Rob Knight

Publications of Rob Knight

• The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites.

  Authors: Luke K Ursell, Jose C Clemente, Jai Ram Rideout, Dirk Gevers, J Gregory Caporaso, Rob Knight

  The Journal of allergy and clinical immunology. 05/2012; 129(5):1204-8.

  The human body harbors 10 to 100 trillion microbes, mainly bacteria in our gut, which greatly outnumber our own human cells. This bacterial assemblage, referred to as the human microbiota, plays aThe human body harbors 10 to 100 trillion microbes, mainly bacteria in our gut, which greatly outnumber our own human cells. This bacterial assemblage, referred to as the human microbiota, plays a fundamental role in our well-being. Deviations from healthy microbial compositions (dysbiosis) have been linked with important human diseases, including inflammation-linked disorders, such as allergies, obesity, and inflammatory bowel disease. Characterizing the temporal variations and community membership of the healthy human microbiome is critical to accurately identify the significant deviations from normality that could be associated with disease states. However, the diversity of the human microbiome varies between body sites, between patients, and over time. Environmental differences have also been shown to play a role in shaping the human microbiome in different cultures, requiring that the healthy human microbiome be characterized across life spans, ethnicities, nationalities, cultures, and geographic locales. In this article we summarize our knowledge on the microbial composition of the 5 best-characterized body sites (gut, skin, oral, airways, and vagina), focusing on interpersonal and intrapersonal variations and our current understanding of the sources of this variation.

• The impact of the gut microbiota on human health: an integrative view.

  Authors: Jose C Clemente, Luke K Ursell, Laura Wegener Parfrey, Rob Knight

  Cell. 03/2012; 148(6):1258-70.

  The human gut harbors diverse microbes that play a fundamental role in the well-being of their host. The constituents of the microbiota-bacteria, viruses, and eukaryotes-have been shown to interactThe human gut harbors diverse microbes that play a fundamental role in the well-being of their host. The constituents of the microbiota-bacteria, viruses, and eukaryotes-have been shown to interact with one another and with the host immune system in ways that influence the development of disease. We review these interactions and suggest that a holistic approach to studying the microbiota that goes beyond characterization of community composition and encompasses dynamic interactions between all components of the microbiota and host tissue over time will be crucial for building predictive models for diagnosis and treatment of diseases linked to imbalances in our microbiota.

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

  Authors: 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, Geoff Smith, Rob Knight

  The ISME journal. 03/2012;

  DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community ampliconDNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community amplicon sequencing on the HiSeq2000 and MiSeq Illumina platforms, and apply that protocol to sequence 24 microbial communities from host-associated and free-living environments. A critical question as more sequencing platforms become available is whether biological conclusions derived on one platform are consistent with what would be derived on a different platform. We show that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the HiSeq2000 versus the MiSeq) and across the sequenced regions of amplicons.

• Experimental and analytical tools for studying the human microbiome.

  Authors: Justin Kuczynski, Christian L Lauber, William A Walters, Laura Wegener Parfrey, José C Clemente, Dirk Gevers, Rob Knight

  Nature reviews. Genetics. 01/2012; 13(1):47-58.

  The human microbiome substantially affects many aspects of human physiology, including metabolism, drug interactions and numerous diseases. This realization, coupled with ever-improving nucleotideThe human microbiome substantially affects many aspects of human physiology, including metabolism, drug interactions and numerous diseases. This realization, coupled with ever-improving nucleotide sequencing technology, has precipitated the collection of diverse data sets that profile the microbiome. In the past 2 years, studies have begun to include sufficient numbers of subjects to provide the power to associate these microbiome features with clinical states using advanced algorithms, increasing the use of microbiome studies both individually and collectively. Here we discuss tools and strategies for microbiome studies, from primer selection to bioinformatics analysis.

• Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys.

  Authors: Jeffrey J Werner, Dennis Zhou, J Gregory Caporaso, Rob Knight, Largus T Angenent

  The ISME journal. 12/2011;

• Advancing analytical algorithms and pipelines for billions of microbial sequences.

  Authors: Antonio Gonzalez, Rob Knight

  Current opinion in biotechnology. 12/2011; 23(1):64-71.

  The vast number of microbial sequences resulting from sequencing efforts using new technologies require us to re-assess currently available analysis methodologies and tools. Here we describe trendsThe vast number of microbial sequences resulting from sequencing efforts using new technologies require us to re-assess currently available analysis methodologies and tools. Here we describe trends in the development and distribution of software for analyzing microbial sequence data. We then focus on one widely used set of methods, dimensionality reduction techniques, which allow users to summarize and compare these vast datasets. We conclude by emphasizing the utility of formal software engineering methods for the development of computational biology tools, and the need for new algorithms for comparing microbial communities. Such large-scale comparisons will allow us to fulfill the dream of rapid integration and comparison of microbial sequence data sets, in a replicable analytical environment, in order to describe the microbial world we inhabit.

• SitePainter: a tool for exploring biogeographical patterns.

  Authors: Antonio Gonzalez, Jesse Stombaugh, Christian L Lauber, Noah Fierer, Rob Knight

  Bioinformatics (Oxford, England). 12/2011; 28(3):436-8.

  As microbial ecologists take advantage of high-throughput analytical techniques to describe microbial communities across ever-increasing numbers of samples, the need for new analysis tools thatAs microbial ecologists take advantage of high-throughput analytical techniques to describe microbial communities across ever-increasing numbers of samples, the need for new analysis tools that reveal the intrinsic spatial patterns and structures of these populations is crucial. Here we present SitePainter, an interactive graphical tool that allows investigators to create or upload pictures of their study site, load diversity analyses data and display both diversity and taxonomy results in a spatial context. Features of SitePainter include: visualizing α -diversity, using taxonomic summaries; visualizing β -diversity, using results from multidimensional scaling methods; and animating relationships among microbial taxa or pathways overtime. SitePainter thus increases the visual power and ability to explore spatially explicit studies. AVAILABILITY: https://sourceforge.net/projects/sitepainter SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: antoniog@colorado.edu, Rob.Knight@colorado.edu.

• Characterizing microbial communities through space and time.

  Authors: Antonio Gonzalez, Andrew King, Michael S Robeson Ii, Sejin Song, Ashley Shade, Jessica L Metcalf, Rob Knight

  Current opinion in biotechnology. 12/2011;

  Until recently, the study of microbial diversity has mainly been limited to descriptive approaches, rather than predictive model-based analyses. The development of advanced analytical tools andUntil recently, the study of microbial diversity has mainly been limited to descriptive approaches, rather than predictive model-based analyses. The development of advanced analytical tools and decreasing cost of high-throughput multi-omics technologies has made the later approach more feasible. However, consensus is lacking as to which spatial and temporal scales best facilitate understanding of the role of microbial diversity in determining both public and environmental health. Here, we review the potential for combining these new technologies with both traditional and nascent spatio-temporal analysis methods. The fusion of proper spatio-temporal sampling, combined with modern multi-omics and computational tools, will provide insight into the tracking, development and manipulation of microbial communities.

• Using QIIME to analyze 16S rRNA gene sequences from microbial communities.

  Authors: Justin Kuczynski, Jesse Stombaugh, William Anton Walters, Antonio González, J Gregory Caporaso, Rob Knight

  Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]. 12/2011; Chapter 10:Unit 10.7..

  QIIME (canonically pronounced "chime") is a software application that performs microbial community analysis. It is an acronym for Quantitative Insights Into Microbial Ecology, and has been used toQIIME (canonically pronounced "chime") is a software application that performs microbial community analysis. It is an acronym for Quantitative Insights Into Microbial Ecology, and has been used to analyze and interpret nucleic acid sequence data from fungal, viral, bacterial, and archaeal communities. The following protocols describe how to install QIIME on a single computer and use it to analyze microbial 16S sequence data from nine distinct microbial communities.

• Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients.

  Authors: Noah Fierer, Christian L Lauber, Kelly S Ramirez, Jesse Zaneveld, Mark A Bradford, Rob Knight

  The ISME journal. 12/2011;

  Terrestrial ecosystems are receiving elevated inputs of nitrogen (N) from anthropogenic sources and understanding how these increases in N availability affect soil microbial communities is criticalTerrestrial ecosystems are receiving elevated inputs of nitrogen (N) from anthropogenic sources and understanding how these increases in N availability affect soil microbial communities is critical for predicting the associated effects on belowground ecosystems. We used a suite of approaches to analyze the structure and functional characteristics of soil microbial communities from replicated plots in two long-term N fertilization experiments located in contrasting systems. Pyrosequencing-based analyses of 16S rRNA genes revealed no significant effects of N fertilization on bacterial diversity, but significant effects on community composition at both sites; copiotrophic taxa (including members of the Proteobacteria and Bacteroidetes phyla) typically increased in relative abundance in the high N plots, with oligotrophic taxa (mainly Acidobacteria) exhibiting the opposite pattern. Consistent with the phylogenetic shifts under N fertilization, shotgun metagenomic sequencing revealed increases in the relative abundances of genes associated with DNA/RNA replication, electron transport and protein metabolism, increases that could be resolved even with the shallow shotgun metagenomic sequencing conducted here (average of 75 000 reads per sample). We also observed shifts in the catabolic capabilities of the communities across the N gradients that were significantly correlated with the phylogenetic and metagenomic responses, indicating possible linkages between the structure and functioning of soil microbial communities. Overall, our results suggest that N fertilization may, directly or indirectly, induce a shift in the predominant microbial life-history strategies, favoring a more active, copiotrophic microbial community, a pattern that parallels the often observed replacement of K-selected with r-selected plant species with elevated N.

• An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.

  Authors: Daniel McDonald, Morgan N Price, Julia Goodrich, Eric P Nawrocki, Todd Z Desantis, Alexander Probst, Gary L Andersen, Rob Knight, Philip Hugenholtz

  The ISME journal. 12/2011; 6(3):610-8.

  Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate.Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a 'taxonomy to tree' approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408 315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/.

• The Western English Channel contains a persistent microbial seed bank.

  Authors: J Gregory Caporaso, Konrad Paszkiewicz, Dawn Field, Rob Knight, Jack A Gilbert

  The ISME journal. 11/2011;

  Robust seasonal dynamics in microbial community composition have previously been observed in the English Channel L4 marine observatory. These could be explained either by seasonal changes in the taxaRobust seasonal dynamics in microbial community composition have previously been observed in the English Channel L4 marine observatory. These could be explained either by seasonal changes in the taxa present at the L4 site, or by the continuous modulation of abundance of taxa within a persistent microbial community. To test these competing hypotheses, deep sequencing of 16S rRNA from one randomly selected time point to a depth of 10 729 927 reads was compared with an existing taxonomic survey data covering 6 years. When compared against the 6-year survey of 72 shallow sequenced time points, the deep sequenced time point maintained 95.4% of the combined shallow OTUs. Additionally, on average, 99.75%±0.06 (mean±s.d.) of the operational taxonomic units found in each shallow sequenced sample were also found in the single deep sequenced sample. This suggests that the vast majority of taxa identified in this ecosystem are always present, but just in different proportions that are predictable. Thus observed changes in community composition are actually variations in the relative abundance of taxa, not, as was previously believed, demonstrating extinction and recolonization of taxa in the ecosystem through time.

• Human Immunodeficiency Virus nef Signature Sequences Are Associated with Pulmonary Hypertension.

  Authors: Sharilyn Almodovar, Rob Knight, Amanda A Allshouse, Sarah Roemer, Catherine Lozupone, Daniel McDonald, Jeremy Widmann, Norbert F Voelkel, Robert J Shelton, Edu B Suarez, Kenneth W Hammer, Cecile Goujard, Nicola Petrosillo, Gerald Simonneau, Priscilla Y Hsue, Marc Humbert, Sonia C Flores

  AIDS research and human retroviruses. 11/2011;

  Abstract Severe pulmonary hypertension (PH) associated with vascular remodeling is a long-term complication of HIV infection (HIV-PH) affecting 1/200 infected individuals vs. 1/200,000 frequency inAbstract Severe pulmonary hypertension (PH) associated with vascular remodeling is a long-term complication of HIV infection (HIV-PH) affecting 1/200 infected individuals vs. 1/200,000 frequency in the uninfected population. Factors accounting for increased PH susceptibility in HIV-infected individuals are unknown. Rhesus macaques infected with chimeric SHIVnef virions but not with SIV display PH-like pulmonary vascular remodeling suggesting that HIV-Nef is associated with PH; these monkeys showed changes in nef sequences that correlated with pathogenesis after passage in vivo. We further examined whether HIV-nef alleles in HIV-PH subjects have signature sequences associated with the disease phenotype. We evaluated specimens from participants with and without HIV-PH from European Registries and validated results with samples collected as part of the Lung-HIV Studies in San Francisco. We found that 10 polymorphisms in nef were overrepresented in blood cells or lung tissue specimens from European HIV-PH individuals but significantly less frequent in HIV-infected individuals without PH. These polymorphisms mapped to known functional domains in Nef. In the validation cohort, 7/10 polymorphisms in the HIV-nef gene were confirmed; these polymorphisms arose independently from viral load, CD4(+) T cell counts, length of infection, and antiretroviral therapy status. Two out of 10 polymorphisms were previously reported in macaques with PH-like pulmonary vascular remodeling. Cloned recombinant Nef proteins from clinical samples down-regulated CD4, suggesting that these primary isolates are functional. This study offers new insights into the association between Nef polymorphisms in functional domains and the HIV-PH phenotype. The utility of these polymorphisms as predictors of PH should be examined in a larger population.

• The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins.

  Authors: Nathan P McNulty, Tanya Yatsunenko, Ansel Hsiao, Jeremiah J Faith, Brian D Muegge, Andrew L Goodman, Bernard Henrissat, Raish Oozeer, Stéphanie Cools-Portier, Guillaume Gobert, Christian Chervaux, Dan Knights, Catherine A Lozupone, Rob Knight, Alexis E Duncan, James R Bain, Michael J Muehlbauer, Christopher B Newgard, Andrew C Heath, Jeffrey I Gordon

  Science translational medicine. 10/2011; 3(106):106ra106.

  Understanding how the human gut microbiota and host are affected by probiotic bacterial strains requires carefully controlled studies in humans and in mouse models of the gut ecosystem whereUnderstanding how the human gut microbiota and host are affected by probiotic bacterial strains requires carefully controlled studies in humans and in mouse models of the gut ecosystem where potentially confounding variables that are difficult to control in humans can be constrained. Therefore, we characterized the fecal microbiomes and metatranscriptomes of adult female monozygotic twin pairs through repeated sampling 4 weeks before, 7 weeks during, and 4 weeks after consumption of a commercially available fermented milk product (FMP) containing a consortium of Bifidobacterium animalis subsp. lactis, two strains of Lactobacillus delbrueckii subsp. bulgaricus, Lactococcus lactis subsp. cremoris, and Streptococcus thermophilus. In addition, gnotobiotic mice harboring a 15-species model human gut microbiota whose genomes contain 58,399 known or predicted protein-coding genes were studied before and after gavage with all five sequenced FMP strains. No significant changes in bacterial species composition or in the proportional representation of genes encoding known enzymes were observed in the feces of humans consuming the FMP. Only minimal changes in microbiota configuration were noted in mice after single or repeated gavage with the FMP consortium. However, RNA-Seq analysis of fecal samples and follow-up mass spectrometry of urinary metabolites disclosed that introducing the FMP strains into mice results in significant changes in expression of microbiome-encoded enzymes involved in numerous metabolic pathways, most prominently those related to carbohydrate metabolism. B. animalis subsp. lactis, the dominant persistent member of the FMP consortium in gnotobiotic mice, up-regulates a locus in vivo that is involved in the catabolism of xylooligosaccharides, a class of glycans widely distributed in fruits, vegetables, and other foods, underscoring the importance of these sugars to this bacterial species. The human fecal metatranscriptome exhibited significant changes, confined to the period of FMP consumption, that mirror changes in gnotobiotic mice, including those related to plant polysaccharide metabolism. These experiments illustrate a translational research pipeline for characterizing the effects of FMPs on the human gut microbiome.

• Human-associated microbial signatures: examining their predictive value.

  Authors: Dan Knights, Laura Wegener Parfrey, Jesse Zaneveld, Catherine Lozupone, Rob Knight

  Cell host & microbe. 10/2011; 10(4):292-6.

  Host-associated microbial communities are unique to individuals, affect host health, and correlate with disease states. Although advanced technologies capture detailed snapshots of microbialHost-associated microbial communities are unique to individuals, affect host health, and correlate with disease states. Although advanced technologies capture detailed snapshots of microbial communities, high within- and between-subject variation hampers discovery of microbial signatures in diagnostic or forensic settings. We suggest turning to machine learning and discuss key directions toward harnessing human-associated microbial signatures.

• Co-habiting amphibian species harbor unique skin bacterial communities in wild populations.

  Authors: Valerie J McKenzie, Robert M Bowers, Noah Fierer, Rob Knight, Christian L Lauber

  The ISME journal. 09/2011; 6(3):588-96.

  Although all plant and animal species harbor microbial symbionts, we know surprisingly little about the specificity of microbial communities to their hosts. Few studies have compared the microbiomesAlthough all plant and animal species harbor microbial symbionts, we know surprisingly little about the specificity of microbial communities to their hosts. Few studies have compared the microbiomes of different species of animals, and fewer still have examined animals in the wild. We sampled four pond habitats in Colorado, USA, where multiple amphibian species were present. In total, 32 amphibian individuals were sampled from three different species including northern leopard frogs (Lithobates pipiens), western chorus frogs (Pseudacris triseriata) and tiger salamanders (Ambystoma tigrinum). We compared the diversity and composition of the bacterial communities on the skin of the collected individuals via barcoded pyrosequencing of the 16S rRNA gene. Dominant bacterial phyla included Acidobacteria, Actinobacteria, Bacteriodetes, Cyanobacteria, Firmicutes and Proteobacteria. In total, we found members of 18 bacterial phyla, comparable to the taxonomic diversity typically found on human skin. Levels of bacterial diversity varied strongly across species: L. pipiens had the highest diversity; A. tigrinum the lowest. Host species was a highly significant predictor of bacterial community similarity, and co-habitation within the same pond was not significant, highlighting that the skin-associated bacterial communities do not simply reflect those bacterial communities found in their surrounding environments. Innate species differences thus appear to regulate the structure of skin bacterial communities on amphibians. In light of recent discoveries that some bacteria on amphibian skin have antifungal activity, our finding suggests that host-specific bacteria may have a role in the species-specific resistance to fungal pathogens.

• TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata.

  Authors: Meg Pirrung, Ryan Kennedy, J Gregory Caporaso, Jesse Stombaugh, Doug Wendel, Rob Knight

  Bioinformatics (Oxford, England). 09/2011; 27(21):3067-9.

  Microbial community profiling is a highly active area of research, but tools that facilitate visualization of phylogenetic trees and associated environmental data have not kept up with the increasingMicrobial community profiling is a highly active area of research, but tools that facilitate visualization of phylogenetic trees and associated environmental data have not kept up with the increasing quantity of data generated in these studies. TopiaryExplorer supports the visualization of very large phylogenetic trees, including features such as the automated coloring of branches by environmental data, manipulation of trees and incorporation of per-tip metadata (e.g. taxonomic labels). http://topiaryexplorer.sourceforge.net. rob.knight@colorado.edu.

• Linking long-term dietary patterns with gut microbial enterotypes.

  Authors: Gary D Wu, Jun Chen, Christian Hoffmann, Kyle Bittinger, Ying-Yu Chen, Sue A Keilbaugh, Meenakshi Bewtra, Dan Knights, William A Walters, Rob Knight, Rohini Sinha, Erin Gilroy, Kernika Gupta, Robert Baldassano, Lisa Nessel, Hongzhe Li, Frederic D Bushman, James D Lewis

  Science (New York, N.Y.). 09/2011; 334(6052):105-8.

  Diet strongly affects human health, partly by modulating gut microbiome composition. We used diet inventories and 16S rDNA sequencing to characterize fecal samples from 98 individuals. FecalDiet strongly affects human health, partly by modulating gut microbiome composition. We used diet inventories and 16S rDNA sequencing to characterize fecal samples from 98 individuals. Fecal communities clustered into enterotypes distinguished primarily by levels of Bacteroides and Prevotella. Enterotypes were strongly associated with long-term diets, particularly protein and animal fat (Bacteroides) versus carbohydrates (Prevotella). A controlled-feeding study of 10 subjects showed that microbiome composition changed detectably within 24 hours of initiating a high-fat/low-fiber or low-fat/high-fiber diet, but that enterotype identity remained stable during the 10-day study. Thus, alternative enterotype states are associated with long-term diet.

• Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation.

  Authors: Jesse R R Zaneveld, Laura Wegener Parfrey, Will Van Treuren, Catherine Lozupone, Jose C Clemente, Dan Knights, Jesse Stombaugh, Justin Kuczynski, Rob Knight

  Trends in microbiology. 08/2011; 19(10):472-82.

  High-throughput sequencing technologies provide new opportunities to address longstanding questions about habitat adaptation in microbial organisms. How have microbes managed to adapt to such a wideHigh-throughput sequencing technologies provide new opportunities to address longstanding questions about habitat adaptation in microbial organisms. How have microbes managed to adapt to such a wide range of environments, and what genomic features allow for such adaptation? We review recent large-scale studies of habitat adaptation, with emphasis on those that utilize phylogenetic techniques. On the basis of current trends, we summarize methodological challenges faced by investigators, and the tools, techniques and analytical approaches available to overcome them. Phylogenetic approaches and detailed information about each environmental sample will be crucial as the ability to collect genome sequences continues to expand.

• Defining seasonal marine microbial community dynamics.

  Authors: Jack A Gilbert, Joshua A Steele, J Gregory Caporaso, Lars Steinbrück, Jens Reeder, Ben Temperton, Susan Huse, Alice C McHardy, Rob Knight, Ian Joint, Paul Somerfield, Jed A Fuhrman, Dawn Field

  The ISME journal. 08/2011; 6(2):298-308.

  Here we describe, the longest microbial time-series analyzed to date using high-resolution 16S rRNA tag pyrosequencing of samples taken monthly over 6 years at a temperate marine coastal site offHere we describe, the longest microbial time-series analyzed to date using high-resolution 16S rRNA tag pyrosequencing of samples taken monthly over 6 years at a temperate marine coastal site off Plymouth, UK. Data treatment effected the estimation of community richness over a 6-year period, whereby 8794 operational taxonomic units (OTUs) were identified using single-linkage preclustering and 21 130 OTUs were identified by denoising the data. The Alphaproteobacteria were the most abundant Class, and the most frequently recorded OTUs were members of the Rickettsiales (SAR 11) and Rhodobacteriales. This near-surface ocean bacterial community showed strong repeatable seasonal patterns, which were defined by winter peaks in diversity across all years. Environmental variables explained far more variation in seasonally predictable bacteria than did data on protists or metazoan biomass. Change in day length alone explains >65% of the variance in community diversity. The results suggested that seasonal changes in environmental variables are more important than trophic interactions. Interestingly, microbial association network analysis showed that correlations in abundance were stronger within bacterial taxa rather than between bacteria and eukaryotes, or between bacteria and environmental variables.