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499
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.
- Appl. Environ. Microbiol.
, 2007
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Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale
- APPLIED AND ENVIRONMENTAL MICROBIOLOGY
, 2009
"... Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work h ..."
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Cited by 189 (21 self)
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Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r � 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R 2 � 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
- Genome Res
, 2009
"... This article cites 109 articles, 59 of which can be accessed free at: service Email alerting click heretop right corner of the article or Receive free email alerts when new articles cite this article- sign up in the box at the ..."
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Cited by 97 (4 self)
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This article cites 109 articles, 59 of which can be accessed free at: service Email alerting click heretop right corner of the article or Receive free email alerts when new articles cite this article- sign up in the box at the
Short pyrosequencing reads suffice for accurate microbial community analysis
- Nucleic Acids Res
, 2007
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Human gut microbiome viewed across age and geography. Nature
, 2012
"... Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy ..."
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Cited by 50 (1 self)
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Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono-and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization. Genetic variation between human populations is typically viewed as differences in the allele frequencies of shared Homo sapiens genes. Another source of genetic and metabolic diversity resides in differences in the representation of the millions of genes and myriad gene functions within our gut microbial communities 1-3 . Sampling a broad population of healthy humans representing different ages and cultural traditions offers an opportunity to discover how our gut microbiomes evolve within a lifespan, vary between populations, and respond to our changing lifestyles
The human gut virome: Inter-individual variation and dynamic response to diet
- GENOME RES.
, 2011
"... Immense populations of viruses are present in the human gut and other body sites. Understanding the role of these populations (the human ‘‘virome’’) in health and disease requires a much deeper understanding of their composition and dynamics in the face of environmental perturbation. Here, we invest ..."
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Cited by 38 (5 self)
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Immense populations of viruses are present in the human gut and other body sites. Understanding the role of these populations (the human ‘‘virome’’) in health and disease requires a much deeper understanding of their composition and dynamics in the face of environmental perturbation. Here, we investigate viromes from human subjects on a controlled feeding regimen. Longitudinal fecal samples were analyzed by metagenomic sequencing of DNA from virus-like particles (VLP) and total microbial communities. Assembly of 336 Mb of VLP sequence yielded 7175 contigs, many identifiable as complete or partial bacteriophage genomes. Contigs were rich in viral functions required in lytic and lysogenic growth, as well as unexpected functions such as viral CRISPR arrays and genes for antibiotic resistance. The largest source of variance among virome samples was interpersonal variation. Parallel deep-sequencing analysis of bacterial populations showed covaration of the virome with the larger microbiome. The dietary intervention was associated with a change in the virome community to a new state, in which individuals on the same diet converged. Thus these data provide an overview of the composition of the human gut virome and associate virome structure with diet.
The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis
- PLoS Pathog
, 2008
"... The vertebrate gut harbors a vast community of bacterial mutualists, the composition of which is modulated by the host immune system. Many gastrointestinal (GI) diseases are expected to be associated with disruptions of hostbacterial interactions, but relatively few comprehensive studies have been r ..."
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Cited by 37 (4 self)
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The vertebrate gut harbors a vast community of bacterial mutualists, the composition of which is modulated by the host immune system. Many gastrointestinal (GI) diseases are expected to be associated with disruptions of hostbacterial interactions, but relatively few comprehensive studies have been reported. We have used the rhesus macaque model to investigate forces shaping GI bacterial communities. We used DNA bar coding and pyrosequencing to characterize 141,000 sequences of 16S rRNA genes obtained from 100 uncultured GI bacterial samples, allowing quantitative analysis of community composition in health and disease. Microbial communities of macaques were distinct from those of mice and humans in both abundance and types of taxa present. The macaque communities differed among samples from intestinal mucosa, colonic contents, and stool, paralleling studies of humans. Communities also differed among animals, over time within individual animals, and between males and females. To investigate changes associated with disease, samples of colonic contents taken at necropsy were compared between healthy animals and animals with colitis and undergoing antibiotic therapy. Communities from diseased and healthy animals also differed significantly in composition. This work provides comprehensive data and improved methods for studying the role of commensal microbiota in macaque models of GI diseases and provides a model for the large-scale
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
- BMC bioinfo
"... Background: Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short reads from next-generation sequencing due to computa ..."
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Cited by 33 (3 self)
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Background: Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short reads from next-generation sequencing due to computational complexity issues and lack of phylogenetic signal. “Phylogenetic placement, ” where a reference tree is fixed and the unknown query sequences are placed onto the tree via a reference alignment, is a way to bring the inferential power offered by likelihood-based approaches to large data sets. Results: This paper introduces pplacer, a software package for phylogenetic placement and subsequent visual-ization. The algorithm can place twenty thousand short reads on a reference tree of one thousand taxa per hour per processor, has essentially linear time and memory complexity in the number of reference taxa, and is easy to run in parallel. Pplacer features calculation of the posterior probability of a placement on an edge, which is a statistically rigorous way of quantifying uncertainty on an edge-by-edge basis. It also can inform the user of the positional uncertainty for query sequences by calculating expected distance between placement locations, which is crucial in the estimation of uncertainty with a well-sampled reference tree. The software provides visualizations using branch thickness and color to represent number of placements and their uncertainty. A simulation study using reads generated from 631 COG alignments shows a high level of accuracy for phylogenetic placement over a wide range of alignment diversity, and the power of edge uncertainty estimates to measure placement confidence. 1 ar
Short-term temporal variability in airborne bacterial and fungal populations
- Applied and Environmental Microbiology
, 2008
"... Airborne microorganisms have been studied for centuries, but the majority of this research has relied on cultivation-dependent surveys that may not capture all of the microbial diversity in the atmosphere. As a result, our understanding of airborne microbial ecology is limited despite the relevance ..."
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Cited by 30 (7 self)
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Airborne microorganisms have been studied for centuries, but the majority of this research has relied on cultivation-dependent surveys that may not capture all of the microbial diversity in the atmosphere. As a result, our understanding of airborne microbial ecology is limited despite the relevance of airborne microbes to human health, various ecosystem functions, and environmental quality. Cultivation-independent surveys of small-subunit rRNA genes were conducted in order to identify the types of airborne bacteria and fungi found at a single site (Boulder, CO) and the temporal variability in the microbial assemblages over an 8-day period. We found that the air samples were dominated by ascomycete fungi of the Hypocreales order and a diverse array of bacteria, including members of the proteobacterial and Cytophaga-Flavobacterium-Bacteroides groups that are commonly found in comparable culture-independent surveys of airborne bacteria. Bacterium/fungus ratios varied by 2 orders of magnitude over the sampling period, and we observed large shifts in the phylogenetic diversity of bacteria present in the air samples collected on different dates, shifts that were not likely to be related to local meteorological conditions. We observed more phylogenetic similarity between bacteria collected from geographically distant sites than between bacteria collected from the same site on different days. These results suggest that outdoor air may harbor similar types of bacteria regardless of location and that the
A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput Biol. 2013; 9:e1002863. doi
"... Recent analyses of human-associated bacterial diversity have categorized individuals into ‘enterotypes ’ or clusters based on the abundances of key bacterial genera in the gut microbiota. There is a lack of consensus, however, on the analytical basis for enterotypes and on the interpretation of thes ..."
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Cited by 26 (1 self)
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Recent analyses of human-associated bacterial diversity have categorized individuals into ‘enterotypes ’ or clusters based on the abundances of key bacterial genera in the gut microbiota. There is a lack of consensus, however, on the analytical basis for enterotypes and on the interpretation of these results. We tested how the following factors influenced the detection of enterotypes: clustering methodology, distance metrics, OTU-picking approaches, sequencing depth, data type (whole genome shotgun (WGS) vs.16S rRNA gene sequence data), and 16S rRNA region. We included 16S rRNA gene sequences from the Human Microbiome Project (HMP) and from 16 additional studies and WGS sequences from the HMP and MetaHIT. In most body sites, we observed smooth abundance gradients of key genera without discrete clustering of samples. Some body habitats displayed bimodal (e.g., gut) or multimodal (e.g., vagina) distributions of sample abundances, but not all clustering methods and workflows accurately highlight such clusters. Because identifying enterotypes in datasets depends not only on the structure of the data but is also sensitive to the methods applied to identifying clustering strength, we
