Parallelization of MAFFT for large-scale multiple sequence alignments

Bioinformatics, Journal Year: 2018, Volume and Issue: 34(14), P. 2490 - 2492

Published: Feb. 28, 2018

Abstract Summary We report an update for the MAFFT multiple sequence alignment program to enable parallel calculation of large numbers sequences. The G-INS-1 option was recently reported have higher accuracy than other methods data, but this method has been impractical most large-scale analyses, due requirement computational resources. introduce a scalable variant, G-large-INS-1, which equivalent and is applicable 50 000 or more Availability implementation This feature available in versions 7.355 later at https://mafft.cbrc.jp/alignment/software/mpi.html. Supplementary information data are Bioinformatics online.

Language: Английский

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Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem

Microbiome, Journal Year: 2018, Volume and Issue: 6(1)

Published: Feb. 26, 2018

The 16S ribosomal RNA gene is the most widely used marker in microbial ecology. Counts of sequence variants, often PCR amplicons, are to estimate proportions bacterial and archaeal taxa communities. Because different organisms contain copy numbers (GCNs), variant counts biased towards clades with greater GCNs. Several tools have recently been developed for predicting GCNs using phylogenetic methods based on sequenced genomes, order correct these biases. However, accuracy those predictions has not independently assessed. Here, we systematically evaluate predictability across clades, ∼ 6,800 public genomes several methods. Further, assess predicted by three published (PICRUSt, CopyRighter, PAPRICA) over a wide range 635 communities from varied environments. We find that regardless method tested, could only be accurately limited fraction taxa, namely closely moderately related representatives (≲15% divergence rRNA gene). Consistent this observation, all considered exhibit low predictive when evaluated against completely some cases explaining less than 10% variance. Substantial disagreement was also observed between (R2<0.5) majority tested nearest taxon index (NSTI) communities, i.e., average distance genome, strong predictor agreement GCN prediction non-animal-associated samples, but moderate animal-associated samples. recommend correcting microbiome surveys default, unless OTUs sufficiently or need true OTU warrants additional noise introduced, so community profiles remain interpretable comparable studies.

Language: Английский

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Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling

Microbiome, Journal Year: 2019, Volume and Issue: 7(1)

Published: Nov. 7, 2019

Abstract Background Rhizosphere microbial communities are key regulators of plant performance, yet few studies have assessed the impact different management approaches on rhizosphere microbiomes major crops. shaped by interactions between agricultural and host selection processes, but often consider these factors individually rather than in combination. We tested impacts (M) effects (R) community structure co-occurrence networks maize roots collected from long-term conventionally organically managed maize-tomato agroecosystems. also explored interaction (M × R) how it diversity composition, differential abundance, indicator taxa, network structure, nitrogen-cycling processes. Results Host processes moderate influence communities, although bacteria fungi respond differently to management. found that plants recruit management-system-specific taxa shift N-cycling pathways rhizosphere, distinguishing this soil compartment bulk soil. conventional organic systems were more similar their respective soils, composition was affected both M R effects. In contrast, fungal only management, selection. Quantification six genes ( nifH , amoA [bacterial archaeal], nirK nrfA nosZ ) revealed abundance higher system. Conclusions Plant interacts with practices shape patterns, at least one process. Reframing research priorities better understand adaptive plant-microbe feedbacks include as a significant moderating outcomes could help guide plant-oriented strategies improve productivity agroecosystem sustainability.

Language: Английский

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Lack of detection of a human placenta microbiome in samples from preterm and term deliveries

Microbiome, Journal Year: 2018, Volume and Issue: 6(1)

Published: Oct. 30, 2018

Historically, the human womb has been thought to be sterile in healthy pregnancies, but this idea challenged by recent studies using DNA sequence-based methods, which have suggested that is colonized with bacteria. For example, analysis of from placenta samples yielded small proportions microbial sequences were proposed represent normal bacterial colonization. However, an our group showed no distinction between background negative controls and samples. Also supporting observation germ-free mammals can generated delivery neonates into a isolator, after remain germ-free, would seem provide strong data support sterility womb. To probe further investigate possible placental colonization associated spontaneous preterm birth, we carried out another study comparing microbiota 20 term deliveries. Both 16S rRNA marker gene sequencing shotgun metagenomic used characterize control We first quantified absolute amounts quantitative PCR (qPCR). As previous study, levels found low indistinguishable controls. Analysis did not yield microbiome distinct controls, either as work, or sequencing. Several types artifacts, including erroneous read classifications barcode misattribution, needed identified removed clarify point. Our findings do existence consistent microbiome, deliveries births.

Language: Английский

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Reintroducing mothur: 10 Years Later

Applied and Environmental Microbiology, Journal Year: 2019, Volume and Issue: 86(2)

Published: Nov. 8, 2019

More than 10 years ago, we published the paper describing mothur software package in Applied and Environmental Microbiology . Our goal was to create a comprehensive that allowed users analyze amplicon sequence data using most robust methods available. has helped lead community through ongoing sequencing revolution continues provide this service microbial ecology community.

Language: Английский

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Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages

Microbiome, Journal Year: 2018, Volume and Issue: 6(1)

Published: June 8, 2018

As a recently discovered member of the DPANN superphylum, Woesearchaeota account for wide diversity 16S rRNA gene sequences, but their ecology, evolution, and metabolism remain largely unknown. Here, we assembled 133 global clone libraries/studies 19 publicly available genomes to profile these patterns Woesearchaeota. Phylogenetic analysis shows high with 26 proposed subgroups this archaeal phylum, which are widely distributed in different biotopes primarily inland anoxic environments. Ecological ancestor state reconstruction specific reveal that oxic status environments is key factor driving distribution evolutionary A selective an adaptive colonization from can be supported by evidence presence ferredoxin-dependent pathways only not biotopes. Metabolic reconstructions support anaerobic heterotrophic lifestyle conspicuous metabolic deficiencies, suggesting requirement complementarity other microbes. Both lineage abundance co-occurrence network analyses across diverse confirmed complementation revealed potential syntrophic relationship between methanogens, modeling. If correct, may impact methanogenesis ecosystems. The findings provide ecological framework at scale indicate roles, especially methanogenesis.

Language: Английский

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A census-based estimate of Earth's bacterial and archaeal diversity

PLoS Biology, Journal Year: 2019, Volume and Issue: 17(2), P. e3000106 - e3000106

Published: Feb. 4, 2019

The global diversity of Bacteria and Archaea, the most ancient widespread forms life on Earth, is a subject intense controversy. This controversy stems largely from fact that existing estimates are entirely based theoretical models or extrapolations small biased data sets. Here, in an attempt to census bulk Earth's bacterial archaeal ("prokaryotic") clades estimate their overall richness, we analyzed over 1.7 billion 16S ribosomal RNA amplicon sequences V4 hypervariable region obtained 492 studies worldwide, covering multitude environments using multiple alternative primers. From this set, recovered 739,880 prokaryotic operational taxonomic units (OTUs, 16S-V4 gene clusters at 97% similarity), commonly used measure microbial richness. Using several statistical approaches, there exist globally about 0.8-1.6 million OTUs, which somewhere between 47%-96%, representing >99.98% cells. Consistent with conclusion, our set independently "recaptured" 91%-93% previous surveys, including PCR-independent metagenomic surveys. distribution relative OTU abundances consistent log-normal model observed larger organisms; total number OTUs predicted by also richness estimates. By combining ratio full-length versus partial-length (V4) sequence SILVA database, further 2.2-4.3 worldwide. When restricting analysis Americas, while controlling for studies, obtain similar as suggesting distributed. Qualitatively results other similarity thresholds (90%, 95%, 99%). Our constrain extent poorly quantified rare biosphere refute recent predictions trillions OTUs.

Language: Английский

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MiDAS 3: An ecosystem-specific reference database, taxonomy and knowledge platform for activated sludge and anaerobic digesters reveals species-level microbiome composition of activated sludge

Water Research, Journal Year: 2020, Volume and Issue: 182, P. 115955 - 115955

Published: May 28, 2020

The function of the microbiomes in wastewater treatment systems and anaerobic digesters is dictated by physiological activity their members complex interactions between them. Since functional traits are often conserved at low taxonomic ranks (genus, species, strain), high resolution classification crucial to understand role microbes any ecosystem. Here we present MiDAS 3, a comprehensive 16S rRNA gene reference database based on full-length amplicon sequence variants (FL-ASVs) derived from activated sludge digester Denmark. new proposes unique provisional names for all unclassified microorganisms down species level, providing much-needed tool microbiome research. 3 was used analyze 20 Danish plants with nutrient removal, sampled over 13 years. 50 most abundant belonged 42 genera, including 14 genera 'midas' name. Of those, have no known system, which highlights need more efforts towards elucidating important ecosystems. also forms backbone Field Guide – an online resource linking identity available data related importance. field guide contains complete list (>1800) (>4200) found Denmark, but relevant across world. linked information, where available, website provides possibility BLAST sequences against database. collaborative platform acting as knowledge repository, facilitating understanding ecosystem function.

Language: Английский

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Genetic risk for autoimmunity is associated with distinct changes in the human gut microbiome

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: Aug. 9, 2019

Susceptibility to many human autoimmune diseases is under strong genetic control by class II leukocyte antigen (HLA) allele combinations. These genes remain far the greatest risk factors in development of type 1 diabetes and celiac disease. Despite this, little known about HLA influences on composition gut microbiome, a potential source environmental influence Here, using general population cohort from All Babies Southeast Sweden study, we report that for developing autoimmunity associated with distinct changes microbiome. Both core microbiome beta diversity differ group genotype. In addition, protective haplotypes are bacterial genera Intestinibacter Romboutsia. Thus, cohorts valuable identifying triggers or may otherwise be masked control.

Language: Английский

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Mining microbes for mental health: Determining the role of microbial metabolic pathways in human brain health and disease

Neuroscience & Biobehavioral Reviews, Journal Year: 2021, Volume and Issue: 125, P. 698 - 761

Published: March 5, 2021

There is increasing knowledge regarding the role of microbiome in modulating brain and behaviour. Indeed, actions microbial metabolites are key for appropriate gut-brain communication humans. Among these metabolites, short-chain fatty acids, tryptophan, bile acid metabolites/pathways show strong preclinical evidence involvement various aspects function With identification neuroactive modules, new predictive tools can be applied to existing datasets. We identified 278 studies relating human microbiota-gut-brain axis which included sequencing data. This spanned across psychiatric neurological disorders with a small number also focused on normal behavioural development. consistent bioinformatics pipeline, thirty-five datasets were reanalysed from publicly available raw files remainder summarised collated. studies, we uncovered disease-related alterations metabolic pathways Alzheimer's Disease, schizophrenia, anxiety depression. Amongst that could not reanalysed, many technical limitations hindered discovery specific biomarkers microbes or conserved studies. Future warranted confirm our findings. propose guidelines future analysis increase reproducibility consistency within field.

Language: Английский

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