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

Anaerobic fungi contain abundant, diverse, and transcriptionally active Long Terminal Repeat retrotransposons

Long Terminal Repeat (LTR) retrotransposons are a class of repetitive elements that are widespread in the genomes of plants and many fungi. LTR retrotransposons have been associated with rapidly evolving gene clusters in plants and virulence factor transfer in fungal-plant parasite-host interactions. We report here the abundance and transcriptional activity of LTR retrotransposons across several species of the early-branching Neocallimastigomycota, otherwise known as the anaerobic gut fungi (AGF). The ubiquity of LTR retrotransposons in these genomes suggests key evolutionary roles in these rumen-dwelling biomass degraders, whose genomes also contain many enzymes that are horizontally transferred from other rumen-dwelling prokaryotes. Up to 10% of anaerobic fungal genomes consist of LTR retrotransposons, and the mapping of sequences from LTR retrotransposons to transcriptomes shows that the majority of clusters are transcribed, with some exhibiting expression greater than 104 reads per kilobase million mapped reads (rpkm). Many LTR retrotransposons are strongly differentially expressed upon heat stress during fungal cultivation, with several exhibiting a nearly three-log10 fold increase in expression, whereas growth substrate variation modulated transcription to a lesser extent. We show that some LTR retrotransposons contain carbohydrate-active enzymes (CAZymes), and the expansion of CAZymes within genomes and among anaerobic fungal species may be linked to retrotransposon activity. We further discuss how these widespread sequences may be a source of promoters and other parts towards the bioengineering of anaerobic fungi.

Anaerobic fungi in the tortoise alimentary tract illuminate early stages of host-fungal symbiosis and Neocallimastigomycota evolution

Anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tract of herbivores. While their presence in mammals is well documented, evidence for their occurrence in non-mammalian hosts is currently sparse. Culture-independent surveys of AGF in tortoises identified a unique community, with three novel deep-branching genera representing >90% of sequences in most samples. Representatives of all genera were successfully isolated under strict anaerobic conditions. Transcriptomics-enabled phylogenomic and molecular dating analyses indicated an ancient, deep-branching position in the AGF tree for these genera, with an evolutionary divergence time estimate of 104-112 million years ago (Mya). Such estimates push the establishment of animal-Neocallimastigomycota symbiosis from the late to the early Cretaceous. Further, tortoise-associated isolates (T-AGF) exhibited limited capacity for plant polysaccharides metabolism and lacked genes encoding several carbohydrate-active enzyme (CAZyme) families. Finally, we demonstrate that the observed curtailed degradation capacities and reduced CAZyme repertoire is driven by the paucity of horizontal gene transfer (HGT) in T-AGF genomes, compared to their mammalian counterparts. This reduced capacity was reflected in an altered cellulosomal production capacity in T-AGF. Our findings provide insights into the phylogenetic diversity, ecological distribution, evolutionary history, evolution of fungal-host nutritional symbiosis, and dynamics of genes acquisition in Neocallimastigomycota.

Rumen microbes, enzymes, metabolisms, and application in lignocellulosic waste conversion - A comprehensive review

The rumen of ruminants is a natural anaerobic fermentation system that efficiently degrades lignocellulosic biomass and mainly depends on synergistic interactions between multiple microbes and their secreted enzymes. Ruminal microbes have been employed as biomass waste converters and are receiving increasing attention because of their degradation performance. To explore the application of ruminal microbes and their secreted enzymes in biomass waste, a comprehensive understanding of these processes is required. Based on the degradation capacity and mechanism of ruminal microbes and their secreted lignocellulose enzymes, this review concentrates on elucidating the main enzymatic strategies that ruminal microbes use for lignocellulose degradation, focusing mainly on polysaccharide metabolism-related gene loci and cellulosomes. Hydrolysis, acidification, methanogenesis, interspecific H2 transfer, and urea cycling in ruminal metabolism are also discussed. Finally, we review the research progress on the conversion of biomass waste into biofuels (bioethanol, biohydrogen, and biomethane) and value-added chemicals (organic acids) by ruminal microbes. This review aims to provide new ideas and methods for ruminal microbe and enzyme applications, biomass waste conversion, and global energy shortage alleviation.

Life at the borderlands: microbiomes of interfaces critical to One Health

Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome-host relationships, specifically at interfaces critical to One Health-a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.

Yeoman C, Grace S, Borgogna JLC, Foote AP, Nagy YI, Kashef MT, Yassin AS, Elshahed MS, Youssef NH. Diversity and community structure of anaerobic gut fungi in the rumen of wild and domesticated herbivores

The rumen houses a diverse community that plays a major role in the digestion process in ruminants. Anaerobic gut fungi (AGF) are key contributors to plant digestion in the rumen. Here, we present a global amplicon-based survey of the rumen AGF mycobiome by examining 206 samples from 15 animal species, 15 countries, and 6 continents. The rumen AGF mycobiome was highly diverse, with 81 out of 88 currently recognized AGF genera or candidate genera identified. However, only six genera (Neocallimastix, Orpinomyces, Caecomyces, Cyllamyces, NY9, and Piromyces) were present at >4% relative abundance. AGF diversity was higher in members of the families Antilocapridae and Cervidae compared to Bovidae. Community structure analysis identified a pattern of phylosymbiosis, where host family (10% of total variance) and species (13.5%) partially explained the rumen mycobiome composition. As well, diet composition (9%-19%), domestication (11.14%), and biogeography (14.1%) also partially explained AGF community structure; although sampling limitation, geographic range restrictions, and direct association between different factors hindered accurate elucidation of the relative contribution of each factor. Pairwise comparison of rumen and fecal samples obtained from the same subject (n = 13) demonstrated greater diversity and inter-sample variability in rumen versus fecal samples. The genera Neocallimastix and Orpinomyces were present in higher abundance in rumen samples, while Cyllamyces and Caecomyces were enriched in fecal samples. Comparative analysis of global rumen and feces data sets revealed a similar pattern. Our results provide a global view of AGF community in the rumen and identify patterns of AGF variability between rumen and feces in herbivores Gastrointestinal (GI) tract.IMPORTANCERuminants are highly successful and economically important mammalian suborder. Ruminants are herbivores that digest plant material with the aid of microorganisms residing in their GI tract. In ruminants, the rumen compartment represents the most important location where microbially mediated plant digestion occurs, and is known to house a bewildering array of microbial diversity. An important component of the rumen microbiome is the anaerobic gut fungi (AGF), members of the phylum Neocallimastigomycota. So far, studies examining AGF diversity have mostly employed fecal samples, and little is currently known regarding the identity of AGF residing in the rumen compartment, factors that impact the observed patterns of diversity and community structure of AGF in the rumen, and how AGF communities in the rumen compare to AGF communities in feces. Here, we examined the rumen AGF diversity using an amplicon-based survey targeting a wide range of wild and domesticated ruminants (n = 206, 15 different animal species) obtained from 15 different countries. Our results demonstrate that while highly diverse, no new AGF genera were identified in the rumen mycobiome samples examined. Our analysis also indicate that animal host phylogeny, diet, biogeography, and domestication status could play a role in shaping AGF community structure. Finally, we demonstrate that a greater level of diversity and higher inter-sample variability was observed in rumen compared to fecal samples, with two genera (Neocallimastix and Orpinomyces) present in higher abundance in rumen samples, and two others (Cyllamyces and Caecomyces) enriched in fecal samples. Our results provide a global view of the identity, diversity, and community structure of AGF in ruminants, elucidate factors impacting diversity and community structure of the rumen mycobiome, and identify patterns of AGF community variability between the rumen and feces in the herbivorous GI tract.

Breakdown of hardly degradable carbohydrates (lignocellulose) in a two-stage anaerobic digestion plant is favored in the main fermenter

The yield and productivity of biogas plants depend on the degradation performance of their microbiomes. The spatial separation of the anaerobic digestion (AD) process into a separate hydrolysis and a main fermenter should improve cultivation conditions of the microorganisms involved in the degradation of complex substrates like lignocellulosic biomass (LCB) and, thus, the performance of anaerobic digesters. However, relatively little is known about such two-stage processes. Here, we investigated the process performance of a two-stage agricultural AD over one year, focusing on chemical and technical process parameters and metagenome-centric metaproteomics. Technical and chemical parameters indicated stable operation of the main fermenter but varying conditions for the open hydrolysis fermenter. Matching this, the microbiome in the hydrolysis fermenter has a higher dynamic than in the main fermenter. Metaproteomics-based microbiome analysis revealed a partial separation between early and common steps in carbohydrate degradation and primary fermentation in the hydrolysis fermenter but complex carbohydrate degradation, secondary fermentation, and methanogenesis in the main fermenter. Detailed metagenomics and metaproteomics characterization of the single metagenome-assembled genomes showed that the species focus on specific substrate niches and do not utilize their full genetic potential to degrade, for example, LCB. Overall, it seems that a separation of AD in a hydrolysis and a main fermenter does not improve the cleavage of complex substrates but significantly improves the overall process performance. In contrast, the remaining methanogenic activity in the hydrolysis fermenter may cause methane losses.

Unravelling the temporal and spatial variation of fungal phylotypes from embryo to adult stages in Atlantic salmon

Early microbial colonization has a profound impact on host physiology during different stages of ontogeny. Although several studies have focused on early bacterial colonization and succession, the composition and role of fungal communities are poorly known in fish. Here, we sequenced the internal transcribed spacer 2 (ITS2) region of fungi to profile the mycobiome associated with the eggs, hatchlings and intestine of Atlantic salmon at various freshwater and marine stages. In most of the stages studied, fungal diversity was lower than bacterial diversity. There were several stage-specific fungal phylotypes belonging to different stages of ontogeny but some groups, such as Candida tropicalis, Saccharomyces cerevisiae, Alternaria metachromatica, Davidiella tassiana and Humicola nigrescens, persisted during successive stages of ontogeny. We observed significant changes in the intestinal fungal communities during the first feeding. Prior to first feeding, Humicola nigrescens dominated, but Saccharomyces cerevisiae (10 weeks post hatch) and Candida tropicalis (12 weeks post hatch) became dominant subsequently. Seawater transfer resulted in a decrease in alpha diversity and an increase in Candida tropicalis abundance. We also observed notable variations in beta diversity and composition between the different farms. Overall, the present study sheds light on the fungal communities of Atlantic salmon from early ontogeny to adulthood. These novel findings will also be useful in future studies investigating host-microbiota interactions in the context of developing better nutritional and health management strategies for Atlantic salmon farming.

Analysis of Rumen Degradation Characteristics, Attached Microbial Community, and Cellulase Activity Changes of Garlic Skin and Artemisia argyi Stalk

The purpose of this study was to study the chemical composition, rumen degradation characteristics, surface attached microbial community and cellulase activity of garlic skin (GS) and Artemisia argyi stalk (AS), in order to explain their feeding value. Four 14-month-old healthy Min Dong male goats with permanent rumen fistula were selected as experimental animals. The rumen degradation characteristics of GS and AS were determined by using the nylon bag method, and the bacterial composition, cellulase activity and their relationship on the surface of the two groups were analyzed with high-throughput sequencing of 16S rRNA gene. The results showed that in GS and AS, the effective degradation rate (ED) values of dry matter (DM) were 42.53% and 37.12%, the ED values of crude protein (CP) were 37.19% and 43.38%, the ED values of neutral detergent fiber (NDF) were 36.83% and 36.23%, and the ED values of acid detergent fiber (ADF) were 33.81% and 34.77%. During rumen degradation, the richness and evenness of bacteria attached to the AS surface were higher. At the phylum level, Bacteroidetes and Firmicutes were always the main rumen bacteria in the two groups. At the genus level, fiber-degrading bacteria such as Prevotella, Treponema, and Ruminococcus showed higher levels in GS (p < 0.05). Compared with GS, the activity of β-glucosidase (BG enzyme), endo-β-1,4-glucanase (C1 enzyme), exo-β-1,4-glucanase (Cx enzyme) and neutral xylanase (NEX enzyme) attached to AS surface showed a higher trend. Correlation analysis showed that the relative abundance of Succinivibrio and Rikenellaceae_RC9_gut_group was positively correlated with the rumen degradability of nutrients in GS, and the relative abundance of Christensenellaceae R-7_group, Succinivibrio and Ruminococcus was positively correlated with the rumen degradability of nutrients in AS. The conclusion of this study shows that AS has more potential to become ruminant roughage than GS. In addition, this study also revealed the relationship between cellulase activity and bacteria, which provided new information for us to better analyze the effects of GS and AS on the rumen of ruminants and provided an important theoretical basis for the development and utilization of agricultural by-products.

Carbohydrate flow through agricultural ecosystems: Implications for synthesis and microbial conversion of carbohydrates

Carbohydrates are chemically and structurally diverse biomolecules, serving numerous and varied roles in agricultural ecosystems. Crops and horticulture products are inherent sources of carbohydrates that are consumed by humans and non-human animals alike; however carbohydrates are also present in other agricultural materials, such as soil and compost, human and animal tissues, milk and dairy products, and honey. The biosynthesis, modification, and flow of carbohydrates within and between agricultural ecosystems is intimately related with microbial communities that colonize and thrive within these environments. Recent advances in -omics techniques have ushered in a new era for microbial ecology by illuminating the functional potential for carbohydrate metabolism encoded within microbial genomes, while agricultural glycomics is providing fresh perspective on carbohydrate-microbe interactions and how they influence the flow of functionalized carbon. Indeed, carbohydrates and carbohydrate-active enzymes are interventions with unrealized potential for improving carbon sequestration, soil fertility and stability, developing alternatives to antimicrobials, and circular production systems. In this manner, glycomics represents a new frontier for carbohydrate-based biotechnological solutions for agricultural systems facing escalating challenges, such as the changing climate.

Abiotic and Biotic Drivers of Soil Fungal Communities in Response to Dairy Manure Amendment

Modern agriculture often relies on large inputs of synthetic fertilizers to maximize crop yield potential, yet their intensive use has led to nutrient losses and impaired soil health. Alternatively, manure amendments provide plant available nutrients, build organic carbon, and enhance soil health. However, we lack a clear understanding of how consistently manure impacts fungal communities, the mechanisms via which manure impacts soil fungi, and the fate of manure-borne fungi in soils. We assembled soil microcosms using five soils to investigate how manure amendments impact fungal communities over a 60-day incubation. Further, we used autoclaving treatments of soils and manure to determine if observed changes in soil fungal communities were due to abiotic or biotic properties, and if indigenous soil communities constrained colonization of manure-borne fungi. We found that manure amended soil fungal communities diverged from nonamended communities over time, often in concert with a reduction in diversity. Fungal communities responded to live and autoclaved manure in a similar manner, suggesting that abiotic forces are primarily responsible for the observed dynamics. Finally, manure-borne fungi declined quickly in both live and autoclaved soil, indicating that the soil environment is unsuitable for their survival. IMPORTANCE Manure amendments in agricultural systems can impact soil microbial communities via supplying growth substrates for indigenous microbes or by introducing manure-borne taxa. This study explores the consistency of these impacts on soil fungal communities and the relative importance of abiotic and biotic drivers across distinct soils. Different fungal taxa responded to manure among distinct soils, and shifts in soil fungal communities were driven largely by abiotic factors, rather than introduced microbes. This work demonstrates that manure may have inconsistent impacts on indigenous soil fungi, and that abiotic properties of soils render them largely resistant to invasion by manure-borne fungi.

Metagenomic analysis reveals the efficient digestion mechanism of corn stover in Angus bull rumen: Microbial community succession, CAZyme composition and functional gene expression

Ruminant rumen is a biological fermentation system that can efficiently degrade lignocellulosic biomass. The knowledge about mechanisms of efficient lignocellulose degradation with rumen microorganisms is still limited. In this study, composition and succession of bacteria and fungi, carbohydrate-active enzymes (CAZymes), and functional genes involved in hydrolysis and acidogenesis were revealed during fermentation in Angus bull rumen via metagenomic sequencing. Results showed that degradation efficiency of hemicellulose and cellulose reached 61.2% and 50.4% at 72 h fermentation, respectively. Main bacterial genera were composed of Prevotella, Butyrivibrio, Ruminococcus, Eubacterium, and Fibrobacter, and main fungal genera were composed of Piromyces, Neocallimastix, Anaeromyces, Aspergillus, and Orpinomyces. Principal coordinates analysis indicated that community structure of bacteria and fungi dynamically changed during 72 h fermentation. Bacterial networks with higher complexity had stronger stability than fungal networks. Most CAZyme families showed a significant decrease trend after 48 h fermentation. Functional genes related to hydrolysis decreased at 72 h, while functional genes involved in acidogenesis did not change significantly. These findings provide a in-depth understanding of mechanisms of lignocellulose degradation in Angus bull rumen, and may guide the construction and enrichment of rumen microorganisms in anaerobic fermentation of waste biomass.

Metabolic influence of core ciliates within the rumen microbiome

Protozoa comprise a major fraction of the microbial biomass in the rumen microbiome, of which the entodiniomorphs (order: Entodiniomorphida) and holotrichs (order: Vestibuliferida) are consistently observed to be dominant across a diverse genetic and geographical range of ruminant hosts. Despite the apparent core role that protozoal species exert, their major biological and metabolic contributions to rumen function remain largely undescribed in vivo. Here, we have leveraged (meta)genome-centric metaproteomes from rumen fluid samples originating from both cattle and goats fed diets with varying inclusion levels of lipids and starch, to detail the specific metabolic niches that protozoa occupy in the context of their microbial co-habitants. Initial proteome estimations via total protein counts and label-free quantification highlight that entodiniomorph species Entodinium and Epidinium as well as the holotrichs Dasytricha and Isotricha comprise an extensive fraction of the total rumen metaproteome. Proteomic detection of protozoal metabolism such as hydrogenases (Dasytricha, Isotricha, Epidinium, Enoploplastron), carbohydrate-active enzymes (Epidinium, Diplodinium, Enoploplastron, Polyplastron), microbial predation (Entodinium) and volatile fatty acid production (Entodinium and Epidinium) was observed at increased levels in high methane-emitting animals. Despite certain protozoal species having well-established reputations for digesting starch, they were unexpectedly less detectable in low methane emitting-animals fed high starch diets, which were instead dominated by propionate/succinate-producing bacterial populations suspected of being resistant to predation irrespective of host. Finally, we reaffirmed our abovementioned observations in geographically independent datasets, thus illuminating the substantial metabolic influence that under-explored eukaryotic populations have in the rumen, with greater implications for both digestion and methane metabolism.

Lignocellulose degradation by rumen bacterial communities: New insights from metagenome analyses

Ruminant animals house a dense and diverse community of microorganisms in their rumen, an enlarged compartment in their stomach, which provides a supportive environment for the storage and microbial fermentation of ingested feeds dominated by plant materials. The rumen microbiota has acquired diverse and functionally overlapped enzymes for the degradation of plant cell wall polysaccharides. In rumen Bacteroidetes, enzymes involved in degradation are clustered into polysaccharide utilization loci to facilitate coordinated expression when target polysaccharides are available. Firmicutes use free enzymes and cellulosomes to degrade the polysaccharides. Fibrobacters either aggregate lignocellulose-degrading enzymes on their cell surface or release them into the extracellular medium in membrane vesicles, a mechanism that has proven extremely effective in the breakdown of recalcitrant cellulose. Based on current metagenomic analyses, rumen Bacteroidetes and Firmicutes are categorized as generalist microbes that can degrade a wide range of polysaccharides, while other members adapted toward specific polysaccharides. Particularly, there is ample evidence that Verrucomicrobia and Spirochaetes have evolved enzyme systems for the breakdown of complex polysaccharides such as xyloglucans, peptidoglycans, and pectin. It is concluded that diversity in degradation mechanisms is required to ensure that every component in feeds is efficiently degraded, which is key to harvesting maximum energy by host animals.

Effects of Dietary Nonfibrous Carbohydrate/Neutral Detergent Fiber Ratio on Methanogenic Archaea and Cellulose-Degrading Bacteria in the Rumen of Karakul Sheep: a 16S rRNA Gene Sequencing Study

The study was conducted to investigate the effects of dietary nonfibrous carbohydrate (NFC)/neutral detergent fiber (NDF) ratio on methanogenic archaea and cellulose-degrading bacteria in Karakul sheep by 16S rRNA gene sequencing. Twelve Karakul sheep were randomly divided into four groups, each group with three replicates, and they were fed with four dietary NFC/NDF ratios at 0.54, 0.96, 1.37, and 1.90 as groups 1, 2, 3, and 4, respectively. The experiment lasted for four periods: I (1 to 18 days), II (19 to 36 days), III (37 to 54 days), and IV (55 to 72 days); during each period, rumen contents were collected before morning feeding to investigate on methanogenic archaea and cellulose-degrading bacteria. The results showed that with an increase in dietary NFC/NDF ratio, the number of rumen archaea operational taxonomic units and the diversity of archaea decrease. The most dominant methanogens did not change with dietary NFC/NDF ratio and prolongation of experimental periods. Methanobrevibacter was the most dominant genus. At the species level, the relative abundance of Methanobrevibacter ruminantium first increased and then decreased when the NFC/NDF ratio increased. When the dietary NFC/NDF ratio was 0.96, the structure of archaea was largely changed, and the relative abundance of Fibrobacter sp. strain UWCM, Ruminococcus flavefaciens, and Ruminococcus albus were the highest. When the dietary NFC/NDF ratio was 1.37, the relative abundance of Butyrivibrio fibrisolvens was higher than for other groups. Based on all the data, we concluded that a dietary NFC/NDF ratio of ca. 0.96 to 1.37 was a suitable ratio to support optimal sheep production. IMPORTANCE CH₄ produced by ruminants aggravates the greenhouse effect and cause wastage of feed energy, and CH₄ emissions are related to methanogens. According to the current literature, there is a symbiotic relationship between methanogens and cellulolytic bacteria, so reducing methane will inevitably affect the degradation of fiber materials. This experiment used 16S rRNA gene high-throughput sequencing technology to explore the balance relationship between methanogens and cellulolytic bacteria for the first time through a long-term feeding period. The findings provide fundamental data, supporting for the diet structures with potential to reduce CH₄ emission.

Understanding the microbial fibre degrading communities & processes in the equine gut

The equine gastrointestinal tract is a self-sufficient fermentation system, housing a complex microbial consortium that acts synergistically and independently to break down complex lignocellulolytic material that enters the equine gut. Despite being strict herbivores, equids such as horses and zebras lack the diversity of enzymes needed to completely break down plant tissue, instead relying on their resident microbes to carry out fibrolysis to yield vital energy sources such as short chain fatty acids. The bulk of equine digestion occurs in the large intestine, where digesta is fermented for 36-48 h through the synergistic activities of bacteria, fungi, and methanogenic archaea. Anaerobic gut dwelling bacteria and fungi break down complex plant polysaccharides through combined mechanical and enzymatic strategies, and notably possess some of the greatest diversity and repertoire of carbohydrate active enzymes among characterized microbes. In addition to the production of enzymes, some equid-isolated anaerobic fungi and bacteria have been shown to possess cellulosomes, powerful multi-enzyme complexes that further enhance break down. The activities of both anaerobic fungi and bacteria are further facilitated by facultatively aerobic yeasts and methanogenic archaea, who maintain an optimal environment for fibrolytic organisms, ultimately leading to increased fibrolytic microbial counts and heightened enzymatic activity. The unique interactions within the equine gut as well as the novel species and powerful mechanisms employed by these microbes makes the equine gut a valuable ecosystem to study fibrolytic functions within complex communities. This review outlines the primary taxa involved in fibre break down within the equine gut and further illuminates the enzymatic strategies and metabolic pathways used by these microbes. We discuss current methods used in analysing fibrolytic functions in complex microbial communities and propose a shift towards the development of functional assays to deepen our understanding of this unique ecosystem.

Long-Read Metagenomics and CAZyme Discovery

Microorganisms play a primary role in regulating biogeochemical cycles and are a valuable source of enzymes that have biotechnological applications, such as carbohydrate-active enzymes (CAZymes). However, the inability to culture the majority of microorganisms that exist in natural ecosystems restricts access to potentially novel bacteria and beneficial CAZymes. While commonplace molecular-based culture-independent methods such as metagenomics enable researchers to study microbial communities directly from environmental samples, recent progress in long-read sequencing technologies are advancing the field. We outline key methodological stages that are required as well as describe specific protocols that are currently used for long-read metagenomic projects dedicated to CAZyme discovery.

Isolation and Preparation of Extracellular Proteins from Lignocellulose-Degrading Fungi for Comparative Proteomic Studies Using Mass Spectrometry

Fungi utilize a unique mechanism of nutrient acquisition involving extracellular digestion. To understand the biology of these microbes, it is important to identify and characterize the function of proteins that are secreted and involved in nutrient acquisition. Mass spectrometry-based proteomics is a powerful tool to study complex mixtures of proteins and understand how the proteins produced by an organism change in response to different conditions. Many fungi are efficient decomposers of plant cell walls, and anaerobic fungi are well recognized for their ability to digest lignocellulose. Here we outline a protocol for the enrichment and isolation of proteins secreted by anaerobic fungi after growth on simple (glucose) and complex (straw and alfalfa hay) carbon sources. We provide detailed instruction on generating protein fragments and preparing these for proteomic analysis using reversed-phase chromatography and mass spectrometry. The interpretation of results and their relevance to a particular biological system is study-dependent and beyond the scope of this protocol.

Suitability of anaerobic fungi culture supernatant or mixed ruminal fluid as novel silage additives

Abstract

This study investigated silage quality characteristics and ruminal fiber degradability of grass and straw ensiled with either anaerobic fungi (AF) supernatant with active fungal enzymes or mixed ruminal fluid as novel silage additives. Compared to control silages, AF supernatant improved the quality of grass and straw silages as evidenced by decreased pH, acetic acid concentration, and dry matter losses. Likewise, mixed ruminal fluid enhanced lactic acid fermentation, which further resulted in lower pH of the treated grass silage. The ruminal fiber degradability was determined using in situ incubations and, compared to controls, the cellulose degradability was higher for grass silage with AF supernatant, whereas ruminal degradability of straw silage was reduced by this treatment. In contrast, mixed ruminal fluid did not influence fiber degradability of silages in the rumen. Concluding, both novel additives improved silage quality, whereas only AF supernatant enhanced ruminal fiber degradability of grass silage and therefore may represent an approach for improving forage utilization by ruminants.

Key points

• Enzymes of anaerobic fungi supernatant improve quality of grass and straw silages.

• Mixed ruminal fluid enhances lactic acid fermentation when ensiling grass and straw.

• Enzymes of anaerobic fungi supernatant increase ruminal grass silage degradability.

Metaproteome plasticity sheds light on the ecology of the rumen microbiome and its connection to host traits

The arsenal of genes that microbes express reflect the way in which they sense their environment. We have previously reported that the rumen microbiome composition and its coding capacity are different in animals having distinct feed efficiency states, even when fed an identical diet. Here, we reveal that many microbial populations belonging to the bacteria and archaea domains show divergent proteome production in function of the feed efficiency state. Thus, proteomic data serve as a strong indicator of host feed efficiency state phenotype, overpowering predictions based on genomic and taxonomic information. We highlight protein production of specific phylogenies associated with each of the feed efficiency states. We also find remarkable plasticity of the proteome both in the individual population and at the community level, driven by niche partitioning and competition. These mechanisms result in protein production patterns that exhibit functional redundancy and checkerboard distribution that are tightly linked to the host feed efficiency phenotype. By linking microbial protein production and the ecological mechanisms that act within the microbiome feed efficiency states, our present work reveals a layer of complexity that bears immense importance to the current global challenges of food security and sustainability.

Rumen Metaproteomics Highlight the Unique Contributions of Microbe-Derived Extracellular and Intracellular Proteins for In Vitro Ruminal Fermentation

Rumen microorganisms can be used in in vitro anaerobic fermentation to encourage the sustainable exploitation of agricultural wastes. However, the understanding of active microbiota under in vitro ruminal fermentation conditions is still insufficient. To investigate how rumen microbes actively participate in the fermentation process in vitro, we resolved the metaproteome generated from ruminal fermentation broth after seven days of in vitro incubation. Herein, the sample-specific database for metaproteomic analysis was constructed according to the metagenomic data of in vitro ruminal fermentation. Based on the sample-specific database, we found in the metaproteome that Bacteroidetes and Firmicutes_A were the most active in protein expression, and over 50% of these proteins were assigned to gene categories involved in energy conversion and basic structures. On the other hand, a variety of bacteria-derived extracellular proteins, which contained carbohydrate-active enzyme domains, were found in the extracellular proteome of fermentation broth. Additionally, the bacterial intracellular/surface moonlighting proteins (ISMPs) and proteins of outer membrane vesicles were detected in the extracellular proteome, and these ISMPs were involved in maintaining microbial population size through potential adherence to substrates. The metaproteomic characterizations of microbial intracellular/extracellular proteins provide new insights into the ability of the rumen microbiome to maintain in vitro ruminal fermentation.

Characterization of fungal microbial diversity in Tibetan sheep, Tibetan gazelle and Tibetan antelope in the Qiangtang region of Tibet

Due to the high crude fiber content, straw of various crops is difficult to become a high quality forage resource. The degradation of cellulose in nature mainly depends on the cellulase secreted by microbes, which degrade cellulose into small molecular substances through chemical action, and the microbes that secrete cellulase mainly include some bacteria, fungi and actinomycetes, etc. The large and diverse microbial population contained in the mammalian gastrointestinal tract plays an important role in nutrient digestion. At present, many cellulose-degrading strains have been screened and obtained from animal digestive system and feces, such as Bacillus subtilis from the feces of Panda, Bacillus amyloliquefaciens from the cecum of goose. In this study, the fungal diversity was analysed in the fresh faeces of Tibetan sheep, Tibetan gazelle and Tibetan antelope in Qiangtang, Tibet. Results showed that the structure and species of gut fungi are different in three animals, which may be related to the different physiological functions among different animals, e.g., Tibetan antelope and Tibetan gazelle have stronger tolerance to rough feeding than Tibetan sheep. This study will lay a foundation for cellulose-degrading fungal development and provides technical support for improving rough feeding tolerance of Tibetan sheep.

Plant cell wall breakdown by hindgut microorganisms: can we get scientific insights from rumen microorganisms?

Equines and ruminants have evolved as grazing herbivores with specialized gastrointestinal tracts capable of utilizing a wide range of fibrous feeds. In China, agricultural by-products, including corn straw, wheat straw, peanut vine, wheat husk, rice husk, and grass hay, have been extensively included in both equine and ruminant diets. These plant materials, which are composed predominantly of cellulose, hemicellulose, noncellulosic polysaccharides, and lignin, are largely undegradable by equines and ruminants themselves. Their breakdown is accomplished by communities of resident microorganisms that live in symbiotic or mutualistic associations with the host. Information relating to microbial composition in the hindgut and rumen has become increasingly available. Rumen fermentation is unique in that plant cell wall breakdown relies on the cooperation between microorganisms that produce fibrolytic enzymes and that ruminant animals provide an anaerobic fermentation chamber. Similar to the rumen, the equine hindgut is also an immensely enlarged fermentative chamber that includes an extremely abundant and highly complex community of microorganisms. However, few studies have characterized the microbial functions and their utilization process of lignocellulosic feeds within the equine hindgut. The process of understanding and describing plant cell wall degradation mechanisms in the equine hindgut ecosystem is important for providing information for proper feeding practices to be implemented. In the present study, we gather existing information on the rumen and equine ecosystem and provide scientific insights for understanding the process of plant cell wall breakdown within the hindgut.

Current Progress in Optimising Sustainable Energy Recovery From Cattle Paunch Contents, a Slaughterhouse Waste Product

Paunch contents are the recalcitrant, lignocellulose-rich, partially-digested feed present in the rumen of ruminant animals. Cattle forage in Europe is primarily from perennial and Italian ryegrasses and/or white clover, so paunch contents from forage-fed cattle in Europe is enriched in these feedstuffs. Globally, due to its underutilisation, the potential energy in cattle paunch contents annually represents an energy loss of 23,216,548,750–27,804,250,000 Megajoules (MJ) and financial loss of up to ~€800,000,000. Therefore, this review aims to describe progress made to-date in optimising sustainable energy recovery from paunch contents. Furthermore, analyses to determine the economic feasibility/potential of recovering sustainable energy from paunch contents was carried out. The primary method used to recover sustainable energy from paunch contents to-date has involved biomethane production through anaerobic digestion (AD). The major bottleneck in its utilisation through AD is its recalcitrance, resulting in build-up of fibrous material. Pre-treatments partially degrade the lignocellulose in lignocellulose-rich wastes, reducing their recalcitrance. Enzyme systems could be inexpensive and more environmentally compatible than conventional solvent pre-treatments. A potential source of enzyme systems is the rumen microbiome, whose efficiency in lignocellulose degradation is attracting significant research interest. Therefore, the application of rumen fluid (liquid derived from dewatering of paunch contents) to improve biomethane production from AD of lignocellulosic wastes is included in this review. Analysis of a study where rumen fluid was used to pre-treat paper sludge from a paper mill prior to AD for biomethane production suggested economic feasibility for CHP combustion, with potential savings of ~€11,000 annually. Meta-genomic studies of bacterial/archaeal populations have been carried out to understand their ruminal functions. However, despite their importance in degrading lignocellulose in nature, rumen fungi remain comparatively under-investigated. Further investigation of rumen microbes, their cultivation and their enzyme systems, and the role of rumen fluid in degrading lignocellulosic wastes, could provide efficient pre-treatments and co-digestion strategies to maximise biomethane yield from a range of lignocellulosic wastes. This review describes current progress in optimising sustainable energy recovery from paunch contents, and the potential of rumen fluid as a pre-treatment and co-substrate to recover sustainable energy from lignocellulosic wastes using AD.

Biotechnological potential of rumen microbiota for sustainable bioconversion of lignocellulosic waste to biofuels and value-added products

Lignocellulosic biomass is an abundant resource with untapped potential for biofuel, enzymes, and chemical production. Its complex recalcitrant structure obstructs its bioconversion into biofuels and other value-added products. For improving its bioconversion efficiency, it is important to deconstruct its complex structure. In natural systems like rumen, diverse microbial communities carry out hydrolysis, acidogenesis, acetogenesis, and methanogenesis of lignocellulosic biomass through physical penetration, synergistic and enzymatic actions enhancing lignocellulose degradation activity. This review article aims to discuss comprehensively the rumen microbial ecosystem, their interactions, enzyme production, and applications for efficient bioconversion of lignocellulosic waste to biofuels. Furthermore, meta 'omics' approaches to elucidate the structure and functions of rumen microorganisms, fermentation mechanisms, microbe-microbe interactions, and host-microbe interactions have been discussed thoroughly. Additionally, feed additives' role in improving ruminal fermentation efficiency and reducing environmental nitrogen losses has been discussed. Finally, the current status of rumen microbiota applications and future perspectives for the development of rumen mimic bioreactors for efficient bioconversion of lignocellulosic wastes to biofuels and chemicals have been highlighted.

Glycan processing in gut microbiomes

Microbiomes and their enzymes process many of the nutrients accessible in the gastrointestinal tract of bilaterians and play an essential role in host health and nutrition. In this review, we describe recent insights into nutrient processing in microbiomes across three exemplary yet contrasting gastrointestinal ecosystems (humans, ruminants and insects), with focus on bacterial mechanisms for the utilization of common and atypical dietary glycans as well as host-derived mucus glycans. In parallel, we discuss findings from multi-omic studies that have provided new perspectives on understanding glycan-dependent interactions and the complex food-webs of microbial populations in their natural habitat. Using key examples, we emphasize how increasing understanding of glycan processing by gut microbiomes can provide critical insights to assist 'microbiome reprogramming', a growing field that seeks to leverage diet to improve animal growth and host health.

Immunomodulation Potential of Probiotics: A Novel Strategy for Improving Livestock Health, Immunity, and Productivity

Over the past decade, the use of probiotics as feed supplements in animal production has increased considerably due to the ban on antibiotic growth promoters in livestock. This review provides an overview of the current situation, limitation, and prospects for probiotic formulations applied to livestock. Recently, the use of probiotics in livestock has been suggested to significantly improve their health, immunity, growth performance, nutritional digestibility, and intestinal microbial balance. Furthermore, it was reported that the use of probiotics in animals was helpful in equilibrating their beneficial microbial population and microbial turnover via stimulating the host immune response through specific secretions and competitive exclusion of potentially pathogenic bacteria in the digestive tract. Recently, there has been great interest in the understanding of probiotics targeted diet and its ability to compete with harmful microbes and acquire their niches. Therefore, the present review explores the most commonly used probiotic formulations in livestock feed and their effect on animal health. In summary, this article provides an in-depth knowledge about the formulation of probiotics as a step toward a better alternative to antibiotic healthy growth strategies.

Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides

The largest living rodent, capybara, can efficiently depolymerize and utilize lignocellulosic biomass through microbial symbiotic mechanisms yet elusive. Herein, we elucidate the microbial community composition, enzymatic systems and metabolic pathways involved in the conversion of dietary fibers into short-chain fatty acids, a main energy source for the host. In this microbiota, the unconventional enzymatic machinery from Fibrobacteres seems to drive cellulose degradation, whereas a diverse set of carbohydrate-active enzymes from Bacteroidetes, organized in polysaccharide utilization loci, are accounted to tackle complex hemicelluloses typically found in gramineous and aquatic plants. Exploring the genetic potential of this community, we discover a glycoside hydrolase family of β-galactosidases (named as GH173), and a carbohydrate-binding module family (named as CBM89) involved in xylan binding that establishes an unprecedented three-dimensional fold among associated modules to carbohydrate-active enzymes. Together, these results demonstrate how the capybara gut microbiota orchestrates the depolymerization and utilization of plant fibers, representing an untapped reservoir of enzymatic mechanisms to overcome the lignocellulose recalcitrance, a central challenge toward a sustainable and bio-based economy.

Here, Cabral et al., perform a multi-omics analysis of the gut microbiome of capybara, the largest living rodent, unveiling enzymatic mechanisms for the breakdown of lignocellulosic biomass, and report two undescribed families of carbohydrate-active enzymes.

Concepts and Consequences of a Core Gut Microbiota for Animal Growth and Development

Animal microbiomes are occasionally considered as an extension of host anatomy, physiology, and even their genomic architecture. Their compositions encompass variable and constant portions when examined across multiple hosts. The latter, termed the core microbiome, is viewed as more accommodated to its host environment and suggested to benefit host fitness. Nevertheless, discrepancies in its definitions, characteristics, and importance to its hosts exist across studies. We survey studies that characterize the core microbiome, detail its current definitions and available methods to identify it, and emphasize the crucial need to upgrade and standardize the methodologies among studies. We highlight ruminants as a case study and discuss the link between the core microbiome and host physiology and genetics, as well as potential factors that shape it. We conclude with main directives of action to better understand the host-core microbiome axis and acquire the necessary insights into its controlled modulation. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Microbial communities and their enzymes facilitate degradation of recalcitrant polymers in anaerobic digestion

Microbial consortia efficiently degrade complex biopolymers found in the organic fraction of municipal solid waste (OFMSW). Through enzyme production and division of labor during anaerobic digestion, microbial communities break down recalcitrant polymers and make fermentation products, including methane. However, microbial communities remain underutilized for waste degradation as it remains difficult to characterize and predict microbial interactions during waste breakdown, especially as cultivation conditions change drastically throughout anaerobic digestion. This review discusses recent progress and opportunities in cultivating natural and engineered consortia for OFMSW hydrolysis, including how recalcitrant substrates are degraded by enzymes as well as the critical factors that govern microbial interactions and culture stability. Methods to measure substrate degradation are also reviewed, and we demonstrate the need for increased standardization to enable comparisons across different environments.

Lignocellulolytic microbiomes for augmenting lignocellulose degradation in anaerobic digestion

Bioaugmenting lignocellulose digestion with potent lignocellulolytic microbiomes (LMs) facilitates efficient biomethanation. Assessing the metabolic roles of microbial communities of the LMs and their complex interactions with the indigenous anaerobic digester microbiome is pivotal in implementing bioaugmentation. Multiple meta-omics are the frontline approaches to investigating gene functions, metabolic roles, and the ecological niches of LMs.

The role of gut mycobiome in health and diseases

The gut microbiome comprised of microbes from multiple kingdoms, including bacteria, fungi, and viruses. Emerging evidence suggests that the intestinal fungi (the gut "mycobiome") play an important role in host immunity and inflammation. Advances in next generation sequencing methods to study the fungi in fecal samples and mucosa tissues have expanded our understanding of gut fungi in intestinal homeostasis and systemic immunity in health and their contribution to different human diseases. In this review, the current status of gut mycobiome in health, early life, and different diseases including inflammatory bowel disease, colorectal cancer, and metabolic diseases were summarized.

Hydrolysis of lignocellulose by anaerobic fungi produces free sugars and organic acids for two-stage fine chemical production with Kluyveromyces marxianus

Development of the bioeconomy is driven by our ability to access the energy-rich carbon trapped in recalcitrant plant materials. Current strategies to release this carbon rely on expensive enzyme cocktails and physicochemical pretreatment, producing inhibitory compounds that hinder subsequent microbial bioproduction. Anaerobic fungi are an appealing solution as they hydrolyze crude, untreated biomass at ambient conditions into sugars that can be converted into value-added products by partner organisms. However, some carbon is lost to anaerobic fungal fermentation products. To improve efficiency and recapture this lost carbon, we built a two-stage bioprocessing system pairing the anaerobic fungus Piromyces indianae with the yeast Kluyveromyces marxianus, which grows on a wide range of sugars and fermentation products. In doing so we produce fine and commodity chemicals directly from untreated lignocellulose. P. indianae efficiently hydrolyzed substrates such as corn stover and poplar to generate sugars, fermentation acids, and ethanol, which K. marxianus consumed while producing 2.4 g/L ethyl acetate. An engineered strain of K. marxianus was also able to produce 550 mg/L 2-phenylethanol and 150 mg/L isoamyl alcohol from P. indianae hydrolyzed lignocellulosic biomass. Despite the use of crude untreated plant material, production yields were comparable to optimized rich yeast media due to the use of all available carbon including organic acids, which formed up to 97% of free carbon in the fungal hydrolysate. This work demonstrates that anaerobic fungal pretreatment of lignocellulose can sustain the production of fine chemicals at high efficiency by partnering organisms with broad substrate versatility.

The Present Role and New Potentials of Anaerobic Fungi in Ruminant Nutrition

The ruminal microbiota allows ruminants to utilize fibrous feeds and is in the limelight of ruminant nutrition research for many years. However, the overwhelming majority of investigations have focused on bacteria, whereas anaerobic fungi (AF) have been widely neglected by ruminant nutritionists. Anaerobic fungi are not only crucial fiber degraders but also important nutrient sources for the host. This review summarizes the current findings on AF and, most importantly, discusses their new application potentials in modern ruminant nutrition. Available data suggest AF can be applied as direct-fed microbials to enhance ruminal fiber degradation, which is indeed of interest for high-yielding dairy cows that often show depressed ruminal fibrolysis in response to high-grain feeding. Moreover, these microorganisms have relevance for the nutrient supply and reduction of methane emissions. However, to reach AF-related improvements in ruminal fiber breakdown and animal performance, obstacles in large-scale AF cultivation and applicable administration options need to be overcome. At feedstuff level, silage production may benefit from the application of fungal enzymes that cleave lignocellulosic structures and consequently enable higher energy exploitation from forages in the rumen. Concluding, AF hold several potentials in improving ruminant feeding and future research efforts are called for to harness these potentials.

Combined whole cell wall analysis and streamlined in silico carbohydrate-active enzyme discovery to improve biocatalytic conversion of agricultural crop residues

The production of biofuels as an efficient source of renewable energy has received considerable attention due to increasing energy demands and regulatory incentives to reduce greenhouse gas emissions. Second-generation biofuel feedstocks, including agricultural crop residues generated on-farm during annual harvests, are abundant, inexpensive, and sustainable. Unlike first-generation feedstocks, which are enriched in easily fermentable carbohydrates, crop residue cell walls are highly resistant to saccharification, fermentation, and valorization. Crop residues contain recalcitrant polysaccharides, including cellulose, hemicelluloses, pectins, and lignin and lignin-carbohydrate complexes. In addition, their cell walls can vary in linkage structure and monosaccharide composition between plant sources. Characterization of total cell wall structure, including high-resolution analyses of saccharide composition, linkage, and complex structures using chromatography-based methods, nuclear magnetic resonance, -omics, and antibody glycome profiling, provides critical insight into the fine chemistry of feedstock cell walls. Furthermore, improving both the catalytic potential of microbial communities that populate biodigester reactors and the efficiency of pre-treatments used in bioethanol production may improve bioconversion rates and yields. Toward this end, knowledge and characterization of carbohydrate-active enzymes (CAZymes) involved in dynamic biomass deconstruction is pivotal. Here we overview the use of common "-omics"-based methods for the study of lignocellulose-metabolizing communities and microorganisms, as well as methods for annotation and discovery of CAZymes, and accurate prediction of CAZyme function. Emerging approaches for analysis of large datasets, including metagenome-assembled genomes, are also discussed. Using complementary glycomic and meta-omic methods to characterize agricultural residues and the microbial communities that digest them provides promising streams of research to maximize value and energy extraction from crop waste streams.

Aestipascuomyces dupliciliberans gen. nov, sp. nov., the First Cultured Representative of the Uncultured SK4 Clade from Aoudad Sheep and Alpaca

We report on the isolation of the previously-uncultured Neocallimastigomycota SK4 lineage, by two independent research groups, from a wild aoudad sheep rumen sample (Texas, USA) and an alpaca fecal sample (Baden-Württemberg, Germany). Isolates from both locations showed near-identical morphological and microscopic features, forming medium-sized (2-5 mm) white filamentous colonies with a white center of sporangia, on agar roll tubes and a heavy biofilm in liquid media. Microscopic analysis revealed monocentric thalli, and spherical polyflagellated zoospores with 7-20 flagella. Zoospore release occurred through an apical pore as well as by sporangial wall rupturing, a duality that is unique amongst described anaerobic gut fungal strains. Isolates were capable of growing on a wide range of mono-, oligo-, and polysaccharide substrates as the sole carbon source. Phylogenetic assessment based on the D1-D2 28S large rRNA gene subunit (D1-D2 LSU) and internal transcribed spacer-1 (ITS-1) regions demonstrated high sequence identity (minimum identity of 99.07% and 96.96%, respectively) between all isolates; but low sequence identity (92.4% and 86.7%, respectively) to their closest cultured relatives. D1-D2 LSU phylogenetic trees grouped the isolates as a new monophyletic clade within the Orpinomyces-Neocallimastix-Pecoramyces-Feramyces-Ghazallamyces supragenus group. D1-D2 LSU and ITS-1 sequences recovered from the obtained isolates were either identical or displayed extremely high sequence similarity to sequences recovered from the same aoudad sheep sample on which isolation was conducted, as well as several sequences recovered from domestic sheep and few other herbivores. Interestingly, members of the SK4 clade seem to be encountered preferably in animals grazing on summer pasture. We hence propose accommodating these novel isolates in a new genus, Aestipascuomyces (derived from the Latin word for "summer pasture"), and a new species, A. dupliciliberans. The type strain is Aestipascuomycesdupliciliberans strain R4.

Anaerobic Fungi: Past, Present, and Future

Anaerobic fungi (AF) play an essential role in feed conversion due to their potent fiber degrading enzymes and invasive growth. Much has been learned about this unusual fungal phylum since the paradigm shifting work of Colin Orpin in the 1970s, when he characterized the first AF. Molecular approaches targeting specific phylogenetic marker genes have facilitated taxonomic classification of AF, which had been previously been complicated by the complex life cycles and associated morphologies. Although we now have a much better understanding of their diversity, it is believed that there are still numerous genera of AF that remain to be described in gut ecosystems. Recent marker-gene based studies have shown that fungal diversity in the herbivore gut is much like the bacterial population, driven by host phylogeny, host genetics and diet. Since AF are major contributors to the degradation of plant material ingested by the host animal, it is understandable that there has been great interest in exploring the enzymatic repertoire of these microorganisms in order to establish a better understanding of how AF, and their enzymes, can be used to improve host health and performance, while simultaneously reducing the ecological footprint of the livestock industry. A detailed understanding of AF and their interaction with other gut microbes as well as the host animal is essential, especially when production of affordable high-quality protein and other animal-based products needs to meet the demands of an increasing human population. Such a mechanistic understanding, leading to more sustainable livestock practices, will be possible with recently developed -omics technologies that have already provided first insights into the different contributions of the fungal and bacterial population in the rumen during plant cell wall hydrolysis.