Publications

common contaminants in next-generation sequencing that hinder discovery of low-abundance microbes.	unbiased high-throughput sequencing of whole metagenome shotgun dna libraries is a promising new approach to identifying microbes in clinical specimens, which, unlike other techniques, is not limited to known sequences. unlike most sequencing applications, it is highly sensitive to laboratory contaminants as these will appear to originate from the clinical specimens. to assess the extent and diversity of sequence contaminants, we aligned 57 "1000 genomes project" sequencing runs from six centers ...	2014	24837716
risk assessment of the schmutzdecke of biosand filters: identification of an opportunistic pathogen in schmutzdecke developed by an unsafe water source.	the biosand filter (bsf) is widely applied in developing counties as an appropriate technology-based product for supplying "safe" water. biosand filters exhibit relatively high purifying efficiency because of the schmutzdecke (biofilm) embedded in them. however, schmutzdecke should be cleaned or discarded on a regular basis to maintain the purifying efficiency of the bsf. due to its role in bsfs, the purifying function of schmutzdecke, rather than its potential risk when not properly discarded, ...	2014	24534769
evaluation of microbial bacterial and fungal diversity in cerebrospinal fluid shunt infection.	cerebrospinal fluid shunt infection can be recalcitrant. recurrence is common despite appropriate therapy for the pathogens identified by culture. improved diagnostic and therapeutic approaches are required, and culture-independent molecular approaches to cerebrospinal fluid shunt infections have not been described.	2014	24421877
parallel histories of horizontal gene transfer facilitated extreme reduction of endosymbiont genomes in sap-feeding insects.	bacteria confined to intracellular environments experience extensive genome reduction. in extreme cases, insect endosymbionts have evolved genomes that are so gene-poor that they blur the distinction between bacteria and endosymbiotically derived organelles such as mitochondria and plastids. to understand the host's role in this extreme gene loss, we analyzed gene content and expression in the nuclear genome of the psyllid pachypsylla venusta, a sap-feeding insect that harbors an ancient endosym ...	2014	24398322
growth conditions determine the dnf2 requirement for symbiosis.	rhizobia and legumes are able to interact in a symbiotic way leading to the development of root nodules. within nodules, rhizobia fix nitrogen for the benefit of the plant. these interactions are efficient because spectacularly high densities of nitrogen fixing rhizobia are maintained in the plant cells. dnf2, a medicago truncatula gene has been described as required for nitrogen fixation, bacteroid's persistence and to prevent defense-like reactions in the nodules. this manuscript shows that a ...	2014	24632747
symbiotic effectiveness of inoculation with bradyrhizobium isolates on soybean [glycine max (l.) merrill] genotypes with different maturities.	the influence of soybean genotypes with different maturity groups on the symbiotic effectiveness of bradyrhizobium spp under high native soil n is not well known. therefore, the objective of this work was to evaluate the influence of maturity time of soybean genotypes on the symbiotic effectiveness of bradyrhizobium spp. at higher soil n. three isolates of bradyrhizobium spp. (uk-isolate, tal-379 isolate and local-isolate) and six soybean genotypes, three late maturing (wogayen, tgx-1336424 and ...	2014	26034703
genome sequence of bradyrhizobium sp. wsm1253; a microsymbiont of ornithopus compressus from the greek island of sifnos.	bradyrhizobium sp. wsm1253 is a novel n2-fixing bacterium isolated from a root nodule of the herbaceous annual legume ornithopus compressus that was growing on the greek island of sifnos. wsm1253 emerged as a strain of interest in an australian program that was selecting inoculant quality bradyrhizobial strains for inoculation of mediterranean species of lupins (lupinus angustifolius, l. princei, l. atlanticus, l. pilosus). in this report we describe, for the first time, the genome sequence info ...	2015	26629308
a genomic encyclopedia of the root nodule bacteria: assessing genetic diversity through a systematic biogeographic survey.	root nodule bacteria are free-living soil bacteria, belonging to diverse genera within the alphaproteobacteria and betaproteobacteria, that have the capacity to form nitrogen-fixing symbioses with legumes. the symbiosis is specific and is governed by signaling molecules produced from both host and bacteria. sequencing of several model rnb genomes has provided valuable insights into the genetic basis of symbiosis. however, the small number of sequenced rnb genomes available does not currently ref ...	2015	25685260
how genome complexity can explain the difficulty of aligning reads to genomes.	although it is frequently observed that aligning short reads to genomes becomes harder if they contain complex repeat patterns, there has not been much effort to quantify the relationship between complexity of genomes and difficulty of short-read alignment. existing measures of sequence complexity seem unsuitable for the understanding and quantification of this relationship.	2015	26678826
evaluation of 3 dental unit waterline contamination testing methods.	previous studies have found inconsistent results from testing methods used to measure heterotrophic plate count (hpc) bacteria in dental unit waterline (duwl) samples. this study used 63 samples to compare the results obtained from an in-office chairside method and 2 currently used commercial laboratory hpc methods (standard methods 9215c and 9215e). the results suggest that the standard method 9215e is not suitable for application to duwl quality monitoring, due to the detection of limited numb ...	2015	25574718
enzymological characterization of atm, the first laccase from agrobacterium sp. s5-1, with the ability to enhance in vitro digestibility of maize straw.	laccase is an enzyme that catalyzes oxidation of phenolic compounds, diamines and aromatic amines. in this study, a novel laccase-like gene (atm) in a ligninolyitic isolate agrobacterium sp. s5-1 from soil humus was identified and heterologously expressed in escherichia coli. atm exhibited its maximal activity at ph 4.5 and at 50°c. this enzyme was tolerant to high temperature, a broad range of ph, heavy metal ions (co3+, mn2+, cu2+ and ni2+, 20 mm) and all tested organic solvents. furthermore, ...	2015	26010258
rhizobium leguminosarum bv. viciae 3841 adapts to 2,4-dichlorophenoxyacetic acid with "auxin-like" morphological changes, cell envelope remodeling and upregulation of central metabolic pathways.	there is a growing need to characterize the effects of environmental stressors at the molecular level on model organisms with the ever increasing number and variety of anthropogenic chemical pollutants. the herbicide 2,4-dichlorophenoxyacetic acid (2,4-d), as one of the most widely applied pesticides in the world, is one such example. this herbicide is known to have non-targeted undesirable effects on humans, animals and soil microbes, but specific molecular targets at sublethal levels are unkno ...	2015	25919284
variable nitrogen fixation in wild populus.	the microbiome of plants is diverse, and like that of animals, is important for overall health and nutrient acquisition. in legumes and actinorhizal plants, a portion of essential nitrogen (n) is obtained through symbiosis with nodule-inhabiting, n2-fixing microorganisms. however, a variety of non-nodulating plant species can also thrive in natural, low-n settings. some of these species may rely on endophytes, microorganisms that live within plants, to fix n2 gas into usable forms. here we repor ...	2016	27196608
genome-wide discovery of putative srnas in paracoccus denitrificans expressed under nitrous oxide emitting conditions.	nitrous oxide (n2o) is a stable, ozone depleting greenhouse gas. emissions of n2o into the atmosphere continue to rise, primarily due to the use of nitrogen-containing fertilizers by soil denitrifying microbes. it is clear more effective mitigation strategies are required to reduce emissions. one way to help develop future mitigation strategies is to address the currently poor understanding of transcriptional regulation of the enzymes used to produce and consume n2o. with this ultimate aim in mi ...	2016	27895629
detection of novel integrons in the metagenome of human saliva.	integrons are genetic elements capable of capturing and expressing open reading frames (orfs) embedded within gene cassettes. they are involved in the dissemination of antibiotic resistance genes (args) in clinically important pathogens. although the args are common in the oral cavity the association of integrons and antibiotic resistance has not been reported there. in this work, a pcr-based approach was used to investigate the presence of integrons and associated gene cassettes in human oral m ...	2016	27304457
novel european free-living, non-diazotrophic bradyrhizobium isolates from contrasting soils that lack nodulation and nitrogen fixation genes - a genome comparison.	the slow-growing genus bradyrhizobium is biologically important in soils, with different representatives found to perform a range of biochemical functions including photosynthesis, induction of root nodules and symbiotic nitrogen fixation and denitrification. consequently, the role of the genus in soil ecology and biogeochemical transformations is of agricultural and environmental significance. some isolates of bradyrhizobium have been shown to be non-symbiotic and do not possess the ability to ...	2016	27162150
characterisation of candida within the mycobiome/microbiome of the lower respiratory tract of icu patients.	whether the presence of candida spp. in lower respiratory tract (lrt) secretions is a marker of underlying disease, intensive care unit (icu) treatment and antibiotic therapy or contributes to poor clinical outcome is unclear. we investigated healthy controls, patients with proposed risk factors for candida growth in lrt (antibiotic therapy, icu treatment with and without antibiotic therapy), icu patients with pneumonia and antibiotic therapy and candidemic patients (for comparison of truly inva ...	2016	27206014
pyruvic oxime dioxygenase from heterotrophic nitrifier alcaligenes faecalis is a nonheme fe((ii))-dependent enzyme homologous to class ii aldolase.	pyruvic oxime dioxygenase (pod), a key enzyme in heterotrophic nitrification, was purified from alcaligenes faecalis, and the molecular and catalytic characteristics were reexamined. pod was purified as the homotetramer of the subunit whose molecular weight was 30,000. the deduced amino acid sequence of pod was homologous with a class ii aldolase that has been regarded as the zn((ii))-dependent enzyme catalyzing aldol reactions. the recombinant protein showed weak pod activity, and was activated ...	2017	28059164
assessment of common and emerging bioinformatics pipelines for targeted metagenomics.	targeted metagenomics, also known as metagenetics, is a high-throughput sequencing application focusing on a nucleotide target in a microbiome to describe its taxonomic content. a wide range of bioinformatics pipelines are available to analyze sequencing outputs, and the choice of an appropriate tool is crucial and not trivial. no standard evaluation method exists for estimating the accuracy of a pipeline for targeted metagenomics analyses. this article proposes an evaluation protocol containing ...	2017	28052134