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Article ; Online: Terabase-scale metagenome coassembly with MetaHipMer

Steven Hofmeyr / Rob Egan / Evangelos Georganas / Alex C. Copeland / Robert Riley / Alicia Clum / Emiley Eloe-Fadrosh / Simon Roux / Eugene Goltsman / Aydın Buluç / Daniel Rokhsar / Leonid Oliker / Katherine Yelick

Scientific Reports, Vol 10, Iss 1, Pp 1-

2020 Volume 11

Abstract: Abstract Metagenome sequence datasets can contain terabytes of reads, too many to be coassembled together on a single shared-memory computer; consequently, they have only been assembled sample by sample (multiassembly) and combining the results is ... ...

Abstract	Abstract Metagenome sequence datasets can contain terabytes of reads, too many to be coassembled together on a single shared-memory computer; consequently, they have only been assembled sample by sample (multiassembly) and combining the results is challenging. We can now perform coassembly of the largest datasets using MetaHipMer, a metagenome assembler designed to run on supercomputers and large clusters of compute nodes. We have reported on the implementation of MetaHipMer previously; in this paper we focus on analyzing the impact of very large coassembly. In particular, we show that coassembly recovers a larger genome fraction than multiassembly and enables the discovery of more complete genomes, with lower error rates, whereas multiassembly recovers more dominant strain variation. Being able to coassemble a large dataset does not preclude one from multiassembly; rather, having a fast, scalable metagenome assembler enables a user to more easily perform coassembly and multiassembly, and assemble both abundant, high strain variation genomes, and low-abundance, rare genomes. We present several assemblies of terabyte datasets that could never be coassembled before, demonstrating MetaHipMer’s scaling power. MetaHipMer is available for public use under an open source license and all datasets used in the paper are available for public download.
Keywords	Medicine ; R ; Science ; Q
Subject code	004
Language	English
Publishing date	2020-07-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

Marc W. Van Goethem / Andrew R. Osborn / Benjamin P. Bowen / Peter F. Andeer / Tami L. Swenson / Alicia Clum / Robert Riley / Guifen He / Maxim Koriabine / Laura Sandor / Mi Yan / Chris G. Daum / Yuko Yoshinaga / Thulani P. Makhalanyane / Ferran Garcia-Pichel / Axel Visel / Len A. Pennacchio / Ronan C. O’Malley / Trent R. Northen

Communications Biology, Vol 4, Iss 1, Pp 1-

2021 Volume 10

Abstract: Marc Van Goethem et al. combine short- and long-read sequencing from biocrust samples to report nearly 3,000 biosynthetic gene clusters (BGCs) encoding microbial secondary metabolites. Their results demonstrate the advantage of integrated ... ...

Abstract	Marc Van Goethem et al. combine short- and long-read sequencing from biocrust samples to report nearly 3,000 biosynthetic gene clusters (BGCs) encoding microbial secondary metabolites. Their results demonstrate the advantage of integrated metatranscriptomic and long-read metagenomic sequencing in analyzing BGCs and provides insight into the role of secondary metabolites in maintaining phylogenetic niches in biocrusts.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A single-cell genomics pipeline for environmental microbial eukaryotes

iScience, Vol 24, Iss 4, Pp 102290- (2021)

2021

Abstract: Summary: Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key ... ...

Abstract	Summary: Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes.
Keywords	Genomics ; Geomicrobiology ; Microbiology ; Science ; Q
Subject code	333
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genetic determinants of endophytism in the Arabidopsis root mycobiome

Nature Communications, Vol 12, Iss 1, Pp 1-

2021 Volume 15

Abstract: Plant roots host diverse fungal communities that affect plant health. Here, Mesny et al. use comparative genomics and transcriptomics of fungal isolates from the Arabidopsis thaliana root mycobiota, together with root colonization assays, to identify ... ...

Abstract	Plant roots host diverse fungal communities that affect plant health. Here, Mesny et al. use comparative genomics and transcriptomics of fungal isolates from the Arabidopsis thaliana root mycobiota, together with root colonization assays, to identify genetic determinants of endophytism.
Keywords	Science ; Q
Language	English
Publishing date	2021-12-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies

Scientific Data, Vol 6, Iss 1, Pp 1-

2019 Volume 9

Abstract: Measurement(s)metagenomic data • sequence_assemblyTechnology Type(s)ONT MinION • Illumina sequencing • PacBio RS IIFactor Type(s)sequencing platformSample Characteristic - OrganismBacteriaSample Characteristic - Environmentmock community Machine- ... ...

Abstract	Measurement(s)metagenomic data • sequence_assemblyTechnology Type(s)ONT MinION • Illumina sequencing • PacBio RS IIFactor Type(s)sequencing platformSample Characteristic - OrganismBacteriaSample Characteristic - Environmentmock community Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.10260740
Keywords	Science ; Q
Language	English
Publishing date	2019-11-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Draft genome sequence of Actinotignum schaalii DSM 15541T

Atteyet F Yassin / Stefan Langenberg / Marcel Huntemann / Alicia Clum / Manoj Pillay / Krishnaveni Palaniappan / Neha Varghese / Natalia Mikhailova / Supratim Mukherjee / T B K Reddy / Chris Daum / Nicole Shapiro / Natalia Ivanova / Tanja Woyke / Nikos C Kyrpides

PLoS ONE, Vol 12, Iss 12, p e

Genetic insights into the lifestyle, cell fitness and virulence.

2017 Volume 0188914

Abstract: The permanent draft genome sequence of Actinotignum schaalii DSM 15541T is presented. The annotated genome includes 2,130,987 bp, with 1777 protein-coding and 58 rRNA-coding genes. Genome sequence analysis revealed absence of genes encoding for: ... ...

Abstract	The permanent draft genome sequence of Actinotignum schaalii DSM 15541T is presented. The annotated genome includes 2,130,987 bp, with 1777 protein-coding and 58 rRNA-coding genes. Genome sequence analysis revealed absence of genes encoding for: components of the PTS systems, enzymes of the TCA cycle, glyoxylate shunt and gluconeogensis. Genomic data revealed that A. schaalii is able to oxidize carbohydrates via glycolysis, the nonoxidative pentose phosphate and the Entner-Doudoroff pathways. Besides, the genome harbors genes encoding for enzymes involved in the conversion of pyruvate to lactate, acetate and ethanol, which are found to be the end products of carbohydrate fermentation. The genome contained the gene encoding Type I fatty acid synthase required for de novo FAS biosynthesis. The plsY and plsX genes encoding the acyltransferases necessary for phosphatidic acid biosynthesis were absent from the genome. The genome harbors genes encoding enzymes responsible for isoprene biosynthesis via the mevalonate (MVA) pathway. Genes encoding enzymes that confer resistance to reactive oxygen species (ROS) were identified. In addition, A. schaalii harbors genes that protect the genome against viral infections. These include restriction-modification (RM) systems, type II toxin-antitoxin (TA), CRISPR-Cas and abortive infection system. A. schaalii genome also encodes several virulence factors that contribute to adhesion and internalization of this pathogen such as the tad genes encoding proteins required for pili assembly, the nanI gene encoding exo-alpha-sialidase, genes encoding heat shock proteins and genes encoding type VII secretion system. These features are consistent with anaerobic and pathogenic lifestyles. Finally, resistance to ciprofloxacin occurs by mutation in chromosomal genes that encode the subunits of DNA-gyrase (GyrA) and topisomerase IV (ParC) enzymes, while resistant to metronidazole was due to the frxA gene, which encodes NADPH-flavin oxidoreductase.
Keywords	Medicine ; R ; Science ; Q
Subject code	572 ; 570
Language	English
Publishing date	2017-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Impact of Soil Salinity on the Cowpea Nodule-Microbiome and the Isolation of Halotolerant PGPR Strains to Promote Plant Growth under Salinity Stress

Salma Mukhtar / Ann M. Hirsch / Noor Khan / Kauser A. Malik / Ethan A. Humm / Matteo Pellegrini / Baochen Shi / Leah Briscoe / Marcel Huntemann / Alicia Clum / Brian Foster / Bryce Foster / Simon Roux / Krishnaveni Palaniappan / Neha Varghese / Supratim Mukherjee / T.B.K. Reddy / Chris Daum / Alex Copeland /

Natalia N. Ivanova / Nikos C. Kyrpides / Nicole Shapiro / Emiley A. Eloe-Fadrosh / Maskit Maymon / Muhammad S. Mirza / Samina Mehnaz

Phytobiomes Journal, Vol 4, Iss 4, Pp 364-

2020 Volume 374

Abstract: Cowpea is one of the major legumes cultivated in arid and semiarid regions of the world. Four soil-microbial samples (SS-1 through SS-4) collected from semiarid soils in Punjab, Pakistan were planted with cowpea (Vigna unguiculata) crops, which were ... ...

Abstract	Cowpea is one of the major legumes cultivated in arid and semiarid regions of the world. Four soil-microbial samples (SS-1 through SS-4) collected from semiarid soils in Punjab, Pakistan were planted with cowpea (Vigna unguiculata) crops, which were grown under salinity stress to analyze bacterial composition in the rhizosphere and within nodules using cultivation-dependent and -independent methods. Two varieties, 603 and the salt-tolerant CB 46, were each inoculated with or without the four different native soil samples or grown in medium either N-deficient (−N) or supplemented with N (+N). Plants inoculated with soil samples SS-2 and SS-4 grew better than plants inoculated with SS-1- and SS-3 and grew comparably with the +N controls. Environmental DNA (eDNA) was isolated from SS-1 and SS-4, and, by 16S ribosomal RNA sequencing, the soil microbiomes consisted mainly of Actinobacteria, Firmicutes, Proteobacteria, and other nonproteobacterial genera. However, analysis of eDNA isolated from cowpea nodules established by the trap plants showed that the nodule microbiome consisted almost exclusively of proteobacterial sequences, particularly species of Bradyrhizobium. Bacteria were isolated from both soils and nodules, and 34 of the 51 isolates tested positive for plant-growth-promoting rhizobacteria traits in plate assays. Many could serve as future inocula for crops in arid soils. The discrepancy between the types of bacteria isolated by culturing bacteria isolated from surface-sterilized cowpea nodules (proteobacteria and nonproteobacteria) versus those detected by sequencing DNA isolated from the nodules (proteobacteria) from cowpea nodules (proteobacteria and nonproteobacteria) versus those detected in the nodule microbiome (proteobacteria) needs further study.
Keywords	Plant culture ; SB1-1110 ; Microbial ecology ; QR100-130 ; Plant ecology ; QK900-989
Subject code	580
Language	English
Publishing date	2020-08-01T00:00:00Z
Publisher	The American Phytopathological Society
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades

Briana S. Abraham / Deniz Caglayan / Natalie V. Carrillo / Matthew C. Chapman / Claire T. Hagan / Skye T. Hansen / Ralph O. Jeanty / Alexander A. Klimczak / Marcos J. Klingler / Thomas P. Kutcher / Sydney H. Levy / Angel A. Millard-Bruzos / Thomas B. Moore / David J. Prentice / Matthew E. Prescott / Richard Roehm / Jordan A. Rose / Mulan Yin / Ayumi Hyodo /

Kathleen Lail / Christopher Daum / Alicia Clum / Alex Copeland / Rekha Seshadri / Tijana Glavina del Rio / Emiley A. Eloe-Fadrosh / Jonathan B. Benskin

Environmental Microbiome, Vol 15, Iss 1, Pp 1-

2020 Volume 10

Abstract: Abstract Background Currently, much is unknown about the taxonomic diversity and the mechanisms of methane metabolism in the Florida Everglades ecosystem. The Loxahatchee National Wildlife Refuge is a section of the Florida Everglades that is almost ... ...

Abstract	Abstract Background Currently, much is unknown about the taxonomic diversity and the mechanisms of methane metabolism in the Florida Everglades ecosystem. The Loxahatchee National Wildlife Refuge is a section of the Florida Everglades that is almost entirely unstudied in regard to taxonomic profiling. This short report analyzes the metagenome of soil samples from this Refuge to investigate the predominant taxa, as well as the abundance of genes involved in environmentally significant metabolic pathways related to methane production (nitrogen fixation and dissimilatory sulfite reduction). Methods Shotgun metagenomic sequencing using the Illumina platform was performed on 17 soil samples from four different sites within the Loxahatchee National Wildlife Refuge, and underwent quality control, assembly, and annotation. The soil from each sample was tested for water content and concentrations of organic carbon and nitrogen. Results The three most common phyla of bacteria for every site were Actinobacteria, Acidobacteria, and Proteobacteria; however, there was variation in relative phylum composition. The most common phylum of Archaea was Euryarchaeota for all sites. Alpha and beta diversity analyses indicated significant congruity in taxonomic diversity in most samples from Sites 1, 3, and 4 and negligible congruity between Site 2 and the other sites. Shotgun metagenomic sequencing revealed the presence of biogeochemical biomarkers of particular interest (e.g., mrcA, nifH, and dsrB) within the samples. The normalized abundances of mcrA, nifH, and dsrB exhibited a positive correlation with nitrogen concentration and water content, and a negative correlation with organic carbon concentration. Conclusion This Everglades soil metagenomic study allowed examination of wetlands biological processes and showed expected correlations between measured organic constituents and prokaryotic gene frequency. Additionally, the taxonomic profile generated gives a basis for the diversity of prokaryotic microbial life throughout the ...
Keywords	Shotgun metagenomics ; Methane production ; Nitrogen fixation ; Everglades ; Soil metagenome ; Prokaryotes ; Environmental sciences ; GE1-350 ; Microbiology ; QR1-502
Subject code	500
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot

Antonio Pedro Camargo / Rafael Soares Correa de Souza / Patrícia de Britto Costa / Isabel Rodrigues Gerhardt / Ricardo Augusto Dante / Grazielle Sales Teodoro / Anna Abrahão / Hans Lambers / Marcelo Falsarella Carazzolle / Marcel Huntemann / Alicia Clum / Brian Foster / Bryce Foster / Simon Roux / Krishnaveni Palaniappan / Neha Varghese / Supratim Mukherjee / T. B. K. Reddy / Chris Daum /

Alex Copeland / I.-Min A. Chen / Natalia N. Ivanova / Nikos C. Kyrpides / Christa Pennacchio / Emiley A. Eloe-Fadrosh / Paulo Arruda / Rafael Silva Oliveira

Scientific Data, Vol 6, Iss 1, Pp 1-

2019 Volume 11

Abstract: Design Type(s)strain comparison design • stimulus or stress designMeasurement Type(s)soil metagenomeTechnology Type(s)DNA sequencing • amplicon sequencingFactor Type(s)Sample Characteristic(s)plant metagenome • Brazil • soil • Vellozia epidendroides • ... ...

Abstract	Design Type(s)strain comparison design • stimulus or stress designMeasurement Type(s)soil metagenomeTechnology Type(s)DNA sequencing • amplicon sequencingFactor Type(s)Sample Characteristic(s)plant metagenome • Brazil • soil • Vellozia epidendroides • leaf • root • rhizosphere • stem • rock • Barbacenia Machine-accessible metadata file describing the reported data (ISA-Tab format)
Keywords	Science ; Q
Language	English
Publishing date	2019-07-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom

Brent Nowinski / Christa B. Smith / Courtney M. Thomas / Kaitlin Esson / Roman Marin / Christina M. Preston / James M. Birch / Christopher A. Scholin / Marcel Huntemann / Alicia Clum / Brian Foster / Bryce Foster / Simon Roux / Krishnaveni Palaniappan / Neha Varghese / Supratim Mukherjee / T. B. K. Reddy / Chris Daum / Alex Copeland /

I.-Min A. Chen / Natalia N. Ivanova / Nikos C. Kyrpides / Tijana Glavina del Rio / William B. Whitman / Ronald P. Kiene / Emiley A. Eloe-Fadrosh / Mary Ann Moran

Scientific Data, Vol 6, Iss 1, Pp 1-

2019 Volume 7

Abstract: Design Type(s)transcription profiling design • sequence assembly objective • biodiversity assessment objectiveMeasurement Type(s)transcription profiling assay • marine metagenome • microbial communityTechnology Type(s)RNA sequencing • DNA sequencing • ... ...

Abstract	Design Type(s)transcription profiling design • sequence assembly objective • biodiversity assessment objectiveMeasurement Type(s)transcription profiling assay • marine metagenome • microbial communityTechnology Type(s)RNA sequencing • DNA sequencing • amplicon sequencingFactor Type(s)assay protocol • temporal_instantSample Characteristic(s)marine metagenome • Monterey Bay • ocean biome Machine-accessible metadata file describing the reported data (ISA-Tab format)
Keywords	Science ; Q
Language	English
Publishing date	2019-07-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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