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37
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
The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery
- Am J Clin Nutr. 2012;96:544–551. 10 Nutrition ReviewsVR
"... ABSTRACT Background: Breast milk is recognized as the most important postpartum element in metabolic and immunologic programming of health of neonates. The factors influencing the milk microbiome and the potential impact of microbes on infant health have not yet been uncovered. Objective: Our objec ..."
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ABSTRACT Background: Breast milk is recognized as the most important postpartum element in metabolic and immunologic programming of health of neonates. The factors influencing the milk microbiome and the potential impact of microbes on infant health have not yet been uncovered. Objective: Our objective was to identify pre-and postnatal factors that can potentially influence the bacterial communities inhabiting human milk. Design: We characterized the milk microbial community at 3 different time points by pyrosequencing and quantitative polymerase chain reaction in mothers (n = 18) who varied in BMI, weight gain, and mode of delivery. Results: We found that the human milk microbiome changes over lactation. Weisella, Leuconostoc, Staphylococcus, Streptococcus, and Lactococcus were predominant in colostrum samples, whereas in 1-and 6-mo milk samples the typical inhabitants of the oral cavity (eg, Veillonella, Leptotrichia, and Prevotella) increased significantly. Milk from obese mothers tended to contain a different and less diverse bacterial community compared with milk from normalweight mothers. Milk samples from elective but not from nonelective mothers who underwent cesarean delivery contained a different bacterial community than did milk samples from individuals giving birth by vaginal delivery, suggesting that it is not the operation per se but rather the absence of physiological stress or hormonal signals that could influence the microbial transmission process to milk. Conclusions: Our results indicate that milk bacteria are not contaminants and suggest that the milk microbiome is influenced by several factors that significantly skew its composition. Because bacteria present in breast milk are among the very first microbes entering the human body, our data emphasize the necessity to understand the biological role that the milk microbiome could potentially play for human health. Am J Clin Nutr 2012;96:544-51.
TD: The human intestinal microbiome: a new frontier of human biology
- DNA Res
"... To analyze the vast number and variety of microorganisms inhabiting the human intestine, emerging metagenomic technologies are extremely powerful. The intestinal microbes are taxonomically complex and constitute an ecologically dynamic community (microbiota) that has long been believed to possess a ..."
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Cited by 24 (0 self)
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To analyze the vast number and variety of microorganisms inhabiting the human intestine, emerging metagenomic technologies are extremely powerful. The intestinal microbes are taxonomically complex and constitute an ecologically dynamic community (microbiota) that has long been believed to possess a strong impact on human physiology. Furthermore, they are heavily involved in the maturation and pro-liferation of human intestinal cells, helping to maintain their homeostasis and can be causative of various diseases, such as inflammatory bowel disease and obesity. A simplified animal model system has provided the mechanistic basis for the molecular interactions that occur at the interface between such microbes and host intestinal epithelia. Through metagenomic analysis, it is now possible to comprehensively explore the genetic nature of the intestinal microbiome, the mutually interacting system comprising the host cells and the residing microbial community. The human microbiome project was recently launched as an international collaborative research effort to further promote this newly developing field and to pave the way to a new frontier of human biology, which will provide new strategies for the maintenance of human health. Key words: microbiome; microbiota; gut; metagenomics 1.
Structural modulation of gut microbiota in life-long calorie-restricted mice
"... Calorie restriction has been regarded as the only experimental regimen that can effectively lengthen lifespan in various animal models, but the actual mechanism remains controversial. The gut microbiota has been shown to have a pivotal role in host health, and its structure is mostly shaped by diet. ..."
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Cited by 6 (0 self)
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Calorie restriction has been regarded as the only experimental regimen that can effectively lengthen lifespan in various animal models, but the actual mechanism remains controversial. The gut microbiota has been shown to have a pivotal role in host health, and its structure is mostly shaped by diet. Here we show that life-long calorie restriction on both high-fat or low-fat diet, but not voluntary exercise, significantly changes the overall structure of the gut microbiota of C57BL/6 J mice. Calorie restriction enriches phylotypes positively correlated with lifespan, for example, the genus Lactobacillus on low-fat diet, and reduces phylotypes negatively correlated with lifespan. These calorie restriction-induced changes in the gut microbiota are concomitant with significantly reduced serum levels of lipopolysaccharide-binding protein, suggesting that animals under calorie restriction can establish a structurally balanced architecture of gut microbiota that may exert a health benefit to the host via
Hepatitis C virus transmission bottlenecks analyzed by deep sequencing
- J Virol
, 2010
"... Hepatitis C virus (HCV) replication in infected patients produces large and diverse viral populations, which give rise to drug-resistant and immune escape variants. Here, we analyzed HCV populations during trans-mission and diversification in longitudinal and cross-sectional samples using 454/Roche ..."
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Hepatitis C virus (HCV) replication in infected patients produces large and diverse viral populations, which give rise to drug-resistant and immune escape variants. Here, we analyzed HCV populations during trans-mission and diversification in longitudinal and cross-sectional samples using 454/Roche pyrosequencing, in total analyzing 174,185 sequence reads. To sample diversity, four locations in the HCV genome were analyzed, ranging from high diversity (the envelope hypervariable region 1 [HVR1]) to almost no diversity (the 5 untranslated region [UTR]). For three longitudinal samples for which early time points were available, we found that only 1 to 4 viral variants were present, suggesting that productive infection was initiated by a very small number of HCV particles. Sequence diversity accumulated subsequently, with the 5 UTR showing almost no diversification while the envelope HVR1 showed>100 variants in some subjects. Calculation of the transmission probability for only a single variant, taking into account the measured population structure within patients, confirmed initial infection by one or a few viral particles. These findings provide the most detailed sequence-based analysis of HCV transmission bottlenecks to date. The analytical methods described here are broadly applicable to studies of viral diversity using deep sequencing. Hepatitis C virus (HCV) is a positive-strand enveloped RNA virus of the flavivirus family. HCV infects 170 million people
Microbial diversity in deep-sea methane seep sediments presented by SSU rRNA gene tag sequencing. Microb Environ 27
, 2012
"... Microbial community structures in methane seep sediments in the Nankai Trough were analyzed by tag-sequencing analysis for the small subunit (SSU) rRNA gene using a newly developed primer set. The dominant members of ..."
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Microbial community structures in methane seep sediments in the Nankai Trough were analyzed by tag-sequencing analysis for the small subunit (SSU) rRNA gene using a newly developed primer set. The dominant members of
Microbiome diversity in the bronchial tracts of patients with chronic obstructive pulmonary disease
- J Clin Microbiol
, 2012
"... Culture of bacteria from bronchial secretions in respiratory patients has low sensitivity and does not allow for complete assess-ment of microbial diversity across different bronchial compartments. In addition, a significant number of clinical studies are based on sputum samples, and it is not known ..."
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Culture of bacteria from bronchial secretions in respiratory patients has low sensitivity and does not allow for complete assess-ment of microbial diversity across different bronchial compartments. In addition, a significant number of clinical studies are based on sputum samples, and it is not known to what extent they describe the real diversity of the mucosa. In order to identify previously unrecognized lower airway bacteria and to investigate the complexity and distribution of microbiota in patients with chronic obstructive pulmonary disease (COPD), we performed PCR amplification and pyrosequencing of the 16S rRNA gene in patients not showing signs or symptoms of infection. Four types of respiratory samples (sputum, bronchial aspirate, bronchoal-veolar lavage, and bronchial mucosa) were taken from each individual, obtaining on average>1,000 16S rRNA sequences per sample. The total number of genera per patient was>100, showing a high diversity, with Streptococcus, Prevotella,Moraxella, Haemophilus, Acinetobacter, Fusobacterium, andNeisseria being the most commonly identified. Sputum samples showed signif-icantly lower diversity than the other three sample types. Lower-bronchial-tree samples, i.e., bronchoalveolar lavage and bron-chial mucosa, showed a very similar bacterial compositions in contrast to sputum and bronchial aspirate samples. Thus, sputum and bronchial aspirate samples are upper bronchial tree samples that are not representative of the lower bronchial mucosa flora,
Ejection summary
- Flying Safety
, 2003
"... I, the undersigned, hereby declare that the work contained in this dissertation is my own original work and that I have not previously in its entirety or in part submitted it at any university for a degree. ..."
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I, the undersigned, hereby declare that the work contained in this dissertation is my own original work and that I have not previously in its entirety or in part submitted it at any university for a degree.
Bacterial Community Profiling of Milk Samples as a Means to Understand Culture-Negative Bovine Clinical
"... Inflammation and infection of bovine mammary glands, commonly known as mastitis, imposes significant losses each year in the dairy industry worldwide. While several different bacterial species have been identified as causative agents of mastitis, many clinical mastitis cases remain culture negative, ..."
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Inflammation and infection of bovine mammary glands, commonly known as mastitis, imposes significant losses each year in the dairy industry worldwide. While several different bacterial species have been identified as causative agents of mastitis, many clinical mastitis cases remain culture negative, even after enrichment for bacterial growth. To understand the basis for this increasingly common phenomenon, the composition of bacterial communities from milk samples was analyzed using culture independent pyrosequencing of amplicons of 16S ribosomal RNA genes (16S rDNA). Comparisons were made of the microbial community composition of culture negative milk samples from mastitic quarters with that of non-mastitic quarters from the same animals. Genomic DNA from culture-negative clinical and healthy quarter sample pairs was isolated, and amplicon libraries were prepared using indexed primers specific to the V1–V2 region of bacterial 16S rRNA genes and sequenced using the Roche 454 GS FLX with titanium chemistry. Evaluation of the taxonomic composition of these samples revealed significant differences in the microbiota in milk from mastitic and healthy quarters. Statistical analysis identified seven bacterial genera that may be mainly responsible for the observed microbial community differences between mastitic and healthy quarters. Collectively, these results provide evidence that cases of culture negative mastitis can be associated with bacterial species that may be present below culture detection thresholds used here. The application of culture-independent bacterial community profiling represents a powerful approach to understand long-standing questions in
COMPUTATIONAL APPROACHES TO STOCHASTIC SYSTEMS IN PHYSICS AND ECOLOGY
, 2012
"... In this dissertation, I devise computational approaches to model and understand two very different sys-tems which exhibit stochastic behavior: quantum fluids with topological defects arising during quenches and forcing, and complex microbial communities living and evolving withing the gastrointestin ..."
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In this dissertation, I devise computational approaches to model and understand two very different sys-tems which exhibit stochastic behavior: quantum fluids with topological defects arising during quenches and forcing, and complex microbial communities living and evolving withing the gastrointestinal tracts of vertebrates. As such, this dissertation is organized into two parts. In Part I, I create a model for quantum fluids, which incorporates a conservative and dissipative part, and I also allow the fluid to be externally forced by a normal fluid. I use then this model to calculate scaling laws arising from the stochastic interactions of the topological defects exhibited by the modeled fluid while undergoing a quench. In Chapter 2 I give a detailed description of this model of quantum fluids. Unlike more traditional approaches, this model is based on Cell Dynamical Systems (CDS), an approach that captures relevant physical features of the system and allows for long time steps during its evolution. I devise a two step CDS model, implementing both conservative and dissipative dynamics present in quantum fluids. I also couple the model with an external normal fluid field that drives the system. I then validate the results of the model by measuring different scaling laws predicted for quantum fluids. I also propose an extension of the
