Abstract:
BACKGROUND:The study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder of these sequence-based approaches is the presence of contamination in DNA extraction kits and other laboratory reagents. RESULTS:In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits and other laboratory reagents, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass. Contamination impacts both PCR-based 16S rRNA gene surveys and shotgun metagenomics. We provide an extensive list of potential contaminating genera, and guidelines on how to mitigate the effects of contamination. CONCLUSIONS:These results suggest that caution should be advised when applying sequence-based techniques to the study of microbiota present in low biomass environments. Concurrent sequencing of negative control samples is strongly advised.
journal_name
BMC Bioljournal_title
BMC biologyauthors
Salter SJ,Cox MJ,Turek EM,Calus ST,Cookson WO,Moffatt MF,Turner P,Parkhill J,Loman NJ,Walker AWdoi
10.1186/s12915-014-0087-zsubject
Has Abstractpub_date
2014-11-12 00:00:00pages
87issn
1741-7007pii
s12915-014-0087-zjournal_volume
12pub_type
杂志文章相关文献
BMC BIOLOGY文献大全abstract:BACKGROUND:Affinity purification followed by mass spectrometry (AP/MS) is a widely used approach to identify protein interactions and complexes. In multicellular organisms, the accurate identification of protein complexes by AP/MS is complicated by the potential heterogeneity of complexes in different tissues. Here, we...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-016-0286-x
更新日期:2016-08-09 00:00:00
abstract::Protein conformational dynamics simultaneously allow promiscuity and specificity in binding. The multiple conformations of the free EphA4 ligand-binding domain observed in two new EphA4 crystal structures provide a unique insight into the conformational dynamics of EphA4 and its signaling pathways. The heterogeneous e...
journal_title:BMC biology
pub_type: 社论
doi:10.1186/1741-7007-10-2
更新日期:2012-01-25 00:00:00
abstract::Joel Dacks is an Associate Professor and Canada Research Chair in Evolutionary Cell Biology at the University of Alberta, a Scientific Associate at the Natural History Museum (London), and the current President of the International Society for Evolutionary Protistology. His research group studies the evolution and div...
journal_title:BMC biology
pub_type: 传,历史文章,面试
doi:10.1186/s12915-018-0586-4
更新日期:2018-11-01 00:00:00
abstract:BACKGROUND:The next big challenge in human genetics is understanding the 98% of the genome that comprises non-coding DNA. Hidden in this DNA are sequences critical for gene regulation, and new experimental strategies are needed to understand the functional role of gene-regulation sequences in health and disease. In thi...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-11-106
更新日期:2013-10-14 00:00:00
abstract:BACKGROUND:ESCRT-III is a membrane remodelling filament with the unique ability to cut membranes from the inside of the membrane neck. It is essential for the final stage of cell division, the formation of vesicles, the release of viruses, and membrane repair. Distinct from other cytoskeletal filaments, ESCRT-III filam...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-019-0700-2
更新日期:2019-10-22 00:00:00
abstract:BACKGROUND:A genome-wide association study (GWAS) is the foremost strategy used for finding genes that control human diseases and agriculturally important traits, but it often reports false positives. In contrast, its complementary method, linkage analysis, provides direct genetic confirmation, but with limited resolut...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-015-0187-4
更新日期:2015-09-21 00:00:00
abstract:BACKGROUND:The green algae Chlamydomonas reinhardtii and Volvox carteri are important models for studying light perception and response, expressing many different photoreceptors. More than 10 opsins were reported in C. reinhardtii, yet only two-the channelrhodopsins-were functionally characterized. Characterization of ...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-018-0613-5
更新日期:2018-12-06 00:00:00
abstract::Cells are highly complex and orderly machines, with defined shapes and a startling variety of internal organizations. Complex geometry is a feature of both free-living unicellular organisms and cells inside multicellular animals. Where does the geometry of a cell come from? Many of the same questions that arise in dev...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-9-57
更新日期:2011-08-31 00:00:00
abstract:BACKGROUND:Membrane proteins form key nodes in mediating the cell's interaction with the surroundings, which is one of the main reasons why the majority of drug targets are membrane proteins. RESULTS:Here we mined the human proteome and identified the membrane proteome subset using three prediction tools for alpha-hel...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-7-50
更新日期:2009-08-13 00:00:00
abstract:BACKGROUND:Nucleostemin is a nucleolus residing GTPase that is considered to be an important cancer stem/progenitor cell marker protein due to its high expression levels in breast cancer stem cells and its role in tumor-initiation of human mammary tumor cells. It has been proposed that nucleostemin may represent a valu...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-014-0072-6
更新日期:2014-09-12 00:00:00
abstract:BACKGROUND:Mate choice is of central importance to most animals, influencing population structure, speciation, and ultimately the survival of a species. Mating behavior of male brachionid rotifers is triggered by the product of a chemosensory gene, a glycoprotein on the body surface of females called the mate recogniti...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-7-60
更新日期:2009-09-09 00:00:00
abstract::The authors of this paper were interested to see whether the expression of three proteins (A, B and C) was altered in a knockout mouse model of a gene encoding Protein X. Each experiment measured the expression of a different protein and the results seem to show a clear increase in protein expression in the mutant mou...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-016-0254-5
更新日期:2016-04-07 00:00:00
abstract::The circadian clock enhances fitness through temporal organization of plant gene expression, metabolism and physiology. Two recent studies, one in BMC Evolutionary Biology, demonstrate through phylogenetic analysis of the CCA1/LHY and TOC1/PRR gene families that the common ancestor of monocots and eudicots had compone...
journal_title:BMC biology
pub_type: 评论,杂志文章,评审
doi:10.1186/1741-7007-8-55
更新日期:2010-05-07 00:00:00
abstract:BACKGROUND:ADP-ribosylation is a ubiquitous post-translational modification that involves both mono- and poly-ADP-ribosylation. ARTD10, also known as PARP10, mediates mono-ADP-ribosylation (MARylation) of substrate proteins. A previous screen identified protein kinase C delta (PKCδ) as a potential ARTD10 substrate, amo...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-020-00878-1
更新日期:2020-10-15 00:00:00
abstract::Mitochondria are highly dynamic and structurally complex organelles that provide multiple essential metabolic functions. Mitochondrial dysfunction is associated with neurodegenerative conditions such as Parkinson's disease, as well as bacterial infection. Here, we explore the roles of mitochondrial autophagy (mitophag...
journal_title:BMC biology
pub_type: 杂志文章,评审
doi:10.1186/s12915-015-0129-1
更新日期:2015-04-03 00:00:00
abstract:BACKGROUND:Within chromatin, the histone variant H2A.Z plays a role in many diverse nuclear processes including transcription, preventing the spread of heterochromatin and epigenetic transcriptional memory. The molecular mechanisms of how H2A.Z mediates its effects are not entirely understood. However, it is now known ...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-7-86
更新日期:2009-12-14 00:00:00
abstract::The vertebrate nervous system is deeply divided into 'somatic' and 'visceral' subsystems that respond to external and internal stimuli, respectively. Molecular characterization of neurons in different groups of mollusks by Nomaksteinsky and colleagues, published in this issue of BMC Biology, reveals that the viscero-s...
journal_title:BMC biology
pub_type: 评论,杂志文章
doi:10.1186/1741-7007-11-54
更新日期:2013-04-30 00:00:00
abstract:BACKGROUND:The traditional concept that heritability occurs exclusively from the transfer of germline-restricted genetics is being challenged by the increasing accumulation of evidence confirming the existence of experience-dependent transgenerational inheritance. However, questions remain unanswered as to how heritabl...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-020-00780-w
更新日期:2020-04-30 00:00:00
abstract:BACKGROUND:The ParaHox gene cluster is the evolutionary sister to the Hox cluster. Whilst the role of the Hox cluster in patterning the anterior-posterior axis of bilaterian animals is well established, and the organisation of vertebrate Hox clusters is intimately linked to gene regulation, much less is known about the...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-7-43
更新日期:2009-07-23 00:00:00
abstract:BACKGROUND:Microarray analysis and 454 cDNA sequencing were used to investigate a centuries-old problem in regenerative biology: the basis of nerve-dependent limb regeneration in salamanders. Innervated (NR) and denervated (DL) forelimbs of Mexican axolotls were amputated and transcripts were sampled after 0, 5, and 14...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-7-1
更新日期:2009-01-13 00:00:00
abstract:BACKGROUND:Methods for assigning strains to bacterial species are cumbersome and no longer fit for purpose. The concatenated sequences of multiple house-keeping genes have been shown to be able to define and circumscribe bacterial species as sequence clusters. The advantage of this approach (multilocus sequence analysi...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-7-3
更新日期:2009-01-26 00:00:00
abstract:BACKGROUND:Corticotropin-releasing factor (CRF) is typically considered to mediate aversive aspects of stress, fear and anxiety. However, CRF release in the brain is also elicited by natural rewards and incentive cues, raising the possibility that some CRF systems in the brain mediate an independent function of positiv...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-4-8
更新日期:2006-04-13 00:00:00
abstract:BACKGROUND:Accurate determination of mouse positions from video data is crucial for various types of behavioral analyses. While detection of body positions is straightforward, the correct identification of nose positions, usually more informative, is far more challenging. The difficulty is largely due to variability in...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-017-0377-3
更新日期:2017-05-15 00:00:00
abstract:BACKGROUND:The discharge of the Cnidarian stinging organelle, the nematocyst, is one of the fastest processes in biology and involves volume changes of the highly pressurised (150 bar) capsule of up to 50%. Hitherto, the molecular basis for the unusual biomechanical properties of nematocysts has been elusive, as their ...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-014-0113-1
更新日期:2015-01-16 00:00:00
abstract:BACKGROUND:Gq is a heterotrimeric G protein that plays an important role in numerous physiological processes. To delineate the molecular mechanisms and kinetics of signalling through this protein, its activation should be measurable in single living cells. Recently, fluorescence resonance energy transfer (FRET) sensors...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-9-32
更新日期:2011-05-27 00:00:00
abstract:BACKGROUND:Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by both motor and non-motor symptoms. Gastrointestinal tract dysfunction is one of the non-motor features, where constipation is reported as the most common gastrointestinal symptom. Aromatic bacterial metabolites are attracti...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-020-00876-3
更新日期:2020-10-20 00:00:00
abstract:BACKGROUND:TPA Induced Sequence 7 acts as a transcriptional co-regulator controlling the expression of genes involved in differentiation of various cell types, including skeletal myoblasts. We and others have shown that TIS7 regulates adult myogenesis through MyoD, one of the essential myogenic regulatory factors. RES...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-016-0318-6
更新日期:2016-10-25 00:00:00
abstract:BACKGROUND:The hormone adiponectin (ApN) exerts powerful anti-inflammatory effects on skeletal muscle and can reverse devastating myopathies, like Duchenne muscular dystrophy (DMD), where inflammation exacerbates disease progression. The NLRP3 inflammasome plays a key role in the inflammation process, and its aberrant ...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-018-0501-z
更新日期:2018-03-20 00:00:00
abstract::There are many reasons to be interested in stem cells, one of the most prominent being their potential use in finding better drugs to treat human disease. This article focuses on how this may be implemented. Recent advances in the production of reprogrammed adult cells and their regulated differentiation to disease-re...
journal_title:BMC biology
pub_type: 杂志文章,评审
doi:10.1186/1741-7007-9-42
更新日期:2011-06-07 00:00:00
abstract:BACKGROUND:The transmissible spongiform encephalopathies, otherwise known as prion diseases, occur following the conversion of the cellular prion protein (PrPC) to an alternatively folded, disease-associated isoform (PrPSc). Recent studies suggest that this conversion occurs via a cholesterol-sensitive process, as chol...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-6-39
更新日期:2008-09-12 00:00:00