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1.  Immune status, antibiotic medication and pH are associated with changes in the stomach fluid microbiota 
The ISME Journal  2013;7(7):1354-1366.
The stomach acts as a barrier to ingested microbes, thereby influencing the microbial ecology of the entire gastrointestinal (GI) tract. The stomach microbiota and the role of human host and environmental factors, such as health status or medications, in shaping its composition remain largely unknown. We sought to characterize the bacterial and fungal microbiota in the stomach fluid in order to gain insights into the role of the stomach in GI homeostasis. Gastric fluid was collected from 25 patients undergoing clinically indicated upper endoscopy. DNA isolates were used for PCR amplification of bacterial 16S ribosomal RNA (rRNA) genes and fungal internal transcribed spacers (ITS). RNA isolates were used for 16S rRNA cDNA generation and subsequent PCR amplification. While all stomach fluid samples are dominated by the phyla Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Fusobacteria (>99% of sequence reads), the transcriptionally active microbiota shows significant reduction in Actinobacteria (34%) and increase in Campylobacter (444%) (P<0.003), specifically the oral commensal and suspected intestinal pathogen Campylobacter concisus. Bacterial but not fungal diversity is reduced by antibiotic treatment (28% P<0.02), immunosuppression in transplant recipients and HIV/AIDS patients (42% P<0.001) and gastric fluid pH >4 (70% P<0.05). Immunosuppression correlates with decreased abundance of Prevotella (24%), Fusobacterium (2%) and Leptotrichia (6%) and increased abundance of Lactobacillus (3844%) (P<0.003). We have generated the first in-depth characterization of the human gastric fluid microbiota, using bacterial 16S rRNA gene and transcript, and fungal ITS amplicon sequencing and provide evidence for a significant impact of the host immune status on its composition with likely consequences for human health.
doi:10.1038/ismej.2013.33
PMCID: PMC3695299  PMID: 23466701
stomach fluid; microbiome; ITS; 16S rRNA; immunosuppression; Helicobacter pylori
2.  Safety of an IV Formulation of Carbamazepine 
Epilepsy research  2009;84(0):242-244.
An intravenous formulation of carbamazepine (CBZ) was administered to 113 (60 male; 53 female) persons with epilepsy aged 19 to 87 years. Subjects received 100 mg of study drug as replacement for 100 mg of their usual morning dose of CBZ. There were no significant changes in blood pressure or heart rate suggesting that this formulation can be developed as replacement therapy for persons unable to take oral CBZ.
doi:10.1016/j.eplepsyres.2009.01.013
PMCID: PMC3973440  PMID: 19299110
Carbamazepine; intravenous; epilepsy; elderly; adults
3.  Syndromes or Flexibility: Behavior during a Life History Transition of a Coral Reef Fish 
PLoS ONE  2013;8(12):e84262.
The theory of behavioral syndromes focuses on quantifying variation in behavior within and among individual organisms and attempts to account for the maintenance of differences in behavior that occur in a consistent manner among individuals. Behavioral syndromes have potentially important ecological consequences (e.g. survivorship tradeoffs) and can be shaped by population dynamics through selective mortality. Here, we search for any evidence for consistency of behavior across situations in juveniles of a common damselfish, Pomacentrus amboinensis (Pomacentridae) at the transition between larval habitats in the plankton and juvenile habitats on the reef. Naïve fish leaving the pelagic phase to settle on reefs were caught by light traps and their behaviors observed using similar methods across three different situations (small aquaria, large aquaria, field setting); all of which represent low risk and well-sheltered environments. Seven behavioral traits were compared within and among individuals across situations to determine if consistent behavioral syndromes existed. No consistency was found in any single or combination of behavioral traits for individuals across all situations. We suggest that high behavioral flexibility is likely beneficial for newly-settled fish at this ontogenetic transition and it is possible that consistent behavioral syndromes are unlikely to emerge in juveniles until environmental experience is gained or certain combinations of behaviors are favored by selective mortality.
doi:10.1371/journal.pone.0084262
PMCID: PMC3874005  PMID: 24386358
4.  Degradation of chemical alarm cues and assessment of risk throughout the day 
Ecology and Evolution  2013;3(11):3925-3934.
The use of chemical information in assessment of predation risk is pervasive across animal taxa. However, by its very nature, chemical information can be temporally unreliable. Chemical cues persist for some period of time after they are released into the environment. Yet, we know surprisingly little about the rate of degradation of chemical cues under natural conditions and hence little about how they function in temporal risk assessment under natural conditions. Here, we conducted an experiment to identify a concentration of fresh alarm cues that evoke a strong antipredator response in coral reef damselfish, Pomacentrus ambonensis. We then tested the rate at which these alarm cues degraded under natural conditions in ocean water, paying attention to whether the rate of degradation varied throughout the day and whether the temporal pattern correlated with physicochemical factors that could influence the rate of degradation. Fresh alarm cues released into ocean water evoke strong avoidance responses in juvenile fish, while those aged for 30 min no longer evoke antipredator responses. Fish exposed to cues aged for 10 or 20 min show intermediate avoidance responses. We found a marked temporal pattern of response throughout the day, with much faster degradation in early to mid-afternoon, the time of day when solar radiation, temperature, dissolved oxygen, and pH are nearing their peak. Ecologists have spent considerable effort elucidating the role of chemical information in mediating predator–prey interactions, yet we know almost nothing about the temporal dynamics of risk assessment using chemical information. We are in dire need of additional comparative field experiments on the rate of breakdown of chemical cues, particularly given that global change in UV radiation, temperature, and water chemistry could be altering the rates of degradation and the potential use of this information in risk assessment.
doi:10.1002/ece3.760
PMCID: PMC3810885  PMID: 24198950
Alarm cues; coral reefs; information use; predator–prey interactions; risk assessment.
5.  Extensively duplicated and transcriptionally active recent lateral gene transfer from a bacterial Wolbachia endosymbiont to its host filarial nematode Brugia malayi 
BMC Genomics  2013;14:639.
Background
Lymphatic filariasis is a neglected tropical disease afflicting more than 120 million people, while another 1.3 billion people are at risk of infection. The nematode worm Brugia malayi is one of the causative agents of the disease and exists in a mutualistic symbiosis with Wolbachia bacteria. Since extensive lateral gene transfer occurs frequently between Wolbachia and its hosts, we sought to measure the extent of such LGT in B. malayi by whole genome sequencing of Wolbachia-depleted worms.
Results
A considerable fraction (at least 115.4-kbp, or 10.6%) of the 1.08-Mbp Wolbachia wBm genome has been transferred to its nematode host and retains high levels of similarity, including 227 wBm genes and gene fragments. Complete open reading frames were transferred for 32 of these genes, meaning they have the potential to produce functional proteins. Moreover, four transfers have evidence of life stage-specific regulation of transcription at levels similar to other nematode transcripts, strengthening the possibility that they are functional.
Conclusions
There is extensive and ongoing transfer of Wolbachia DNA to the worm genome and some transfers are transcribed in a stage-specific manner at biologically relevant levels.
doi:10.1186/1471-2164-14-639
PMCID: PMC3849323  PMID: 24053607
6.  A Comparison of Measures of Boldness and Their Relationships to Survival in Young Fish 
PLoS ONE  2013;8(7):e68900.
Boldness is the propensity of an animal to engage in risky behavior. Many variations of novel-object or novel-environment tests have been used to quantify the boldness of animals, although the relationship between test outcomes has rarely been investigated. Furthermore, the relationship of outcomes to any ecological aspect of fitness is generally assumed, rather than measured directly. Our study is the first to compare how the outcomes of the same test of boldness differ among observers and how different tests of boldness relate to the survival of individuals in the field. Newly-metamorphosed lemon damselfish, Pomacentrus moluccensis, were placed onto replicate patches of natural habitat. Individual behavior was quantified using four tests (composed of a total of 12 different measures of behavior): latency to enter a novel environment, activity in a novel environment, and reactions to threatening and benign novel objects. After behavior was quantified, survival was monitored for two days during which time fish were exposed to natural predators. Variation among observers was low for most of the 12 measures, except distance moved and the threat test (reaction to probe thrust), which displayed unacceptable amounts of inter-observer variation. Overall, the results of the behavioral tests suggested that novel environment and novel object tests quantified similar behaviors, yet these behavioral measures were not interchangeable. Multiple measures of behavior within the context of novel environment or object tests were the most robust way to assess boldness and these measures have a complex relationship with survivorship of young fish in the field. Body size and distance ventured from shelter were the only variables that had a direct and positive relationship with survival.
doi:10.1371/journal.pone.0068900
PMCID: PMC3712919  PMID: 23874804
7.  Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato) 
BMC Microbiology  2013;13:114.
Background
Research to understand and control microbiological risks associated with the consumption of fresh fruits and vegetables has examined many environments in the farm to fork continuum. An important data gap however, that remains poorly studied is the baseline description of microflora that may be associated with plant anatomy either endemically or in response to environmental pressures. Specific anatomical niches of plants may contribute to persistence of human pathogens in agricultural environments in ways we have yet to describe. Tomatoes have been implicated in outbreaks of Salmonella at least 17 times during the years spanning 1990 to 2010. Our research seeks to provide a baseline description of the tomato microbiome and possibly identify whether or not there is something distinctive about tomatoes or their growing ecology that contributes to persistence of Salmonella in this important food crop.
Results
DNA was recovered from washes of epiphytic surfaces of tomato anatomical organs; leaves, stems, roots, flowers and fruits of Solanum lycopersicum (BHN602), grown at a site in close proximity to commercial farms previously implicated in tomato-Salmonella outbreaks. DNA was amplified for targeted 16S and 18S rRNA genes and sheared for shotgun metagenomic sequencing. Amplicons and metagenomes were used to describe “native” bacterial microflora for diverse anatomical parts of Virginia-grown tomatoes.
Conclusions
Distinct groupings of microbial communities were associated with different tomato plant organs and a gradient of compositional similarity could be correlated to the distance of a given plant part from the soil. Unique bacterial phylotypes (at 95% identity) were associated with fruits and flowers of tomato plants. These include Microvirga, Pseudomonas, Sphingomonas, Brachybacterium, Rhizobiales, Paracocccus, Chryseomonas and Microbacterium. The most frequently observed bacterial taxa across aerial plant regions were Pseudomonas and Xanthomonas. Dominant fungal taxa that could be identified to genus with 18S amplicons included Hypocrea, Aureobasidium and Cryptococcus. No definitive presence of Salmonella could be confirmed in any of the plant samples, although 16S sequences suggested that closely related genera were present on leaves, fruits and roots.
doi:10.1186/1471-2180-13-114
PMCID: PMC3680157  PMID: 23705801
Tomato microflora; 16S; 18S; Metagenomics; Phyllosphere; Solanum lycopersicum; Tomato organs; Microbial ecology; Baseline microflora; Tomatome
8.  Characterization of microflora in Latin-style cheeses by next-generation sequencing technology 
BMC Microbiology  2012;12:254.
Background
Cheese contamination can occur at numerous stages in the manufacturing process including the use of improperly pasteurized or raw milk. Of concern is the potential contamination by Listeria monocytogenes and other pathogenic bacteria that find the high moisture levels and moderate pH of popular Latin-style cheeses like queso fresco a hospitable environment. In the investigation of a foodborne outbreak, samples typically undergo enrichment in broth for 24 hours followed by selective agar plating to isolate bacterial colonies for confirmatory testing. The broth enrichment step may also enable background microflora to proliferate, which can confound subsequent analysis if not inhibited by effective broth or agar additives. We used 16S rRNA gene sequencing to provide a preliminary survey of bacterial species associated with three brands of Latin-style cheeses after 24-hour broth enrichment.
Results
Brand A showed a greater diversity than the other two cheese brands (Brands B and C) at nearly every taxonomic level except phylum. Brand B showed the least diversity and was dominated by a single bacterial taxon, Exiguobacterium, not previously reported in cheese. This genus was also found in Brand C, although Lactococcus was prominent, an expected finding since this bacteria belongs to the group of lactic acid bacteria (LAB) commonly found in fermented foods.
Conclusions
The contrasting diversity observed in Latin-style cheese was surprising, demonstrating that despite similarity of cheese type, raw materials and cheese making conditions appear to play a critical role in the microflora composition of the final product. The high bacterial diversity associated with Brand A suggests it may have been prepared with raw materials of high bacterial diversity or influenced by the ecology of the processing environment. Additionally, the presence of Exiguobacterium in high proportions (96%) in Brand B and, to a lesser extent, Brand C (46%), may have been influenced by the enrichment process. This study is the first to define Latin-style cheese microflora using Next-Generation Sequencing. These valuable preliminary data will direct selective tailoring of agar formulations to improve culture-based detection of pathogens in Latin-style cheese.
doi:10.1186/1471-2180-12-254
PMCID: PMC3503605  PMID: 23134566
Latin-style cheese; Next Generation Sequencing; Microflora; Bacteria; Exiguobacterium
9.  Using metagenomic analyses to estimate the consequences of enrichment bias for pathogen detection 
BMC Research Notes  2012;5:378.
Background
Enriching environmental samples to increase the probability of detection has been standard practice throughout the history of microbiology. However, by its very nature, the process of enrichment creates a biased sample that may have unintended consequences for surveillance or resolving a pathogenic outbreak. With the advent of next-generation sequencing and metagenomic approaches, the possibility now exists to quantify enrichment bias at an unprecedented taxonomic breadth.
Findings
We investigated differences in taxonomic profiles of three enriched and unenriched tomato phyllosphere samples taken from three different tomato fields (n = 18). 16S rRNA gene meteganomes were created for each of the 18 samples using 454/Roche’s pyrosequencing platform, resulting in a total of 165,259 sequences. Significantly different taxonomic profiles and abundances at a number of taxonomic levels were observed between the two treatments. Although as many as 28 putative Salmonella sequences were detected in enriched samples, there was no significant difference in the abundance of Salmonella between enriched and unenriched treatments.
Conclusions
Our results illustrate that the process of enriching greatly alters the taxonomic profile of an environmental sample beyond that of the target organism. We also found evidence suggesting that enrichment may not increase the probability of detecting a target. In conclusion, our results further emphasize the need to develop metagenomics as a validated culture independent method for pathogen detection.
doi:10.1186/1756-0500-5-378
PMCID: PMC3441234  PMID: 22839680
Enrichment bias; Metagenomics; Pathogen; Taxonomy
10.  Pyrosequencing of Bacterial Symbionts within Axinella corrugata Sponges: Diversity and Seasonal Variability 
PLoS ONE  2012;7(6):e38204.
Background
Marine sponge species are of significant interest to many scientific fields including marine ecology, conservation biology, genetics, host-microbe symbiosis and pharmacology. One of the most intriguing aspects of the sponge “holobiont” system is the unique physiology, interaction with microbes from the marine environment and the development of a complex commensal microbial community. However, intraspecific variability and temporal stability of sponge-associated bacterial symbionts remain relatively unknown.
Methodology/Principal Findings
We have characterized the bacterial symbiont community biodiversity of seven different individuals of the Caribbean reef sponge Axinella corrugata, from two different Florida reef locations during variable seasons using multiplex 454 pyrosequencing of 16 S rRNA amplicons. Over 265,512 high-quality 16 S rRNA sequences were generated and analyzed. Utilizing versatile bioinformatics methods and analytical software such as the QIIME and CloVR packages, we have identified 9,444 distinct bacterial operational taxonomic units (OTUs). Approximately 65,550 rRNA sequences (24%) could not be matched to bacteria at the class level, and may therefore represent novel taxa. Differentially abundant classes between seasonal Axinella communities included Gammaproteobacteria, Flavobacteria, Alphaproteobacteria, Cyanobacteria, Acidobacter and Nitrospira. Comparisons with a proximal outgroup sponge species (Amphimedon compressa), and the growing sponge symbiont literature, indicate that this study has identified approximately 330 A. corrugata-specific symbiotic OTUs, many of which are related to the sulfur-oxidizing Ectothiorhodospiraceae. This family appeared exclusively within A. corrugata, comprising >34.5% of all sequenced amplicons. Other A. corrugata symbionts such as Deltaproteobacteria, Bdellovibrio, and Thiocystis among many others are described.
Conclusions/Significance
Slight shifts in several bacterial taxa were observed between communities sampled during spring and fall seasons. New 16 S rDNA sequences and concomitant identifications greatly expand the microbial community profile for this model reef sponge, and will likely be useful as a baseline for any future comparisons regarding sponge microbial community dynamics.
doi:10.1371/journal.pone.0038204
PMCID: PMC3373494  PMID: 22701613
11.  Proof of Concept of Microbiome-Metabolome Analysis and Delayed Gluten Exposure on Celiac Disease Autoimmunity in Genetically At-Risk Infants 
PLoS ONE  2012;7(3):e33387.
Celiac disease (CD) is a unique autoimmune disorder in which the genetic factors (DQ2/DQ8) and the environmental trigger (gluten) are known and necessary but not sufficient for its development. Other environmental components contributing to CD are poorly understood. Studies suggest that aspects of gluten intake might influence the risk of CD occurrence and timing of its onset, i.e., the amount and quality of ingested gluten, together with the pattern of infant feeding and the age at which gluten is introduced in the diet. In this study, we hypothesize that the intestinal microbiota as a whole rather than specific infections dictates the switch from tolerance to immune response in genetically susceptible individuals. Using a sample of infants genetically at risk of CD, we characterized the longitudinal changes in the microbial communities that colonize infants from birth to 24 months and the impact of two patterns of gluten introduction (early vs. late) on the gut microbiota and metabolome, and the switch from gluten tolerance to immune response, including onset of CD autoimmunity. We show that infants genetically susceptible to CD who are exposed to gluten early mount an immune response against gluten and develop CD autoimmunity more frequently than at-risk infants in which gluten exposure is delayed until 12 months of age. The data, while derived from a relatively small number of subjects, suggest differences between the developing microbiota of infants with genetic predisposition for CD and the microbiota from infants with a non-selected genetic background, with an overall lack of bacteria of the phylum Bacteriodetes along with a high abundance of Firmicutes and microbiota that do not resemble that of adults even at 2 years of age. Furthermore, metabolomics analysis reveals potential biomarkers for the prediction of CD. This study constitutes a definite proof-of-principle that these combined genomic and metabolomic approaches will be key to deciphering the role of the gut microbiota on CD onset.
doi:10.1371/journal.pone.0033387
PMCID: PMC3303818  PMID: 22432018
12.  Transoral Resection of a Retropharyngeal Myxoma: A Case Report 
Skull Base Reports  2011;1(2):139-144.
This study was conducted to describe a retropharyngeal myxoma and discuss clinical concerns regarding this pathology and a retropharyngeal site of occurrence. We present a case report and review of literature. A 71-year-old woman presented with mild right neck pressure for 3 weeks. Imaging studies and head neck examination confirmed a 5.3 × 3.1 × 1.0 cm retropharyngeal mass with no communication to the vertebral column but was intimately involved with the pharyngeal mucosa. A transoral fine needle aspiration biopsy suggested a possible spindle cell neoplasm. A presurgical swallowing consultation was obtained. A transoral excision of the tumor was possible with no intraoperative complications. Histopathology was a cellular myxoma. Postoperative dysphagia required swallowing therapy and nasogastric tube feeding for 2 weeks before oral intake was possible. The patient has no evidence of clinical or radiological recurrence more than 1 year after surgical intervention. We present the second case of a myxoma in the retropharynx reported in English literature. Transoral excision was safe, feasible, and cosmetically appealing option in our patient. Additional clinical data are required to valid its safety and utility as an approach to tumors in the retropharynx. Postoperative dysphagia can be significant and consequently we recommend preoperative swallowing evaluation and counseling.
doi:10.1055/s-0031-1287685
PMCID: PMC3743605  PMID: 23984217
Retropharyngeal; myxoma; transoral surgery; retropharynx
13.  Resources and Costs for Microbial Sequence Analysis Evaluated Using Virtual Machines and Cloud Computing 
PLoS ONE  2011;6(10):e26624.
Background
The widespread popularity of genomic applications is threatened by the “bioinformatics bottleneck” resulting from uncertainty about the cost and infrastructure needed to meet increasing demands for next-generation sequence analysis. Cloud computing services have been discussed as potential new bioinformatics support systems but have not been evaluated thoroughly.
Results
We present benchmark costs and runtimes for common microbial genomics applications, including 16S rRNA analysis, microbial whole-genome shotgun (WGS) sequence assembly and annotation, WGS metagenomics and large-scale BLAST. Sequence dataset types and sizes were selected to correspond to outputs typically generated by small- to midsize facilities equipped with 454 and Illumina platforms, except for WGS metagenomics where sampling of Illumina data was used. Automated analysis pipelines, as implemented in the CloVR virtual machine, were used in order to guarantee transparency, reproducibility and portability across different operating systems, including the commercial Amazon Elastic Compute Cloud (EC2), which was used to attach real dollar costs to each analysis type. We found considerable differences in computational requirements, runtimes and costs associated with different microbial genomics applications. While all 16S analyses completed on a single-CPU desktop in under three hours, microbial genome and metagenome analyses utilized multi-CPU support of up to 120 CPUs on Amazon EC2, where each analysis completed in under 24 hours for less than $60. Representative datasets were used to estimate maximum data throughput on different cluster sizes and to compare costs between EC2 and comparable local grid servers.
Conclusions
Although bioinformatics requirements for microbial genomics depend on dataset characteristics and the analysis protocols applied, our results suggests that smaller sequencing facilities (up to three Roche/454 or one Illumina GAIIx sequencer) invested in 16S rRNA amplicon sequencing, microbial single-genome and metagenomics WGS projects can achieve cost-efficient bioinformatics support using CloVR in combination with Amazon EC2 as an alternative to local computing centers.
doi:10.1371/journal.pone.0026624
PMCID: PMC3197577  PMID: 22028928
14.  CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing 
BMC Bioinformatics  2011;12:356.
Background
Next-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and scalable for high-throughput applications. Cloud computing platforms provide on-demand access to computing infrastructure over the Internet and can be used in combination with custom built virtual machines to distribute pre-packaged with pre-configured software.
Results
We describe the Cloud Virtual Resource, CloVR, a new desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. In a case study, we demonstrate the use of CloVR to automatically process next-generation sequencing data on multiple cloud computing platforms.
Conclusion
The CloVR VM and associated architecture lowers the barrier of entry for utilizing complex analysis protocols on both local single- and multi-core computers and cloud systems for high throughput data processing.
doi:10.1186/1471-2105-12-356
PMCID: PMC3228541  PMID: 21878105
15.  Bacterial community diversity and variation in spray water sources and the tomato fruit surface 
BMC Microbiology  2011;11:81.
Background
Tomato (Solanum lycopersicum) consumption has been one of the most common causes of produce-associated salmonellosis in the United States. Contamination may originate from animal waste, insects, soil or water. Current guidelines for fresh tomato production recommend the use of potable water for applications coming in direct contact with the fruit, but due to high demand, water from other sources is frequently used. We sought to describe the overall bacterial diversity on the surface of tomato fruit and the effect of two different water sources (ground and surface water) when used for direct crop applications by generating a 454-pyrosequencing 16S rRNA dataset of these different environments. This study represents the first in depth characterization of bacterial communities in the tomato fruit surface and the water sources commonly used in commercial vegetable production.
Results
The two water sources tested had a significantly different bacterial composition. Proteobacteria was predominant in groundwater samples, whereas in the significantly more diverse surface water, abundant phyla also included Firmicutes, Actinobacteria and Verrucomicrobia. The fruit surface bacterial communities on tomatoes sprayed with both water sources could not be differentiated using various statistical methods. Both fruit surface environments had a high representation of Gammaproteobacteria, and within this class the genera Pantoea and Enterobacter were the most abundant.
Conclusions
Despite the major differences observed in the bacterial composition of ground and surface water, the season long use of these very different water sources did not have a significant impact on the bacterial composition of the tomato fruit surface. This study has provided the first next-generation sequencing database describing the bacterial communities living in the fruit surface of a tomato crop under two different spray water regimes, and therefore represents an important step forward towards the development of science-based metrics for Good Agricultural Practices.
doi:10.1186/1471-2180-11-81
PMCID: PMC3108269  PMID: 21510867
16.  Alignment and clustering of phylogenetic markers - implications for microbial diversity studies 
BMC Bioinformatics  2010;11:152.
Background
Molecular studies of microbial diversity have provided many insights into the bacterial communities inhabiting the human body and the environment. A common first step in such studies is a survey of conserved marker genes (primarily 16S rRNA) to characterize the taxonomic composition and diversity of these communities. To date, however, there exists significant variability in analysis methods employed in these studies.
Results
Here we provide a critical assessment of current analysis methodologies that cluster sequences into operational taxonomic units (OTUs) and demonstrate that small changes in algorithm parameters can lead to significantly varying results. Our analysis provides strong evidence that the species-level diversity estimates produced using common OTU methodologies are inflated due to overly stringent parameter choices. We further describe an example of how semi-supervised clustering can produce OTUs that are more robust to changes in algorithm parameters.
Conclusions
Our results highlight the need for systematic and open evaluation of data analysis methodologies, especially as targeted 16S rRNA diversity studies are increasingly relying on high-throughput sequencing technologies. All data and results from our study are available through the JGI FAMeS website http://fames.jgi-psf.org/.
doi:10.1186/1471-2105-11-152
PMCID: PMC2859756  PMID: 20334679
17.  Extensive Genome Rearrangements and Multiple Horizontal Gene Transfers in a Population of Pyrococcus Isolates from Vulcano Island, Italy▿ †  
Applied and Environmental Microbiology  2008;74(20):6447-6451.
The extent of chromosome rearrangements in Pyrococcus isolates from marine hydrothermal vents in Vulcano Island, Italy, was evaluated by high-throughput genomic methods. The results illustrate the dynamic nature of the genomes of the genus Pyrococcus and raise the possibility of a connection between rapidly changing environmental conditions and adaptive genomic properties.
doi:10.1128/AEM.01024-08
PMCID: PMC2570278  PMID: 18723649
18.  Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps 
PLoS ONE  2008;3(3):e1836.
The assembly methods used for whole-genome shotgun (WGS) data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of “reliable” overlaps based on identifying repeat k-mers. To demonstrate the benefits of using reliable overlaps, we have created a version of the Phrap assembly program that uses only overlaps from a specific list. We call this version PhrapUMD. Integrating PhrapUMD and our “reliable-overlap” algorithm with the Baylor College of Medicine assembler, Atlas, we assemble the BACs from the Rattus norvegicus genome project. Starting with the same data as the Nov. 2002 Atlas assembly, we compare our results and the Atlas assembly to the 4.3 Mb of rat sequence in the 21 BACs that have been finished. Our version of the draft assembly of the 21 BACs increases the coverage of finished sequence from 93.4% to 96.3%, while simultaneously reducing the base error rate from 4.5 to 1.1 errors per 10,000 bases. There are a number of ways of assessing the relative merits of assemblies when the finished sequence is available. If one views the overall quality of an assembly as proportional to the inverse of the product of the error rate and sequence missed, then the assembly presented here is seven times better. The UMD Overlapper with options for reliable overlaps is available from the authors at http://www.genome.umd.edu. We also provide the changes to the Phrap source code enabling it to use only the reliable overlaps.
doi:10.1371/journal.pone.0001836
PMCID: PMC2266800  PMID: 18350171

Results 1-19 (19)