Shotgun metagenomic sequencing from Manao-Pee cave, Thailand, reveals insight into the microbial community structure and its metabolic potential

Methanogenesis

(2018) Zhe Lyu et al.   CURRENT BIOLOGY

Bacterial Diversity and Phylogenetic Analysis of Type II Polyketide Synthase Gene from Manao-Pee Cave, Thailand

(2018) Apirak Wiseschart et al.   GEOMICROBIOLOGY JOURNAL

Evaluating the Information Content of Shallow Shotgun Metagenomics

(2018) Benjamin Hillmann et al.   mSystems

Biodegradation of polyethylene by bacterial strains isolated from Kashmir Cave, Buner, Pakistan

(2017) Syed Umair ullah Jamil et al.   JOURNAL OF CAVE AND KARST STUDIES

Paulomycin G, a New Natural Product with Cytotoxic Activity against Tumor Cell Lines Produced by Deep-Sea Sediment Derived Micromonospora matsumotoense M-412 from the Avilés Canyon in the Cantabrian Sea

(2017) Aida Sarmiento-Vizcaíno et al.   Marine Drugs

Actinomycetes: still a source of novel antibiotics

(2017) Olga Genilloud   NATURAL PRODUCT REPORTS

Seasonal total methane depletion in limestone caves

(2017) Chris L. Waring et al.   Scientific Reports

Assessment of the Potential Role of Streptomyces in Cave Moonmilk Formation

(2017) Marta Maciejewska et al.   Frontiers in Microbiology

Plant growth-promoting actinobacteria: a new strategy for enhancing sustainable production and protection of grain legumes

(2017) Arumugam Sathya et al.   3 Biotech

Plant growth-promoting actinobacteria: a new strategy for enhancing sustainable production and protection of grain legumes

(2017) Arumugam Sathya et al.   3 Biotech

Actinobacterial Rare Biospheres and Dark Matter Revealed in Habitats of the Chilean Atacama Desert

(2017) Hamidah Idris et al.   Scientific Reports

Biotechnological potential of Actinobacteria from Canadian and Azorean volcanic caves

(2016) Cristina Riquelme et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

(2016) Ravi Ranjan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Metagenome-scale analysis yields insights into the structure and function of microbial communities in a copper bioleaching heap

(2016) Xian Zhang et al.   BMC GENETICS

Metabolic versatility of microbial methane oxidation for biocatalytic methane conversion

(2016) Taek Jin Kang et al.   JOURNAL OF INDUSTRIAL AND ENGINEERING CHEMISTRY

Novel insights into the origin and diversification of photosynthesis based on analyses of conserved indels in the core reaction center proteins

(2016) Bijendra Khadka et al.   PHOTOSYNTHESIS RESEARCH

Vikodak - A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets

(2016) Sunil Nagpal et al.   PLoS One

Natural Products as a Source for Novel Antibiotics

(2016) Mark G. Moloney   TRENDS IN PHARMACOLOGICAL SCIENCES

A Phenotypic and Genotypic Analysis of the Antimicrobial Potential of Cultivable Streptomyces Isolated from Cave Moonmilk Deposits

(2016) Marta Maciejewska et al.   Frontiers in Microbiology

Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante's Cave, Northern Sweden

(2016) Marie Lisandra Zepeda Mendoza et al.   PLoS One

Actinobacteria Isolated from an Underground Lake and Moonmilk Speleothem from the Biggest Conglomeratic Karstic Cave in Siberia as Sources of Novel Biologically Active Compounds

(2016) Denis V. Axenov-Gibanov et al.   PLoS One

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis

(2016) Adam G. Clooney et al.   PLoS One

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.

(2015) Kathrin P. Aßhauer et al.   BIOINFORMATICS

Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting: Applications, microbes and future research needs

(2015) Ming Chen et al.   BIOTECHNOLOGY ADVANCES

Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities

(2015) Michael A. Peabody et al.   BMC BIOINFORMATICS

The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies

(2015) J Paul Brooks et al.   BMC MICROBIOLOGY

Microbial Diversity in Caves

(2015) Karolina Tomczyk-Żak et al.   GEOMICROBIOLOGY JOURNAL

Evidence for the presence of key chlorophyll-biosynthesis-related proteins in the genus Rubrobacter (Phylum Actinobacteria) and its implications for the evolution and origin of photosynthesis

(2015) Radhey S. Gupta et al.   PHOTOSYNTHESIS RESEARCH

High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats

(2015) Jizhong Zhou et al.   mBio

Microbial mediation of complex subterranean mineral structures

(2015) Nicola Tisato et al.   Scientific Reports

Actinobacterial Diversity in Volcanic Caves and Associated Geomicrobiological Interactions

(2015) Cristina Riquelme et al.   Frontiers in Microbiology

Thermophilic and alkaliphilic Actinobacteria: biology and potential applications

(2015) L. Shivlata et al.   Frontiers in Microbiology

Are changes in sulfate assimilation pathway needed for evolution of C4 photosynthesis?

(2015) Silke C. Weckopp et al.   Frontiers in Plant Science

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Niche differentiation in nitrogen metabolism among methanotrophs within an operational taxonomic unit

(2014) Sven Hoefman et al.   BMC MICROBIOLOGY

Mechanism of Nitrogen Fixation by Nitrogenase: The Next Stage

(2014) Brian M. Hoffman et al.   CHEMICAL REVIEWS

Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics

(2014) Rachel Poretsky et al.   PLoS One

An introduction to the analysis of shotgun metagenomic data

(2014) Thomas J. Sharpton   Frontiers in Plant Science

Effects of actinobacteria on plant disease suppression and growth promotion

(2013) Sasikumar Arunachalam Palaniyandi et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Antibiotics at subinhibitory concentrations improve the quorum sensing behavior ofChromobacterium violaceum

(2013) Zhanjun Liu et al.   FEMS MICROBIOLOGY LETTERS

Actinobacteria—An Ancient Phylum Active in Volcanic Rock Weathering

(2013) Charles S. Cockell et al.   GEOMICROBIOLOGY JOURNAL

Nitrogen fixation in distinct microbial niches within a chemoautotrophy-driven cave ecosystem

(2013) Mahesh S Desai et al.   ISME Journal

Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave

(2013) Marianyoly Ortiz et al.   ISME Journal

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

Subinhibitory Antibiotic Concentrations Mediate Nutrient Use and Competition among Soil Streptomyces

(2013) Patricia Vaz Jauri et al.   PLoS One

Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data

(2013) Lauren M. Bragg et al.   PLoS Computational Biology

The multifaceted roles of antibiotics and antibiotic resistance in nature

(2013) Saswati Sengupta et al.   Frontiers in Microbiology

The biogeochemical role of Actinobacteria in Altamira Cave, Spain

(2012) Soledad Cuezva et al.   FEMS MICROBIOLOGY ECOLOGY

Profiling Bacterial Diversity and Taxonomic Composition on Speleothem Surfaces in Kartchner Caverns, AZ

(2012) Marianyoly Ortiz et al.   MICROBIAL ECOLOGY

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Antibiotic Resistance Is Prevalent in an Isolated Cave Microbiome

(2012) Kirandeep Bhullar et al.   PLoS One

OTU Analysis Using Metagenomic Shotgun Sequencing Data

(2012) Xiaolin Hao 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

Methanogens: a window into ancient sulfur metabolism

(2012) Yuchen Liu et al.   TRENDS IN MICROBIOLOGY

Ecological Aspects of the Distribution of Different Autotrophic CO2Fixation Pathways

(2011) Ivan A. Berg   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

(2011) Y. Zhao et al.   BIOINFORMATICS

Rare actinomycetes: a potential storehouse for novel antibiotics

(2011) Kavita Tiwari et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

Autotrophic, sulfur-oxidizing actinobacteria in acidic environments

(2011) Paul R. Norris et al.   EXTREMOPHILES

Diverse Metabolic Profiles of aStreptomycesStrain Isolated from a Hyper-arid Environment

(2011) Mostafa E. Rateb et al.   JOURNAL OF NATURAL PRODUCTS

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

The chlorosome: a prototype for efficient light harvesting in photosynthesis

(2010) Gert T. Oostergetel et al.   PHOTOSYNTHESIS RESEARCH

Pathways of nitrogen utilization by soil microorganisms – A review

(2010) Daniel Geisseler et al.   SOIL BIOLOGY & BIOCHEMISTRY

Life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave

(2009) Yin Chen et al.   ISME Journal

Abundance, composition, diversity and novelty of soil Proteobacteria

(2009) Anne M Spain et al.   ISME Journal

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

(2009) Peter J. A. Cock et al.   NUCLEIC ACIDS RESEARCH

The ecology and biotechnology of sulphate-reducing bacteria

(2008) Gerard Muyzer et al.   NATURE REVIEWS MICROBIOLOGY