Abstract:
BACKGROUND:As an important nosocomial pathogen, Enterococcus faecium has received increasing attention in recent years. However, a large number of studies have focused on the hospital-associated isolates and ignored isolates originated from the natural environments. RESULTS:In this study, comparative genomic analysis was conducted on 161 isolates originated from human, animal, and naturally fermented dairy products. The results showed that the environment played an important role in shaping the genomes of Enterococcus faecium. The isolates from human had the largest average genome size, while the isolates from dairy products had the smallest average genome size and fewest antibiotic resistance genes. A phylogenetic tree was reconstructed based on the genomes of these isolates, which revealed new insights into the phylogenetic relationships among the dairy isolates and those from hospitals, communities, and animals. Furthermore, 202 environment-specific genes were identified, including 136 dairy-specific, 31 human blood-specific, and 35 human gastrointestinal-specific genes. Interestingly, five dairy-specific genes (namely lacF, lacA/B, lacD, lacG, and lacC) that constituted an integrated lactose metabolism pathway existed in almost all dairy isolates. The pathway conservation demonstrated an active role of the environment in shaping the genomes of Enterococcus faecium. CONCLUSIONS:This study shows that the Enterococcus faecium species has great genomic plasticity and high versatility to occupy broad ecological roles, dwelling as non-harmful dairy and animal gut commensals as well as significant nosocomial pathogens that disseminate antibiotic resistance genes.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Zhong Z,Kwok LY,Hou Q,Sun Y,Li W,Zhang H,Sun Zdoi
10.1186/s12864-019-5975-8subject
Has Abstractpub_date
2019-07-22 00:00:00pages
602issue
1issn
1471-2164pii
10.1186/s12864-019-5975-8journal_volume
20pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Boar taint is observed in a high proportion of uncastrated male pigs and is characterized by an unpleasant odor/flavor in cooked meat, primarily caused by elevated levels of androstenone and skatole. Androstenone is a steroid produced in the testis in parallel with biosynthesis of other sex steroids like tes...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-362
更新日期:2011-07-13 00:00:00
abstract:BACKGROUND:Bananas (Musa spp.) are an important crop worldwide. Most modern cultivars resulted from a complex polyploidization history that comprised three whole genome duplications (WGDs) shaping the haploid Musa genome, followed by inter- and intra-specific crosses between Musa acuminata and M. balbisiana (A and B ge...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5618-0
更新日期:2019-03-27 00:00:00
abstract:BACKGROUND:RNA sequencing (RNA-seq) and microarrays are two transcriptomics techniques aimed at the quantification of transcribed genes and their isoforms. Here we compare the latest Affymetrix HTA 2.0 microarray with Illumina 2000 RNA-seq for the analysis of patient samples - normal lung epithelium tissue and squamous...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3819-y
更新日期:2017-06-06 00:00:00
abstract:BACKGROUND:The contribution of a gene to the fitness of a bacterium can be assayed by whether and to what degree the bacterium tolerates transposon insertions in that gene. We use this fact to compare the fitness of syntenic homologous genes among related Salmonella strains and thereby reveal differences not apparent a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-212
更新日期:2012-05-30 00:00:00
abstract:BACKGROUND:Heat shock proteins (Hsps) are molecular chaperones that are involved in many normal cellular processes and stress responses, and heat shock factors (Hsfs) are the transcriptional activators of Hsps. Hsfs and Hsps are widely coordinated in various biological processes. Although the roles of Hsfs and Hsps in ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1398-3
更新日期:2015-03-14 00:00:00
abstract:BACKGROUND:Marek's disease (MD) is a lymphoproliferative disease in chickens caused by Marek's disease virus (MDV) and characterized by T cell lymphoma and infiltration of lymphoid cells into various organs such as liver, spleen, peripheral nerves and muscle. Resistance to MD and disease risk have long been thought to ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-501
更新日期:2011-10-12 00:00:00
abstract:BACKGROUND:Whole-exome sequencing (WES) is rapidly evolving into a tool of choice for rapid, and inexpensive identification of molecular genetic lesions within targeted regions of the human genome. While biases in WES coverage of nucleotides in targeted regions are recognized, it is not well understood how repetition o...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2107-y
更新日期:2015-11-25 00:00:00
abstract:BACKGROUND:Characterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types and methods are available to detect these structural variants (SVs), they remain less characterized than smaller variants because of SV diversity, complexity,...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1479-3
更新日期:2015-04-11 00:00:00
abstract:BACKGROUND:Among viruses, bacteriophages are a group of special interest due to their capacity of infecting bacteria that are important for biotechnology and human health. Composting is a microbial-driven process in which complex organic matter is converted into humus-like substances. In thermophilic composting, the de...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3729-z
更新日期:2017-05-04 00:00:00
abstract:BACKGROUND:Leishmania (L) are intracellular protozoan parasites that are able to survive and replicate within the harsh and potentially hostile phagolysosomal environment of mammalian mononuclear phagocytes. A complex interplay then takes place between the macrophage (MPhi) striving to eliminate the pathogen and the pa...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-238
更新日期:2008-05-21 00:00:00
abstract:BACKGROUND:The incidence of congenital heart disease (CHD) is continuously increasing among infants born alive nowadays, making it one of the leading causes of infant morbidity worldwide. Various studies suggest that both genetic and environmental factors lead to CHD, and therefore identifying its candidate genes and d...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-592
更新日期:2011-12-02 00:00:00
abstract:BACKGROUND:Prolactin is a polypeptide hormone secreted by the anterior pituitary gland that plays an essential role in lactation, tissue growth, and suppressing apoptosis to increase cell survival. Prolactin serves as a key player in many life-critical processes, including immune system and reproduction. Prolactin is a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2785-0
更新日期:2016-06-29 00:00:00
abstract:BACKGROUND:The Pregnancy-associated glycoproteins (PAGs) belong to a large family of aspartic peptidases expressed exclusively in the placenta of species in the Artiodactyla order. In cattle, the PAG gene family is comprised of at least 22 transcribed genes, as well as some variants. Phylogenetic analyses have shown th...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-185
更新日期:2009-04-24 00:00:00
abstract:BACKGROUND:The gut of phloem feeding insects is critical for nutrition uptake and xenobiotics degradation. However, partly due to its tiny size, genomic information for the gut of phloem feeding insects is limited. RESULTS:In this study, the gut transcriptomes of two species of invasive whiteflies in the Bemisia tabac...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-370
更新日期:2014-05-15 00:00:00
abstract:BACKGROUND:The 2009 pandemic H1N1 influenza virus emerged in swine and quickly became a major global health threat. In mouse, non human primate, and swine infection models, the pH1N1 virus efficiently replicates in the lung and induces pro-inflammatory host responses; however, whether similar or different cellular path...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-627
更新日期:2012-11-15 00:00:00
abstract:BACKGROUND:Hard ticks (family Ixodidae) are obligatory hematophagous ectoparasites of worldwide medical and veterinary importance. The haploid genomes of multiple species of ixodid ticks exceed 1 Gbp, prompting questions regarding gene, segmental and whole genome duplication in this phyletic group. The availability of ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2350-2
更新日期:2016-03-16 00:00:00
abstract:BACKGROUND:Microarray technology is limited to monitoring the expression of previously annotated genes that have corresponding probes on the array. Computationally annotated genes have not fully been validated, because ESTs and full-length cDNAs cannot cover entire transcribed regions. Here, mRNA-Seq (an Illumina cDNA ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-683
更新日期:2010-12-02 00:00:00
abstract:BACKGROUND:Understanding how and why genetic variation is partitioned across geographic space is of fundamental importance to understanding the nature of biological species. How geographical isolation and local adaptation contribute to the formation of ecotypically differentiated groups of plants is just beginning to b...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5179-7
更新日期:2018-11-01 00:00:00
abstract:BACKGROUND:Chinese bayberry (Myrica rubra Sieb. and Zucc.) is a subtropical evergreen tree originating in China. It has been cultivated in southern China for several thousand years, and annual production has reached 1.1 million tons. The taste and high level of health promoting characters identified in the fruit in rec...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-201
更新日期:2012-05-23 00:00:00
abstract:BACKGROUND:In higher eukaryotes, small RNAs play a role in regulating gene expression. Overexpression (OE) lines of Arabidopsis thaliana purple acid phosphatase 2 (AtPAP2) were shown to grow faster and exhibit higher ATP and sugar contents. Leaf microarray studies showed that many genes involved in microRNAs (miRNAs) a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-116
更新日期:2014-02-10 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) post-transcriptionally regulate a variety of genes involved in eukaryotic cell growth, development, metabolism and other biological processes, and numerous miRNAs are implicated in the initiation and progression of cancer. Enzootic nasal adenocarcinoma (ENA), an epithelial tumor induced in...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3238-5
更新日期:2016-11-08 00:00:00
abstract:BACKGROUND:Skeletal muscle mass can be markedly reduced through a process called atrophy, as a consequence of many diseases or critical physiological and environmental situations. Atrophy is characterised by loss of contractile proteins and reduction of fiber volume. Although in the last decade the molecular aspects un...
journal_title:BMC genomics
pub_type: 杂志文章,meta分析
doi:10.1186/1471-2164-9-630
更新日期:2008-12-23 00:00:00
abstract:BACKGROUND:Genome-wide association studies (GWAS) have identified many common polymorphisms associated with complex traits. However, these associated common variants explain only a small fraction of the phenotypic variances, leaving a substantial portion of genetic heritability unexplained. As a result, searches for "m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-S1-S1
更新日期:2013-01-01 00:00:00
abstract:BACKGROUND:The European spruce bark beetle, Ips typographus, and the North American mountain pine beetle, Dendroctonus ponderosae (Coleoptera: Curculionidae: Scolytinae), are severe pests of coniferous forests. Both bark beetle species utilize aggregation pheromones to coordinate mass-attacks on host trees, while odora...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-198
更新日期:2013-03-21 00:00:00
abstract:BACKGROUND:Pyrethroid resistance in Anopheles funestus populations has led to an increase in malaria transmission in southern Africa. Resistance has been attributed to elevated activities of cytochrome P450s but the molecular basis underlying this metabolic resistance is unknown. Microsatellite and SNP markers were use...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-34
更新日期:2007-01-29 00:00:00
abstract:BACKGROUND:The human zinc finger protein 191 (ZNF191) is a member of the SCAN domain family of Krüppel-like zinc finger transcription factors. ZNF191 shows 94% identity to its mouse homologue zinc finger protein 191(Zfp191), which is the most highly conserved among the human-mouse SCAN family member orthologues pairs. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-241
更新日期:2009-05-22 00:00:00
abstract:BACKGROUND:The food spoilage yeast species Zygosaccharomyces bailii exhibits an extraordinary capacity to tolerate weak acids, in particular acetic acid. In Saccharomyces cerevisiae, the transcription factor Haa1 (ScHaa1) is considered the main player in genomic expression reprogramming in response to acetic acid stres...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3443-2
更新日期:2017-01-13 00:00:00
abstract:BACKGROUND:The bacterial CRISPR system is fast becoming the most popular genetic and epigenetic engineering tool due to its universal applicability and adaptability. The desire to deploy CRISPR-based methods in a large variety of species and contexts has created an urgent need for the development of easy, time- and cos...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3268-z
更新日期:2016-11-14 00:00:00
abstract:BACKGROUND:Oxidative stress is a common stress encountered by living organisms and is due to an imbalance between intracellular reactive oxygen and nitrogen species (ROS, RNS) and cellular antioxidant defence. To defend themselves against ROS/RNS, bacteria possess a subsystem of detoxification enzymes, which are classi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-637
更新日期:2008-12-31 00:00:00
abstract:BACKGROUND:Obesity and phenotypic traits associated with this condition exhibit significant heritability in natural populations of most organisms. While a number of genes and genetic pathways have been implicated to play a role in obesity associated traits, the genetic architecture that underlies the natural variation ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-297
更新日期:2010-05-11 00:00:00