolution gives the opportunity to test for the presence of some eukaryotic taxa in environments where they have not been found using c...

journal_title：Environmental microbiology

authors： Lejzerowicz F,Pawlowski J,Fraissinet-Tachet L,Marmeisse R

更新日期：2010-09-01 00:00:00

abstract：:How to explore protein sequence space efficiently and how to generate high-quality mutant libraries that allow to identify improved variants with current screening technologies are key questions for any directed protein evolution experiment. High-quality mutant libraries can be generated through improved random mutage...

journal_title：Environmental microbiology

authors： Wong TS,Roccatano D,Schwaneberg U

更新日期：2007-11-01 00:00:00

abstract：:Fragilariopsis is a dominating psychrophilic diatom genus in polar sea ice. The two species Fragilariopsis cylindrus and Fragilariopsis curta are able to grow and divide below freezing temperature of sea water and above average sea water salinity. Here we show that antifreeze proteins (AFPs), involved in cold adaptati...

journal_title：Environmental microbiology

authors： Bayer-Giraldi M,Uhlig C,John U,Mock T,Valentin K

更新日期：2010-04-01 00:00:00

abstract：:The genome of the soil bacterium Pseudomonas putida strain KT2440 has been erased of various determinants of resistance to antibiotics encoded in its extant chromosome. To this end, we employed a coherent genetic platform that allowed the precise deletion of multiple genomic segments in a large variety of Gram-negativ...

journal_title：Environmental microbiology

authors： Martínez-García E,de Lorenzo V

更新日期：2011-10-01 00:00:00