Cocultivation of Anaerobic Fungi with Rumen Bacteria Establishes an Antagonistic Relationship

mBio ◽

10.1128/mbio.01442-21 ◽

2021 ◽

Author(s):

Candice L. Swift ◽

Katherine B. Louie ◽

Benjamin P. Bowen ◽

Casey A. Hooker ◽

Kevin V. Solomon ◽

...

Keyword(s):

Rumen Bacteria ◽

Anaerobic Fungi ◽

Rumen Microbiome

Anaerobic fungi are outnumbered by bacteria by 4 orders of magnitude in the herbivore rumen. Despite their numerical disadvantage, they are resilient members of the rumen microbiome.

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Cellulose degradation by two rumen anaerobic fungi in monoculture or in coculture with rumen bacteria

Animal Feed Science and Technology ◽

10.1016/0377-8401(91)90016-l ◽

1991 ◽

Vol 32 (1-3) ◽

pp. 131-136 ◽

Cited By ~ 22

Author(s):

Annick Bernalier ◽

G. Fonty ◽

Ph. Gouet

Keyword(s):

Cellulose Degradation ◽

Rumen Bacteria ◽

Anaerobic Fungi

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Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

The ISME Journal ◽

10.1038/s41396-020-00769-x ◽

2020 ◽

Cited By ~ 3

Author(s):

Live H. Hagen ◽

Charles G. Brooke ◽

Claire A. Shaw ◽

Angela D. Norbeck ◽

Hailan Piao ◽

...

Keyword(s):

Plant Cell Wall ◽

Plant Biomass ◽

Soluble Sugars ◽

Rumen Bacteria ◽

Anaerobic Fungi ◽

Host Animal ◽

Bacterial Populations ◽

Domain Specific ◽

Gene Catalog ◽

Ruminal Degradation

Abstract The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa, and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 h in nylon bags within the rumen of cannulated dairy cows. Across a gene catalog covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of hemicelluloses, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo- and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8, and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryote-selected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggest that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.

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The genomic and proteomic landscape of the rumen microbiome revealed by comprehensive genome-resolved metagenomics

10.1101/489443 ◽

2018 ◽

Cited By ~ 8

Author(s):

Robert D. Stewart ◽

Marc D. Auffret ◽

Amanda Warr ◽

Alan W. Walker ◽

Rainer Roehe ◽

...

Keyword(s):

Sequence Data ◽

Structure And Function ◽

Comprehensive Analysis ◽

Rumen Bacteria ◽

Future Studies ◽

Rumen Microbiota ◽

Rumen Microbiome ◽

Public Datasets ◽

And Function

AbstractRuminants provide essential nutrition for billions of people worldwide. The rumen is a specialised stomach adapted to the breakdown of plant-derived complex polysaccharides, and collectively the rumen microbiota encode the thousands of enzymes responsible. Here we present a comprehensive analysis of over 6.5 terabytes of Illumina and Nanopore sequence data, including assembly of 4941 metagenome-assembled genomes, and several single-contig, whole-chromosome assemblies of novel rumen bacteria. We also present the largest dataset of predicted proteins from the rumen, and provide rich annotation against public datasets. Together these data will form an essential part of future studies of rumen microbiome structure and function.

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Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

10.1101/2020.01.16.907998 ◽

2020 ◽

Cited By ~ 1

Author(s):

Live H. Hagen ◽

Charles G. Brooke ◽

Claire Shaw ◽

Angela D. Norbeck ◽

Hailan Piao ◽

...

Keyword(s):

Plant Cell Wall ◽

Plant Biomass ◽

Soluble Sugars ◽

Rumen Bacteria ◽

Anaerobic Fungi ◽

Host Animal ◽

Bacterial Populations ◽

Domain Specific ◽

Gene Catalogue ◽

Ruminal Degradation

AbstractThe rumen harbors a complex microbial mixture of archaea, bacteria, protozoa and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 hours in nylon bags within the rumen of cannulated dairy cows. Across a gene catalogue covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of polysaccharides such as hemicellulose, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo- and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8 and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryote-selected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggests that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.

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Mining Novel Specific Rumen Bacteria to Enhance the Bioactive Function of Mulberry Leaf in Promoting Host Antioxidant Activity and Immunomodulatory

10.21203/rs.3.rs-36704/v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Bing Wang ◽

Hailing Luo

Keyword(s):

Antioxidant Capacity ◽

Strong Association ◽

Taxonomic Composition ◽

Rumen Bacteria ◽

Mulberry Leaf ◽

Β Diversity ◽

Rumen Microbiome ◽

Group A ◽

Microbial Analysis ◽

Host Metabolism

Abstract Background: Rumen is a natural fermentation system and the microorganisms inside can effectively utilize plant bioresource and interact with host metabolism. Here, analysis of rumen microbiome, together with animal performance and serum metabolism in a lamb model were performed to identify the potential use of mulberry leaf silage (MS) to replace alfalfa silage (AS) as a new functional feed resource and to mining the novel specific mulberry leaf associated rumen bacteria interact with host metabolism. Results: The lambs fed with MS diet showed improved antioxidant capacity and immune function compared to those fed AS diet. The MS diet significantly altered rumen microbiota α- and β-diversity and taxonomic composition. Microbial analysis revealed that Bifidobacterium, Lactobacillus and Schwartzia were enhanced, and Ruminococcaceae UCG-010 and Lachnospiraceae_XPB1014_group were down-regulated in the rumen of MS group. A strong association was also found between these rumen microbial taxa and host antioxidant capacity and immunomodulatory. Conclusion: These findings indicated that mulberry leaf silage can be a high-quality feed source or bioactive pharmaceutical that is responsible for ruminants health benefits by modifying the rumen microbial community with potentially enhanced probiotics and inhibited biohydrogenation and methane emission.

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The Effect of a High-Grain Diet on the Rumen Microbiome of Goats with a Special Focus on Anaerobic Fungi

Microorganisms ◽

10.3390/microorganisms9010157 ◽

2021 ◽

Vol 9 (1) ◽

pp. 157

Author(s):

Katerina O. Fliegerova ◽

Sabine M. Podmirseg ◽

Julia Vinzelj ◽

Diego J. Grilli ◽

Simona Kvasnová ◽

...

Keyword(s):

High Throughput Sequencing ◽

Microbial Interactions ◽

Rumen Content ◽

Special Focus ◽

Rrna Gene ◽

Anaerobic Fungi ◽

Diet Change ◽

Host Animal ◽

Rumen Microbiome ◽

Significant Augmentation

This work investigated the changes of the rumen microbiome of goats switched from a forage to a concentrate diet with special attention to anaerobic fungi (AF). Female goats were fed an alfalfa hay (AH) diet (0% grain; n = 4) for 20 days and were then abruptly shifted to a high-grain (HG) diet (40% corn grain, 60% AH; n = 4) and treated for another 10 days. Rumen content samples were collected from the cannulated animals at the end of each diet period (day 20 and 30). The microbiome structure was studied using high-throughput sequencing for bacteria, archaea (16S rRNA gene) and fungi (ITS2), accompanied by qPCR for each group. To further elucidate unclassified AF, clone library analyses were performed on the ITS1 spacer region. Rumen pH was significantly lower in HG diet fed goats, but did not induce subacute ruminal acidosis. HG diet altered prokaryotic communities, with a significant increase of Bacteroidetes and a decrease of Firmicutes. On the genus level Prevotella 1 was significantly boosted. Methanobrevibacter and Methanosphaera were the most abundant archaea regardless of the diet and HG induced a significant augmentation of unclassified Thermoplasmatales. For anaerobic fungi, HG triggered a considerable rise in Feramyces observed with both ITS markers, while a decline of Tahromyces was detected by ITS2 and decrease of Joblinomyces by ITS1 only. The uncultured BlackRhino group revealed by ITS1 and further elucidated in one sample by LSU analysis, formed a considerable part of the AF community of goats fed both diets. Results strongly indicate that the rumen ecosystem still acts as a source for novel microorganisms and unexplored microbial interactions and that initial rumen microbiota of the host animal considerably influences the reaction pattern upon diet change.

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