Abstract:
:Illumina and nanopore sequencing technologies are powerful tools that can be used to determine the bacterial composition of complex microbial communities. In this study, we compared nasal microbiota results at genus level using both Illumina and nanopore 16S rRNA gene sequencing. We also monitored the progression of nanopore sequencing in the accurate identification of species, using pure, single species cultures, and evaluated the performance of the nanopore EPI2ME 16S data analysis pipeline. Fifty-nine nasal swabs were sequenced using Illumina MiSeq and Oxford Nanopore 16S rRNA gene sequencing technologies. In addition, five pure cultures of relevant bacterial species were sequenced with the nanopore sequencing technology. The Illumina MiSeq sequence data were processed using bioinformatics modules present in the Mothur software package. Albacore and Guppy base calling, a workflow in nanopore EPI2ME (Oxford Nanopore Technologies-ONT, Oxford, UK) and an in-house developed bioinformatics script were used to analyze the nanopore data. At genus level, similar bacterial diversity profiles were found, and five main and established genera were identified by both platforms. However, probably due to mismatching of the nanopore sequence primers, the nanopore sequencing platform identified Corynebacterium in much lower abundance compared to Illumina sequencing. Further, when using default settings in the EPI2ME workflow, almost all sequence reads that seem to belong to the bacterial genus Dolosigranulum and a considerable part to the genus Haemophilus were only identified at family level. Nanopore sequencing of single species cultures demonstrated at least 88% accurate identification of the species at genus and species level for 4/5 strains tested, including improvements in accurate sequence read identification when the basecaller Guppy and Albacore, and when flowcell versions R9.4 (Oxford Nanopore Technologies-ONT, Oxford, UK) and R9.2 (Oxford Nanopore Technologies-ONT, Oxford, UK) were compared. In conclusion, the current study shows that the nanopore sequencing platform is comparable with the Illumina platform in detection bacterial genera of the nasal microbiota, but the nanopore platform does have problems in detecting bacteria within the genus Corynebacterium. Although advances are being made, thorough validation of the nanopore platform is still recommendable.
journal_name
Genes (Basel)journal_title
Genesauthors
Heikema AP,Horst-Kreft D,Boers SA,Jansen R,Hiltemann SD,de Koning W,Kraaij R,de Ridder MAJ,van Houten CB,Bont LJ,Stubbs AP,Hays JPdoi
10.3390/genes11091105subject
Has Abstractpub_date
2020-09-21 00:00:00issue
9issn
2073-4425pii
genes11091105journal_volume
11pub_type
杂志文章相关文献
Genes文献大全abstract::For medical genetic counseling, estimating the chance of a child being born with chromosome abnormality is crucially important. Cytogenetic diagnostics of parents with a balanced karyotype are a special case. Such chromosome rearrangements cannot be detected with comprehensive chromosome screening. In the current pape...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11121511
更新日期:2020-12-17 00:00:00
abstract::Pyrethroid resistance in major malaria vectors such as Anopheles funestus threatens malaria control efforts in Africa. Cytochrome P450-mediated metabolic resistance is best understood for CYP6P9 genes in southern Africa in An. funestus. However, we do not know if this resistance mechanism is spreading across Africa an...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11111314
更新日期:2020-11-05 00:00:00
abstract::Limb-girdle muscular dystrophies (LGMD) are clinically and genetically heterogeneous conditions, presenting with a wide clinical spectrum, leading to progressive proximal weakness caused by loss of muscle fibers. MiR-206 is a member of myomiRNAs, a group of miRNAs with important function in skeletal muscle. Our aim is...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes12010085
更新日期:2021-01-12 00:00:00
abstract::Transfer RNAs (tRNAs) are abundant small non-coding RNAs that are crucially important for decoding genetic information. Besides fulfilling canonical roles as adaptor molecules during protein synthesis, tRNAs are also the source of a heterogeneous class of small RNAs, tRNA-derived small RNAs (tsRNAs). Occurrence and th...
journal_title:Genes
pub_type: 杂志文章,评审
doi:10.3390/genes9120607
更新日期:2018-12-05 00:00:00
abstract::Hypertrophic cardiomyopathy associated with damaging variants in the ALPK3 gene is a fairly recent discovery, and only a small number of patients have been described thus far. Here we present two additional patients with hypertrophic cardiomyopathy caused by biallelic variants in ALPK3. Genetic investigation was perfo...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11101201
更新日期:2020-10-15 00:00:00
abstract::The histone-like nucleoid structuring protein (H-NS) has played a key role in shaping the evolution of Shigella spp., and provides the backdrop to the regulatory cascade that controls virulence by silencing many genes found on the large virulence plasmid. H-NS and its paralogue StpA are present in all four Shigella sp...
journal_title:Genes
pub_type: 杂志文章,评审
doi:10.3390/genes7120112
更新日期:2016-12-01 00:00:00
abstract::Cytokinin oxidase/dehydrogenases (CKXs) play a critical role in the irreversible degradation of cytokinins, thereby regulating plant growth and development. Brassica napus is one of the most widely cultivated oilseed crops worldwide. With the completion of whole-genome sequencing of B. napus, genome-wide identificatio...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes9030168
更新日期:2018-03-16 00:00:00
abstract::The mutation parameter θ is fundamental and ubiquitous in the analysis of population samples of DNA sequences. This paper presents a new highly efficient estimator of θ by utilizing the phylogenetic information among distinct alleles in a sample of DNA sequences. The new estimator, called Allelic BLUE, is derived from...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes5030561
更新日期:2014-07-22 00:00:00
abstract::The filamenting temperature-sensitive Z proteins (FtsZs) play an important role in plastid division. In this study, three FtsZ genes were isolated from the cassava genome, and named MeFtsZ1, MeFtsZ2-1, and MeFtsZ2-2, respectively. Based on phylogeny, the MeFtsZs were classified into two groups (FtsZ1 and FtsZ2). MeFts...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes8120391
更新日期:2017-12-15 00:00:00
abstract::A major technological shift in the research community in the past decade has been the adoption of high throughput (HT) technologies to interrogate the genome, epigenome, transcriptome, and proteome in a massively parallel fashion [...]. ...
journal_title:Genes
pub_type: 社论
doi:10.3390/genes11030245
更新日期:2020-02-26 00:00:00
abstract::The revolution in next-generation DNA sequencing technologies is leading to explosive data growth in genomics, posing a significant challenge to the computing infrastructure and software algorithms for genomics analysis. Various big data technologies have been explored to scale up/out current bioinformatics solutions ...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes10121017
更新日期:2019-12-06 00:00:00
abstract::Model-based clustering with finite mixture models has become a widely used clustering method. One of the recent implementations is MCLUST. When objects to be clustered are summary statistics, such as regression coefficient estimates, they are naturally associated with estimation errors, whose covariance matrices can o...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11020185
更新日期:2020-02-10 00:00:00
abstract::The accurate repair of DNA is critical for genome stability and cancer prevention. DNA double-strand breaks are one of the most toxic lesions; however, they can be repaired using homologous recombination. Homologous recombination is a high-fidelity DNA repair pathway that uses a homologous template for repair. One cen...
journal_title:Genes
pub_type: 杂志文章,评审
doi:10.3390/genes9120629
更新日期:2018-12-13 00:00:00
abstract::Genetic adaptation to extremes is a fascinating topic. Nevertheless, few studies have explored the genetic adaptation of closely related species respectively inhabiting distinct extremes. With deep transcriptome sequencing, we attempt to detect the genetic architectures of tadpoles of five closely related toad species...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11020123
更新日期:2020-01-22 00:00:00
abstract::Background: The C34T polymorphism (rs 17602729) in adenosine monophosphate deaminase 1 gene (AMPD1) is associated with muscular energy metabolism in exercise. However, the role of its potential modifying impact on exercise-induced changes in obesity related parameters is unknown. The aim of the study was to determine ...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11050558
更新日期:2020-05-16 00:00:00
abstract::Candida albicans mutants deficient in homologous recombination (HR) are extremely sensitive to the alkylating agent methyl-methane-sulfonate (MMS). Here, we have investigated the role of HR genes in the protection and repair of C. albicans chromosomes by taking advantage of the heat-labile property (55 °C) of MMS-indu...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes9090447
更新日期:2018-09-07 00:00:00
abstract::Prader-Willi syndrome (PWS) is a complex multisystemic condition caused by a lack of paternal expression of imprinted genes from the 15q11.2-q13 region. Limited literature exists on the association between molecular classes, growth hormone use, and the prevalence of psychiatric phenotypes in PWS. In this study, we ana...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11111250
更新日期:2020-10-23 00:00:00
abstract::In addition to its wide geographical distribution, osteoglossiform fishes represent one of the most ancient freshwater teleost lineages; making it an important group for systematic and evolutionary studies. These fishes had a Gondwanan origin and their past distribution may have contributed to the diversity present in...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes9060306
更新日期:2018-06-19 00:00:00
abstract::The heavy impact of obesity on both the population general health and the economy makes clarifying the underlying mechanisms, identifying pharmacological targets, and developing efficient therapies for obesity of high importance. The main struggle facing obesity research is that the underlying mechanistic pathways are...
journal_title:Genes
pub_type: 杂志文章,评审
doi:10.3390/genes11080875
更新日期:2020-07-31 00:00:00
abstract::Shiga toxin-producing Escherichia coli (STEC) are foodborne pathogens associated with outbreaks and hemolytic-uremic syndrome. Cattle and meat foods are the main reservoir and infection source, respectively. Pathogenicity islands (PAIs) play an important role in STEC pathogenicity, and non-locus of the enterocyte effa...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes9020081
更新日期:2018-02-10 00:00:00
abstract::Our current knowledge of B chromosome biology has been augmented by an increase in the number and diversity of species observed to carry B chromosomes as well as the use of next-generation sequencing for B chromosome genomic analysis. Within the genus Drosophila, B chromosomes have been observed in a handful of specie...
journal_title:Genes
pub_type: 杂志文章,评审
doi:10.3390/genes9100470
更新日期:2018-09-27 00:00:00
abstract::Divergent selection between ecologically dissimilar habitats promotes local adaptation, which can lead to reproductive isolation (RI). Populations in the Poecilia mexicana species complex have independently adapted to toxic hydrogen sulfide and show varying degrees of RI. Here, we examined the variation in the mate ch...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes9050232
更新日期:2018-05-02 00:00:00
abstract::Fig wasps are a peculiar group of insects which, for millions of years, have inhabited the enclosed syconia of fig trees. Considering the relatively closed and dark environment of fig syconia, we hypothesize that the fig wasps' oxidative phosphorylation (OXPHOS) pathway, which is the main oxygen consumption and adenos...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11111353
更新日期:2020-11-15 00:00:00
abstract::Meat eating quality with a healthy composition hinges on intramuscular fat (IMF), fat melting point (FMP), tenderness, juiciness, flavour and omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA) content. These health-beneficial n-3 LC-PUFA play significant roles in optimal cardiovascular, retinal, maternal and...
journal_title:Genes
pub_type: 杂志文章,评审
doi:10.3390/genes11050587
更新日期:2020-05-25 00:00:00
abstract::Smoltification and early seawater phase are critical developmental periods with physiological and biochemical changes in Atlantic salmon that facilitates survival in saltwater. MicroRNAs (miRNAs) are known to have important roles in development, but whether any miRNAs are involved in regulation of gene expression duri...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11091059
更新日期:2020-09-08 00:00:00
abstract::Death investigations often include an effort to establish the postmortem interval (PMI) in cases in which the time of death is uncertain. The postmortem interval can lead to the identification of the deceased and the validation of witness statements and suspect alibis. Recent research has demonstrated that microbes pr...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes9020104
更新日期:2018-02-16 00:00:00
abstract::The southern elephant seal Mirounga leonina is the largest phocid seal and one of the two species of elephant seals. They are listed as 'least concern' by the International Union for Conservation of Nature (IUCN) Red List of Threatened Species 2015. Here, we have assembled the reference genome for M. leonina using the...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11020160
更新日期:2020-02-03 00:00:00
abstract::Cell size affects almost all biosynthetic processes by controlling the size of organelles and disrupting the nutrient uptake process. Yeast cells must reach a critical size to be able to enter a new cell cycle stage. Abnormal changes in cell size are often observed under pathological conditions such as cancer disease....
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11040430
更新日期:2020-04-16 00:00:00
abstract::Exposure to Formaldehyde (FA) results in many pathophysiological symptoms, however the underlying mechanisms are not well understood. Given the complicated modulatory role of intestinal microbiota on human health, we hypothesized that interactions between FA and the gut microbiome may account for FA's toxicity. Balb/c...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes9040192
更新日期:2018-04-03 00:00:00
abstract::Telomere maintenance mechanisms (TMM) are used by cancer cells to avoid apoptosis, 85-90% reactivate telomerase, while 10-15% use the alternative lengthening of telomeres (ALT). Due to anti-telomerase-based treatments, some tumors switch from a telomerase-dependent mechanism to ALT; in fact, the co-existence between b...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11070834
更新日期:2020-07-21 00:00:00