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BMC Research Notes Nov 2014Over the past ten years, there has been an explosion of microbiome research. Many software packages for analyzing microbial sequences such as the 16S gene from 454... (Review)
Review
BACKGROUND
Over the past ten years, there has been an explosion of microbiome research. Many software packages for analyzing microbial sequences such as the 16S gene from 454 sequencers and Illumina platforms are available. But for a new researcher, it is difficult to know which package to choose. We present a systematic review of packages for the analysis of molecular sequences used to describe and compare microbial communities. This review gives students and researchers information to help choose the best analytic pipeline for their project. To the best of our knowledge, this is the first review of such software.
FINDINGS
Seven software packages met our inclusion criteria of being cost free and publically available, offering analysis functions from platform sequencing to results presentation, and included documentation and data security. We installed and executed each of the software packages and describe the installation, documentation, features, and functions of each.
CONCLUSIONS
For the user, pipeline choices may be limited because some packages only run on select operating systems. Users should be aware of the availability of features and functions of each package. Of utmost importance is that the user must be aware of the default settings and underlying assumptions of each function. All packages are lacking sufficient methods for longitudinal analysis.Researchers can do well using any one of these seven packages. However, two packages are outstanding; mothur and QIIME, due not only to the comprehensive suite of functions and procedures incorporated into the pipelines but also because of the accompanying documentation.
Topics: Animals; DNA Contamination; Humans; Sequence Analysis, DNA; Software
PubMed: 25421430
DOI: 10.1186/1756-0500-7-830 -
PloS One 2014We conducted a systematic review of the Medline database (U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, U.S.A) to determine if... (Meta-Analysis)
Meta-Analysis Review
We conducted a systematic review of the Medline database (U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, U.S.A) to determine if consistent molecular vaginal microbiota (VMB) composition patterns can be discerned after a decade of molecular testing, and to evaluate demographic, behavioral and clinical determinants of VMB compositions. Studies were eligible when published between 1 January 2008 and 15 November 2013, and if at least one molecular technique (sequencing, PCR, DNA fingerprinting, or DNA hybridization) was used to characterize the VMB. Sixty three eligible studies were identified. These studies have now conclusively shown that lactobacilli-dominated VMB are associated with a healthy vaginal micro-environment and that bacterial vaginosis (BV) is best described as a polybacterial dysbiosis. The extent of dysbiosis correlates well with Nugent score and vaginal pH but not with the other Amsel criteria. Lactobacillus crispatus is more beneficial than L. iners. Longitudinal studies have shown that a L. crispatus-dominated VMB is more likely to shift to a L. iners-dominated or mixed lactobacilli VMB than to full dysbiosis. Data on VMB determinants are scarce and inconsistent, but dysbiosis is consistently associated with HIV, human papillomavirus (HPV), and Trichomonas vaginalis infection. In contrast, vaginal colonization with Candida spp. is more common in women with a lactobacilli-dominated VMB than in women with dysbiosis. Cervicovaginal mucosal immune responses to molecular VMB compositions have not yet been properly characterized. Molecular techniques have now become more affordable, and we make a case for incorporating them into larger epidemiological studies to address knowledge gaps in etiology and pathogenesis of dysbiosis, associations of different dysbiotic states with clinical outcomes, and to evaluate interventions aimed at restoring and maintaining a lactobacilli-dominated VMB.
Topics: Adolescent; Adult; Cluster Analysis; Female; Humans; Microbial Consortia; Microbiota; Pregnancy; Vagina; Vaginosis, Bacterial
PubMed: 25148517
DOI: 10.1371/journal.pone.0105998 -
BMC Infectious Diseases Jun 2010Invasive meningococcal disease (IMD), is a widely distributed, complex human disease affecting all age categories. The causative agent, Neisseria meningitidis, is spread... (Review)
Review
BACKGROUND
Invasive meningococcal disease (IMD), is a widely distributed, complex human disease affecting all age categories. The causative agent, Neisseria meningitidis, is spread through aerosol respiratory droplets. 13 different serogroups have been identified, each with varying epidemiological features including prevalence, virulence, immunogenicity, geographical and temporal distribution. Although preventative measures are available for several of the serogroups, meningococcal disease caused by serogroup B is of particular interest due to the challenge it presents concerning vaccine development.
METHODS
A systematic review of peer reviewed studies and reports, the collection of data from national and international health resources, along with the analysis of the Multi Locus Sequence Typing database was carried out aimed at collecting information concerning serogroup B IMD and the epidemiology attached to it.
RESULTS
A continuous output of related and novel STs occurring worldwide in terms of the hypervirulent clonal complexes was observed both in published studies and the MLST database in this case using the eburst software, which highlights the genetically diverse nature of serogroup B strains.
CONCLUSIONS
With the recent dominance of serogroup B IMD seen in many countries, along with the presence of antibiotic resistance, vaccine development needs to target areas of the bacterium which tackle this widespread and heterogeneous aspect of meningococcal meningitis disease.
Topics: Adolescent; Adult; Aged; Aged, 80 and over; Bacterial Typing Techniques; Child; Child, Preschool; Cluster Analysis; DNA Fingerprinting; Drug Resistance, Bacterial; Genotype; Humans; Infant; Infant, Newborn; Meningitis, Meningococcal; Middle Aged; Neisseria meningitidis, Serogroup B; Young Adult
PubMed: 20565757
DOI: 10.1186/1471-2334-10-175 -
Tropical Medicine & International... Aug 2009The proportion of tuberculosis cases in a population that are clustered (i.e. share identical strains of Mycobacterium tuberculosis) reflects ongoing M. tuberculosis... (Meta-Analysis)
Meta-Analysis Review
OBJECTIVES
The proportion of tuberculosis cases in a population that are clustered (i.e. share identical strains of Mycobacterium tuberculosis) reflects ongoing M. tuberculosis transmission. It varies markedly, but it is unclear how much of this variation reflects measurable differences in study design, setting and the patient population. We aimed to assess the relative impact of these factors and develop a tool to improve interpretation of the proportion clustered from an individual study.
METHODS
We systematically reviewed all population-based TB clustering studies that used IS6110 RFLP as their main DNA fingerprinting technique. Meta-regression was used to see how much of the variation in the proportion clustered between studies could be explained by variables describing study design, setting and population. We compared expected clustering, based on study design and setting, with that observed.
RESULTS
Forty-six studies were included. Just four factors related to study design and setting-study duration, sampling fraction, handling of low band strains and tuberculosis incidence-explained 28% of the variation in the proportion clustered. Additionally including average patient age and proportion foreign born explained 60% of the variation in clustering for industrialized countries. Comparison of expected and observed proportions showed that for some studies the expected proportion clustered differed strongly from that observed.
CONCLUSIONS
We were able to account for much of the variation in the proportion clustered. The comparison of expected and observed clustering allows for a more valid comparison of studies and provides a tool for identifying outliers that warrant further investigation.
Topics: Adult; Aged; Analysis of Variance; DNA Fingerprinting; DNA, Bacterial; Epidemiologic Studies; Female; Humans; Male; Middle Aged; Mycobacterium tuberculosis; Tuberculosis
PubMed: 19702595
DOI: 10.1111/j.1365-3156.2009.02316.x