DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples.

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 Rep

journal_title

Scientific reports

authors

Shaw LM,Blanchard A,Chen Q,An X,Davies P,Tötemeyer S,Zhu YG,Stekel DJ

doi

10.1038/s41598-019-38873-4

subject

Has Abstract

pub_date

2019-02-20 00:00:00

pages

2373

issue

1

issn

2045-2322

pii

10.1038/s41598-019-38873-4

journal_volume

9

pub_type

杂志文章
  • Tracing Mycobacterium tuberculosis transmission by whole genome sequencing in a high incidence setting: a retrospective population-based study in East Greenland.

    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

    authors: Bjorn-Mortensen K,Soborg B,Koch A,Ladefoged K,Merker M,Lillebaek T,Andersen AB,Niemann S,Kohl TA

    更新日期:2016-09-12 00:00:00

  • N2 fixation dominates nitrogen cycling in a mangrove fiddler crab holobiont.

    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

    authors: Zilius M,Bonaglia S,Broman E,Chiozzini VG,Samuiloviene A,Nascimento FJA,Cardini U,Bartoli M

    更新日期:2020-08-18 00:00:00

  • Novel common variants and susceptible haplotype for exfoliation glaucoma specific to Asian population.

    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

    authors: Nakano M,Ikeda Y,Tokuda Y,Fuwa M,Ueno M,Imai K,Sato R,Omi N,Adachi H,Kageyama M,Mori K,Kinoshita S,Tashiro K

    更新日期:2014-06-18 00:00:00

  • Potential for sub-mm long erbium-doped composite silicon waveguide DFB lasers.

    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

    authors: Tu Z,Zhang J,Rönn J,Alonso-Ramos C,Leroux X,Vivien L,Sun Z,Cassan É

    更新日期:2020-07-02 00:00:00

  • A Single Dose of Modified Vaccinia Ankara expressing Ebola Virus Like Particles Protects Nonhuman Primates from Lethal Ebola Virus Challenge.

    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

    authors: Domi A,Feldmann F,Basu R,McCurley N,Shifflett K,Emanuel J,Hellerstein MS,Guirakhoo F,Orlandi C,Flinko R,Lewis GK,Hanley PW,Feldmann H,Robinson HL,Marzi A

    更新日期:2018-01-16 00:00:00

  • Identification of target genes for RNAi-mediated control of the Twospotted Spider Mite.

    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

    authors: Yoon JS,Sahoo DK,Maiti IB,Palli SR

    更新日期:2018-10-02 00:00:00

  • Trajectory analysis quantifies transcriptional plasticity during macrophage polarization.

    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

    authors: Liu SX,Gustafson HH,Jackson DL,Pun SH,Trapnell C

    更新日期:2020-07-23 00:00:00

  • Bidirectional modulation of hippocampal synaptic plasticity by Dopaminergic D4-receptors in the CA1 area of hippocampus.

    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

    authors: Navakkode S,Chew KCM,Tay SJN,Lin Q,Behnisch T,Soong TW

    更新日期:2017-11-14 00:00:00

  • Tuning bandgap and surface wettability of NiFe2O4 driven by phase transition.

    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

    authors: Tong SK,Chi PW,Kung SH,Wei DH

    更新日期:2018-01-22 00:00:00

  • Wnt7a induces satellite cell expansion, myofiber hyperplasia and hypertrophy in rat craniofacial muscle.

    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

    authors: Cheng X,Huang H,Luo X,Shi B,Li J

    更新日期:2018-07-13 00:00:00

  • Reorganization of early visual cortex functional connectivity following selective peripheral and central visual loss.

    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

    authors: Sabbah N,Sanda N,Authié CN,Mohand-Saïd S,Sahel JA,Habas C,Amedi A,Safran AB

    更新日期:2017-02-24 00:00:00

  • Effects of the Qinghai-Tibet Railway on the Landscape Genetics of the Endangered Przewalski's Gazelle (Procapra przewalskii).

    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

    authors: Yu H,Song S,Liu J,Li S,Zhang L,Wang D,Luo SJ

    更新日期:2017-12-21 00:00:00

  • A metabolomics cell-based approach for anticipating and investigating drug-induced liver injury.

    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

    authors: García-Cañaveras JC,Castell JV,Donato MT,Lahoz A

    更新日期:2016-06-06 00:00:00

  • X-ray based virtual histology allows guided sectioning of heavy ion stained murine lungs for histological analysis.

    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

    authors: Albers J,Markus MA,Alves F,Dullin C

    更新日期:2018-05-16 00:00:00

  • Cyclotron resonance in the high mobility GaAs/AlGaAs 2D electron system over the microwave, mm-wave, and terahertz- bands.

    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

    authors: Kriisa A,Samaraweera RL,Heimbeck MS,Everitt HO,Reichl C,Wegscheider W,Mani RG

    更新日期:2019-02-20 00:00:00

  • Non-reliance of metazoans on stromatolite-forming microbial mats as a food resource.

    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

    authors: Rishworth GM,Perissinotto R,Bird MS,Strydom NA,Peer N,Miranda NA,Raw JL

    更新日期:2017-02-16 00:00:00

  • ADAM17-dependent proteolysis of L-selectin promotes early clonal expansion of cytotoxic T cells.

    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

    authors: Mohammed RN,Wehenkel SC,Galkina EV,Yates EK,Preece G,Newman A,Watson HA,Ohme J,Bridgeman JS,Durairaj RRP,Moon OR,Ladell K,Miners KL,Dolton G,Troeberg L,Kashiwagi M,Murphy G,Nagase H,Price DA,Matthews RJ,Knäuper V

    更新日期:2019-04-02 00:00:00

  • Multi-pass transmission electron microscopy.

    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

    authors: Juffmann T,Koppell SA,Klopfer BB,Ophus C,Glaeser RM,Kasevich MA

    更新日期:2017-05-10 00:00:00

  • Bioaggregate of photo-fermentative bacteria for enhancing continuous hydrogen production in a sequencing batch photobioreactor.

    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

    authors: Xie GJ,Liu BF,Wang RQ,Ding J,Ren HY,Zhou X,Ren NQ

    更新日期:2015-11-05 00:00:00

  • Verteporfin inhibits growth of human glioma in vitro without light activation.

    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

    authors: Al-Moujahed A,Brodowska K,Stryjewski TP,Efstathiou NE,Vasilikos I,Cichy J,Miller JW,Gragoudas E,Vavvas DG

    更新日期:2017-08-08 00:00:00

  • Wide Band Low Noise Love Wave Magnetic Field Sensor System.

    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

    authors: Kittmann A,Durdaut P,Zabel S,Reermann J,Schmalz J,Spetzler B,Meyners D,Sun NX,McCord J,Gerken M,Schmidt G,Höft M,Knöchel R,Faupel F,Quandt E

    更新日期:2018-01-10 00:00:00

  • In silico re-assessment of a diagnostic RT-qPCR assay for universal detection of Influenza A viruses.

    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

    authors: Nagy A,Jiřinec T,Jiřincová H,Černíková L,Havlíčková M

    更新日期:2019-02-07 00:00:00

  • Quantitative proteomic characterization of cellular pathways associated with altered insulin sensitivity in skeletal muscle following high-fat diet feeding and exercise training.

    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

    authors: Kleinert M,Parker BL,Jensen TE,Raun SH,Pham P,Han X,James DE,Richter EA,Sylow L

    更新日期:2018-07-16 00:00:00

  • Assessing fuel properties effects of 2,5-dimethylfuran on microscopic and macroscopic characteristics of oxygenated fuel/diesel blends spray.

    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

    authors: Zhang P,Su X,Chen H,Geng L,Zhao X

    更新日期:2020-01-29 00:00:00

  • Magnetically-induced ferroelectricity in the (ND4)2[FeCl5(D2O)] molecular compound.

    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

    authors: Alberto Rodríguez-Velamazán J,Fabelo Ó,Millán Á,Campo J,Johnson RD,Chapon L

    更新日期:2015-09-29 00:00:00

  • Ocular toxoplasmosis: susceptibility in respect to the genes encoding the KIR receptors and their HLA class I ligands.

    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

    authors: Ayo CM,Frederico FB,Siqueira RC,Brandão de Mattos CC,Previato M,Barbosa AP,Murata FH,Silveira-Carvalho AP,de Mattos LC

    更新日期:2016-11-09 00:00:00

  • Cytoskeletal disorganization underlies PABPN1-mediated myogenic disability.

    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

    authors: Olie CS,van der Wal E,Domagoj C,Maton L,de Greef JC,Lin IH,Chen YF,Kareem E,Penninger JM,Kessler BM,Raz V

    更新日期:2020-10-19 00:00:00

  • Pelvic bone morphometric analysis in the dugong (Dugong dugon).

    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

    authors: Nganvongpanit K,Cherdsukjai P,Boonsri B,Buddhachat K,Kaewmong P,Kittiwattanawong K

    更新日期:2020-11-09 00:00:00

  • PKC-ѳ is dispensable for OX40L-induced TCR-independent Treg proliferation but contributes by enabling IL-2 production from effector T-cells.

    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

    authors: Alharshawi K,Marinelarena A,Kumar P,El-Sayed O,Bhattacharya P,Sun Z,Epstein AL,Maker AV,Prabhakar BS

    更新日期:2017-07-26 00:00:00

  • Ex vivo evaluation of an atherosclerotic human coronary artery via histology and high-resolution hard X-ray tomography.

    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

    authors: Buscema M,Hieber SE,Schulz G,Deyhle H,Hipp A,Beckmann F,Lobrinus JA,Saxer T,Müller B

    更新日期:2019-10-04 00:00:00