Abstract:
:High throughput genomics technologies are applied widely to microbiomes in humans, animals, soil and water, to detect changes in bacterial communities or the genes they carry, between different environments or treatments. We describe a method to test the statistical significance of differences in bacterial population or gene composition, applicable to metagenomic or quantitative polymerase chain reaction data. Our method goes beyond previous published work in being universally most powerful, thus better able to detect statistically significant differences, and through being more reliable for smaller sample sizes. It can also be used for experimental design, to estimate how many samples to use in future experiments, again with the advantage of being universally most powerful. We present three example analyses in the area of antimicrobial resistance. The first is to published data on bacterial communities and antimicrobial resistance genes (ARGs) in the environment; we show that there are significant changes in both ARG and community composition. The second is to new data on seasonality in bacterial communities and ARGs in hooves from four sheep. While the observed differences are not significant, we show that a minimum group size of eight sheep would provide sufficient power to observe significance of similar changes in further experiments. The third is to published data on bacterial communities surrounding rice crops. This is a much larger data set and is used to verify the new method. Our method has broad uses for statistical testing and experimental design in research on changing microbiomes, including studies on antimicrobial resistance.
journal_name
Sci Repjournal_title
Scientific reportsauthors
Shaw LM,Blanchard A,Chen Q,An X,Davies P,Tötemeyer S,Zhu YG,Stekel DJdoi
10.1038/s41598-019-38873-4subject
Has Abstractpub_date
2019-02-20 00:00:00pages
2373issue
1issn
2045-2322pii
10.1038/s41598-019-38873-4journal_volume
9pub_type
杂志文章abstract::In East Greenland, a dramatic increase of tuberculosis (TB) incidence has been observed in recent years. Classical genotyping suggests a genetically similar Mycobacterium tuberculosis (Mtb) strain population as cause, however, precise transmission patterns are unclear. We performed whole genome sequencing (WGS) of Mtb...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep33180
更新日期:2016-09-12 00:00:00
abstract::Mangrove forests are among the most productive and diverse ecosystems on the planet, despite limited nitrogen (N) availability. Under such conditions, animal-microbe associations (holobionts) are often key to ecosystem functioning. Here, we investigated the role of fiddler crabs and their carapace-associated microbial...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-70834-0
更新日期:2020-08-18 00:00:00
abstract::The common variants in lysyl oxidase-like 1 gene (LOXL1) are associated with exfoliation glaucoma (XFG) patients developed through exfoliation syndrome (XFS). However, the risk allele of a variant in LOXL1 has been found to be inverted between Asian and Caucasian populations. Therefore, we newly performed a genome-wid...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep05340
更新日期:2014-06-18 00:00:00
abstract::Compact silicon integrated lasers are of significant interest for various applications. We present a detailed investigation for realizing sub-mm long on-chip laser structures operating at λ = 1.533 µm on the silicon-on-insulator photonic platform by combining a multi-segment silicon waveguide structure and a recently ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-67722-y
更新日期:2020-07-02 00:00:00
abstract::Ebola virus (EBOV), isolate Makona, was the causative agent of the West African epidemic devastating predominantly Guinea, Liberia and Sierra Leone from 2013-2016. While several experimental vaccine and treatment approaches have been accelerated through human clinical trials, there is still no approved countermeasure ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-19041-y
更新日期:2018-01-16 00:00:00
abstract::RNA interference (RNAi) is being developed for the management of pests that destroy crops. The twospotted Spider Mite (TSSM), Tetranychus urticae is a worldwide pest due to its unique physiological and behavioral characteristics including extraordinary ability to detoxify a wide range of pesticides and feed on many ho...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-32742-2
更新日期:2018-10-02 00:00:00
abstract::In recent years, macrophages have been shown to be tremendously plastic in both in vitro and in vivo settings; however, it remains unclear whether macrophages retain any persistent memory of past polarization states which may then impact their future repolarization to new states. Here, we perform deep transcriptomic p...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-68766-w
更新日期:2020-07-23 00:00:00
abstract::Long-term potentiation (LTP) is the persistent increase in the strength of the synapses. However, the neural networks would become saturated if there is only synaptic strenghthening. Synaptic weakening could be facilitated by active processes like long-term depression (LTD). Molecular mechanisms that facilitate the we...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-15917-1
更新日期:2017-11-14 00:00:00
abstract::Stress variation induced bandgap tuning and surface wettability switching of spinel nickel ferrite (NiFe2O4, NFO) films were demonstrated and directly driven by phase transition via a post-annealing process. Firstly, the as-deposited NFO films showed hydrophilic surface with water contact angle (CA) value of 80 ± 1°. ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-19319-9
更新日期:2018-01-22 00:00:00
abstract::Craniofacial muscles drive critical functions in the head, including speech, feeding and expression. Compared with their counterparts in trunk and limbs, craniofacial muscles are of distinct embryonic origins, which might consequently lead to different growth patterns and regenerative potential. In this study, rat lev...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-28917-6
更新日期:2018-07-13 00:00:00
abstract::Behavioral alterations emerging after central or peripheral vision loss suggest that cerebral reorganization occurs for both the afferented and deafferented early visual cortex (EVC). We explored the functional reorganization of the central and peripheral EVC following visual field defects specifically affecting centr...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep43223
更新日期:2017-02-24 00:00:00
abstract::The Przewalski's gazelle (Procapra przewalskii) is one of the most endangered ungulates in the world, with fewer than 2,000 individuals surviving in nine habitat fragments on the Qinghai-Tibet Plateau and isolated by human settlements and infrastructure. In particular, the Qinghai-Tibet railway, which crosses the larg...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-18163-7
更新日期:2017-12-21 00:00:00
abstract::In preclinical stages of drug development, anticipating potential adverse drug effects such as toxicity is an important issue for both saving resources and preventing public health risks. Current in vitro cytotoxicity tests are restricted by their predictive potential and their ability to provide mechanistic informati...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep27239
更新日期:2016-06-06 00:00:00
abstract::Examination of histological or immunohistochemically stained 2D sections of embedded tissue is one of the most frequently used tools in biomedical research and clinical routine. Since to date, targeted sectioning of specific regions of interest (ROI) in the sample is not possible, we aimed at developing a guided secti...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-26086-0
更新日期:2018-05-16 00:00:00
abstract::The reflected microwave power from the photo-excited high mobility GaAs/AlGaAs 2D device has been measured over the wide frequency band spanning from 30 to 330 GHz simultaneously along with diagonal magnetoresistance as a function of the magnetic field. Easily distinguishable resonances in the reflected power signal a...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-39186-2
更新日期:2019-02-20 00:00:00
abstract::Grazing and burrowing organisms usually homogenise microalgal mats that form on benthic sediments of many aquatic ecosystems. In the absence of this disruption, microalgal mats can accrete laminated deposits (stromatolites). Stromatolites are rare in modern coastal ecosystems, but persist at locations where metazoans ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep42614
更新日期:2017-02-16 00:00:00
abstract::L-selectin on T-cells is best known as an adhesion molecule that supports recruitment of blood-borne naïve and central memory cells into lymph nodes. Proteolytic shedding of the ectodomain is thought to redirect activated T-cells from lymph nodes to sites of infection. However, we have shown that activated T-cells re-...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-41811-z
更新日期:2019-04-02 00:00:00
abstract::Feynman once asked physicists to build better electron microscopes to be able to watch biology at work. While electron microscopes can now provide atomic resolution, electron beam induced specimen damage precludes high resolution imaging of sensitive materials, such as single proteins or polymers. Here, we use simulat...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-01841-x
更新日期:2017-05-10 00:00:00
abstract::Hydrogen recovery through solar-driven biomass conversion by photo-fermentative bacteria (PFB) has been regarded as a promising way for sustainable energy production. However, a considerable fraction of organic substrate was consumed for the growth of PFB as biocatalysts, furthermore, these PFB were continuously washe...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep16174
更新日期:2015-11-05 00:00:00
abstract::Verteporfin (VP), a light-activated drug used in photodynamic therapy for the treatment of choroidal neovascular membranes, has also been shown to be an effective inhibitor of malignant cells. Recently, studies have demonstrated that, even without photo-activation, VP may still inhibit certain tumor cell lines, includ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-07632-8
更新日期:2017-08-08 00:00:00
abstract::We present a comprehensive study of a magnetic sensor system that benefits from a new technique to substantially increase the magnetoelastic coupling of surface acoustic waves (SAW). The device uses shear horizontal acoustic surface waves that are guided by a fused silica layer with an amorphous magnetostrictive FeCoS...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-18441-4
更新日期:2018-01-10 00:00:00
abstract::The ongoing evolution of microbial pathogens represents a significant issue in diagnostic PCR/qPCR. Many assays are burdened with false negativity due to mispriming and/or probe-binding failures. Therefore, PCR/qPCR assays used in the laboratory should be periodically re-assessed in silico on public sequences to evalu...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-37869-w
更新日期:2019-02-07 00:00:00
abstract::Regular exercise elicits advantageous metabolic adaptations in skeletal muscle, such as improved insulin sensitivity. However, the underpinning molecular mechanisms and the effect of diet on muscle exercise training benefits are unclear. We therefore characterized the skeletal muscle proteome following exercise traini...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-28540-5
更新日期:2018-07-16 00:00:00
abstract::2,5-Dimethylfuran (DMF) is a type of attractive sustainable green energy for diesel engines that is designed to reduce soot emission. This study investigated the effect of fuel properties on the macroscopic and microscopic spray characteristics of four test blends under injection pressures of 90, 120 and 150 MPa and a...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-58119-y
更新日期:2020-01-29 00:00:00
abstract::The number of magnetoelectric multiferroic materials reported to date is scarce, as magnetic structures that break inversion symmetry and induce an improper ferroelectric polarization typically arise through subtle competition between different magnetic interactions. The (NH4)2[FeCl5(H2O)] compound is a rare case wher...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep14475
更新日期:2015-09-29 00:00:00
abstract::The objective of this study was to investigate the influence of the genes encoding the KIR receptors and their HLA ligands in the susceptibility of ocular toxoplasmosis. A total of 297 patients serologically-diagnosed with toxoplasmosis were selected and stratified according to the presence (n = 148) or absence (n = 1...
journal_title:Scientific reports
pub_type: 临床试验,杂志文章
doi:10.1038/srep36632
更新日期:2016-11-09 00:00:00
abstract::Muscle wasting and atrophy are regulated by multiple molecular processes, including mRNA processing. Reduced levels of the polyadenylation binding protein nucleus 1 (PABPN1), a multifactorial regulator of mRNA processing, cause muscle atrophy. A proteomic study in muscles with reduced PABPN1 levels suggested dysregula...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-74676-8
更新日期:2020-10-19 00:00:00
abstract::The dugong (Dugong dugon Müller) is recognized as an endangered marine mammal. There is limited available anatomical data on the dugong's skeletal system, while what is available has not been well established due to the limited number of archived samples and limited access to them. Importantly, there are certain key q...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-76545-w
更新日期:2020-11-09 00:00:00
abstract::We have previously shown that OX40L/OX40 interaction is critical for TCR-independent selective proliferation of Foxp3+ Tregs, but not Foxp3- effector T-cells (Teff), when CD4+ T-cells are co-cultured with GM-CSF derived bone marrow dendritic cells (G-BMDCs). Events downstream of OX40L/OX40 interaction in Tregs respons...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-05254-8
更新日期:2017-07-26 00:00:00
abstract::Atherosclerotic arteries exhibit characteristic constrictions and substantial deviations from cylindrical shape. Therefore, determining the artery's cross-section along the centerline is challenging, although high-resolution isotropic three-dimensional data are available. Herein, we apply high-resolution computed tomo...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-50711-1
更新日期:2019-10-04 00:00:00