Error filtering, pair assembly and error correction for next-generation sequencing reads

Bioinformatics, Год журнала: 2015, Номер 31(21), С. 3476 - 3482

Опубликована: Июль 2, 2015

Abstract Motivation: Next-generation sequencing produces vast amounts of data with errors that are difficult to distinguish from true biological variation when coverage is low. Results: We demonstrate large reductions in error frequencies, especially for high-error-rate reads, by three independent means: (i) filtering reads according their expected number errors, (ii) assembling overlapping read pairs and (iii) amplicon exploiting unique sequence abundances perform correction. also show most published paired assemblers calculate incorrect posterior quality scores. Availability implementation: These methods implemented the USEARCH package. Binaries freely available at http://drive5.com/usearch. Contact: [email protected] Supplementary information: Bioinformatics online.

Язык: Английский

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Diversity, structure and convergent evolution of the global sponge microbiome

Nature Communications, Год журнала: 2016, Номер 7(1)

Опубликована: Июнь 16, 2016

Abstract Sponges (phylum Porifera) are early-diverging metazoa renowned for establishing complex microbial symbioses. Here we present a global Porifera microbiome survey, set out to establish the ecological and evolutionary drivers of these host–microbe interactions. We show that sponges reservoir exceptional diversity major contributors total world’s oceans. Little commonality in species composition or structure is evident across phylum, although symbiont communities characterized by specialists generalists rather than opportunists. Core sponge microbiomes stable generalist symbionts exhibiting amensal and/or commensal Symbionts phylogenetically unique do not disproportionally contribute core microbiome, host phylogeny impacts complexity community. Our findings support model independent assembly evolution entire with convergent forces resulting analogous community organization

Язык: Английский

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Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

The ISME Journal, Год журнала: 2014, Номер 9(4), С. 968 - 979

Опубликована: Окт. 17, 2014

Abstract Molecular microbial ecology investigations often employ large marker gene datasets, for example, ribosomal RNAs, to represent the occurrence of single-cell genomes in communities. Massively parallel DNA sequencing technologies enable extensive surveys libraries that sometimes include nearly identical sequences. Computational approaches rely on pairwise sequence alignments similarity assessment and de novo clustering with facto thresholds partition high-throughput datasets constrain fine-scale resolution descriptions Minimum Entropy Decomposition (MED) provides a computationally efficient means into ‘MED nodes’, which homogeneous operational taxonomic units. By employing Shannon entropy, MED uses only information-rich nucleotide positions across reads iteratively partitions while omitting stochastic variation. When applied analyses microbiomes from two deep-sea cryptic sponges Hexadella dedritifera Hexadellacf. dedritifera, resolved key Gammaproteobacteria cluster multiple nodes are specific different sponges, revealed these closely related sympatric sponge species maintain distinct analysis previously published human oral microbiome dataset also taxa separated by less than 1% variation distributed niches cavity. The information theory-guided decomposition process behind algorithm enables sensitive discrimination organisms amplicon without relying computational heuristics user supervision.

Язык: Английский

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Oligotyping analysis of the human oral microbiome

Proceedings of the National Academy of Sciences, Год журнала: 2014, Номер 111(28)

Опубликована: Июнь 25, 2014

The Human Microbiome Project provided a census of bacterial populations in healthy individuals, but an understanding the biomedical significance this has been hindered by limited taxonomic resolution. A high-resolution method termed oligotyping overcomes limitation evaluating individual nucleotide positions using Shannon entropy to identify most information-rich positions, which then define oligotypes. We have applied comprehensively analyze oral microbiome. Using 16S rRNA gene sequence data for nine sites cavity, we identified 493 oligotypes from V1-V3 and 360 V3-V5 data. associated these with species-level taxon names comparison Oral Database. discovered closely related oligotypes, differing sometimes as little single nucleotide, that showed dramatically different distributions among individuals. also detected potentially pathogenic taxa high abundance samples. Numerous were preferentially located plaque, others keratinized gingiva or buccal mucosa, some characteristic habitat groupings such throat, tonsils, tongue dorsum, hard palate, saliva. suggest level ecological functional biodiversity not previously recognized. conclude approach capacity entire microbiomes, discriminate between distinct and, combination analysis, provide deep insight into microbial communities health disease.

Язык: Английский

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The Sponge Hologenome

mBio, Год журнала: 2016, Номер 7(2)

Опубликована: Апрель 22, 2016

A paradigm shift has recently transformed the field of biological science; molecular advances have revealed how fundamentally important microorganisms are to many aspects a host's phenotype and evolution. In process, an era "holobiont" research emerged investigate intricate network interactions between host its symbiotic microbial consortia. Marine sponges early-diverging metazoa known for hosting dense, specific, often highly diverse communities. Here we synthesize current thoughts about environmental evolutionary forces that influence diversity, specificity, distribution symbionts within sponge holobiont, explore physiological pathways contribute holobiont function, describe mechanisms underpin establishment maintenance these partnerships. The collective genomes form hologenome, highlight define sponge's in fact act on genomic interplay different components holobiont.

Язык: Английский

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Making a microbiome: the many determinants of host-associated microbial community composition

Current Opinion in Microbiology, Год журнала: 2016, Номер 35, С. 23 - 29

Опубликована: Ноя. 28, 2016

Язык: Английский

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An introduction to phylosymbiosis

Proceedings of the Royal Society B Biological Sciences, Год журнала: 2020, Номер 287(1922), С. 20192900 - 20192900

Опубликована: Март 4, 2020

Phylosymbiosis was recently formulated to support a hypothesis-driven framework for the characterization of new, cross-system trend in host-associated microbiomes. Defining phylosymbiosis as ‘microbial community relationships that recapitulate phylogeny their host’, we review relevant literature and data last decade, emphasizing frequently used methods regular patterns observed analyses. Quantitative is provided by statistical evaluating higher microbiome variation between host species than within species, topological similarities dendrogram, positive association genetic beta diversity. Significant degrees are prevalent, but not universal, microbiomes plants animals from terrestrial aquatic habitats. Consistent with natural selection shaping phylosymbiosis, transplant experiments demonstrate reduced performance and/or fitness upon host–microbiome mismatches. Hybridization can also disrupt phylosymbiotic cause hybrid pathologies. The pervasiveness carries several important implications advancing knowledge eco-evolutionary processes impact interactions future applications precision microbiology. Important steps will be examine beyond bacterial communities, apply evolutionary modelling an increasingly sophisticated understanding unravel microbial mechanisms contribute pattern. This serves gateway experimental, conceptual quantitative themes outlines opportunities ripe investigation diversity disciplines.

Язык: Английский

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Community assembly of a euryhaline fish microbiome during salinity acclimation

Molecular Ecology, Год журнала: 2015, Номер 24(10), С. 2537 - 2550

Опубликована: Март 29, 2015

Abstract Microbiomes play a critical role in promoting range of host functions. Microbiome function, turn, is dependent on its community composition. Yet, how microbiome taxa are assembled from their regional species pool remains unclear. Many possible drivers have been hypothesized, including deterministic processes competition, stochastic colonization and migration, physiological ‘host‐effect’ habitat filters. The contribution each to assembly nascent or perturbed microbiomes important for understanding host–microbe interactions health. In this study, we characterized the bacterial communities euryhaline fish surrounding tank water during salinity acclimation. To assess relative influence versus assembly, manipulated around by changing aquarium water. Our results show complete repeatable turnover dominant individuals same after acclimation salinity. We that changes not correlated with corresponding abundant rare aquatic surroundings, vice versa . suggest best able compete within unique environment at given appropriate most niche space, independent abundance communities. experiment, appear drive little evidence colonization.

Язык: Английский

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Evaluating the core microbiota in complex communities: A systematic investigation

Environmental Microbiology, Год журнала: 2017, Номер 19(4), С. 1450 - 1462

Опубликована: Янв. 12, 2017

Summary The study of complex microbial communities poses unique conceptual and analytical challenges, with species potentially numbering in the thousands. With transient or allochthonous microorganisms often adding to this complexity, a ‘core’ microbiota approach, focusing only on stable permanent members community, is becoming increasingly popular. Given various ways defining core microbiota, it prudent examine whether definition impacts upon results obtained. Here we used marine sponge microbiotas undertook systematic evaluation degree which different factors define influenced conclusions. Significant differences alpha‐ beta‐diversity were detected using some but not all definitions. However, findings related host specificity environmental quality largely insensitive major changes definition. Furthermore, none applied definitions altered our perception ecological networks summarising interactions among bacteria within sponges. These suggest that, while care should still be taken interpretation, approach surprisingly robust, at least for comparing closely samples.

Язык: Английский

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Predicting the HMA-LMA Status in Marine Sponges by Machine Learning

Frontiers in Microbiology, Год журнала: 2017, Номер 8

Опубликована: Май 8, 2017

The dichotomy between high microbial abundance (HMA) and low (LMA) sponges has been observed in sponge-microbe symbiosis, although the extent of this pattern remains poorly unknown. We characterized differences microbiomes HMA (n = 19) LMA 17) (575 specimens) present Sponge Microbiome Project. were associated with richer more diverse than sponges, as indicated by comparison alpha diversity metrics. Microbial community structures differed considering Operational Taxonomic Units (OTU) abundances across taxonomic levels, from phylum to species. largest proportion microbiome variation was explained host identity. Several phyla, classes, OTUs found differentially abundant either group, which considered "HMA indicators" "LMA indicators." Machine learning algorithms (classifiers) trained predict HMA-LMA status sponges. Among nine different classifiers, higher performances achieved Random Forest class abundances. optimized parameters predicted additional 135 sponge species (1,232 without a priori knowledge. These grouped four clusters, two composed consistently 44) 74). In summary, our analyses shown distinct features communities prediction based on profiles demonstrates application machine explore patterns host-associated communities.

Язык: Английский

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