4.8 Article

Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biology

Genomic insights into versatile lifestyle of three new bacterial candidate phyla

Xinxu Zhang et al.

Summary: Metagenomic exploration of the ocean's Yap Trench led to the discovery of three new monophyletic bacterial lineages named Candidatus Qinglongiota, Candidatus Heilongiota, and Candidatus Canglongiota. The genomes of these new lineages suggest a versatile lifestyle and a preference for oxygen-limited or particle-attached environments. Evolutionary analysis indicated the importance of gene gain and loss events, as well as horizontal gene transfer, in shaping the genomic and metabolic features of these new phyla.

SCIENCE CHINA-LIFE SCIENCES (2022)

Article Microbiology

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

Zhichao Zhou et al.

Summary: Advances in microbiome science have been driven by the ability to study and infer microbial ecology from genomes. METABOLIC is a scalable software that allows for the study of microbial ecology and biogeochemistry using genomes at the resolution of individual organisms and/or microbial communities. It provides annotation of microbial genomes, metabolic pathway analyses, and determination of microbial contributions to biogeochemical transformations and cycles. METABOLIC is a versatile tool that can be used with various metagenomic datasets, from diverse environments such as marine subsurface, terrestrial subsurface, and human gut.

MICROBIOME (2022)

Article Gastroenterology & Hepatology

Hybrid, ultra-deep metagenomic sequencing enables genomic and functional characterization of low-abundance species in the human gut microbiome

Hao Jin et al.

Summary: This study utilized a new metagenomic sequencing approach to investigate the role of low-abundance species in the human gut microbiome. The researchers discovered a significant number of uncultured microbial genomes, as well as individual-specific genomic features.

GUT MICROBES (2022)

Article Biochemistry & Molecular Biology

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

Donovan H. Parks et al.

Summary: The Genome Taxonomy Database (GTDB) provides a phylogenetically consistent taxonomy for prokaryotic genomes sourced from the NCBI database. It includes a large number of bacterial and archaeal genomes, highlights the importance of metagenome-assembled genomes, and discusses improvements to the GTDB website and the procedure for updating species clusters.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemistry & Molecular Biology

KEGG mapping tools for uncovering hidden features in biological data

Minoru Kanehisa et al.

Summary: KEGG relies on human intelligence to develop biological system models through manually creating pathway maps. These models can be used in biological big data analysis to uncover systemic functions in an organism's genome.

PROTEIN SCIENCE (2022)

Article Multidisciplinary Sciences

The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments

Yosuke Nishimura et al.

Summary: The genomic repertoire of marine microorganisms is expanded through the collection and reconstruction of a large number of marine metagenomes, leading to the discovery of novel microbial lineages and a significant increase in known phylogenetic diversity.

SCIENTIFIC DATA (2022)

Article Biotechnology & Applied Microbiology

Improved metagenome binning and assembly using deep variational autoencoders

Jakob Nybo Nissen et al.

Summary: Despite recent advances in metagenomic binning, reconstruction of microbial species from metagenomics data remains challenging. Here we develop variational autoencoders for metagenomic binning (VAMB), a program that outperforms existing state-of-the-art binners in reconstructing near-complete genomes on simulated and real data. VAMB is able to separate closely related strains with high accuracy and showcase different geographical distribution patterns of human gut microbiome species.

NATURE BIOTECHNOLOGY (2021)

Article Microbiology

Marine sediments harbor diverse archaea and bacteria with the potential for anaerobic hydrocarbon degradation via fumarate addition

Chuwen Zhang et al.

Summary: This study identified diverse bacterial and archaeal lineages involved in anaerobic degradation of alkanes and methylated aromatic hydrocarbons in marine sediments, including the presence of fumarate-adding enzymes (FAE). These microorganisms, found in hydrocarbon-impacted sediments, potentially degrade hydrocarbons through sulfate reduction or fermentation, expanding our understanding of the ecological roles of these organisms in marine ecosystems.

FEMS MICROBIOLOGY ECOLOGY (2021)

Article Biotechnology & Applied Microbiology

High-Level Diversity of Basal Fungal Lineages and the Control of Fungal Community Assembly by Stochastic Processes in Mangrove Sediments

Zhi-Feng Zhang et al.

Summary: This study highlights the high diversity of fungal communities in mangroves in eastern to southern China, with the presence of previously unreported basal fungal lineages. Dispersal limitation plays a crucial role in shaping fungal communities in mangrove sediments, while environmental selection has a minor impact. Network analysis revealed highly modular co-occurrence patterns in fungal communities in mangrove sediments.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2021)

Letter Biochemistry & Molecular Biology

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

Mose Manni et al.

Summary: The BUSCO software provides essential methods for assessing the quality of genomic and metagenomic data, offering new functionalities and improvements to streamline the process. It is capable of evaluating both eukaryotic and prokaryotic species, and can be used across various data types including genome assemblies, metagenomic bins, transcriptomes, and gene sets.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Microbiology

A standardized archaeal taxonomy for the Genome Taxonomy Database

Christian Rinke et al.

Summary: The study proposes a standardized archaeal taxonomy derived from a 122-concatenated-protein phylogeny, resolving polyphyletic groups and normalizing ranks. This taxonomy is based on 2,392 archaeal genomes, identifying 16 archaeal phyla and reclassifying major monophyletic units. Rank normalization corrects for up to 30-fold substitution rate variations and addresses incomplete and uneven archaeal classifications through a genome-based approach.

NATURE MICROBIOLOGY (2021)

Article Microbiology

Biogeography, Assembly Patterns, Driving Factors, and Interactions of Archaeal Community in Mangrove Sediments

Zhi-Feng Zhang et al.

Summary: This study systematically analyzed the biogeography, assembly patterns, and driving factors of archaeal communities in seven representative mangroves across southeastern China. The results showed that archaeal communities in mangroves vary in diversity based on latitude and depth, with influences from homogeneous selection and stochastic processes.

MSYSTEMS (2021)

Article Biotechnology & Applied Microbiology

Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep

Ping Chen et al.

Summary: Using deep metagenomics approach, a study on the microbial communities in the sediment of the Challenger Deep in the Mariana Trench revealed new insights into the structure and function of the hadal microbiome. The study also discovered a diverse range of new bacterial and fungal species through large-scale cultivation. This research fills in knowledge gaps and provides valuable information on the ecology and metabolism of eukaryotic and viral components in the deepest biosphere on earth.

GENOME BIOLOGY (2021)

Review Marine & Freshwater Biology

Diversity, metabolism and cultivation of archaea in mangrove ecosystems

Cui-Jing Zhang et al.

Summary: Archaea in mangroves play essential roles in biogeochemical cycles and are crucial for carbon, nitrogen, and sulfur cycling. Innovative cultivation strategies, such as single-cell isolation and high-throughput culturing, provide more opportunities to study previously uncultured archaeal lineages in mangrove wetlands.

MARINE LIFE SCIENCE & TECHNOLOGY (2021)

Article Biochemistry & Molecular Biology

Pfam: The protein families database in 2021

Jaina Mistry et al.

Summary: The Pfam database has recently added a large number of protein families and domains, made revisions for COVID-19 research, and introduced Pfam-B as a supplement. These updates and improvements can help researchers classify protein sequences more effectively and conduct related studies.

NUCLEIC ACIDS RESEARCH (2021)

Review Biochemical Research Methods

New approaches for metagenome assembly with short reads

Martin Ayling et al.

BRIEFINGS IN BIOINFORMATICS (2020)

Article Biochemistry & Molecular Biology

KEGG Mapper for inferring cellular functions from protein sequences

Minoru Kanehisa et al.

PROTEIN SCIENCE (2020)

Article Biochemical Research Methods

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

Pierre-Alain Chaumeil et al.

BIOINFORMATICS (2020)

Article Biochemical Research Methods

NextPolish: a fast and efficient genome polishing tool for long-read assembly

Jiang Hu et al.

BIOINFORMATICS (2020)

Article Environmental Sciences

Exploring the genetic potential of a fosmid metagenomic library from an oil impacted mangrove sediment for metabolism of aromatic compounds

Sanderson Tarciso Pereira de Sousa et al.

ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY (2020)

Article Biochemistry & Molecular Biology

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Bui Quang Minh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Biotechnology & Applied Microbiology

Complete, closed bacterial genomes from microbiomes using nanopore sequencing

Eli L. Moss et al.

NATURE BIOTECHNOLOGY (2020)

Article Biotechnology & Applied Microbiology

A complete domain-to-species taxonomy for Bacteria and Archaea

Donovan H. Parks et al.

NATURE BIOTECHNOLOGY (2020)

Article Microbiology

Roadmap for naming uncultivated Archaea and Bacteria

Alison E. Murray et al.

NATURE MICROBIOLOGY (2020)

Article Multidisciplinary Sciences

Assembly methods for nanopore-based metagenomic sequencing: a comparative study

Adriel Latorre-Perez et al.

SCIENTIFIC REPORTS (2020)

Article Biochemical Research Methods

metaFlye: scalable long-read metagenome assembly using repeat graphs

Mikhail Kolmogorov et al.

NATURE METHODS (2020)

Article Biotechnology & Applied Microbiology

Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale

Wei Zhuang et al.

NPJ BIOFILMS AND MICROBIOMES (2020)

Article Biotechnology & Applied Microbiology

The importance of designating type material for uncultured taxa

Maria Chuvochina et al.

SYSTEMATIC AND APPLIED MICROBIOLOGY (2019)

Review Genetics & Heredity

Clinical metagenomics

Charles Y. Chiu et al.

NATURE REVIEWS GENETICS (2019)

Article Biochemistry & Molecular Biology

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

Ivica Letunic et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biotechnology & Applied Microbiology

Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

Robert D. Stewart et al.

NATURE BIOTECHNOLOGY (2019)

Article Biotechnology & Applied Microbiology

Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing

Sarah Goldstein et al.

BMC GENOMICS (2019)

Article Biotechnology & Applied Microbiology

OrthoFinder: phylogenetic orthology inference for comparative genomics

David M. Emms et al.

GENOME BIOLOGY (2019)

Article Biochemical Research Methods

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

Kazutaka Katoh et al.

BRIEFINGS IN BIOINFORMATICS (2019)

Article Biotechnology & Applied Microbiology

Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation

John Beaulaurier et al.

NATURE BIOTECHNOLOGY (2018)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Editorial Material Biochemistry & Molecular Biology

Using Metagenomics to Characterize an Expanding Virosphere

Yong-Zhen Zhang et al.

Review Ecology

Decomposition as a regulator of carbon accretion in mangroves: a review

Shantelle D. Friesen et al.

ECOLOGICAL ENGINEERING (2018)

Article Biochemistry & Molecular Biology

Genome-reconstruction for eukaryotes from complex natural microbial communities

Patrick T. West et al.

GENOME RESEARCH (2018)

Article Biochemistry & Molecular Biology

GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes

Joel A. Boyd et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

Han Zhang et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Multidisciplinary Sciences

Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes

Panagiotis S. Adam et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Multidisciplinary Sciences

Genome-centric view of carbon processing in thawing permafrost

Ben J. Woodcroft et al.

NATURE (2018)

Article Biotechnology & Applied Microbiology

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

Donovan H. Parks et al.

NATURE BIOTECHNOLOGY (2018)

Software Review Microbiology

MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis

Gherman V. Uritskiy et al.

MICROBIOME (2018)

Review Microbiology

Bathyarchaeota: globally distributed metabolic generalists in anoxic environments

Zhichao Zhou et al.

FEMS MICROBIOLOGY REVIEWS (2018)

Article Biochemistry & Molecular Biology

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

Sergey Koren et al.

GENOME RESEARCH (2017)

Article Ecology

Uncultivated microbes in need of their own taxonomy

Konstantinos T. Konstantinidis et al.

ISME JOURNAL (2017)

Article Microbiology

Metagenomic alkaline protease from mangrove sediment

Tharcilla B. A. Pessoa et al.

JOURNAL OF BASIC MICROBIOLOGY (2017)

Article Biochemical Research Methods

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software

Alexander Sczyrba et al.

NATURE METHODS (2017)

Review Microbiology

Virus taxonomy in the age of metagenomics

Peter Simmonds et al.

NATURE REVIEWS MICROBIOLOGY (2017)

Article Biochemical Research Methods

MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis

Joao F. Matias Rodrigues et al.

BIOINFORMATICS (2017)

Review Chemistry, Analytical

Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

Leighton Pritchard et al.

ANALYTICAL METHODS (2016)

Review Biochemistry & Molecular Biology

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

Minoru Kanehisa et al.

JOURNAL OF MOLECULAR BIOLOGY (2016)

Review Genetics & Heredity

Coming of age: ten years of next-generation sequencing technologies

Sara Goodwin et al.

NATURE REVIEWS GENETICS (2016)

Article Biochemistry & Molecular Biology

Heatmapper: web-enabled heat mapping for all

Sasha Babicki et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Multidisciplinary Sciences

Fast and sensitive taxonomic classification for metagenomics with Kaiju

Peter Menzel et al.

NATURE COMMUNICATIONS (2016)

Article Multidisciplinary Sciences

HydDB: A web tool for hydrogenase classification and analysis

Dan Sondergaard et al.

SCIENTIFIC REPORTS (2016)

Article Biochemistry & Molecular Biology

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Donovan H. Parks et al.

GENOME RESEARCH (2015)

Article Multidisciplinary Sciences

Complete nitrification by a single microorganism

Maartje A. H. J. van Kessel et al.

NATURE (2015)

Article Biochemical Research Methods

Fast and sensitive protein alignment using DIAMOND

Benjamin Buchfink et al.

NATURE METHODS (2015)

Review Geochemistry & Geophysics

Carbon Cycling and Storage in Mangrove Forests

Daniel M. Alongi

ANNUAL REVIEW OF MARINE SCIENCE, VOL 6 (2014)

Article Biochemistry & Molecular Biology

MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

Chengwei Luo et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

TIGRFAMs and Genome Properties in 2013

Daniel H. Haft et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biochemistry & Molecular Biology

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Christian Quast et al.

NUCLEIC ACIDS RESEARCH (2013)

Review Microbiology

Genomic Insights into Syntrophy: The Paradigm for Anaerobic Metabolic Cooperation

Jessica R. Sieber et al.

ANNUAL REVIEW OF MICROBIOLOGY, VOL 66 (2012)

Review Biotechnology & Applied Microbiology

Dissimilatory Reduction of Extracellular Electron Acceptors in Anaerobic Respiration

Katrin Richter et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Multidisciplinary Sciences

The Microbiome of Brazilian Mangrove Sediments as Revealed by Metagenomics

Fernando Dini Andreote et al.

PLOS ONE (2012)

Review Microbiology

Alternative Pathways of Carbon Dioxide Fixation: Insights into the Early Evolution of Life?

Georg Fuchs

ANNUAL REVIEW OF MICROBIOLOGY, VOL 65 (2011)

Article Geosciences, Multidisciplinary

Mangroves among the most carbon-rich forests in the tropics

Daniel C. Donato et al.

NATURE GEOSCIENCE (2011)

Review Microbiology

Microbial Ecology of the Dark Ocean above, at, and below the Seafloor

Beth N. Orcutt et al.

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2011)

Article Biochemistry & Molecular Biology

HMMER web server: interactive sequence similarity searching

Robert D. Finn et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemical Research Methods

Prodigal: prokaryotic gene recognition and translation initiation site identification

Doug Hyatt et al.

BMC BIOINFORMATICS (2010)

Article Engineering, Environmental

Fungal and bacterial mediated denitrification in wetlands: Influence of sediment redox condition

Dong Cheol Seo et al.

WATER RESEARCH (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

BLAST plus : architecture and applications

Christiam Camacho et al.

BMC BIOINFORMATICS (2009)

Article Microbiology

Enzymology of the Wood-Ljungdahl pathway of acetogenesis

Stephen W. Ragsdale

INCREDIBLE ANAEROBES: FROM PHYSIOLOGY TO GENOMICS TO FUELS (2008)

Review Biochemistry & Molecular Biology

Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation

Stephen W. Ragsdale et al.

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2008)

Editorial Material Microbiology

The microbial nitrogen cycle

Mike S. M. Jetten

ENVIRONMENTAL MICROBIOLOGY (2008)

Editorial Material Multidisciplinary Sciences

Microbiology - Metagenomics

Philip Hugenholtz et al.

NATURE (2008)

Review Microbiology

Symbiotic diversity in marine animals: the art of harnessing chemosynthesis

Nicole Dubilier et al.

NATURE REVIEWS MICROBIOLOGY (2008)

Editorial Material Multidisciplinary Sciences

Perspective - Synteny and collinearity in plant genomes

Haibao Tang et al.

SCIENCE (2008)

Article Plant Sciences

Catalysis and regulation in Rubisco

Inger Andersson

JOURNAL OF EXPERIMENTAL BOTANY (2008)

Review Microbiology

Genetic regulation of biological nitrogen fixation

R Dixon et al.

NATURE REVIEWS MICROBIOLOGY (2004)

Article Biochemistry & Molecular Biology

Mauve: Multiple alignment of conserved genomic sequence with rearrangements

ACE Darling et al.

GENOME RESEARCH (2004)

Review Microbiology

Classification and phylogeny of hydrogenases

PM Vignais et al.

FEMS MICROBIOLOGY REVIEWS (2001)

Review Microbiology

Novel forms of anaerobic respiration of environmental relevance

DR Lovley et al.

CURRENT OPINION IN MICROBIOLOGY (2000)

Article Biochemistry & Molecular Biology

KEGG: Kyoto Encyclopedia of Genes and Genomes

M Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2000)