A phylogenetic census of global diversity of gut anaerobic fungi and a new taxonomic framework

Pecoramyces ruminantium, gen. nov., sp. nov., an anaerobic gut fungus from the feces of cattle and sheep

(2017) Radwa A. Hanafy et al.   MYCOLOGIA

An Investigation into Rumen Fungal and Protozoal Diversity in Three Rumen Fractions, during High-Fiber or Grain-Induced Sub-Acute Ruminal Acidosis Conditions, with or without Active Dry Yeast Supplementation

(2017) Suzanne L. Ishaq et al.   Frontiers in Microbiology

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity

(2016) Nam-Phuong Nguyen et al.   npj Biofilms and Microbiomes

A new anaerobic fungus (Oontomyces anksri gen. nov., sp. nov.) from the digestive tract of the Indian camel (Camelus dromedarius)

(2015) Sumit S. Dagar et al.   Fungal Biology

Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa

(2015) Hiran A. Ariyawansa et al.   FUNGAL DIVERSITY

Mycobiome: Approaches to analysis of intestinal fungi

(2015) Jie Tang et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Buwchfawromyces eastonii gen. nov., sp. nov.: a new anaerobic fungus (Neocallimastigomycota) isolated from buffalo faeces

(2015) Gareth Wyn Griffith et al.   MycoKeys

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   BIOINFORMATICS

Anaerobic fungi (phylumNeocallimastigomycota): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential

(2014) Robert J. Gruninger et al.   FEMS MICROBIOLOGY ECOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Internal Transcribed Spacer 1 Secondary Structure Analysis Reveals a Common Core throughout the Anaerobic Fungi (Neocallimastigomycota)

(2014) Christian Koetschan et al.   PLoS One

Bacterial community structure and its regulating factors in the intertidal sediment along the Liaodong Bay of Bohai Sea, China

(2013) Binghui Zheng et al.   MICROBIOLOGICAL RESEARCH

Bacterial census of poultry intestinal microbiome

(2013) S. Wei et al.   POULTRY SCIENCE

Utilizing ITS1 and ITS2 to study environmental fungal diversity using pyrosequencing

(2012) Cécile Monard et al.   FEMS MICROBIOLOGY ECOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

A Proposed Taxonomy of Anaerobic Fungi (Class Neocallimastigomycetes) Suitable for Large-Scale Sequence-Based Community Structure Analysis

(2012) Sandra Kittelmann et al.   PLoS One

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Aligning short reads to reference alignments and trees

(2011) Simon A. Berger et al.   BIOINFORMATICS

Status of the phylogenetic diversity census of ruminal microbiomes

(2011) Minseok Kim et al.   FEMS MICROBIOLOGY ECOLOGY

ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time

(2011) Yunpeng Cai et al.   NUCLEIC ACIDS RESEARCH

PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data

(2011) Thomas J. Sharpton et al.   PLoS Computational Biology

Anaerobic fungi: Neocallimastigomycota

(2011) Gareth W Griffith et al.   IMA Fungus

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores

(2010) Audra S Liggenstoffer et al.   ISME Journal

Fibrolytic potential of anaerobic fungi (Piromycessp.) isolated from wild cattle and blue bulls in pure culture and effect of their addition onin vitrofermentation of wheat straw and methane emission by rumen fluid of buffaloes

(2010) Shyam S Paul et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Diversity of anaerobic gut fungal populations analysed using ribosomal ITS1 sequences in faeces of wild and domesticated herbivores

(2009) Matthew J. Nicholson et al.   ANAEROBE

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Cellulase/Hemicellulase System of the Anaerobic FungusOrpinomycesPC-2 and Aspects of Its Applied Use

(2008) Lars G. Ljungdahl   Annals of the New York Academy of Sciences