UCHIME improves sensitivity and speed of chimera detection

Edgar, Robert C.; Haas, Brian J.; Clemente, José C.; Quince, Christopher; Knight, Rob

doi:10.1093/bioinformatics/btr381

Cited by 13,006 publications

(8,666 citation statements)

References 19 publications

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“…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). Sequences assigned to chloroplasts, mitochondria, archaea, and eukaryotes were removed based on classification against the Greengenes database (release gg_13_8_99, McDonald et al., 2012).…”

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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“…All identical sequences were subsequently collapsed and representative sequences were retained via unique.seqs command in mothur . Chimera sequences were removed with uchime as implemented in mothur (Edgar et al ., 2011). …”

Section: Methodsmentioning

confidence: 99%

Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula

Ziegler

Arif

Burt

et al. 2017

Journal of Biogeography

142

130

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AimCoral reefs rely on the symbiosis between scleractinian corals and intracellular, photosynthetic dinoflagellates of the genus Symbiodinium making the assessment of symbiont diversity critical to our understanding of ecological resilience of these ecosystems. This study characterizes Symbiodinium diversity around the Arabian Peninsula, which contains some of the most thermally diverse and understudied reefs on Earth.LocationShallow water coral reefs throughout the Red Sea (RS), Sea of Oman (SO), and Persian/Arabian Gulf (PAG).MethodsNext‐generation sequencing of the ITS2 marker gene was used to assess Symbiodinium community composition and diversity comprising 892 samples from 46 hard and soft coral genera.ResultsCorals were associated with a large diversity of Symbiodinium, which usually consisted of one or two prevalent symbiont types and many types at low abundance. Symbiodinium communities were strongly structured according to geographical region and to a lesser extent by coral host identity. Overall symbiont communities were composed primarily of species from clade A and C in the RS, clade A, C, and D in the SO, and clade C and D in the PAG, representing a gradual shift from C‐ to D‐dominated coral hosts. The analysis of symbiont diversity in an Operational Taxonomic Unit (OTU)‐based framework allowed the identification of differences in symbiont taxon richness over geographical regions and host genera.Main conclusionsOur study represents a comprehensive overview over biogeography and molecular diversity of Symbiodinium in the Arabian Seas, where coral reefs thrive in one of the most extreme environmental settings on the planet. As such our data will serve as a baseline for further exploration into the effects of environmental change on host–symbiont pairings and the identification and ecological significance of Symbiodinium types from regions already experiencing ‘Future Ocean’ conditions.

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“…After the preliminary filtering process, the resulting sequences were denoised using the “pre.cluster” command (http://www.mothur.org/wiki/Pre.cluster) in MOTHUR. Chimera sequences were detected and removed by UCHIME (Edgar, Haas, Clemente, Quince, & Knight, 2011). To obtain the taxonomic assignments, all of the trimmed reads were clustered into OTUs with ≥97% similarity and aligned to the Greengenes database (McDonald et al., 2012) using the “claasify.seq” command in MOTHUR, with an 80% confidence threshold.…”

Section: Methodsmentioning

confidence: 99%

Diversity and resilience of the wood‐feeding higher termite Mironasutitermes shangchengensis gut microbiota in response to temporal and diet variations

Wang

Huang

et al. 2016

Ecology and Evolution

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Termites are considered among the most efficient bioreactors, with high capacities for lignocellulose degradation and utilization. Recently, several studies have characterized the gut microbiota of diverse termites. However, the temporal dynamics of the gut microbiota within a given termite with dietary diversity are poorly understood. Here, we employed 16S rDNA barcoded pyrosequencing analysis to investigate temporal changes in bacterial diversity and richness of the gut microbiota of wood‐feeding higher termite Mironasutitermes shangchengensis under three lignocellulose content‐based diets that feature wood, corn stalks, and filter paper. Compositions of the predominant termite gut residents were largely constant among the gut microbiomes under different diets, but each diet caused specific changes in the bacterial composition over time. Notably, microbial communities exhibited an unexpectedly strong resilience during continuous feeding on both corn stalks and filter paper. Members of five bacterial phyla, that is, Spirochaetes, Firmicutes, Actinobacteria, Tenericutes, and Acidobacteria, were strongly associated with the resilience. These findings provide insights into the stability of the gut microbiota in higher termites and have important implications for the future design of robust bioreactors for lignocellulose degradation and utilization.

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UCHIME improves sensitivity and speed of chimera detection

Cited by 13,006 publications

References 19 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

Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula

Diversity and resilience of the wood‐feeding higher termite Mironasutitermes shangchengensis gut microbiota in response to temporal and diet variations

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