Huse Susan M.

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Huse

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Susan M.

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Shifts in the microbial community composition of Gulf Coast beaches following beach oiling

(Public Library of Science, 2013-09-10) Newton, Ryan J. ; Huse, Susan M. ; Morrison, Hilary G. ; Peake, Colin S. ; Sogin, Mitchell L. ; McLellan, Sandra L.

Microorganisms associated with coastal sands serve as a natural biofilter, providing essential nutrient recycling in nearshore environments and acting to maintain coastal ecosystem health. Anthropogenic stressors often impact these ecosystems, but little is known about whether these disturbances can be identified through microbial community change. The blowout of the Macondo Prospect reservoir on April 20, 2010, which released oil hydrocarbons into the Gulf of Mexico, presented an opportunity to examine whether microbial community composition might provide a sensitive measure of ecosystem disturbance. Samples were collected on four occasions, beginning in mid-June, during initial beach oiling, until mid-November from surface sand and surf zone waters at seven beaches stretching from Bay St. Louis, MS to St. George Island, FL USA. Oil hydrocarbon measurements and NOAA shoreline assessments indicated little to no impact on the two most eastern beaches (controls). Sequence comparisons of bacterial ribosomal RNA gene hypervariable regions isolated from beach sands located to the east and west of Mobile Bay in Alabama demonstrated that regional drivers account for markedly different bacterial communities. Individual beaches had unique community signatures that persisted over time and exhibited spatial relationships, where community similarity decreased as horizontal distance between samples increased from one to hundreds of meters. In contrast, sequence analyses detected larger temporal and less spatial variation among the water samples. Superimposed upon these beach community distance and time relationships, was increased variability in bacterial community composition from oil hydrocarbon contaminated sands. The increased variability was observed among the core, resident, and transient community members, indicating the occurrence of community-wide impacts rather than solely an overprinting of oil hydrocarbon-degrading bacteria onto otherwise relatively stable sand population structures. Among sequences classified to genus, Alcanivorax, Alteromonas, Marinobacter, Winogradskyella, and Zeaxanthinibacter exhibited the largest relative abundance increases in oiled sands.
TaxMan : a server to trim rRNA reference databases and inspect taxonomic coverage

(Oxford University Press, 2012-05-22) Brandt, Bernd W. ; Bonder, Marc J. ; Huse, Susan M. ; Zaura, Egija

Amplicon sequencing of the hypervariable regions of the small subunit ribosomal RNA gene is a widely accepted method for identifying the members of complex bacterial communities. Several rRNA gene sequence reference databases can be used to assign taxonomic names to the sequencing reads using BLAST, USEARCH, GAST or the RDP classifier. Next-generation sequencing methods produce ample reads, but they are short, currently ∼100–450 nt (depending on the technology), as compared to the full rRNA gene of ∼1550 nt. It is important, therefore, to select the right rRNA gene region for sequencing. The primers should amplify the species of interest and the hypervariable regions should differentiate their taxonomy. Here, we introduce TaxMan: a web-based tool that trims reference sequences based on user-selected primer pairs and returns an assessment of the primer specificity by taxa. It allows interactive plotting of taxa, both amplified and missed in silico by the primers used. Additionally, using the trimmed sequences improves the speed of sequence matching algorithms. The smaller database greatly improves run times (up to 98%) and memory usage, not only of similarity searching (BLAST), but also of chimera checking (UCHIME) and of clustering the reads (UCLUST). TaxMan is available at http://www.ibi.vu.nl/programs/taxmanwww/.
MIxS-BE : a MIxS extension defining a minimum information standard for sequence data from the built environment

(Nature Publishing Group, 2013-10-24) Glass, Elizabeth M. ; Dribinsky, Yekaterina ; Yilmaz, Pelin ; Levin, Hal ; Van Pelt, Robert ; Wendel, Doug ; Wilke, Andreas ; Eisen, Jonathan A. ; Huse, Susan M. ; Shipanova, Anna ; Sogin, Mitchell L. ; Stajich, Jason ; Knight, Rob ; Meyer, Folker ; Schriml, Lynn M.

The need for metadata standards for microbe sampling in the built environment.
The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing

(Public Library of Science, 2008-11-18) Dethlefsen, Les ; Huse, Susan M. ; Sogin, Mitchell L. ; Relman, David A.

The intestinal microbiota is essential to human health, with effects on nutrition, metabolism, pathogen resistance, and other processes. Antibiotics may disrupt these interactions and cause acute disease, as well as contribute to chronic health problems, although technical challenges have hampered research on this front. Several recent studies have characterized uncultured and complex microbial communities by applying a new, massively parallel technology to obtain hundreds of thousands of sequences of a specific variable region within the small subunit rRNA gene. These shorter sequences provide an indication of diversity. We used this technique to track changes in the intestinal microbiota of three healthy humans before and after treatment with the antibiotic ciprofloxacin, with high sensitivity and resolution, and without sacrificing breadth of coverage. Consistent with previous results, we found that the microbiota of these individuals was similar at the genus level, but interindividual differences were evident at finer scales. Ciprofloxacin reduced the diversity of the intestinal microbiota, with significant effects on about one-third of the bacterial taxa. Despite this pervasive disturbance, the membership of the communities had largely returned to the pretreatment state within 4 weeks.
A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes

(Public Library of Science, 2009-07-27) Amaral-Zettler, Linda A. ; McCliment, Elizabeth A. ; Ducklow, Hugh W. ; Huse, Susan M.

Massively parallel pyrosequencing of amplicons from the V6 hypervariable regions of small-subunit (SSU) ribosomal RNA (rRNA) genes is commonly used to assess diversity and richness in bacterial and archaeal populations. Recent advances in pyrosequencing technology provide read lengths of up to 240 nucleotides. Amplicon pyrosequencing can now be applied to longer variable regions of the SSU rRNA gene including the V9 region in eukaryotes. We present a protocol for the amplicon pyrosequencing of V9 regions for eukaryotic environmental samples for biodiversity inventories and species richness estimation. The International Census of Marine Microbes (ICoMM) and the Microbial Inventory Research Across Diverse Aquatic Long Term Ecological Research Sites (MIRADA-LTERs) projects are already employing this protocol for tag sequencing of eukaryotic samples in a wide diversity of both marine and freshwater environments. Massively parallel pyrosequencing of eukaryotic V9 hypervariable regions of SSU rRNA genes provides a means of estimating species richness from deeply-sampled populations and for discovering novel species from the environment.
Global distribution and diversity of marine Verrucomicrobia

( 2011-12-08) Freitas, Sara ; Hatosy, Stephen ; Fuhrman, Jed A. ; Huse, Susan M. ; Mark Welch, David B. ; Sogin, Mitchell L. ; Martiny, Adam C.

Verrucomicrobia is a bacterial phylum that is commonly detected in soil but little is known about the distribution and diversity of this phylum in the marine environment. To address this, we analyzed the marine microbial community composition in 506 samples from the International Census of Marine Microbes as well as eleven coastal samples taken from the California Current. These samples from both the water column and sediments covered a wide range of environmental conditions. Verrucomicrobia were present in 98% of the analyzed samples and thus appeared nearly ubiquitous in the ocean. Based on the occurrence of amplified 16S rRNA sequences, Verrucomicrobia constituted on average 2% of the water column and 1.4% of the sediment bacterial communities. The diversity of Verrucomicrobia displayed a biogeography at multiple taxonomic levels and thus, specific lineages appeared to have clear habitat preference. We found that Subdivision 1 and 4 generally dominated marine bacterial communities, whereas Subdivision 2 was confined to low salinity waters. Within the subdivisions, Verrucomicrobia community composition were significantly different in the water column compared to sediment as well as within the water column along gradients of salinity, temperature, nitrate, depth, and overall water column depth. Although we still know little about the ecophysiology of Verrucomicrobia lineages, the ubiquity of this phylum suggests that it may be important for the biogeochemical cycle of carbon in the ocean.
Accuracy and quality of massively parallel DNA pyrosequencing

(BioMed Central, 2007-07-20) Huse, Susan M. ; Huber, Julie A. ; Morrison, Hilary G. ; Sogin, Mitchell L. ; Mark Welch, David B.

Massively parallel pyrosequencing systems have increased the efficiency of DNA sequencing, although the published per-base accuracy of a Roche GS20 is only 96%. In genome projects, highly redundant consensus assemblies can compensate for sequencing errors. In contrast, studies of microbial diversity that catalogue differences between PCR amplicons of ribosomal RNA genes (rDNA) or other conserved gene families cannot take advantage of consensus assemblies to detect and minimize incorrect base calls. We performed an empirical study of the per-base error rate for the Roche GS20 system using sequences of the V6 hypervariable region from cloned microbial ribosomal DNA (tag sequencing). We calculated a 99.5% accuracy rate in unassembled sequences, and identified several factors that can be used to remove a small percentage of low-quality reads, improving the accuracy to 99.75% or better. By using objective criteria to eliminate low quality data, the quality of individual GS20 sequence reads in molecular ecological applications can surpass the accuracy of traditional capillary methods.
The taxonomic and functional diversity of microbes at a temperate coastal site : a ‘multi-omic’ study of seasonal and diel temporal variation

(Public Library of Science, 2010-11-29) Gilbert, Jack A. ; Field, Dawn ; Swift, Paul ; Thomas, Simon ; Cummings, Denise ; Temperton, Ben ; Weynberg, Karen ; Huse, Susan M. ; Hughes, Margaret ; Joint, Ian ; Somerfield, Paul J. ; Muhling, Martin

How microbial communities change over time in response to the environment is poorly understood. Previously a six-year time series of 16S rRNA V6 data from the Western English Channel demonstrated robust seasonal structure within the bacterial community, with diversity negatively correlated with day-length. Here we determine whether metagenomes and metatranscriptomes follow similar patterns. We generated 16S rRNA datasets, metagenomes (1.2 GB) and metatranscriptomes (157 MB) for eight additional time points sampled in 2008, representing three seasons (Winter, Spring, Summer) and including day and night samples. This is the first microbial ‘multi-omic’ study to combine 16S rRNA amplicon sequencing with metagenomic and metatranscriptomic profiling. Five main conclusions can be drawn from analysis of these data: 1) Archaea follow the same seasonal patterns as Bacteria, but show lower relative diversity; 2) Higher 16S rRNA diversity also reflects a higher diversity of transcripts; 3) Diversity is highest in winter and at night; 4) Community-level changes in 16S-based diversity and metagenomic profiles are better explained by seasonal patterns (with samples closest in time being most similar), while metatranscriptomic profiles are better explained by diel patterns and shifts in particular categories (i.e., functional groups) of genes; 5) Changes in key genes occur among seasons and between day and night (i.e., photosynthesis); but these samples contain large numbers of orphan genes without known homologues and it is these unknown gene sets that appear to contribute most towards defining the differences observed between times. Despite the huge diversity of these microbial communities, there are clear signs of predictable patterns and detectable stability over time. Renewed and intensified efforts are required to reveal fundamental deterministic patterns in the most complex microbial communities. Further, the presence of a substantial proportion of orphan sequences underscores the need to determine the gene products of sequences with currently unknown function.
The seasonal structure of microbial communities in the Western English Channel

( 2009-06-05) Gilbert, Jack A. ; Field, Dawn ; Swift, Paul ; Newbold, Lindsay K. ; Oliver, Anna E. ; Smyth, Tim J. ; Somerfield, Paul J. ; Huse, Susan M. ; Joint, Ian

Very few marine microbial communities are well characterized even with the weight of research effort presently devoted to it. Only a small proportion of this effort has been aimed at investigating temporal community structure. Here we present the first report of the application of high-throughput pyrosequencing to investigate intra-annual bacterial community structure. Microbial diversity was determined for 12 time points at the surface of the L4 sampling site in the Western English Channel. This was performed over 11 months during 2007. A total of 182,560 sequences from the V6 hyper-variable region of the small-subunit ribosomal RNA gene (16S rRNA) were obtained; there were between 11,327 and 17,339 reads per sample. Approximately 7000 genera were identified, with one in every 25 reads being attributed to a new genus; yet this level of sampling far from exhausted the total diversity present at any one time point. The total data set contained 17,673 unique sequences. Only 93 (0.5%) were found at all time-points, yet these few lineages comprised 50% of the total reads sequenced. The most abundant phylum was Proteobacteria (50% of all sequenced reads), while the SAR11 clade comprised 21% of the ubiquitous reads and ~12 % of the total sequenced reads. In contrast, 78% of all OTUs were only found at one time-point and 67% were only found once, evidence of a large and transient rare assemblage. This time-series shows evidence of seasonally structured community diversity. There is also evidence for seasonal succession, primarily reflecting changes among dominant taxa. These changes in structure were significantly correlated to a combination of temperature, phosphate and silicate concentrations.
Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing

(Public Library of Science, 2008-11-21) Huse, Susan M. ; Dethlefsen, Les ; Huber, Julie A. ; Mark Welch, David B. ; Relman, David A. ; Sogin, Mitchell L.

Massively parallel pyrosequencing of hypervariable regions from small subunit ribosomal RNA (SSU rRNA) genes can sample a microbial community two or three orders of magnitude more deeply per dollar and per hour than capillary sequencing of full-length SSU rRNA. As with full-length rRNA surveys, each sequence read is a tag surrogate for a single microbe. However, rather than assigning taxonomy by creating gene trees de novo that include all experimental sequences and certain reference taxa, we compare the hypervariable region tags to an extensive database of rRNA sequences and assign taxonomy based on the best match in a Global Alignment for Sequence Taxonomy (GAST) process. The resulting taxonomic census provides information on both composition and diversity of the microbial community. To determine the effectiveness of using only hypervariable region tags for assessing microbial community membership, we compared the taxonomy assigned to the V3 and V6 hypervariable regions with the taxonomy assigned to full-length SSU rRNA sequences isolated from both the human gut and a deep-sea hydrothermal vent. The hypervariable region tags and full-length rRNA sequences provided equivalent taxonomy and measures of relative abundance of microbial communities, even for tags up to 15% divergent from their nearest reference match. The greater sampling depth per dollar afforded by massively parallel pyrosequencing reveals many more members of the “rare biosphere” than does capillary sequencing of the full-length gene. In addition, tag sequencing eliminates cloning bias and the sequences are short enough to be completely sequenced in a single read, maximizing the number of organisms sampled in a run while minimizing chimera formation. This technique allows the cost-effective exploration of changes in microbial community structure, including the rare biosphere, over space and time and can be applied immediately to initiatives, such as the Human Microbiome Project.
VAMPS : a website for visualization and analysis of microbial population structures

(BioMed Central, 2014-02-05) Huse, Susan M. ; Mark Welch, David B. ; Voorhis, Andy ; Shipunova, Anna ; Morrison, Hilary G. ; Eren, A. Murat ; Sogin, Mitchell L.

The advent of next-generation DNA sequencing platforms has revolutionized molecular microbial ecology by making the detailed analysis of complex communities over time and space a tractable research pursuit for small research groups. However, the ability to generate 105–108 reads with relative ease brings with it many downstream complications. Beyond the computational resources and skills needed to process and analyze data, it is difficult to compare datasets in an intuitive and interactive manner that leads to hypothesis generation and testing. We developed the free web service VAMPS (Visualization and Analysis of Microbial Population Structures, http://vamps.mbl.edu webcite) to address these challenges and to facilitate research by individuals or collaborating groups working on projects with large-scale sequencing data. Users can upload marker gene sequences and associated metadata; reads are quality filtered and assigned to both taxonomic structures and to taxonomy-independent clusters. A simple point-and-click interface allows users to select for analysis any combination of their own or their collaborators’ private data and data from public projects, filter these by their choice of taxonomic and/or abundance criteria, and then explore these data using a wide range of analytic methods and visualizations. Each result is extensively hyperlinked to other analysis and visualization options, promoting data exploration and leading to a greater understanding of data relationships. VAMPS allows researchers using marker gene sequence data to analyze the diversity of microbial communities and the relationships between communities, to explore these analyses in an intuitive visual context, and to download data, results, and images for publication. VAMPS obviates the need for individual research groups to make the considerable investment in computational infrastructure and bioinformatic support otherwise necessary to process, analyze, and interpret massive amounts of next-generation sequence data. Any web-capable device can be used to upload, process, explore, and extract data and results from VAMPS. VAMPS encourages researchers to share sequence and metadata, and fosters collaboration between researchers of disparate biomes who recognize common patterns in shared data.
Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure

( 2008-07) Huber, Julie A. ; Morrison, Hilary G. ; Huse, Susan M. ; Neal, Phillip R. ; Sogin, Mitchell L. ; Mark Welch, David B.

PCR-based surveys of microbial communities commonly use regions of the small subunit ribosomal RNA (SSU rRNA) gene to determine taxonomic membership and estimate total diversity. Here we show that the length of the target amplicon has a significant effect on assessments of microbial richness and community membership. Using OTU- and taxonomy-based tools, we compared the V6 hypervariable region of the bacterial SSU rRNA gene of three amplicon libraries of ca. 100 base pair (bp), 400bp, and 1000bp from each of two hydrothermal vent fluid samples. We found that the smallest amplicon libraries contained more unique sequences, higher diversity estimates, and a different community structure than the other two libraries from each sample. We hypothesize that a combination of polymerase dissociation, cloning bias, and mis-priming due to secondary structure accounts for the differences. While this relationship is not linear, it is clear that the smallest amplicon libraries contained more different types of sequences, and accordingly, more diverse members of the community. Because divergent and lower abundant taxa can be more readily detected with smaller amplicons, they may provide better assessments of total community diversity and taxonomic membership than longer amplicons in molecular studies of microbial communities.
DRISEE overestimates errors in metagenomic sequencing data

(Oxford University Press, 2013-05-22) Eren, A. Murat ; Morrison, Hilary G. ; Huse, Susan M. ; Sogin, Mitchell L.

The extremely high error rates reported by Keegan et al. in ‘A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE’ (PLoS Comput Biol 2012;8:e1002541) for many next-generation sequencing datasets prompted us to re-examine their results. Our analysis reveals that the presence of conserved artificial sequences, e.g. Illumina adapters, and other naturally occurring sequence motifs accounts for most of the reported errors. We conclude that DRISEE reports inflated levels of sequencing error, particularly for Illumina data. Tools offered for evaluating large datasets need scrupulous review before they are implemented.
Isolated communities of Epsilonproteobacteria in hydrothermal vent fluids of the Mariana Arc seamounts

( 2010-05) Huber, Julie A. ; Cantin, Holly V. ; Huse, Susan M. ; Mark Welch, David B. ; Sogin, Mitchell L. ; Butterfield, David A.

Low-temperature hydrothermal vent fluids represent access points to diverse microbial communities living in oceanic crust. This study examined the distribution, relative abundance, and diversity of Epsilonproteobacteria in 14 low-temperature vent fluids from 5 volcanically active seamounts of the Mariana Arc using a 454 tag sequencing approach. Most vent fluids were enriched in cell concentrations compared to background seawater, and quantitative PCR results indicated all fluids were dominated by bacteria. Operational taxonomic unit (OTU)-based statistical tools applied to 454 data show that all vents from the northern end of the Marian Arc grouped together, to the exclusion of southern arc seamounts, which were as distinct from one another as they were from northern seamounts. Statistical analysis also showed a significant relationship between seamount and individual vent groupings, suggesting that community membership may be linked to geographical isolation and not geochemical parameters. However, while there may be large-scale geographic differences, distance is not the distinguishing factor in microbial community composition. At the local scale, most vents host a distinct population of Epsilonprotoebacteria, regardless of seamount location. This suggests there may be barriers to exchange and dispersal for these vent endemic microorganisms at hydrothermal seamounts of the Mariana Arc.
Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation

( 2009-03-13) Antonopoulos, Dionysios A. ; Huse, Susan M. ; Morrison, Hilary G. ; Schmidt, Thomas M. ; Sogin, Mitchell L. ; Young, Vincent B.

Shifts in microbial communities are implicated in the pathogenesis of a number of gastrointestinal diseases, but we have limited understanding of the mechanisms that lead to altered community structures. One difficulty with studying these mechanisms in human subjects is the inherent baseline variability of the microbiota in different individuals that arise due to varying life histories. To try and overcome this baseline variability we employed a mouse model to control host genotype, diet and other possible influences on the microbiota. This allowed us to determine if the indigenous microbiota in such mice had a stable baseline community structure and whether this community exhibited a consistent response following antibiotic administration. We employed a tag sequencing strategy targeting the V6 hypervariable region of the bacterial small-subunit (16S) ribosomal RNA combined with massively parallel sequencing to determine the community structure of the gut microbiota. Inbred mice in a controlled environment harbored a reproducible baseline community that was significantly impacted by antibiotic administration. The ability of the gut microbial community to recover to baseline following cessation of antibiotic administration varied according to the antibiotic regimen administered. Severe antibiotic pressure resulted in reproducible long-lasting alterations in the gut microbial community including a decrease in overall diversity. The finding of stereotypic responses of the indigenous microbiota to ecologic stress implies that a better understanding of the factors that govern community structure could lead to strategies for the intentional manipulation of this ecosystem to preserve or restore a healthy microbiota.

Huse Susan M.

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