Ironing out the wrinkles in the rare biosphere through improved OTU clustering

Huse, Susan M.; Welch, David B. Mark; Morrison, Hilary G.; Sogin, Mitchell L.

doi:10.1111/j.1462-2920.2010.02193.x

Cited by 1,203 publications

(1,127 citation statements)

References 30 publications

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“…This resulted in 12,041,000 sequences distributed over 36 coral fragments [3 coral replicates × 4 conditions (control vs. DOC; control vs. DON) × 3 time points] and 36 water samples [3 seawater replicates × 4 conditions (control vs. DOC; control vs. DON) × 3 time points]. Remaining sequences were aligned against the SILVA database (release 119; Pruesse et al., 2007)) and preclustered (2 bp difference; Huse, Welch, Morrison, & Sogin, 2010). Chimeric sequences were removed using the UCHIME command (Edgar et al., 2011).…”

Section: Methodsmentioning

confidence: 99%

Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome

Pogoreutz

Rädecker

Cárdenas

et al. 2018

Ecology and Evolution

120

112

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The importance of Symbiodinium algal endosymbionts and a diverse suite of bacteria for coral holobiont health and functioning are widely acknowledged. Yet, we know surprisingly little about microbial community dynamics and the stability of host‐microbe associations under adverse environmental conditions. To gain insight into the stability of coral host‐microbe associations and holobiont structure, we assessed changes in the community structure of Symbiodinium and bacteria associated with the coral Pocillopora verrucosa under excess organic nutrient conditions. Pocillopora‐associated microbial communities were monitored over 14 days in two independent experiments. We assessed the effect of excess dissolved organic nitrogen (DON) and excess dissolved organic carbon (DOC). Exposure to excess nutrients rapidly affected coral health, resulting in two distinct stress phenotypes: coral bleaching under excess DOC and severe tissue sloughing (>90% tissue loss resulting in host mortality) under excess DON. These phenotypes were accompanied by structural changes in the Symbiodinium community. In contrast, the associated bacterial community remained remarkably stable and was dominated by two Endozoicomonas phylotypes, comprising on average 90% of 16S rRNA gene sequences. This dominance of Endozoicomonas even under conditions of coral bleaching and mortality suggests the bacterial community of P. verrucosa may be rather inflexible and thereby unable to respond or acclimatize to rapid changes in the environment, contrary to what was previously observed in other corals. In this light, our results suggest that coral holobionts might occupy structural landscapes ranging from a highly flexible to a rather inflexible composition with consequences for their ability to respond to environmental change.

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Section: Methodsmentioning

confidence: 99%

Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome

Pogoreutz

Rädecker

Cárdenas

et al. 2018

Ecology and Evolution

120

112

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“…Resulting sequences were filtered for length, quality and chimera removal using the software package mothur (Schloss et al, 2009). High-quality sequences were subjected to operational taxonomic unit (OTU)-based clustering (Huse et al, 2010) and phylogenybased analysis using Fast UniFrac (Hamady et al, 2010) to evaluate the effects of host genetics on bacterial community composition. Details of sequencing and data processing steps are provided in the Supplementary Methods.…”

Section: Micementioning

confidence: 99%

Host genetic and environmental effects on mouse intestinal microbiota

et al. 2012

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The mammalian gut harbors complex and variable microbial communities, across both host phylogenetic space and conspecific individuals. A synergy of host genetic and environmental factors shape these communities and account for their variability, but their individual contributions and the selective pressures involved are still not well understood. We employed barcoded pyrosequencing of V1-2 and V4 regions of bacterial small subunit ribosomal RNA genes to characterize the effects of host genetics and environment on cecum assemblages in 10 genetically distinct, inbred mouse strains. Eight of these strains are the foundation of the Collaborative Cross (CC), a panel of mice derived from a genetically diverse set of inbred founder strains, designed specifically for complex trait analysis. Diversity of gut microbiota was characterized by complementing phylogenetic and distance-based, sequence-clustering approaches. Significant correlations were found between the mouse strains and their gut microbiota, reflected by distinct bacterial communities. Cohabitation and litter had a reduced, although detectable effect, and the microbiota response to these factors varied by strain. We identified bacterial phylotypes that appear to be discriminative and strainspecific to each mouse line used. Cohabitation of different strains of mice revealed an interaction of host genetic and environmental factors in shaping gut bacterial consortia, in which bacterial communities became more similar but retained strain specificity. This study provides a baseline analysis of intestinal bacterial communities in the eight CC progenitor strains and will be linked to integrated host genotype, phenotype and microbiota research on the resulting CC panel.

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“…Kunin et al (2009) argued that much of the diversity described in these initial studies was a result of sequencing error. The error rate of these methods after appropriate quality control procedures, however, is quite low (Huse et al, 2010). Reanalysis of these initial studies with new clustering methods that minimally inflate the number of operational taxonomic units (OTUs) report only slightly lower richness estimates with rank abundance curves that indicate a large abundance of rare taxa (Huse et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates

et al. 2012

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Much of the phylogenetic diversity in microbial systems arises from rare taxa that comprise the long tail of taxon rank distribution curves. This vast diversity presents a challenge to testing hypotheses about the effects of perturbations on microbial community composition because variability of rare taxa among environmental replicates may be sufficiently large that it would require a prohibitive degree of sequencing to discern differences between samples. In this study we used pyrosequencing of 16S rRNA tags to examine the diversity and within-site variability of salt marsh sediment bacteria. Our goal was to determine whether pyrosequencing could produce similar patterns in community composition among replicate environmental samples from the same location. We hypothesized that repeated sampling from the same location would produce different snapshots of the rare community due to incomplete sequencing of the taxonomically rich rare biosphere. We demonstrate that the salt marsh sediments we sampled contain a remarkably diverse array of bacterial taxa and, in contrast to our hypothesis, repeated sampling from within the same site produces reliably similar patterns in bacterial community composition, even among rare organisms. These results demonstrate that deep sequencing of 16s tags is well suited to distinguish sitespecific similarities and differences among rare taxa and is a valuable tool for hypothesis testing in microbial ecology.

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Ironing out the wrinkles in the rare biosphere through improved OTU clustering

Cited by 1,203 publications

References 30 publications

Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome

Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome

Host genetic and environmental effects on mouse intestinal microbiota

Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates

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