Abstract：
BACKGROUND:Next-generation sequencing platforms have revolutionised our ability to investigate the microbiota composition of complex environments, frequently through 16S rRNA gene sequencing of the bacterial component of the community. Numerous factors, including DNA extraction method, primer sequences and sequencing platform employed, can affect the accuracy of the results achieved. The aim of this study was to determine the impact of these three factors on 16S rRNA gene sequencing results, using mock communities and mock community DNA. RESULTS:The use of different primer sequences (V4-V5, V1-V2 and V1-V2 degenerate primers) resulted in differences in the genera and species detected. The V4-V5 primers gave the most comparable results across platforms. The three Ion PGM primer sets detected more of the 20 mock community species than the equivalent MiSeq primer sets. Data generated from DNA extracted using the 2 extraction methods were very similar. CONCLUSIONS:Microbiota compositional data differed depending on the primers and sequencing platform that were used. The results demonstrate the risks in comparing data generated using different sequencing approaches and highlight the merits of choosing a standardised approach for sequencing in situations where a comparison across multiple sequencing runs is required.
journal_name
BMC Microbioljournal_title
BMC microbiologyauthors
Fouhy F,Clooney AG,Stanton C,Claesson MJ,Cotter PDdoi
10.1186/s12866-016-0738-zsubject
Has Abstractpub_date
2016-06-24 00:00:00pages
123issue
1issn
1471-2180pii
10.1186/s12866-016-0738-zjournal_volume
16pub_type
杂志文章相关文献
BMC MICROBIOLOGY文献大全abstract：BACKGROUND:Quinolone resistant Escherichia coli (QREC) have been found in samples from Norwegian broiler chicken, despite quinolones not being administered to poultry in Norway. Biofilm production may be one factor contributing to the observed persistence in the broiler production chain. In the present study, 158 QREC ...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/s12866-020-01730-w
更新日期：2020-03-04 00:00:00
abstract：BACKGROUND:The gut comprises an essential barrier that protects both invertebrate and vertebrate animals from invasion by microorganisms. Disruption of the balanced relationship between indigenous gut microbiota and their host can result in gut bacteria eliciting host responses similar to those caused by invasive patho...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/1471-2180-10-129
更新日期：2010-04-27 00:00:00
abstract：BACKGROUND:There is a rapid emergence of multiple resistant gram-negative bacteria due to overuse of antibiotics in the treatment of infections. Biofilms consist of polymicrobial communities that survive the host's defense system. The key bacteria in biofilms are slow growing and support an attachment and rapid growth ...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/s12866-016-0821-5
更新日期：2016-09-09 00:00:00
abstract：BACKGROUND:It is well known that expression of certain bacterial genes responds rapidly to such stimuli as exposure to toxic chemicals and physical agents. It is generally believed that the proteins encoded in these genes are important for successful survival of the organism under the hostile conditions. Analogously, t...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/1471-2180-3-16
更新日期：2003-08-12 00:00:00
abstract：BACKGROUND:The phenomenon of misdiagnosing tuberculosis (TB) by laboratory cross-contamination when culturing Mycobacterium tuberculosis (MTB) has been widely reported and it has an obvious clinical, therapeutic and social impact. The final confirmation of a cross-contamination event requires the molecular identificati...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/1471-2180-8-30
更新日期：2008-02-14 00:00:00
abstract：BACKGROUND:Accumulation of gyrase cleavage complex in Escherichia coli from the action of quinolone antibiotics induces an oxidative damage cell death pathway. The oxidative cell death pathway has also been shown to be involved in the lethality following accumulation of cleavage complex formed by bacterial topoisomeras...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/1471-2180-11-261
更新日期：2011-12-12 00:00:00
abstract：BACKGROUND:Antimicrobial resistance is currently a major global issue. As the rate of emergence of antimicrobial resistance has superseded the rate of discovery and introduction of new effective drugs, the medical arsenal now is experiencing shortage of effective drugs to combat diseases, particularly against diseases ...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/s12866-017-0936-3
更新日期：2017-02-16 00:00:00
abstract：BACKGROUND:In the present work, we describe a group of anomalous dose-response (DR) profiles and develop a dynamic model that is able to explain them. Responses were obtained from conventional assays of three antimicrobial agents (nisin, pediocin and phenol) against two microorganisms (Carnobacterium piscicola and Leuc...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/1471-2180-10-220
更新日期：2010-08-19 00:00:00
abstract：BACKGROUND:Klebsiella pneumoniae can be found in environmental habitats as well as in hospital settings where it is commonly associated with nosocomial infections. One of the factors that contribute to virulence is its capacity to form biofilms on diverse biotic and abiotic surfaces. The second messenger Bis-(3'-5')-cy...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/1471-2180-12-139
更新日期：2012-07-09 00:00:00
abstract：BACKGROUND:Nontuberculous mycobacteria (NTM) are ubiquitous organisms and the incidence of NTM infections has been increasing in recent years. Mycobacteroides abscessus (M. abscessus) is one of the most antimicrobial-resistant NTM; however, no reliable antibiotic regimen can be officially advocated. We evaluated the ef...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/s12866-020-02000-5
更新日期：2020-10-19 00:00:00
abstract：BACKGROUND:Hepatitis B virus (HBV), because of its error-prone viral polymerase, has a high mutation rate leading to widespread substitutions, deletions, and insertions in the HBV genome. Deletions may significantly change viral biological features complicating the progression of liver diseases. However, the clinical c...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/1471-2180-12-307
更新日期：2012-12-28 00:00:00
abstract：BACKGROUND:Footrot and interdigital dermatitis are endemic infectious diseases in all sheep farming regions, impairing welfare and production. The development of efficacious vaccines against the primary causative pathogen has been hampered by the extensive antigenic diversity of Dichelobacter nodosus. Understanding the...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/s12866-020-01769-9
更新日期：2020-05-01 00:00:00
abstract：BACKGROUND:Listeria monocytogenes is the causative agent of listeriosis, a serious disease affecting both animals and humans. Here, multilocus sequence typing (MLST) was used to characterize the genetic diversity of Listeria monocytogenes strains isolated from the natural environment and animal clinical cases in Europe...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/s12866-019-1676-3
更新日期：2019-12-18 00:00:00
abstract：BACKGROUND:Thermotolerant Campylobacter is among the more prevalent bacterial pathogens that cause foodborne diseases. This study aimed at evaluating the occurrence of thermotolerant Campylobacter contamination in chicken carcasses and processing plant stations (chilling water, scalding water, defeathering machinery, e...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/1471-2180-9-94
更新日期：2009-05-15 00:00:00
abstract：BACKGROUND:Probiotics are increasingly applied to prevent and treat a range of infectious, immune related and gastrointestinal diseases. Despite this, the mechanisms behind the putative effects of probiotics are poorly understood. One of the suggested modes of probiotic action is modulation of the endogenous gut microb...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/s12866-017-1090-7
更新日期：2017-08-17 00:00:00
abstract：BACKGROUND:Whole-genome sequencing using high throughput technologies has revolutionized and speeded up the scientific investigation of bacterial genetics, biochemistry, and molecular biology. Lactic acid bacteria (LABs) have been extensively used in fermentation and more recently as probiotics in food products that pr...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/s12866-020-01980-8
更新日期：2020-10-23 00:00:00
abstract：BACKGROUND:The genus Phytophthora includes a group of agriculturally important pathogens and they are commonly regarded as water molds. They produce motile zoospores that can move via water currents and on their own locomotion in aquatic environments. However, zoosporic response to dissolved oxygen, an important water ...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/1471-2180-14-124
更新日期：2014-05-13 00:00:00
abstract：BACKGROUND:Despite the high prevalence of genotype 1b hepatitis C virus (HCV) among patients, a cell culture system that permits entire viral life cycle of genotype 1b isolates is limited. To develop a cell-cultured hepatitis C virus (HCVcc) of genotype 1b, the proper combination of HCV genomic variants and host cells ...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/s12866-016-0846-9
更新日期：2016-09-27 00:00:00
abstract：BACKGROUND:The functions of proteins are strongly related to their localization in cell compartments (for example the cytoplasm or membranes) but the experimental determination of the sub-cellular localization of proteomes is laborious and expensive. A fast and low-cost alternative approach is in silico prediction, bas...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/1471-2180-10-88
更新日期：2010-03-23 00:00:00
abstract：BACKGROUND:Nucleotide sugar transporters (NSTs) play an essential role in translocating nucleotide sugars into the lumen of the endoplasmic reticulum and Golgi apparatus to be used as substrates in glycosylation reactions. This intracellular transport is an essential step in the biosynthesis of glycoconjugates. RESULT...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/s12866-015-0601-7
更新日期：2015-11-21 00:00:00
abstract：BACKGROUND:Campylobacter jejuni is the predominant cause of antecedent infection in post-infectious neuropathies such as the Guillain-Barré (GBS) and Miller Fisher syndromes (MFS). GBS and MFS are probably induced by molecular mimicry between human gangliosides and bacterial lipo-oligosaccharides (LOS). This study desc...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/1471-2180-6-32
更新日期：2006-04-04 00:00:00
abstract：BACKGROUND:Streptococcus agalactiae or Group B Streptococci (GBS) have the ability to access various host sites, which reflects its adaptability to different environments during the course of infection. This adaptation is due to the expression of virulence factors that are involved with survival, invasion and bacterial...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/1471-2180-13-297
更新日期：2013-12-21 00:00:00
abstract：BACKGROUND:Fluconazole (FLC), a triazole antifungal drug, is widely used for the maintenance therapy of cryptococcal meningoencephalitis, the most common opportunistic infection in AIDS patients. In this study, we examined changes in the gene expression profile of the C. neoformans reference strain H99 (serotype A) fol...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/1471-2180-11-97
更新日期：2011-05-11 00:00:00
abstract：BACKGROUND:Edwardsiella ictaluri is a Gram-negative facultative intracellular anaerobe and the etiologic agent of enteric septicemia of channel catfish (ESC). To the catfish industry, ESC is a devastating disease due to production losses and treatment costs. Identification of virulence mechanisms of E. ictaluri is crit...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/s12866-019-1429-3
更新日期：2019-03-08 00:00:00
abstract：BACKGROUND:Ochrobactrum anthropi is a versatile bacterial species with strains living in very diverse habitats. It is increasingly recognized as opportunistic pathogen in hospitalized patients. The population biology of the species particularly with regard to the characteristics of the human isolates is being investiga...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/1471-2180-9-267
更新日期：2009-12-18 00:00:00
abstract：BACKGROUND:The genus Arsenophonus is a group of symbiotic, mainly insect-associated bacteria with rapidly increasing number of records. It is known from a broad spectrum of hosts and symbiotic relationships varying from parasitic son-killers to coevolving mutualists.The present study extends the currently known diversi...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/1471-2180-9-143
更新日期：2009-07-20 00:00:00
abstract：BACKGROUND:The resurgence of multi-drug resistant tuberculosis (MDR-TB) and HIV associated tuberculosis (TB) are of serious global concern. To contain this situation, new anti-tuberculosis drugs and reduced treatment regimens are imperative. Recently, a nitroimidazole, PA-824, has been shown to be active against both r...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/1471-2180-13-218
更新日期：2013-10-01 00:00:00
abstract：BACKGROUND:The increasing availability of whole genome sequences allows the gene or protein content of different organisms to be compared, leading to burgeoning interest in the relatively new subfield of pan-genomics. However, while several studies have analyzed protein content relationships in specific groups of bacte...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/1471-2180-10-258
更新日期：2010-10-13 00:00:00
abstract：BACKGROUND:Helicobacter pylori forms biofilms on glass surfaces at the air-liquid interface in in vitro batch cultures; however, biofilms of H. pylori have not been well characterized. In the present study, we analyzed the ability of H. pylori strains to form biofilms and characterized the underlying mechanisms of H. p...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/1471-2180-9-197
更新日期：2009-09-15 00:00:00
abstract：BACKGROUND:Bloodstream infections represent serious conditions carrying a high mortality and morbidity rate. Rapid identification of microorganisms and prompt institution of adequate antimicrobial therapy is of utmost importance for a successful outcome. Aiming at the development of a rapid, simplified and efficient pr...
journal_title：BMC microbiology
pub_type： 杂志文章
doi：10.1186/s12866-015-0594-2
更新日期：2015-11-06 00:00:00
