Abstract:
BACKGROUND:Besides the development of comprehensive tools for high-throughput 16S ribosomal RNA amplicon sequence analysis, there exists a growing need for protocols emphasizing alternative phylogenetic markers such as those representing eukaryotic organisms. RESULTS:Here we introduce CloVR-ITS, an automated pipeline for comparative analysis of internal transcribed spacer (ITS) pyrosequences amplified from metagenomic DNA isolates and representing fungal species. This pipeline performs a variety of steps similar to those commonly used for 16S rRNA amplicon sequence analysis, including preprocessing for quality, chimera detection, clustering of sequences into operational taxonomic units (OTUs), taxonomic assignment (at class, order, family, genus, and species levels) and statistical analysis of sample groups of interest based on user-provided information. Using ITS amplicon pyrosequencing data from a previous human gastric fluid study, we demonstrate the utility of CloVR-ITS for fungal microbiota analysis and provide runtime and cost examples, including analysis of extremely large datasets on the cloud. We show that the largest fractions of reads from the stomach fluid samples were assigned to Dothideomycetes, Saccharomycetes, Agaricomycetes and Sordariomycetes but that all samples were dominated by sequences that could not be taxonomically classified. Representatives of the Candida genus were identified in all samples, most notably C. quercitrusa, while sequence reads assigned to the Aspergillus genus were only identified in a subset of samples. CloVR-ITS is made available as a pre-installed, automated, and portable software pipeline for cloud-friendly execution as part of the CloVR virtual machine package (http://clovr.org). CONCLUSION:The CloVR-ITS pipeline provides fungal microbiota analysis that can be complementary to bacterial 16S rRNA and total metagenome sequence analysis allowing for more comprehensive studies of environmental and host-associated microbial communities.
journal_name
Microbiomejournal_title
Microbiomeauthors
White JR,Maddox C,White O,Angiuoli SV,Fricke WFdoi
10.1186/2049-2618-1-6subject
Has Abstractpub_date
2013-02-04 00:00:00pages
6issue
1issn
2049-2618pii
2049-2618-1-6journal_volume
1pub_type
杂志文章相关文献
Microbiome文献大全abstract:BACKGROUND:Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and evolutionary adaptations remain elusive. We recently isolated a novel group of bacterial predators, Br...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-020-00902-0
更新日期:2020-08-31 00:00:00
abstract:BACKGROUND:The caecal microbiota plays a key role in chicken health and performance, influencing digestion and absorption of nutrients, and contributing to defence against colonisation by invading pathogens. Measures of productivity and resistance to pathogen colonisation are directly influenced by chicken genotype, bu...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0501-9
更新日期:2018-06-23 00:00:00
abstract:BACKGROUND:Fecal microbiota transplantation is an effective treatment for recurrent Clostridium difficile infection and is being investigated as a treatment for other microbiota-associated diseases. To facilitate these activities, an international public stool bank has been created, which screens donors and processes s...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-015-0140-3
更新日期:2015-12-17 00:00:00
abstract:BACKGROUND:Lower respiratory tract infection (LRTI) is a major contributor to respiratory failure requiring intubation and mechanical ventilation. LRTI also occurs during mechanical ventilation, increasing the morbidity and mortality of intubated patients. We sought to understand the dynamics of respiratory tract micro...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-016-0151-8
更新日期:2016-02-11 00:00:00
abstract:BACKGROUND:Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the rec...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-017-0270-x
更新日期:2017-05-04 00:00:00
abstract::Following publication of the original article [1], the authors reported an error in Fig. 2. The original Fig. 2 has been incorrectly replaced with the Supplementary Fig. 2. The correct Fig. 2 is presented here. ...
journal_title:Microbiome
pub_type: 杂志文章,已发布勘误
doi:10.1186/s40168-020-00829-6
更新日期:2020-04-06 00:00:00
abstract:BACKGROUND:Clostridium difficile infection (CDI) is the leading infectious cause of nosocomial diarrhea. Hospitalized patients are at increased risk of developing CDI because they are exposed to C. difficile spores through contact with the hospital environment and often receive antibiotics and other medications that ca...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-016-0156-3
更新日期:2016-03-14 00:00:00
abstract:BACKGROUND:Preterm infants are at risk of developing intestinal dysbiosis with an increased proportion of Gammaproteobacteria. In this study, we sought the clinical determinants of the relative abundance of feces-associated Gammaproteobacteria in very low birth weight (VLBW) infants. Fecal microbiome was characterized ...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0547-8
更新日期:2018-09-12 00:00:00
abstract:BACKGROUND:Sub-therapeutic antibiotics are widely used as growth promoters in the poultry industry; however, the resulting antibiotic resistance threatens public health. A plant-derived growth promoter, Macleaya cordata extract (MCE), with effective ingredients of benzylisoquinoline alkaloids, is a potential alternativ...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0590-5
更新日期:2018-11-27 00:00:00
abstract:BACKGROUND:Increasing evidence reveals the importance of the microbiome in health and disease and inseparable host-microbial dependencies. Host-microbe interactions are highly relevant in patients receiving allogeneic hematopoietic stem cell transplantation (HSCT), i.e., a replacement of the cellular components of the ...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0745-z
更新日期:2019-09-13 00:00:00
abstract::Human genome-wide association studies (GWASs) have recurrently estimated lower heritability estimates than familial studies. Many explanations have been suggested to explain these lower estimates, including that a substantial proportion of genetic variation and gene-by-environment interactions are unmeasured in typica...
journal_title:Microbiome
pub_type: 信件
doi:10.1186/s40168-020-00839-4
更新日期:2020-06-08 00:00:00
abstract:BACKGROUND:The nasopharynx is a reservoir for pathogens associated with respiratory illnesses, such as asthma. Next-generation sequencing (NGS) has been used to characterize the nasopharyngeal microbiome during health and disease. Most studies so far have surveyed the nasopharynx as a whole; however, less is known abou...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-016-0170-5
更新日期:2016-06-16 00:00:00
abstract:BACKGROUND:Our understanding of gut microbiota has been limited primarily to findings from human and laboratory animals, but what shapes the gut microbiota in nature remains largely unknown. To fill this gap, we conducted a comprehensive study of gut microbiota of a well-studied North American red squirrel (Tamiasciuru...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-017-0382-3
更新日期:2017-12-21 00:00:00
abstract:BACKGROUND:In microbiome studies, it is important to detect taxa which are associated with pathological outcomes at the lowest definable taxonomic rank, such as genus or species. Traditionally, taxa at the target rank are tested for individual association, followed by the Benjamini-Hochberg (BH) procedure to control fo...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0517-1
更新日期:2018-07-25 00:00:00
abstract:BACKGROUND:Natural gas seeps contribute to global climate change by releasing substantial amounts of the potent greenhouse gas methane and other climate-active gases including ethane and propane to the atmosphere. However, methanotrophs, bacteria capable of utilising methane as the sole source of carbon and energy, pla...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0741-3
更新日期:2019-10-04 00:00:00
abstract::The vaginal microbiota plays a significant role in health and disease of the female reproductive tract. Next-generation sequencing techniques based upon the analysis of bacterial 16S rRNA genes permit in-depth study of vaginal microbial community structure to a level of detail not possible with standard culture-based ...
journal_title:Microbiome
pub_type: 杂志文章,评审
doi:10.1186/s40168-016-0203-0
更新日期:2016-11-01 00:00:00
abstract:BACKGROUND:Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed to ensure sustainable animal production in the future. Methane yield varies naturally in sheep and i...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-016-0201-2
更新日期:2016-10-19 00:00:00
abstract::Human microbiome reference datasets provide epidemiological context for researchers, enabling them to uncover new insights into their own data through meta-analyses. In addition, large and comprehensive reference sets offer a means to develop or test hypotheses and can pave the way for addressing practical study desig...
journal_title:Microbiome
pub_type: 杂志文章,评审
doi:10.1186/s40168-015-0117-2
更新日期:2015-11-04 00:00:00
abstract:BACKGROUND:The microbial populations of the human intestinal tract and their relationship to specific diseases have been extensively studied during the last decade. However, the characterization of the human bile microbiota as a whole has been hampered by difficulties in accessing biological samples and the lack of ade...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0712-8
更新日期:2019-07-04 00:00:00
abstract:BACKGROUND:Current knowledge of the urinary tract microbiome is limited to urine analysis and analysis of biofilms formed on Foley catheters. Bacterial biofilms on ureteral stents have rarely been investigated, and no cultivation-independent data are available on the microbiome of the encrustations on the stents. RESU...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0674-x
更新日期:2019-04-13 00:00:00
abstract:BACKGROUND:Alterations of gut microbiota are associated with colorectal cancer (CRC) in different populations and several bacterial species were found to contribute to the tumorigenesis. The potential use of gut microbes as markers for early diagnosis has also been reported. However, cohort specific noises may distort ...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0451-2
更新日期:2018-04-11 00:00:00
abstract:BACKGROUND:Periodontitis is an infectious and inflammatory disease of polymicrobial etiology that can lead to the destruction of bones and tissues that support the teeth. The management of chronic periodontitis (CP) relies heavily on elimination or at least control of known pathogenic consortia associated with the dise...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/2049-2618-2-32
更新日期:2014-08-26 00:00:00
abstract:BACKGROUND:Archaea are one of the least-studied members of the gut-dwelling autochthonous microbiota. Few studies have reported the dominance of methanogens in the archaeal microbiome (archaeome) of the human gut, although limited information regarding the diversity and abundance of other archaeal phylotypes is availab...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-020-00894-x
更新日期:2020-08-04 00:00:00
abstract:BACKGROUND:The interconnectivities of built and natural environments can serve as conduits for the proliferation and dissemination of antibiotic resistance genes (ARGs). Several studies have compared the broad spectrum of ARGs (i.e., "resistomes") in various environmental compartments, but there is a need to identify u...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0735-1
更新日期:2019-08-29 00:00:00
abstract:BACKGROUND:The vaginal microbiome is an important site of bacterial-mammalian symbiosis. This symbiosis is currently best characterized for humans, where lactobacilli dominate the microbial community and may help defend women against infectious disease. However, lactobacilli do not dominate the vaginal microbiota of an...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-017-0228-z
更新日期:2017-01-19 00:00:00
abstract::An amendment to this paper has been published and can be accessed via the original article. ...
journal_title:Microbiome
pub_type: 已发布勘误
doi:10.1186/s40168-020-00905-x
更新日期:2020-08-20 00:00:00
abstract:BACKGROUND:This proof-of-principle study examines whether postnatal, low-dose exposure to environmental chemicals modifies the composition of gut microbiome. Three chemicals that are widely used in personal care products-diethyl phthalate (DEP), methylparaben (MPB), triclosan (TCS)-and their mixture (MIX) were administ...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-016-0173-2
更新日期:2016-06-14 00:00:00
abstract:BACKGROUND:The role of the gut microbiome in arresting pathogen colonization and growth is important for protection against Clostridium difficile infection (CDI). Observational studies associate proton pump inhibitor (PPI) use and CDI incidence. We hypothesized that PPI use affected the distal gut microbiome over time,...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/2049-2618-2-42
更新日期:2014-11-25 00:00:00
abstract:BACKGROUND:Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial samples, skews the ge...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-016-0197-7
更新日期:2016-10-06 00:00:00
abstract::Following publication of the original article [1], the authors reported an error in Figure 1 and a text on page 13. In Figure 1, some areas are missing and the correct figure is presented here. On page 13, the sentence should be updated to the following (change has been indicated in bold italics). ...
journal_title:Microbiome
pub_type: 已发布勘误
doi:10.1186/s40168-019-0763-x
更新日期:2019-11-14 00:00:00