Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds

Exploring bacterial functionality in mangrove sediments and its capability to overcome anthropogenic activity

(2019) Simone Raposo Cotta et al.   MARINE POLLUTION BULLETIN

The Distribution of Tryptophan-Dependent Indole-3-Acetic Acid Synthesis Pathways in Bacteria Unraveled by Large-Scale Genomic Analysis

(2019) Pengfan Zhang et al.   MOLECULES

NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice

(2019) Jingying Zhang et al.   NATURE BIOTECHNOLOGY

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

High-throughput sequencing and analysis of microbial communities in the mangrove swamps along the coast of Beibu Gulf in Guangxi, China

(2019) Bin Gong et al.   Scientific Reports

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes

(2019) Cui-Jing Zhang et al.   mSystems

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

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

First Insights into the Microbiome of a Mangrove Tree Reveal Significant Differences in Taxonomic and Functional Composition among Plant and Soil Compartments

(2019) Witoon Purahong et al.   Microorganisms

Discovery of recombinases enables genome mining of cryptic biosynthetic gene clusters in Burkholderiales species

(2018) Xue Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences

(2018) Samuel C. Epstein et al.   Standards in Genomic Sciences

Lead Compounds from Mangrove-Associated Microorganisms

(2018) Elena Ancheeva et al.   Marine Drugs

Comparative mangrove metagenome reveals global prevalence of heavy metals and antibiotic resistome across different ecosystems

(2018) Madangchanok Imchen et al.   Scientific Reports

Mangrove Sediment Microbiome: Adaptive Microbial Assemblages and Their Routed Biogeochemical Processes in Yunxiao Mangrove National Nature Reserve, China

(2018) Xiaolan Lin et al.   MICROBIAL ECOLOGY

Rhizosphere microbiome structure alters to enable wilt resistance in tomato

(2018) Min-Jung Kwak et al.   NATURE BIOTECHNOLOGY

The structure and function of the global citrus rhizosphere microbiome

(2018) Jin Xu et al.   Nature Communications

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Safety evaluation of flexirubin from Chryseobacterium artocarpi CECT 8497: Acute, sub-acute toxicity and mutagenicity studies

(2017) Chidambaram Kulandaisamy Venil et al.   PROCESS SAFETY AND ENVIRONMENTAL PROTECTION

Compositions and Abundances of Sulfate-Reducing and Sulfur-Oxidizing Microorganisms in Water-Flooded Petroleum Reservoirs with Different Temperatures in China

(2017) Huimei Tian et al.   Frontiers in Microbiology

Taxonomic structure and functional association of foxtail millet root microbiome

(2017) Tao Jin et al.   GigaScience

Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing

(2017) Chao Fang et al.   GigaScience

SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data

(2017) Yuxin Chen et al.   GigaScience

Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome

(2017) Yunzeng Zhang et al.   Microbiome

Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems

(2017) Madangchanok Imchen et al.   Scientific Reports

Ectoine as a promising protective agent in humans and animals

(2016) Adam Bownik et al.   Arhiv za Higijenu Rada i Toksikologiju-Archives of Industrial Hygiene and Toxicology

Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea

(2016) Hanin Alzubaidy et al.   GENE

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

Potential for Sulfate Reduction in Mangrove Forest Soils: Comparison between Two Dominant Species of the Americas

(2016) Melike Balk et al.   Frontiers in Microbiology

Bacterial Communities in the Rhizospheres of Three Mangrove Tree Species from Beilun Estuary, China

(2016) Peng Wu et al.   PLoS One

Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley

(2015) Davide Bulgarelli et al.   Cell Host & Microbe

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

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

Spatiotemporal Analysis of Bacterial Diversity in Sediments of Sundarbans Using Parallel 16S rRNA Gene Tag Sequencing

(2014) Pijush Basak et al.   MICROBIAL ECOLOGY

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Niche and host-associated functional signatures of the root surface microbiome

(2014) Maya Ofek-Lalzar et al.   Nature Communications

Potential Role of Carotenoids as Antioxidants in Human Health and Disease

(2014) Joanna Fiedor et al.   Nutrients

Relating microbial community structure and environmental variables in mangrove sediments inside Rhizophora mangle L. habitats

(2013) Geórgia Barguil Colares et al.   APPLIED SOIL ECOLOGY

Microbial diversity in Brazilian mangrove sediments: a mini review

(2013) Angela Michelato Ghizelini et al.   BRAZILIAN JOURNAL OF MICROBIOLOGY

Illumina Sequencing of 16S rRNA Tag Revealed Spatial Variations of Bacterial Communities in a Mangrove Wetland

(2013) Xiao-Tao Jiang et al.   MICROBIAL ECOLOGY

GeoChip-based analysis of the functional gene diversity and metabolic potential of soil microbial communities of mangroves

(2012) Shijie Bai et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Structure, fluctuation and magnitude of a natural grassland soil metagenome

(2012) Tom O Delmont et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The Microbiome of Brazilian Mangrove Sediments as Revealed by Metagenomics

(2012) Fernando Dini Andreote et al.   PLoS One

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

(2012) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Organic carbon dynamics in mangrove ecosystems: A review

(2008) Erik Kristensen et al.   AQUATIC BOTANY