Abstract：
:The commensal microbiome is known to influence a variety of host phenotypes. Microbiome profiling followed by differential abundance analysis has been established as an effective approach to study the mechanisms of host-microbiome interactions. However, it is challenging to interpret the collective functions of the resultant microbe-sets due to the lack of well-organized functional characterization of commensal microbiome. We developed microbe-set enrichment analysis (MSEA) to enable the functional interpretation of microbe-sets by examining the statistical significance of their overlaps with annotated groups of microbes that share common attributes such as biological function or phylogenetic similarity. We then constructed microbe-set libraries by query PubMed to find microbe-mammalian gene associations and disease associations by parsing the Disbiome database. To demonstrate the utility of our novel MSEA methodology, we carried out three case studies using publicly available curated knowledge resource and microbiome profiling datasets focusing on human diseases. We found MSEA not only yields consistent findings with the original studies, but also recovers insights about disease mechanisms that are supported by the literature. Overall, MSEA is a useful knowledge-based computational approach to interpret the functions of microbes, which can be integrated with microbiome profiling pipelines to help reveal the underlying mechanism of host-microbiome interactions.
journal_name
Sci Repjournal_title
Scientific reportsauthors
Kou Y,Xu X,Zhu Z,Dai L,Tan Ydoi
10.1038/s41598-020-78511-ysubject
Has Abstractpub_date
2020-12-08 00:00:00pages
21466issue
1issn
2045-2322pii
10.1038/s41598-020-78511-yjournal_volume
10pub_type
杂志文章abstract：:Resistance of cancer cells to radiotherapy is a major clinical problem in cancer treatment. Therefore, understanding the molecular basis of cellular resistance to radiotherapy and identification of novel targets are essential for improving treatment efficacy for cancer patients. Our previous studies have demonstrated ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep14723
更新日期：2015-09-30 00:00:00
abstract：:The Andaman day gecko (Phelsuma andamanensis) is endemic to the Andaman Archipelago, located ~ 6000 km away from Madagascar where the genus Phelsuma likely evolved. We complemented existing phylogenetic data with additional markers to show that this species consistently branches off early in the evolution of the genus...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-68402-7
更新日期：2020-07-16 00:00:00
abstract：:Benign prostatic hyperplasia (BPH) results in a significant public health burden due to the morbidity caused by the disease and many of the available remedies. As much as 70% of men over 70 will develop BPH. Few studies have been conducted to discover the genetic determinants of BPH risk. Understanding the biological ...
journal_title：Scientific reports
pub_type： 杂志文章,多中心研究
doi：10.1038/s41598-019-42427-z
更新日期：2019-04-15 00:00:00
abstract：:Most of the current studies on myocardial strain are mainly applied in patients with sinus rhythm because the image quality of arrhythmias obtained with conventional scanning sequences does not meet diagnostic needs. Here, we intend to assess left ventricular (LV) global myocardial strain in patients with arrhythmias ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-66315-z
更新日期：2020-06-09 00:00:00
abstract：:Serratia marcescens is one of the important nosocomial pathogens which rely on quorum sensing (QS) to regulate the production of biofilm and several virulence factors. Hence, blocking of QS has become a promising approach to quench the virulence of S. marcescens. For the first time, QS inhibitory (QSI) and antibiofilm...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-16507-x
更新日期：2017-11-27 00:00:00
abstract：:Eph receptors have emerged as targets for therapy in both neoplastic and non-neoplastic disease, however, particularly in non-neoplastic diseases, redundancy of function limits the effectiveness of targeting individual Eph proteins. We have shown previously that a soluble fusion protein, where the EphA4 ectodomain was...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-06685-z
更新日期：2017-07-26 00:00:00
abstract：:Lung adenocarcinoma (LUAD) is characterized by high infiltration and rapid growth. The function of the stem cell population is to control and maintain cell regeneration. Therefore, it is necessary to study the prognostic value of stem cell-related genes in LUAD. Signature genes were screened out from 166 stem cell-rel...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-80453-4
更新日期：2021-01-18 00:00:00
abstract：:The evaporation of seawater in arid climates is currently the main accepted driving mechanism for the formation of ancient and recent salt deposits in shallow basins. However, the deposition of huge amounts of marine salts, including the formation of tens of metres of highly soluble types (tachyhydrite and bischofite)...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-48138-9
更新日期：2019-08-12 00:00:00
abstract：:The metal complexes can demonstrate various interesting biological activities in the human body. However, the role of certain metal ions for specific cell activities is still subject to debate. This study is aimed at comparing the thermochemical properties of neotame (artificial sweetener) and α, β-fructose in gas pha...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-54626-9
更新日期：2019-12-05 00:00:00
abstract：:Although the association between social support and postpartum depression has been previously investigated, its causal relationship remains unclear. Therefore, we examined prospectively whether social support during pregnancy affected postpartum depression. Social support and depressive symptoms were assessed by Japan...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep10520
更新日期：2015-05-29 00:00:00
abstract：:Bio-functionalized nanoparticles with semiconducting/metallic core encapsulated in a bio- or bio-derived materials are promising for applications in biology and especially in cancer diagnostic and healing. In this report, we report a facile, single-step, first-time synthesis and in-situ functionalization strategy for ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep18629
更新日期：2015-12-21 00:00:00
abstract：:Intestinal fibrosis is thought to be a consequence of excessive tissue repair, and constitutes a common problem in patients with Crohn's disease (CD). While fibrosis seems to require inflammation as a prerequisite it is unclear whether the severity or persistence of inflammation influences the degree of fibrosis. Our ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-33452-5
更新日期：2018-10-12 00:00:00
abstract：:The mechanism whereby lactic acid bacteria extend the lifespan of Caenorhabditis elegans has previously been elucidated. However, the role of Weissella species has yet not been studied. We show that Weissella koreensis and Weissella cibaria significantly (p < 0.05) extend the lifespan of C. elegans compared with Esche...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep17128
更新日期：2015-11-25 00:00:00
abstract：:Luminescent zeolites exchanged with two distinct and interacted emissive ions are vital but less-studied for the potential applications in white light emitting diodes, solar cells, optical codes, biomedicine and so on. Typical transition metal ion Mn2+ and lanthanide ion Yb3+ are adopted as a case study via their char...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep46219
更新日期：2017-04-10 00:00:00
abstract：:TLR4 location, and bacterial species-derived lipopolysaccharides, play a significant role in the downstream activation of transcription factors, accessory molecules, and products. Here, this is demonstrated through the use of classically-activated and alternatively-activated macrophages. We show that, when polarized, ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-79145-w
更新日期：2021-01-14 00:00:00
abstract：:This study aimed to investigate changes in types of dental arch form during adolescence and explore adolescent changes in size and form of dental arch. Hong Kong Chinese were recruited and digital dental arch models were obtained at ages 12, 15, and 18 years. Geometric morphometrics was used to investigate adolescent ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-55073-2
更新日期：2019-12-06 00:00:00
abstract：:Culture medium of mesenchymal stromal cells (MSCs) is usually supplemented with either human platelet lysate (HPL) or fetal calf serum (FCS). Many studies have demonstrated that proliferation and cellular morphology are affected by these supplements - it is therefore important to determine if they favor outgrowth of d...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-05207-1
更新日期：2017-07-11 00:00:00
abstract：:In the eyeblink conditioning paradigm, cerebellar Purkinje cells learn to respond to the conditional stimulus with an adaptively timed pause in its spontaneous firing. Evidence suggests that the pause is elicited by glutamate released from parallel fibers and acting on metabotropic receptors (mGluR7) which initiates a...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-72581-8
更新日期：2020-09-24 00:00:00
abstract：:Crops have different strategies to acquire poorly-available soil phosphorus (P) which are dependent on their architectural, morphological, and physiological root traits, but their capacity to enhance P acquisition varies with the type of fertilizer applied. The objective of this study was to examine how P-acquisition ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-51204-x
更新日期：2019-10-16 00:00:00
abstract：:Lipopolysaccharide (LPS) is a major component of the outer wall of gram negative bacteria. In high doses LPS contributes to the inflammation in gram negative sepsis, and in low doses contributes to the low grade inflammation characteristic of the metabolic syndrome. We wanted to assess the role of beta2-glycoprotein I...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep33656
更新日期：2016-09-27 00:00:00
abstract：:Highly efficient and specific biomolecular recognition requires both affinity and specificity. Previous quantitative descriptions of biomolecular recognition were mostly driven by improving the affinity prediction, but lack of quantification of specificity. We developed a novel method SPA (SPecificity and Affinity) ba...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep00309
更新日期：2012-01-01 00:00:00
abstract：:The clinical significance of STIM proteins and Orai Ca2+ channels in tumor progression has been demonstrated in different types of cancers. Podosomes are dynamic actin-rich cellular protrusions that facilitate cancer cell invasiveness by degrading extracellular matrix. Whether STIM1-dependent Ca2+ signaling facilitate...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-11273-2
更新日期：2017-09-14 00:00:00
abstract：:The Near-infrared Fluorescence (NIRF) molecular imaging of cancer is known to be superior in sensitivity, deeper penetration, and low phototoxicity compared to other imaging modalities. In view of an increased need for efficient and targeted imaging agents, we synthesized a NAD(P)H quinone oxidoreductase 1 (NQO1)-acti...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-44111-8
更新日期：2019-06-12 00:00:00
abstract：:microRNAs are short, noncoding RNAs that can regulate hundreds of targets and thus shape the expression landscape of a cell. Similar to mRNA, they often exhibit cell type enriched expression and serve to reinforce cellular identity. In tissue with high cellular complexity, such as the central nervous system (CNS), it ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-61307-5
更新日期：2020-03-18 00:00:00
abstract：:Production of fly ash zeolites may be an attractive method for the utilization of solid wastes from the energy sector. Different methods of synthesis often yield a variety of zeolite types, thereby affecting the properties of the resulting materials. The attention paid to carbon dioxide emission reduction technologies...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-58591-6
更新日期：2020-02-04 00:00:00
abstract：:Histone methylation is thought to control the regulation of genetic program and the dysregulation of it has been found to be closely associated with cancer. JMJD3 has been identified as an H3K27 demethylase and its role in cancer development is context specific. The role of JMJD3 in gastric cancer (GC) has not been ex...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-37340-w
更新日期：2019-01-29 00:00:00
abstract：:Assessment of intraventricular pressure gradients (IVPG) using color Doppler M-mode echocardiography has gained increasing interest in the evaluation of cardiac function. However, standardized analysis tools for IVPG quantification are missing. We aimed to evaluate the feasibility, the test-retest observer reproducibi...
journal_title：Scientific reports
pub_type： 临床试验,杂志文章
doi：10.1038/s41598-020-64059-4
更新日期：2020-04-28 00:00:00
abstract：:Deprivation of maternal care during early development markedly affects emotional development, but the underlying neuromolecular mechanisms are not fully understood. In a mouse model of disrupted mother-infant relationship, early weaning causes long-term impacts on pups to exhibit increased corticosterone secretion, an...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-40530-9
更新日期：2019-03-08 00:00:00
abstract：:Spinal cord injury (SCI) is frequently accompanied by a degree of spontaneous functional recovery. The underlying mechanisms through which such recovery is generated remain elusive. In this study, we observed a significant spontaneous motor function recovery 14 to 28 days after spinal cord transection (SCT) in rats. U...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep16911
更新日期：2015-11-23 00:00:00
abstract：:Crystalline atomic layers on solid surfaces are composed of a single building block, unit cell, that is copied and stacked together to form the entire two-dimensional crystal structure. However, it appears that this is not an unique possibility. We report here on synthesis and characterization of the one-atomic-layer-...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep19446
更新日期：2016-01-19 00:00:00
