4.8 Article

Patterns and determinants of the global herbivorous mycobiome

Related references

Note: Only part of the references are listed.
Article Biotechnology & Applied Microbiology

Co-cultivation of anaerobic fungi with Clostridium acetobutylicum bolsters butyrate and butanol production from cellulose and lignocellulose

Jennifer L. Brown et al.

Summary: A system for co-cultivation of anaerobic fungi with anaerobic bacteria was established to produce butyrate and butanol from plant biomass. The co-culture formulations consisted of different fungi with the bacterium Clostridium acetobutylicum, and the simultaneous co-culture promoted the production of butyrate up to 30 mM. Two-stage growth slightly promoted solventogenesis and elevated butanol levels. This study demonstrates the potential of a fungal-bacterial co-culture system for biobutanol and bio-butyrate production from lignocellulose.

JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY (2023)

Article Ecology

Global soil microbiomes: A new frontline of biome-ecology research

Martti Vasar et al.

Summary: Organisms in different ecosystems on Earth form distinct communities, and understanding their patterns and functions is crucial for biodiversity conservation. Current terrestrial biome classifications are insufficient in representing the diversity patterns of soil microbes. In this study, we used high-throughput sequencing and statistical clustering to define soil microbiomes on a global scale. We found strong correlations among different microbial groups and identified pH and temperature as the main environmental drivers of soil microbiome structure. These findings have important implications for theoretical and applied biodiversity research.

GLOBAL ECOLOGY AND BIOGEOGRAPHY (2022)

Article Multidisciplinary Sciences

Rumen sampling methods bias bacterial communities observed

Jill Hagey et al.

Summary: The rumen is an important ecosystem in improving cattle feed efficiency and reducing environmental impacts. This study investigated the bacterial and archaeal communities using different sampling methods and rumen fraction types. The results showed that the abundance of major archaeal communities was not affected by the sampling method, while the bacterial order WCHB1-41 and family Prevotellaceae were enriched in liquid samples. Solid samples with rumen liquid particles resembled the grab samples. Stomach tube samples had higher variability and represented the liquid phase, and fecal samples differed significantly from the rumen samples.

PLOS ONE (2022)

Review Microbiology

Metabolic Enabling and Detoxification by Mammalian Gut Microbes

M. Denise Dearing et al.

Summary: The longstanding interactions between mammals and their symbionts enable thousands of mammal species to consume herbivorous diets and degrade both plant fiber and toxins. However, research on microbial toxin degradation in wild mammals is limited due to constraints on sampling and manipulating the microbial communities.

ANNUAL REVIEW OF MICROBIOLOGY (2022)

Article Biochemical Research Methods

GTDB-Tk v2: memory friendly classification with the genome taxonomy database

Pierre-Alain Chaumeil et al.

Summary: This study presents an updated version of GTDB-Tk that uses a divide-and-conquer approach to reduce memory requirements while minimizing classification impact.

BIOINFORMATICS (2022)

Article Multidisciplinary Sciences

Natural and after colon washing fecal samples: the two sides of the coin for investigating the human gut microbiome

Elisabetta Piancone et al.

Summary: This study compared the effectiveness and accuracy of feces and colon washing feces as sampling matrices for representing the complexity of the human gut microbiome. The results showed inter-individual variability among paired feces and colon washing feces samples, but overall high similarity. Both types of samples exhibited comparable microbial load. This comparative study highlights the potential of using both types of sampling matrices for a more comprehensive understanding of the human gut microbiota.

SCIENTIFIC REPORTS (2022)

Article Microbiology

Simultaneous Metabarcoding and Quantification of Neocallimastigomycetes from Environmental Samples: Insights into Community Composition and Novel Lineages

Diana Young et al.

Summary: This study developed and validated a new specific PCR primer pair targeting Neocallimastigomycetes fungi. The primer pair was evaluated in pure cultures and environmental samples, successfully analyzing previously unknown anaerobic gut fungal taxa.

MICROORGANISMS (2022)

Article Biotechnology & Applied Microbiology

Co-cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates

Jennifer L. Brown et al.

Summary: Anaerobic fungi and methanogenic archaea can form stable synthetic co-cultures with metabolic interactions impacting transcriptional and metabolic changes of anaerobic fungus Caecomyces churrovis, potentially enhancing specific metabolic functions related to biomass breakdown and sugar utilization pathways. Co-culture with methanogen may increase overall transcription of enzymes and domains related to carbohydrates binding and cause upregulation of genes associated with enzymatic machinery across multiple growth substrates, suggesting a potential role in fungal-methanogen physical associations and metabolic functions enhancement.

BIOTECHNOLOGY FOR BIOFUELS (2021)

Article Biotechnology & Applied Microbiology

Non-destructive quantification of anaerobic gut fungi and methanogens in co-culture reveals increased fungal growth rate and changes in metabolic flux relative to mono-culture

Patrick A. Leggieri et al.

Summary: The study presents a microplate-based method to measure AGF and methanogen concentrations in co-culture, demonstrating significant increases in AGF growth rate and degradation rates in the presence of methanogens. This method allows for direct growth measurements and calculation of metabolic fluxes, essential for understanding rumen metabolism and the impact of co-culture on degradation and production processes.

MICROBIAL CELL FACTORIES (2021)

Article Multidisciplinary Sciences

Global donkey and mule populations: Figures and trends

Stuart L. Norris et al.

Summary: This paper provides an update on donkey and mule populations globally, regionally, and at the country level, showing a trend of increasing donkey populations by about 1% per year and decreasing mule populations by about 2% per year. The largest increases in donkey population were observed in sub-Saharan Africa, while the greatest reduction occurred in Eastern Europe, highlighting the influence of socio-economic drivers on changes in equid populations.

PLOS ONE (2021)

Article Microbiology

Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes

Xuefeng Peng et al.

Summary: The study found that microbial consortia dominated by anaerobic fungi outperformed bacterially dominated consortia in methane production and cellulose degradation. Cross-domain partnerships between fungi and methanogens enabled the production of acetate, formate, and methane, while bacterially dominated consortia mainly produced short-chain fatty acids. The division of labor among herbivore anaerobes for plant biomass degradation could be utilized for industrial bioprocessing.

NATURE MICROBIOLOGY (2021)

Article Microbiology

Vertebrate host phylogeny influences gut archaeal diversity

Nicholas D. Youngblut et al.

Summary: Analysis of the archaeal gut microbiota of 110 vertebrate species spanning five taxonomic classes revealed that host phylogeny could explain archaeal diversity.

NATURE MICROBIOLOGY (2021)

Article Ecology

Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem

Ya-Jou Chen et al.

Summary: This study found that habitat generalists tend to dominate in highly dynamic environments, while habitat specialists are restricted to narrower niches in permeable sediments. The ecological theory describing distribution patterns for macroorganisms likely extends to microorganisms, with broad ecological and biogeochemical implications.

ISME JOURNAL (2021)

Article Multidisciplinary Sciences

Anaerobic gut fungi are an untapped reservoir of natural products

Candice L. Swift et al.

Summary: Anaerobic gut fungi, as low-abundance members of the herbivore digestive tract, have been found to potentially synthesize diverse natural products, including antibiotics and antimicrobial peptides. Through a multi-omics approach, genes encoding biosynthetic enzymes for natural products were identified in four representative anaerobic gut fungal species. This suggests that these fungi could serve as a valuable source of antimicrobials and therapeutics.

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

Cocultivation of Anaerobic Fungi with Rumen Bacteria Establishes an Antagonistic Relationship

Candice L. Swift et al.

Summary: In the co-culture environment of anaerobic gut fungi and rumen bacteria, fungi produce antimicrobials while bacteria upregulate self-protective mechanisms.
Article Multidisciplinary Sciences

Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota

Luis Javier Galindo et al.

Summary: The study delves into two atypical parasitic fungi with amoeboid zoospores and long kinetosomes, proposing a new phylum, Sanchytriomycota, based on their distinct phylogenetic position and unique traits. Comparative genomic analyses reveal a reduced metabolic repertoire for the sanchytrids and infer three independent flagellum losses. The research also highlights that most of the hyphal morphogenesis gene repertoire of multicellular fungi had already evolved in early holomycotan lineages.

NATURE COMMUNICATIONS (2021)

Article Microbiology

Unraveling differences in fecal microbiota stability in mammals: from high variable carnivores and consistently stable herbivores

Franziska Zoelzer et al.

Summary: Our study demonstrated significant differences in microbiota consistency and diversity between carnivore and herbivore species. Carnivores show high variability in microbiota composition within and between species, while herbivores exhibit less variation across species boundaries. Low-abundance bacterial families exhibit larger fluctuations in fecal microbiota compared to high-abundance families.

ANIMAL MICROBIOME (2021)

Article Mycology

In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies

Merce Montoliu-Nerin et al.

Summary: A novel workflow was proposed to generate de novo genome assemblies covering seven families of AM fungi by combining genomic data from single nuclei, successfully sequencing the genomes of 15 AM fungal species. Phylogenomic analysis results supported family level classification from previous studies and showed the polyphyly of the order Glomerales.

FRONTIERS IN FUNGAL BIOLOGY (2021)

Article Multidisciplinary Sciences

The systematics of the Cervidae: a total evidence approach

Nicola S. Heckeberg

PEERJ (2020)

Review Microbiology

Toward a Fully Resolved Fungal Tree of Life

Timothy Y. James et al.

ANNUAL REVIEW OF MICROBIOLOGY, VOL 74, 2020 (2020)

Review Microbiology

Anaerobic Fungi: Past, Present, and Future

Matthias Hess et al.

FRONTIERS IN MICROBIOLOGY (2020)

Article Biotechnology & Applied Microbiology

Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage

Chelsea L. Murphy et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2019)

Article Multidisciplinary Sciences

A general framework for quantitatively assessing ecological stochasticity

Daliang Ning et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Multidisciplinary Sciences

Covariation of diet and gut microbiome in African megafauna

Tyler R. Kartzinel et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Mycology

Anaerobic fungal communities differ along the horse digestive tract

Erica Mura et al.

FUNGAL BIOLOGY (2019)

Review Chemistry, Multidisciplinary

Lignocellulosic Biomass: Understanding Recalcitrance and Predicting Hydrolysis

Aya Zoghlami et al.

FRONTIERS IN CHEMISTRY (2019)

Review Biotechnology & Applied Microbiology

Enzymes of early-diverging, zoosporic fungi

Lene Lange et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2019)

Article Biotechnology & Applied Microbiology

The use of extracellular DNA as a proxy for specific microbial activity

Magdalena Nagler et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2018)

Article Biochemistry & Molecular Biology

Genome-reconstruction for eukaryotes from complex natural microbial communities

Patrick T. West et al.

GENOME RESEARCH (2018)

Article Multidisciplinary Sciences

The biomass distribution on Earth

Yinon M. Bar-On et al.

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

Article Evolutionary Biology

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

Andrew Rambaut et al.

SYSTEMATIC BIOLOGY (2018)

Review Biotechnology & Applied Microbiology

The biotechnological potential of anaerobic fungi on fiber degradation and methane production

Yanfen Cheng et al.

WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY (2018)

Article Virology

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10

Marc A. Suchard et al.

VIRUS EVOLUTION (2018)

Review Ecology

Where less may be more: how the rare biosphere pulls ecosystems strings

Alexandre Jousset et al.

ISME JOURNAL (2017)

Review Microbiology

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

Jizhong Zhou et al.

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2017)

Article Multidisciplinary Sciences

A communal catalogue reveals Earth's multiscale microbial diversity

Luke R. Thompson et al.

NATURE (2017)

Article Multidisciplinary Sciences

A genome Tree of Life for the Fungi kingdom

JaeJin Choi et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Microbiology

A parts list for fungal cellulosomes revealed by comparative genomics

Charles H. Haitjema et al.

NATURE MICROBIOLOGY (2017)

Article Biotechnology & Applied Microbiology

Transcriptomic characterization of Caecomyces churrovis: a novel, non-rhizoid-forming lignocellulolytic anaerobic fungus

John K. Henske et al.

BIOTECHNOLOGY FOR BIOFUELS (2017)

Article Agriculture, Dairy & Animal Science

Development and physiology of the rumen and the lower gut: Targets for improving gut health

Michael A. Steele et al.

JOURNAL OF DAIRY SCIENCE (2016)

Article Biochemical Research Methods

A fast and reliable procedure for spore collection from anaerobic fungi: Application for RNA uptake and long-term storage of isolates

Shelby Calkins et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2016)

Article Multidisciplinary Sciences

Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes

Kevin V. Solomon et al.

SCIENCE (2016)

Article Biotechnology & Applied Microbiology

Buccal Swabbing as a Noninvasive Method To Determine Bacterial, Archaeal, and Eukaryotic Microbial Community Structures in the Rumen

Sandra Kittelmann et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2015)

Review Microbiology

Ecology and exploration of the rare biosphere

Michael D. J. Lynch et al.

NATURE REVIEWS MICROBIOLOGY (2015)

Article Multidisciplinary Sciences

Structure and function of the global ocean microbiome

Shinichi Sunagawa et al.

SCIENCE (2015)

Article Biochemistry & Molecular Biology

The Hologenome Concept: Helpful or Hollow?

Nancy A. Moran et al.

PLOS BIOLOGY (2015)

Article Microbiology

Estimating and mapping ecological processes influencing microbial community assembly

James C. Stegen et al.

FRONTIERS IN MICROBIOLOGY (2015)

Editorial Material Biology

The Earth Microbiome project: successes and aspirations

Jack A. Gilbert et al.

BMC BIOLOGY (2014)

Article Ecology

Body mass evolution and diversification within horses (family Equidae)

Lauren Shoemaker et al.

ECOLOGY LETTERS (2014)

Article Biochemical Research Methods

Binning metagenomic contigs by coverage and composition

Johannes Alneberg et al.

NATURE METHODS (2014)

Article Biotechnology & Applied Microbiology

The Genome of the Anaerobic Fungus Orpinomyces sp Strain C1A Reveals the Unique Evolutionary History of a Remarkable Plant Biomass Degrader

Noha H. Youssef et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2013)

Article Agriculture, Dairy & Animal Science

Enzymatic characteristics of crude feruloyl and acetyl esterases of rumen fungus Neocallimastix sp YAK11 isolated from yak (Bos grunniens)

Y. C. Cao et al.

JOURNAL OF ANIMAL PHYSIOLOGY AND ANIMAL NUTRITION (2013)

Review Agriculture, Dairy & Animal Science

Keeping horses in groups: A review

Elke Hartmann et al.

APPLIED ANIMAL BEHAVIOUR SCIENCE (2012)

Article Biochemical Research Methods

CD-HIT: accelerated for clustering the next-generation sequencing data

Limin Fu et al.

BIOINFORMATICS (2012)

Article Green & Sustainable Science & Technology

Evaluating expression and catalytic activity of anaerobic fungal fibrolytic enzymes native topiromyces sp E2 inSaccharomyces cerevisiae

Michelle A. O'Malley et al.

ENVIRONMENTAL PROGRESS & SUSTAINABLE ENERGY (2012)

Article Microbiology

A comparison of the microbiome and the metabolome of different regions of the equine hindgut

Kirsty Dougal et al.

FEMS MICROBIOLOGY ECOLOGY (2012)

Article Biotechnology & Applied Microbiology

Xylanases of Anaerobic Fungus Anaeromyces mucronatus

Z. Novotna et al.

FOLIA MICROBIOLOGICA (2010)

Review Agriculture, Dairy & Animal Science

Invited review: Ruminant ecology and evolution: Perspectives useful to ruminant livestock research and production

T. J. Hackmann et al.

JOURNAL OF DAIRY SCIENCE (2010)

Article Plant Sciences

Correlation analysis of dissimilarity matrices

Sarah C. Goslee

PLANT ECOLOGY (2010)

Article Statistics & Probability

Procrustes methods

John C. Gower

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL STATISTICS (2010)

Article Biochemical Research Methods

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

Salvador Capella-Gutierrez et al.

BIOINFORMATICS (2009)

Article Mycology

A serpin in the cellulosome of the anaerobic fungus Piromyces sp strain E2

Peter J. M. Steenbakkers et al.

MYCOLOGICAL RESEARCH (2008)

Article Biochemistry & Molecular Biology

β-glucosidase in cellulosome of the anaerobic fungus Piromyces sp strain E2 is a family 3 glycoside hydrolase

PJM Steenbakkers et al.

BIOCHEMICAL JOURNAL (2003)

Article Biochemistry & Molecular Biology

Molecular insights into the evolution of the family Bovidae: A nuclear DNA perspective

CA Matthee et al.

MOLECULAR BIOLOGY AND EVOLUTION (2001)

Article Evolutionary Biology

Molecular dating and biogeography of the early placental mammal radiation

E Eizirik et al.

JOURNAL OF HEREDITY (2001)