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A preliminary survey of lichen associated eukaryotes using pyrosequencing

Scott T. BATES, Donna BERG-LYONS, Christian L. LAUBER, William A. WALTERS, Rob KNIGHT, Noah FIERER
2011 The Lichenologist  
associated with lichens and their potential functional roles within the symbiosis (Cardinale et al. 2008; Hodkinson & Lutzoni 2009; Bates et al. 2011; Hodkinson et al. in press; reviewed in Grube & Berg  ... 
doi:10.1017/s0024282911000648 fatcat:aopexen5b5di5ks457rqfie5oa

Examining the global distribution of dominant archaeal populations in soil

Scott T Bates, Donna Berg-Lyons, J Gregory Caporaso, William A Walters, Rob Knight, Noah Fierer
2010 The ISME Journal  
Archaea, primarily Crenarchaeota, are common in soil; however, the structure of soil archaeal communities and the factors regulating their diversity and abundance remain poorly understood. Here, we used barcoded pyrosequencing to comprehensively survey archaeal and bacterial communities in 146 soils, representing a multitude of soil and ecosystem types from across the globe. Relative archaeal abundance, the percentage of all 16S rRNA gene sequences recovered that were archaeal, averaged 2%
more » ... s all soils and ranged from 0% to 410% in individual soils. Soil C:N ratio was the only factor consistently correlated with archaeal relative abundances, being higher in soils with lower C:N ratios. Soil archaea communities were dominated by just two phylotypes from a constrained clade within the Crenarchaeota, which together accounted for 470% of all archaeal sequences obtained in the survey. As one of these phylotypes was closely related to a previously identified putative ammonia oxidizer, we sampled from two long-term nitrogen (N) addition experiments to determine if this taxon responds to experimental manipulations of N availability. Contrary to expectations, the abundance of this dominant taxon, as well as archaea overall, tended to decline with increasing N. This trend was coupled with a concurrent increase in known N-oxidizing bacteria, suggesting competitive interactions between these groups.
doi:10.1038/ismej.2010.171 pmid:21085198 pmcid:PMC3105767 fatcat:ry4vnpetovcelfislcarpbeyka

Moving pictures of the human microbiome

J Gregory Caporaso, Christian L Lauber, Elizabeth K Costello, Donna Berg-Lyons, Antonio Gonzalez, Jesse Stombaugh, Dan Knights, Pawel Gajer, Jacques Ravel, Noah Fierer, Jeffrey I Gordon, Rob Knight
2011 Genome Biology  
Understanding the normal temporal variation in the human microbiome is critical to developing treatments for putative microbiome-related afflictions such as obesity, Crohn's disease, inflammatory bowel disease and malnutrition. Sequencing and computational technologies, however, have been a limiting factor in performing dense time series analysis of the human microbiome. Here, we present the largest human microbiota time series analysis to date, covering two individuals at four body sites over
more » ... 96 timepoints. Results: We find that despite stable differences between body sites and individuals, there is pronounced variability in an individual's microbiota across months, weeks and even days. Additionally, only a small fraction of the total taxa found within a single body site appear to be present across all time points, suggesting that no core temporal microbiome exists at high abundance (although some microbes may be present but drop below the detection threshold). Many more taxa appear to be persistent but non-permanent community members. Conclusions: DNA sequencing and computational advances described here provide the ability to go beyond infrequent snapshots of our human-associated microbial ecology to high-resolution assessments of temporal variations over protracted periods, within and between body habitats and individuals. This capacity will allow us to define normal variation and pathologic states, and assess responses to therapeutic interventions.
doi:10.1186/gb-2011-12-5-r50 pmid:21624126 pmcid:PMC3271711 fatcat:rbrev7hmfnb4ldk7tut6br7kt4

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

William A. Walters, J. Gregory Caporaso, Christian L. Lauber, Donna Berg-Lyons, Noah Fierer, Rob Knight
2011 Computer applications in the biosciences : CABIOS  
Motivation: PCR amplification of DNA is a key preliminary step in many applications of high-throughput sequencing technologies, yet design of novel barcoded primers and taxonomic analysis of novel or existing primers remains a challenging task. Results: PrimerProspector is an open-source software package that allows researchers to develop new primers from collections of sequences and to evaluate existing primers in the context of taxonomic data. Availability: PrimerProspector is open-source software available at
doi:10.1093/bioinformatics/btr087 pmid:21349862 pmcid:PMC3072552 fatcat:5hjzj2h6wfccxanexj2mkyksse

Cohabiting family members share microbiota with one another and with their dogs

Se Jin Song, Christian Lauber, Elizabeth K Costello, Catherine A Lozupone, Gregory Humphrey, Donna Berg-Lyons, J Gregory Caporaso, Dan Knights, Jose C Clemente, Sara Nakielny, Jeffrey I Gordon, Noah Fierer (+1 others)
2013 eLife  
Human-associated microbial communities vary across individuals: possible contributing factors include (genetic) relatedness, diet, and age. However, our surroundings, including individuals with whom we interact, also likely shape our microbial communities. To quantify this microbial exchange, we surveyed fecal, oral, and skin microbiota from 60 families (spousal units with children, dogs, both, or neither). Household members, particularly couples, shared more of their microbiota than
more » ... from different households, with stronger effects of co-habitation on skin than oral or fecal microbiota. Dog ownership significantly increased the shared skin microbiota in cohabiting adults, and dog-owning adults shared more 'skin' microbiota with their own dogs than with other dogs. Although the degree to which these shared microbes have a true niche on the human body, vs transient detection after direct contact, is unknown, these results suggest that direct and frequent contact with our cohabitants may significantly shape the composition of our microbial communities.
doi:10.7554/elife.00458 pmid:23599893 pmcid:PMC3628085 fatcat:b23zk6s3mjdllbg7mruk3476xq

Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection

Alexa Weingarden, Antonio González, Yoshiki Vázquez-Baeza, Sophie Weiss, Gregory Humphry, Donna Berg-Lyons, Dan Knights, Tatsuya Unno, Aleh Bobr, Johnthomas Kang, Alexander Khoruts, Rob Knight (+1 others)
2015 Microbiome  
Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection (CDI) that often fails standard antibiotic therapy. Despite its widespread recent use, however, little is known about the stability of the fecal microbiota following FMT. Results: Here we report on short-and long-term changes and provide kinetic visualization of fecal microbiota composition in patients with multiply recurrent CDI that were refractory to antibiotic therapy and treated
more » ... ing FMT. Fecal samples were collected from four patients before and up to 151 days after FMT, with daily collections until 28 days and weekly collections until 84 days post-FMT. The composition of fecal bacteria was characterized using high throughput 16S rRNA gene sequence analysis, compared to microbiota across body sites in the Human Microbiome Project (HMP) database, and visualized in a movie-like, kinetic format. FMT resulted in rapid normalization of bacterial fecal sample composition from a markedly dysbiotic state to one representative of normal fecal microbiota. While the microbiome appeared most similar to the donor implant material 1 day post-FMT, the composition diverged variably at later time points. The donor microbiota composition also varied over time. However, both post-FMT and donor samples remained within the larger cloud of fecal microbiota characterized as healthy by the HMP. Conclusions: Dynamic behavior is an intrinsic property of normal fecal microbiota and should be accounted for in comparing microbial communities among normal individuals and those with disease states. This also suggests that more frequent sample analyses are needed in order to properly assess success of FMT procedures.
doi:10.1186/s40168-015-0070-0 pmid:25825673 pmcid:PMC4378022 fatcat:6eq3qrwt25cyvdlav44624csdm

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity

Laura Wegener Parfrey, William A. Walters, Christian L. Lauber, Jose C. Clemente, Donna Berg-Lyons, Clotilde Teiling, Chinnappa Kodira, Mohammed Mohiuddin, Julie Brunelle, Mark Driscoll, Noah Fierer, Jack A. Gilbert (+1 others)
2014 Frontiers in Microbiology  
Copyright © 2014 Parfrey, Walters, Lauber, Clemente, Berg-Lyons, Teiling, Kodira, Mohiuddin, Brunelle, Driscoll, Fierer, Gilbert and Knight.  ...  Citation: Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, Kodira C, Mohiuddin M, Brunelle J, Driscoll M, Fierer N, Gilbert JA and Knight R (2014) Communities of microbial eukaryotes  ... 
doi:10.3389/fmicb.2014.00298 pmid:24995004 pmcid:PMC4063188 fatcat:24iz6w7difbgzgwlkcwsci4qla

Advancing Our Understanding of the Human Microbiome Using QIIME [chapter]

José A. Navas-Molina, Juan M. Peralta-Sánchez, Antonio González, Paul J. McMurdie, Yoshiki Vázquez-Baeza, Zhenjiang Xu, Luke K. Ursell, Christian Lauber, Hongwei Zhou, Se Jin Song, James Huntley, Gail L. Ackermann (+4 others)
2013 Methods in Enzymology  
We will discuss a first and general approach for those cases, using the Moving Pictures of the Human Microbiome Dataset (Caporaso, Lauber, Costello, Berg-Lyons, Gonzalez, Stombaugh et al., 2011) , where  ... 
doi:10.1016/b978-0-12-407863-5.00019-8 pmid:24060131 pmcid:PMC4517945 fatcat:w6yem3w3szdwteqmqe7t6z7ikq

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

J Gregory Caporaso, Christian L Lauber, William A Walters, Donna Berg-Lyons, James Huntley, Noah Fierer, Sarah M Owens, Jason Betley, Louise Fraser, Markus Bauer, Niall Gormley, Jack A Gilbert (+2 others)
2012 The ISME Journal  
doi:10.1038/ismej.2012.8 pmid:22402401 pmcid:PMC3400413 fatcat:g7vnsv4jvjgrdfcd3lzn2nk3ju

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

William Walters, Embriette R. Hyde, Donna Berg-Lyons, Gail Ackermann, Greg Humphrey, Alma Parada, Jack A. Gilbert, Janet K. Jansson, J. Gregory Caporaso, Jed A. Fuhrman, Amy Apprill, Rob Knight (+1 others)
2015 mSystems  
Designing primers for PCR-based taxonomic surveys that amplify a broad range of phylotypes in varied community samples is a difficult challenge, and the comparability of data sets amplified with varied primers requires attention. Here, we examined the performance of modified 16S rRNA gene and internal transcribed spacer (ITS) primers for archaea/bacteria and fungi, respectively, with nonaquatic samples. We moved primer bar codes to the 5′ end, allowing for a range of different 3′ primer
more » ... , such as the 515f/926r primer pair, which amplifies variable regions 4 and 5 of the 16S rRNA gene. We additionally demonstrated that modifications to the 515f/806r (variable region 4) 16S primer pair, which improves detection of Thaumarchaeota and clade SAR11 in marine samples, do not degrade performance on taxa already amplified effectively by the original primer set. Alterations to the fungal ITS primers did result in differential but overall improved performance compared to the original primers. In both cases, the improved primers should be widely adopted for amplicon studies. Importance We continue to uncover a wealth of information connecting microbes in important ways to human and environmental ecology. As our scientific knowledge and technical abilities improve, the tools used for microbiome surveys can be modified to improve the accuracy of our techniques, ensuring that we can continue to identify groundbreaking connections between microbes and the ecosystems they populate, from ice caps to the human body. It is important to confirm that modifications to these tools do not cause new, detrimental biases that would inhibit the field rather than continue to move it forward. We therefore demonstrated that two recently modified primer pairs that target taxonomically discriminatory regions of bacterial and fungal genomic DNA do not introduce new biases when used on a variety of sample types, from soil to human skin. This confirms the utility of these primers for maintaining currently recommended microbiome research techniques as the state of the art.
doi:10.1128/msystems.00009-15 pmid:27822518 pmcid:PMC5069754 fatcat:omizerahlrc3ldpentonx4inwm

A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system

Jessica L Metcalf, Laura Wegener Parfrey, Antonio Gonzalez, Christian L Lauber, Dan Knights, Gail Ackermann, Gregory C Humphrey, Matthew J Gebert, Will Van Treuren, Donna Berg-Lyons, Kyle Keepers, Yan Guo (+4 others)
2013 eLife  
Establishing the time since death is critical in every death investigation, yet existing techniques are susceptible to a range of errors and biases. For example, forensic entomology is widely used to assess the postmortem interval (PMI), but errors can range from days to months. Microbes may provide a novel method for estimating PMI that avoids many of these limitations. Here we show that postmortem microbial community changes are dramatic, measurable, and repeatable in a mouse model system,
more » ... owing PMI to be estimated within approximately 3 days over 48 days. Our results provide a detailed understanding of bacterial and microbial eukaryotic ecology within a decomposing corpse system and suggest that microbial community data can be developed into a forensic tool for estimating PMI.
doi:10.7554/elife.01104 pmid:24137541 pmcid:PMC3796315 fatcat:ixzi4fijvrb2xpsntvkg2ob7s4

Composition of Human Skin Microbiota Affects Attractiveness to Malaria Mosquitoes

Niels O. Verhulst, Yu Tong Qiu, Hans Beijleveld, Chris Maliepaard, Dan Knights, Stefan Schulz, Donna Berg-Lyons, Christian L. Lauber, Willem Verduijn, Geert W. Haasnoot, Roland Mumm, Harro J. Bouwmeester (+7 others)
2011 PLoS ONE  
The African malaria mosquito Anopheles gambiae sensu stricto continues to play an important role in malaria transmission, which is aggravated by its high degree of anthropophily, making it among the foremost vectors of this disease. In the current study we set out to unravel the strong association between this mosquito species and human beings, as it is determined by odorant cues derived from the human skin. Microbial communities on the skin play key roles in the production of human body odour.
more » ... We demonstrate that the composition of the skin microbiota affects the degree of attractiveness of human beings to this mosquito species. Bacterial plate counts and 16S rRNA sequencing revealed that individuals that are highly attractive to An. gambiae s.s. have a significantly higher abundance, but lower diversity of bacteria on their skin than individuals that are poorly attractive. Bacterial genera that are correlated with the relative degree of attractiveness to mosquitoes were identified. The discovery of the connection between skin microbial populations and attractiveness to mosquitoes may lead to the development of new mosquito attractants and personalized methods for protection against vectors of malaria and other infectious diseases.
doi:10.1371/journal.pone.0028991 pmid:22216154 pmcid:PMC3247224 fatcat:eity3jnburelhh5r4wuzjdzg3i

Molecular cartography of the human skin surface in 3D

Amina Bouslimani, Carla Porto, Christopher M. Rath, Mingxun Wang, Yurong Guo, Antonio Gonzalez, Donna Berg-Lyon, Gail Ackermann, Gitte Julie Moeller Christensen, Teruaki Nakatsuji, Lingjuan Zhang, Andrew W. Borkowski (+7 others)
2015 Proceedings of the National Academy of Sciences of the United States of America  
The human skin is an organ with a surface area of 1.5-2 m 2 that provides our interface with the environment. The molecular composition of this organ is derived from host cells, microbiota, and external molecules. The chemical makeup of the skin surface is largely undefined. Here we advance the technologies needed to explore the topographical distribution of skin molecules, using 3D mapping of mass spectrometry data and microbial 16S rRNA amplicon sequences. Our 3D maps reveal that the
more » ... composition of skin has diverse distributions and that the composition is defined not only by skin cells and microbes but also by our daily routines, including the application of hygiene products. The technological development of these maps lays a foundation for studying the spatial relationships of human skin with hygiene, the microbiota, and environment, with potential for developing predictive models of skin phenotypes tailored to individual health. human skin | 3D mapping | mass spectrometry | 16S rRNA
doi:10.1073/pnas.1424409112 pmid:25825778 pmcid:PMC4418856 fatcat:yockcwu3kza2tgncowb6jkueiq

Characterizing genetic variants for clinical action

Erin M. Ramos, Corina Din-Lovinescu, Jonathan S. Berg, Lisa D. Brooks, Audrey Duncanson, Michael Dunn, Peter Good, Tim J.P. Hubbard, Gail P. Jarvik, Christopher O'Donnell, Stephen T. Sherry, Naomi Aronson (+23 others)
2014 American Journal of Medical Genetics. Part C, Seminars in Medical Genetics  
Elaine Lyon is an associate professor of Pathology at the University of Utah School of Medicine.  ...  This prioritization should include an upfront assessment of the likelihood of clinical value based on standardized frameworks such as the method proposed by Berg et al [Berg et al., 2011] .  ... 
doi:10.1002/ajmg.c.31386 pmid:24634402 pmcid:PMC4158437 fatcat:gebtnuuwljdoxnb5dtrkbmauda

L'opéra, miroir des sociétés européennes

Clémence Schupp
2016 Genre, Sexualité et Société  
de Lyon, 2010.  ...  SCHNEIDER Michel, Prima Donna, Opéra et inconscient , Paris, Odile Jacob, 2001.  ... 
doi:10.4000/gss.3788 fatcat:utjcwohzcbgjrp4ntiksidrfra
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