Trends in bacterial and fungal communities in ant nests observed with Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and Next Generation Sequencing (NGS) techniques—validity and compatibility in ecological studies

Uncovering the Horseshoe Effect in Microbial Analyses

(2017) James T. Morton et al.   mSystems

Effect of short term variation in temperature and water content on the bacterial community in a tropical soil

(2016) Yasoga Supramaniam et al.   APPLIED SOIL ECOLOGY

Diversity of fungi from the mound nests of Formica ulkei and adjacent non-nest soils

(2016) Lyndon B. Duff et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

(2016) Sophie Weiss et al.   ISME Journal

Ericoid Roots and Mycospheres Govern Plant-Specific Bacterial Communities in Boreal Forest Humus

(2016) Sari Timonen et al.   MICROBIAL ECOLOGY

Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences

(2016) Vinita Deshpande et al.   MYCOLOGIA

Reconstruction of the Metabolic Potential of Acidophilic Sideroxydans Strains from the Metagenome of an Microaerophilic Enrichment Culture of Acidophilic Iron-Oxidizing Bacteria from a Pilot Plant for the Treatment of Acid Mine Drainage Reveals Metabolic Versatility and Adaptation to Life at Low pH

(2016) Martin Mühling et al.   Frontiers in Microbiology

Temporally Variable Geographical Distance Effects Contribute to the Assembly of Root-Associated Fungal Communities

(2016) Christopher J. Barnes et al.   Frontiers in Microbiology

New Primers for Discovering Fungal Diversity Using Nuclear Large Ribosomal DNA

(2016) Asma Asemaninejad et al.   PLoS One

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

Metagenomics meets time series analysis: unraveling microbial community dynamics

(2015) Karoline Faust et al.   CURRENT OPINION IN MICROBIOLOGY

The Community Structures of Prokaryotes and Fungi in Mountain Pasture Soils are Highly Correlated and Primarily Influenced by pH

(2015) Anders Lanzén et al.   Frontiers in Microbiology

Structures of Microbial Communities in Alpine Soils: Seasonal and Elevational Effects

(2015) Anna Lazzaro et al.   Frontiers in Microbiology

Long-term forest soil warming alters microbial communities in temperate forest soils

(2015) Kristen M. DeAngelis et al.   Frontiers in Microbiology

Standardizing metadata and taxonomic identification in metabarcoding studies

(2015) Leho Tedersoo et al.   GigaScience

Impact of T-RFLP data analysis choices on assessments of microbial community structure and dynamics

(2014) Nils Johan Fredriksson et al.   BMC BIOINFORMATICS

Community fingerprinting in a sequencing world

(2014) Josie van Dorst et al.   FEMS MICROBIOLOGY ECOLOGY

A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses

(2014) Pier Luigi Buttigieg et al.   FEMS MICROBIOLOGY ECOLOGY

Technicalities and Glitches of Terminal Restriction Fragment Length Polymorphism (T-RFLP)

(2014) Om Prakash et al.   INDIAN JOURNAL OF MICROBIOLOGY

Resource Availability and Spatial Heterogeneity Control Bacterial Community Response to Nutrient Enrichment in Lakes

(2014) KathiJo Jankowski et al.   PLoS One

Pros and Cons of Ion-Torrent Next Generation Sequencing versus Terminal Restriction Fragment Length Polymorphism T-RFLP for Studying the Rumen Bacterial Community

(2014) Gabriel de la Fuente et al.   PLoS One

Bacterial Community Composition of Size-Fractioned Aggregates within the Phycosphere of Cyanobacterial Blooms in a Eutrophic Freshwater Lake

(2014) Haiyuan Cai et al.   PLoS One

Soil biodiversity and soil community composition determine ecosystem multifunctionality

(2014) C. Wagg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Linking ecosystem modification by the yellow meadow ant (Lasius flavus) to microbial assemblages in different soil environments

(2013) Bas Boots et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide

(2013) Björn D. Lindahl et al.   NEW PHYTOLOGIST

Meta-analysis of deep-sequenced fungal communities indicates limited taxon sharing between studies and the presence of biogeographic patterns

(2013) Anjuli Meiser et al.   NEW PHYTOLOGIST

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

A Metatranscriptomic Approach to the Identification of Microbiota Associated with the Ant Formica exsecta

(2013) Helena Johansson et al.   PLoS One

Evaluation of molecular community analysis methods for discerning fecal sources and human waste

(2013) Yiping Cao et al.   WATER RESEARCH

Controls on soil microbial community stability under climate change

(2013) Franciska T. de Vries et al.   Frontiers in Microbiology

Surveying the Microbiome of Ants: Comparing 454 Pyrosequencing with Traditional Methods To Uncover Bacterial Diversity

(2012) Stefanie Kautz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data

(2012) David G Weissbrodt et al.   BMC MICROBIOLOGY

Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective

(2012) H. Teeling et al.   BRIEFINGS IN BIOINFORMATICS

Bacteria Associated with Gut Lumen of Camponotus japonicus Mayr

(2012) Hong He et al.   ENVIRONMENTAL ENTOMOLOGY

New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities

(2012) Katarina Ihrmark et al.   FEMS MICROBIOLOGY ECOLOGY

Ant Interactions with Soil Organisms and Associated Semiochemicals

(2012) Robert Vander Meer   JOURNAL OF CHEMICAL ECOLOGY

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Testing the Limits of 454 Pyrotag Sequencing: Reproducibility, Quantitative Assessment and Comparison to T-RFLP Fingerprinting of Aquifer Microbes

(2012) Giovanni Pilloni et al.   PLoS One

Dynamics of Microbial Community Structure of and Enhanced Biological Phosphorus Removal by Aerobic Granules Cultivated on Propionate or Acetate

(2011) Graciela Gonzalez-Gil et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

INBREEDING AND REPRODUCTIVE INVESTMENT IN THE ANT FORMICA EXSECTA

(2011) Emma Vitikainen et al.   EVOLUTION

Biochar induced soil microbial community change: Implications for biogeochemical cycling of carbon, nitrogen and phosphorus

(2011) Craig R. Anderson et al.   PEDOBIOLOGIA

Unique soil microbial assemblages associated with grassland ant species with different nesting and foraging strategies

(2011) Bas Boots et al.   PEDOBIOLOGIA

Soil bacterial communities in native and regenerated perhumid montane forests

(2010) Yu-Te Lin et al.   APPLIED SOIL ECOLOGY

A review of molecular methods to study the microbiota of soil and the mycosphere

(2010) J.D. van Elsas et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

The diversity of ant-associated black yeasts: insights into a newly discovered world of symbiotic interactions

(2010) Hermann Voglmayr et al.   Fungal Biology

Possible interactions between bacterial diversity, microbial activity and supraglacial hydrology of cryoconite holes in Svalbard

(2010) Arwyn Edwards et al.   ISME Journal

Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

(2010) ANTHONY S. AMEND et al.   MOLECULAR ECOLOGY

Quantitative Community Fingerprinting Methods for Estimating the Abundance of Operational Taxonomic Units in Natural Microbial Communities

(2009) A. Ramette   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

T-REX: software for the processing and analysis of T-RFLP data

(2009) Steven W Culman et al.   BMC BIOINFORMATICS

Compaction of forest soils with heavy logging machinery affects soil bacterial community structure

(2009) Beat Frey et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

The ITS region as a target for characterization of fungal communities using emerging sequencing technologies

(2009) Rolf Henrik Nilsson et al.   FEMS MICROBIOLOGY LETTERS

Initial community evenness favours functionality under selective stress

(2009) Lieven Wittebolle et al.   NATURE

454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity

(2009) M. Buée et al.   NEW PHYTOLOGIST

Bacterial gut symbionts are tightly linked with the evolution of herbivory in ants

(2009) Jacob A. Russell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities

(2008) Ursel M. E. Schütte et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

How to get more out of molecular fingerprints: practical tools for microbial ecology

(2008) Massimo Marzorati et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity rankings among bacterial lineages in soil

(2008) Noha H Youssef et al.   ISME Journal

Organic mound-building ants: their impact on soil properties in temperate and boreal forests

(2008) M. F. Jurgensen et al.   JOURNAL OF APPLIED ENTOMOLOGY

Spatial scaling of functional gene diversity across various microbial taxa

(2008) J. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use

(2008) V. Acosta-Martínez et al.   SOIL BIOLOGY & BIOCHEMISTRY

Spatial distribution of fungal communities in a coastal grassland soil

(2008) Clare H. Robinson et al.   SOIL BIOLOGY & BIOCHEMISTRY