A5029254834- Gut microbiota and health
- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Parasitic Infections and Diagnostics
- Clostridium difficile and Clostridium perfringens research
- Diet and metabolism studies
- Oral microbiology and periodontitis research
- Molecular Biology Techniques and Applications
- Cystic Fibrosis Research Advances
- Salivary Gland Disorders and Functions
- Oral Health Pathology and Treatment
- Methane Hydrates and Related Phenomena
- Infant Nutrition and Health
- Protist diversity and phylogeny
- Environmental DNA in Biodiversity Studies
- Probiotics and Fermented Foods
- Bacteriophages and microbial interactions
- Mycobacterium research and diagnosis
- Fecal contamination and water quality
- Plant and Fungal Interactions Research
- Cancer Genomics and Diagnostics
- Pediatric health and respiratory diseases
- RNA modifications and cancer
- Nutrition, Genetics, and Disease
- Bioinformatics and Genomic Networks
Marine Biological Laboratory
2015-2024
Cardiff University
2024
University of Tennessee at Knoxville
2023
University of South Alabama
2023
Max Planck Institute for Chemistry
2023
Dauphin Island Sea Lab
2023
Lawrence Berkeley National Laboratory
2023
Oregon State University
2023
University of Alberta
2021
Rutgers Sexual and Reproductive Health and Rights
2020
The evolution of marine microbes over billions years predicts that the composition microbial communities should be much greater than published estimates a few thousand distinct kinds per liter seawater. By adopting massively parallel tag sequencing strategy, we show bacterial deep water masses North Atlantic and diffuse flow hydrothermal vents are one to two orders magnitude more complex previously reported for any environment. A relatively small number different populations dominate all...
Advances in high-throughput sequencing and 'omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations lifestyles require the ability to interactively organize visualize genetic information incorporate subtle differences that enable greater resolution complex data. Here we introduce anvi'o, an advanced analysis visualization platform offers automated human-guided characterization genomes metagenomic assemblies, with interactive...
Deep sequencing of PCR amplicon libraries facilitates the detection low-abundance populations in environmental DNA surveys complex microbial communities. At same time, deep can lead to overestimates diversity through generation low-frequency, error-prone reads. Even with error rates below 0.005 per nucleotide position, common method generating operational taxonomic units (OTUs) by multiple sequence alignment and complete-linkage clustering significantly increases number predicted OTUs...
Abstract Background Massively parallel pyrosequencing systems have increased the efficiency of DNA sequencing, although published per-base accuracy a Roche GS20 is only 96%. In genome projects, highly redundant consensus assemblies can compensate for sequencing errors. contrast, studies microbial diversity that catalogue differences between PCR amplicons ribosomal RNA genes (rDNA) or other conserved gene families cannot take advantage to detect and minimize incorrect base calls. Results We...
The analytical power of environmental DNA sequences for modeling microbial ecosystems depends on accurate assessments population structure, including diversity (richness) and relative abundance (evenness). We investigated both aspects structure communities at two neighboring hydrothermal vents by examining the more than 900,000 small-subunit ribosomal RNA amplicons. vent have different structures that reflect local geochemical regimes. Descriptions archaeal were nearly exhaustive, but...
The genome of the eukaryotic protist Giardia lamblia, an important human intestinal parasite, is compact in structure and content, contains few introns or mitochondrial relics, has simplified machinery for DNA replication, transcription, RNA processing, most metabolic pathways. Protein kinases comprise single largest protein class reflect Giardia's requirement a complex signal transduction network coordinating differentiation. Lateral gene transfer from bacterial archaeal donors shaped...
Bacteria comprise the most diverse domain of life on Earth, where they occupy nearly every possible ecological niche and play key roles in biological chemical processes. Studying composition ecology bacterial ecosystems understanding their function is prime importance. High-throughput sequencing technologies enable comprehensive descriptions diversity through 16S ribosomal RNA gene amplicons. Analyses these communities generally rely upon taxonomic assignments reference databases, or...
Abstract We characterize and extend a highly efficient method for constructing shotgun fragment libraries in which transposase catalyzes vitro DNA fragmentation adaptor incorporation simultaneously. apply this to sequencing human genome find that coverage biases are comparable those of conventional protocols. also its capabilities by developing protocols sub-nanogram library construction, exome capture from 50 ng input DNA, PCR-free colony PCR 96-plex sample indexing.
Abstract Molecular microbial ecology investigations often employ large marker gene datasets, for example, ribosomal RNAs, to represent the occurrence of single-cell genomes in communities. Massively parallel DNA sequencing technologies enable extensive surveys libraries that sometimes include nearly identical sequences. Computational approaches rely on pairwise sequence alignments similarity assessment and de novo clustering with facto thresholds partition high-throughput datasets constrain...
ABSTRACT Shifts in microbial communities are implicated the pathogenesis of a number gastrointestinal diseases, but we have limited understanding mechanisms that lead to altered community structures. One difficulty with studying these human subjects is inherent baseline variability microbiota different individuals. In an effort overcome this variability, employed mouse model control host genotype, diet, and other possible influences on microbiota. This allowed us determine whether indigenous...
ABSTRACT Pulmonary damage caused by chronic colonization of the cystic fibrosis (CF) lung microbial communities is proximal cause respiratory failure. While there has been an effort to document microbiome CF in pediatric and adult patients, little known regarding developing microflora infants. We examined intestinal microbiota development infants with from birth 21 months. Distinct genera dominated gut compared those tract, yet some bacteria overlapped, demonstrating a core Veillonella...
The exploration of microbial communities by sequencing 16S rRNA genes has expanded with low-cost, high-throughput instruments. Illumina-based gene recently gained popularity over 454 pyrosequencing due to its lower costs, higher accuracy and greater throughput. Although recent reports suggest that Illumina provide similar beta diversity measures, it remains be demonstrated pre-existing workflows can transfer directly from MiSeq simply changing the adapters primers. In this study, we modified...
Consensus between independent reads improves the accuracy of genome and transcriptome analyses, however lack consensus very similar sequences in metagenomic studies can often does represent natural variation biological significance. The common use machine-assigned quality scores on next generation platforms not necessarily correlate with accuracy. Here, we describe using overlap paired-end, short sequence to identify error-prone marker gene analyses their contribution spurious OTUs following...
The intestinal microbiome plays a critical role in infant development, and delivery mode feeding method (breast milk vs formula) are determinants of its composition. However, the importance beyond first days life is unknown, studies associations between composition have been generally limited to comparisons exclusively breastfed formula-fed infants, with little consideration given combination both breast formula.To examine at approximately 6 weeks life.Prospective observational study 102...
ABSTRACT Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other characteristics, but resources for marker gene studies consider trends among populations scale number individuals sampled each population. As an alternative strategy sampling populations, we examined whether sewage accurately reflects microbial a mixture samples. We used oligotyping high-throughput 16S rRNA...
The gut microbiome has an important role in infant health and immune development may be affected by early-life exposures. Maternal diet influence the through vertical transfer of maternal microbes to infants during vaginal delivery breastfeeding. We aimed examine association pregnancy with 6 weeks post-delivery mother-infant dyads enrolled New Hampshire Birth Cohort Study. Infant stool samples were collected from 145 infants, prenatal was assessed using a food frequency questionnaire. used...
The advent of next-generation DNA sequencing platforms has revolutionized molecular microbial ecology by making the detailed analysis complex communities over time and space a tractable research pursuit for small groups. However, ability to generate 105–108 reads with relative ease brings it many downstream complications. Beyond computational resources skills needed process analyze data, is difficult compare datasets in an intuitive interactive manner that leads hypothesis generation...
Abstract Introduction Microbial residents of the human oral cavity have long been a major focus microbiology due to their influence on host health and intriguing patterns site specificity amidst lack dispersal limitation. However, determinants niche partitioning in this habitat are yet be fully understood, especially among taxa that belong recently discovered branches microbial life. Results Here, we assemble metagenomes from tongue dental plaque samples multiple individuals reconstruct 790...
Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest the gut microbiome. However, establishing reproducible insights into determinants succession has been formidable challenge.
GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia Trichomonas vaginalis, respectively, represent latest additions to EuPathDB (http://EuPathDB.org) family of functional genomic databases. employ same framework as other sites (CryptoDB, PlasmoDB ToxoDB), supporting fully integrated searchable Genomic-scale data available via these resources may be queried based on BLAST searches, annotation keywords gene ID GO terms, sequence...
An accurate reconstruction of the eukaryotic tree life is essential to identify innovations underlying diversity microbial and macroscopic (e.g., plants animals) eukaryotes. Previous work has divided into a small number high-level "supergroups," many which receive strong support in phylogenomic analyses. However, abundance data analyses can lead highly supported but incorrect relationships due systematic phylogenetic error. Furthermore, paucity major lineages (19 or fewer) included these...
Diverse microbial communities chronically colonize the lungs of cystic fibrosis patients. Pyrosequencing amplicons for hypervariable regions in 16S rRNA gene generated taxonomic profiles bacterial sputum genomic DNA samples from 22 patients during a state clinical stability (outpatients) and 13 acute exacerbation (inpatients). We employed quantitative PCR (qPCR) to confirm detection Pseudomonas aeruginosa Streptococcus by pyrosequencing data human oral microbe identification microarray...
Summary We evaluated the population structure and temporal dynamics of dominant community members within sewage influent from two wastewater treatment plants (WWTPs) in Milwaukee, WI. generated > 1.1 M bacterial pyrotag sequences V6 hypervariable region 16S rRNA genes 38 samples taken upstream sanitary sewer system. Only a small fraction pyrotags (∼ 15%) matched human faecal samples. The components included enriched populations Lactococcus Enterobacteriaceae relative to their fractional...