Cellulose Degradation by Ruminal Microorganisms

Natural Foraging Selection and Gut Microecology of Two Subterranean Rodents from the Eurasian Steppe in China

As the most abundant group of mammals, rodents possess a very rich ecotype, which makes them ideal for studying the relationship between diet and host gut microecology. Zokors are specialized herbivorous rodents adapted to living underground. Unlike more generalized herbivorous rodents, they feed on the underground parts of grassland plants. There are two species of the genus Myospalax in the Eurasian steppes in China: one is Myospalax psilurus, which inhabits meadow grasslands and forest edge areas, and the other is M. aspalax, which inhabits typical grassland areas. How are the dietary choices of the two species adapted to long-term subterranean life, and what is the relationship of this diet with gut microbes? Are there unique indicator genera for their gut microbial communities? Relevant factors, such as the ability of both species to degrade cellulose, are not yet clear. In this study, we analyzed the gut bacterial communities and diet compositions of two species of zokors using 16S amplicon technology combined with macro-barcoding technology. We found that the diversity of gut microbial bacterial communities in M. psilurus was significantly higher than that in M. aspalax, and that the two species of zokors possessed different gut bacterial indicator genera. Differences in the feeding habits of the two species of zokors stem from food composition rather than diversity. Based on the results of Mantel analyses, the gut bacterial community of M. aspalax showed a significant positive correlation with the creeping-rooted type food, and there was a complementary relationship between the axis root-type-food- and the rhizome-type-food-dominated (containing bulb types and tuberous root types) food groups. Functional prediction based on KEGG found that M. psilurus possessed a stronger degradation ability in the same cellulose degradation pathway. Neutral modeling results show that the gut flora of the M. psilurus has a wider ecological niche compared to that of the M. aspalax. This provides a new perspective for understanding how rodents living underground in grassland areas respond to changes in food conditions.

Invited review: "Probiotic" approaches to improving dairy production: Reassessing "magic foo-foo dust"

The gastrointestinal microbial consortium in dairy cattle is critical to determining the energetic status of the dairy cow from birth through her final lactation. The ruminant's microbial community can degrade a wide variety of feedstuffs, which can affect growth, as well as production rate and efficiency on the farm, but can also affect food safety, animal health, and environmental impacts of dairy production. Gut microbial diversity and density are powerful tools that can be harnessed to benefit both producers and consumers. The incentives in the United States to develop Alternatives to Antibiotics for use in food-animal production have been largely driven by the Veterinary Feed Directive and have led to an increased use of probiotic approaches to alter the gastrointestinal microbial community composition, resulting in improved heifer growth, milk production and efficiency, and animal health. However, the efficacy of direct-fed microbials or probiotics in dairy cattle has been highly variable due to specific microbial ecological factors within the host gut and its native microflora. Interactions (both synergistic and antagonistic) between the microbial ecosystem and the host animal physiology (including epithelial cells, immune system, hormones, enzyme activities, and epigenetics) are critical to understanding why some probiotics work but others do not. Increasing availability of next-generation sequencing approaches provides novel insights into how probiotic approaches change the microbial community composition in the gut that can potentially affect animal health (e.g., diarrhea or scours, gut integrity, foodborne pathogens), as well as animal performance (e.g., growth, reproduction, productivity) and fermentation parameters (e.g., pH, short-chain fatty acids, methane production, and microbial profiles) of cattle. However, it remains clear that all direct-fed microbials are not created equal and their efficacy remains highly variable and dependent on stage of production and farm environment. Collectively, data have demonstrated that probiotic effects are not limited to the simple mechanisms that have been traditionally hypothesized, but instead are part of a complex cascade of microbial ecological and host animal physiological effects that ultimately impact dairy production and profitability.

Effect of concentrates level on digestibility, ruminal fermentation, and bacterial community in growing camels

Understanding the rumen microbiota of camels under different feeding conditions is necessary to optimize rumen fermentation and productivity. This study aims to investigate the effects of different concentrate supplement levels on digestion, rumen fermentation and bacteria in growing camels. Fifteen growing camels were divided into three groups and were fed alfalfa hay in addition to one of the three concentrate supplement levels based on body weight (BW): low (0.7%), medium (1%), and high (1.3%). Increasing the concentrate supplement level in the diet increased total dry matter intake but had no effect on nutrients digestibility, except for crude protein digestibility, which was enhanced with the high concentrate level. Growing camels at low-level had considerably higher rumen pH than those fed medium or high levels. Increasing the supplement level also increased rumen propionic acid but decreased acetic acid concentration. Principal coordinate analysis showed that concentrate levels clearly separated the ruminal bacterial communities where Bacteroidetes and Firmicutes were the dominant phyla and Prevotella, Ruminococcus, Butyrivibrio, RC9_gut_group, and Fibrobacteres were the dominant bacterial genera. This study expands our knowledge regarding the rumen microbiota of growing camels under different concentrate levels and reveals that medium concentrate levels could be appropriate for growing camels.

Forages and pastures symposium: forage biodegradation: advances in ruminal microbial ecology

The rumen microbial ecosystem provides ruminants a selective advantage, the ability to utilize forages, allowing them to flourish worldwide in various environments. For many years, our understanding of the ruminal microbial ecosystem was limited to understanding the microbes (usually only laboratory-amenable bacteria) grown in pure culture, meaning that much of our understanding of ruminal function remained a "black box." However, the ruminal degradation of plant cell walls is performed by a consortium of bacteria, archaea, protozoa, and fungi that produces a wide variety of carbohydrate-active enzymes (CAZymes) that are responsible for the catabolism of cellulose, hemicellulose, and pectin. The past 15 years have seen the development and implementation of numerous next-generation sequencing (NGS) approaches (e.g., pyrosequencing, Illumina, and shotgun sequencing), which have contributed significantly to a greater level of insight regarding the microbial ecology of ruminants fed a variety of forages. There has also been an increase in the utilization of liquid chromatography and mass spectrometry that revolutionized transcriptomic approaches, and further improvements in the measurement of fermentation intermediates and end products have advanced with metabolomics. These advanced NGS techniques along with other analytic approaches, such as metaproteomics, have been utilized to elucidate the specific role of microbial CAZymes in forage degradation. Other methods have provided new insights into dynamic changes in the ruminal microbial population fed different diets and how these changes impact the assortment of products presented to the host animal. As more omics-based data has accumulated on forage-fed ruminants, the sequence of events that occur during fiber colonization by the microbial consortium has become more apparent, with fungal populations and fibrolytic bacterial populations working in conjunction, as well as expanding understanding of the individual microbial contributions to degradation of plant cell walls and polysaccharide components. In the future, the ability to predict microbial population and enzymatic activity and end products will be able to support the development of dynamic predictive models of rumen forage degradation and fermentation. Consequently, it is imperative to understand the rumen's microbial population better to improve fiber degradation in ruminants and, thus, stimulate more sustainable production systems.

Bioconversion of cellulose into bisabolene using Ruminococcus flavefaciens and Rhodosporidium toruloides

In this study, organic acids were demonstrated as a promising carbon source for bisabolene production by the non-conventional yeast, Rhodosporidium toruloides, at microscale with a maximum titre of 1055 ± 7 mg/L. A 125-fold scale-up of the optimal process, enhanced bisabolene titres 2.5-fold to 2606 mg/L. Implementation of a pH controlled organic acid feeding strategy at this scale lead to a further threefold improvement in bisabolene titre to 7758 mg/L, the highest reported microbial titre. Finally, a proof-of-concept sequential bioreactor approach was investigated. Firstly, the cellulolytic bacterium Ruminococcus flavefaciens was employed to ferment cellulose, yielding 4.2 g/L of organic acids. R. toruloides was subsequently cultivated in the resulting supernatant, producing 318 ± 22 mg/L of bisabolene. This highlights the feasibility of a sequential bioprocess for the bioconversion of cellulose, into biojet fuel candidates. Future work will focus on enhancing organic acid yields and the use of real lignocellulosic feedstocks to further enhance bisabolene production.

Modulation of rumen bacterial community and feed utilization in camel and sheep using combined supplementation of live yeast and microalgae

The combination of live yeast and microalgae as feed supplementation could improve rumen fermentation and animal productivity. This study aimed to investigate the impact of a mixture of (YA) yeast (Saccharomyces cerevisiae) and microalgae (Spirulina platensis and Chlorella vulgaris) as feed supplementation on feed intake, rumen disappearance of barley straw, bacteria, and fermentation, blood parameters of camels and sheep. Three fistulated camels and three fistulated rams were fed a concentrates mixture and ad libitum barley straw as a basal diet alone or supplemented with YA mixture. The dietary supplementation improved the feed intake, rumen disappearance of barley straw nutrients, and the blood immunity parameters. The YA supplementation affected rumen fermentation as well as the composition and diversity of rumen bacteria; however, the response to the supplementation varied according to animal species. Principle Coordinate Analysis (PCoA) separated bacterial communities based on animal species and feeding treatment. Phylum Bacteroidetes and Firmicutes dominated the bacterial community; and the dominant genera were Prevotella, RC9_gut_group, Butyrivibrio, Ruminococcus, Saccharofermentans, Christensenellaceae_R-7_group, and Succiniclasticum. Our results suggest positive impacts of YA supplementation in rumen fermentation and animal performance.

A fungal symbiont converts provisioned cellulose into edible yield for its leafcutter ant farmers

While ants are dominant consumers in terrestrial habitats, only the leafcutters practice herbivory. Leafcutters do this by provisioning a fungal cultivar (Leucoagaricus gongylophorus) with freshly cut plant fragments and harnessing its metabolic machinery to convert plant mulch into edible fungal tissue (hyphae and swollen hyphal cells called gongylidia). The cultivar is known to degrade cellulose, but whether it assimilates this ubiquitous but recalcitrant molecule into its nutritional reward structures is unknown. We use in vitro experiments with isotopically labelled cellulose to show that fungal cultures from an Atta colombica leafcutter colony convert cellulose-derived carbon into gongylidia, even when potential bacterial symbionts are excluded. A laboratory feeding experiment showed that cellulose assimilation also occurs in vivo in A. colombica colonies. Analyses of publicly available transcriptomic data further identified a complete, constitutively expressed, cellulose-degradation pathway in the fungal cultivar. Confirming leafcutters use cellulose as a food source sheds light on the eco-evolutionary success of these important herbivores.

Understanding the Role of Prevotella Genus in the Digestion of Lignocellulose and Other Substrates in Vietnamese Native Goats' Rumen by Metagenomic Deep Sequencing

Simple Summary

Prevotella is an abundant genus which plays an important role for lignocellulose digestion in goat rumen and is significant to the yield and quality of milk and meat in cows. In a previous study, we sequenced bacterial metagenome from Vietnamese native goat rumen to get 8.4 GB clean data and found very diverse genes related to lignocellulose degradation. However, due to the limitation in the metagenomic size, low amount of complete lignocellulase genes, and high bacterial diversity, further analysis was restricted. In this study, metagenomic deep sequencing was used to obtain 48.66 GB of reliable data, thus some lignocellulolytic enzymes were first seen and a picture of bacterial enzymes involved in lignocellulose digestion in the goat rumen was drawn. The loci for galactan-, xylan-, and arabinan-processing in Prevotella were observed for the first time. We confirm that Prevotella plays pivotal role for hemicellulose digestion and significantly participates in starch, cellulose, hemicellulose, and pectin conversion in the goat rumen. A gene coding endoxylanase was expressed in E. coli. The recombinant enzyme was tolerant with some salts, detergents, and had high activity, thus is a good candidate for lignocellulose processing and as an animal feed food additive to effectively improve xylooligosaccharide production.

Abstract

Bacteria in rumen play pivotal roles in the digestion of nutrients to support energy for the host. In this study, metagenomic deep sequencing of bacterial metagenome extracted from the goats’ rumen generated 48.66 GB of data with 3,411,867 contigs and 5,367,270 genes. The genes were mainly functionally annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) Carbohydrate-Active enZYmes (CAZy), and HMMER database, and taxonomically classified by MEGAN. As a result, 65,554 genes encoding for 30 enzymes/proteins related to lignocellulose conversion were exploited, in which nine enzymes were seen for the first time in goat rumen. Prevotella was the most abundant genus, contributing 30% hemicellulases and 36% enzymes/proteins for lignocellulose pretreatment, and supporting 98.8% of feruloyl esterases and 71.7% acetylxylan esterases. In addition, 18 of the 22 most lignocellulose digesting- potential contigs belonged to Prevotella. Besides, Prevotella possessed many genes coding for amylolytic enzymes. One gene encoding for endoxylanase was successfully expressed in E. coli. The recombinant enzyme had high Vmax, was tolerant to some salts and detergents, worked better at pH 5.5–6.5, temperature 40–50 °C, and was capable to be used in practices. Based on these findings, we confirm that Prevotella plays a pivotal role for hemicellulose digestion and significantly participates in starch, cellulose, hemicellulose, and pectin digestion in the goat rumen.

Non-fiber Carbohydrates in Forages and Their Influence on Beef Production Systems

Forages can provide a complete diet for ruminant animals, increasing the sustainability of beef production systems worldwide while reducing competition with humans for agricultural land or grain crops. Much of the emphasis on the nutritional characteristics of forages has been on the fiber, sugars, starch, and protein they supply to the rumen, despite the fact that other less-explored constituents, i.e., neutral detergent soluble fiber (NDSF) and other non-structural or non-fiber carbohydrates (NFC) also play a key role in the nutrition of ruminants. This paper explores the less investigated potential of temperate legumes to accumulate levels of NFC comparable to corn silage or beet pulp in cool, dry environments under irrigation, and its implications for forage-based beef production systems. We conclude that genetic or managerial interventions (i.e., breeding programs, defoliation frequency) or ecological conditions (i.e., climate, elevation) that increase concentrations of NFC in legumes can enhance beef production, meat quality, and the efficiency of nitrogen utilization by ruminants while reducing environmental impacts.

Systematic Analysis of Escherichia coli Isolates from Sheep and Cattle Suggests Adaption to the Rumen Niche

The commonly used laboratory bacterium Escherichia coli normally does not produce and secrete cellulases due to its complex bilayer membrane structure and poor secretory apparatus. In our previous study, the cellulolytic E. coli strain ZH-4 with extracellular cellulase activity was found in the bovine rumen. In this study, we demonstrate that the secretion of cellulase is a common feature of E. coli isolates from the rumen of animals such as sheep and cattle. Physiological phenotype characterization of these E. coli isolates, together with genome, transcriptome, and comparative genomics analysis, suggests their adaption to the rumen niche. The higher growth rate of the isolated strains under aerobic conditions meets the competitive requirements of the strains in rumen microecosystem, while anaerobic accumulation of reduced H₂ and succinate is hypothesized to be the results of adaptation to the rumen environment. Cellulase secretion increased significantly when the molecular chaperone genes ibpA and ibpB were overexpressed. This was also revealed by the transcriptomic data. A possible mechanism for cellulase secretion by E. coli isolates was proposed based on the transcriptomic data and molecular experiments.IMPORTANCE As an important intestinal microorganism, E. coli is present in the intestinal tract of animals and in many other environments. However, it normally does not produce and secret cellulases due to its complex bilayer membrane structure and poor secretory apparatus. Here, we proved that E. coli is widely present in the rumen of sheep and cattle. Systematic analysis of the isolates indicated that they have adapted to the rumen niche, with phenotypes that include secretion of cellulase and fermentative accumulation of succinate and H₂ The finding that overexpression of small heat shock protein genes ibpA and ibpB could facilitate cellulase BcsZ secretion, which provides a possible insight into the protein secretion mechanism of rumen-colonizing E. coli.

Relationships between chemical composition and in vitro gas production parameters of maize leaves and stems

This study investigated the chemical composition (proximate and Van Soest analysis) and in vitro gas production parameters of maize leaves and stems separately, and related the in vitro gas production parameters with the chemical composition, of thirteen maize cultivars. After harvest in September 2016, all plants were separated into two morphological fractions: leaves and stems. The crude protein (CP) content was greater, and the ratio of acid detergent lignin (ADL) to potentially rumen degradable fibre (calculated as the difference between neutral detergent fibre and ADL; ADL:pRDF) was lower in the leaves than in the stems in all 13 cultivars. For the leaves, the cumulative gas production between 3 and 20 hr (A2), representing cell wall fermentation in the rumen fluid, and the cumulative 72‐hr gas production (GP72), representing total organic matter (OM) degradation, were moderately to weakly correlated with the chemical composition, including hemicellulose, cellulose, ADL and CP content (R² < 0.40), whilst the best relationship between the half‐time value (B2), representing the rate of cell wall degradation, and chemical composition had an R² of 0.63. For the stems, the best relationship between A2, B2 and GP72 with chemical composition was greater (R² ≥ 0.74) and the best relationship included hemicellulose (A2 only), cellulose and ADL (GP72 and A2 only) contents. In conclusion, maize leaves and stems differed in chemical composition, in particular CP content and ADL:pRDF. The A2 and GP72 of the stems, but not of the leaves, were highly correlated with the chemical composition, indicating that the cell wall and OM degradation of maize stems can be better predicted by its chemical composition.

Amino Acids and Ribose: Drivers of Protein and RNA Fermentation by Ingested Bacteria of a Primitive Gut Ecosystem

Animal health is linked to gut ecosystems whose primary function is normally the digestion of dietary matter. Earthworms are representative of one of the oldest known animal lineages and, despite their primitive nature, have unique environmental impact by virtue of their dietary consumption of their habitat, i.e., soil-associated matter. A resident gut community is a hallmark of many gut ecosystems of evolutionarily more advanced animals, but the alimentary canal of earthworms is dominated by ingested transient soil microbes. Protein and RNA are (i) the primary organic components of microbial cells that are subject to lysis during gut passage and (ii) fermentable dietary substrates in the alimentary canal. This study examined the gut-associated fermentation of constituents of these biopolymers to determine how their fermentation is integrated to the microbiological dynamics of the gut and might contribute to earthworm-linked transformations of organic matter in the terrestrial biosphere.

Earthworms are among the most primitive animals and are of fundamental importance to the turnover of organic matter in the terrestrial biosphere. These invertebrates ingest materials that are colonized by microbes, some of which are subject to disruption by the crop/gizzard or other lytic events during gut passage. Protein and RNA are dominant polymers of disrupted microbial cells, and these biopolymers facilitate robust fermentations by surviving ingested bacteria. To further resolve these fermentations, amino acids and ribose (as fermentable constituents of protein and RNA, respectively) were evaluated as potential drivers of fermentation in gut content of the model earthworm Lumbricus terrestris (taxa were examined with 16S rRNA-based analyses). Of eight amino acids tested, glutamate, aspartate, and threonine were most stimulatory and yielded dissimilar fermentations facilitated by contrasting taxa (e.g., glutamate stimulated the Fusobacteriaceae and yielded H₂ and formate, whereas aspartate stimulated the Aeromonadaceae and yielded succinate and propionate). A marginal Stickland fermentation was associated with the Peptostreptococcaceae and Lachnospiraceae. Ribose fermentation yielded a complex product profile facilitated primarily by the Aeromonadaceae. The transient nature of succinate was linked to its decarboxylation to propionate and the Fusobacteriaceae, whereas the transient nature of formate was linked to formate-hydrogen lyase activity and the Peptostreptococcaceae. These findings reinforce the likelihood that (i) the animal host and hosted fermentative bacteria compete for the constituents of protein and RNA in the alimentary canal and (ii) diverse gut fermenters engaged in the fermentation of these constituents produce products that can be utilized by earthworms.

IMPORTANCE Animal health is linked to gut ecosystems whose primary function is normally the digestion of dietary matter. Earthworms are representative of one of the oldest known animal lineages and, despite their primitive nature, have unique environmental impact by virtue of their dietary consumption of their habitat, i.e., soil-associated matter. A resident gut community is a hallmark of many gut ecosystems of evolutionarily more advanced animals, but the alimentary canal of earthworms is dominated by ingested transient soil microbes. Protein and RNA are (i) the primary organic components of microbial cells that are subject to lysis during gut passage and (ii) fermentable dietary substrates in the alimentary canal. This study examined the gut-associated fermentation of constituents of these biopolymers to determine how their fermentation is integrated to the microbiological dynamics of the gut and might contribute to earthworm-linked transformations of organic matter in the terrestrial biosphere.

The Phylogenomic Diversity of Herbivore-Associated Fibrobacter spp. Is Correlated to Lignocellulose-Degrading Potential

Members of the genus Fibrobacter are cellulose-degrading bacteria and common constituents of the gastrointestinal microbiota of herbivores. Although considerable phylogenetic diversity is observed among members of this group, few functional differences explaining the distinct ecological distributions of specific phylotypes have been described. In this study, we sequenced and performed a comparative analysis of whole genomes from 38 novel Fibrobacter strains against the type strains for the two formally described Fibrobacter species F. succinogenes strain S85 and F. intestinalis strain NR9. Significant differences in the number of genes encoding carbohydrate-active enzyme families involved in plant cell wall polysaccharide degradation were observed among Fibrobacter phylotypes. F. succinogenes genomes were consistently enriched in genes encoding carbohydrate-active enzymes compared to those of F. intestinalis strains. Moreover, genomes of F. succinogenes phylotypes that are dominant in the rumen had significantly more genes annotated to major families involved in hemicellulose degradation (e.g., CE6, GH10, and GH43) than did the genomes of F. succinogenes phylotypes typically observed in the lower gut of large hindgut-fermenting herbivores such as horses. Genes encoding a putative urease were also identified in 12 of the Fibrobacter genomes, which were primarily isolated from hindgut-fermenting hosts. Screening for growth on urea as the sole source of nitrogen provided strong evidence that the urease was active in these strains. These results represent the strongest evidence reported to date for specific functional differences contributing to the ecology of Fibrobacter spp. in the herbivore gut.IMPORTANCE The herbivore gut microbiome is incredibly diverse, and a functional understanding of this diversity is needed to more reliably manipulate this community for specific gain, such as increased production in ruminant livestock. Microbial degraders of plant cell wall polysaccharides in the herbivore gut, particularly Fibrobacter spp., are of fundamental importance to their hosts for digestion of a diet consisting primarily of recalcitrant plant fibers. Considerable phylogenetic diversity exists among members of the genus Fibrobacter, but much of this diversity remains cryptic. Here, we used comparative genomics, applied to a diverse collection of recently isolated Fibrobacter strains, to identify a robust association between carbohydrate-active enzyme gene content and the Fibrobacter phylogeny. Our results provide the strongest evidence reported to date for functional differences among Fibrobacter phylotypes associated with either the rumen or the hindgut and emphasize the general significance of carbohydrate-active enzymes in the evolution of fiber-degrading bacteria.

Prediction of Lignin Content in Ruminant Diets and Fecal Samples Using Rapid Analytical Techniques

The measurement of lignin content in ruminant diet and fecal samples is important for digestibility studies, but it is typically time-consuming and costly. The work reported involves correlation of traditional wet chemistry data with those from three rapid instrumental techniques, Fourier transform infrared spectroscopy (FTIR), conventional thermogravimteric analysis (TGA), and high-resolution TGA (MaxRes TGA) to predict the lignin content of diets and feces from digestibility trials. Calibration and performance data indicate that the FTIR model is acceptable for screening, while the conventional and MaxRes TGA predictions are high accuracy for quantitative analysis. Cross validation and model performance data reveal that MaxRes TGA provides the best-performing predictive model. This work shows that MaxRes TGA can accurately predict lignin content in ruminant diet and fecal samples with distinct advantages over traditional wet chemistry: namely, the requirement of small sample size, ease of sample preparation, speed of analysis, and high sample throughput at considerably lower cost.

Incorporating the influent cellulose fraction in activated sludge modelling

Cellulose represents a significant fraction of domestic wastewater, but it is not considered as a separate state variable in the conventional Activated Sludge Models (ASM). Cellulose is a very slowly degradable substrate that in traditional wastewater characterisation methods would be characterised partly as slowly biodegradable and partly as inert material. This can be problematic when the same model is used under different temperature conditions or different solid retention times. Also with the emerging attention for cellulose recovery, inclusion of this compound in models helps to assess the impact of cellulose recovery on operations and on operational costs. But also in membrane bioreactors, sieves are used in order to remove fibrous material, mainly cellulose. In this study a modification of ASM1 is proposed, where cellulose is introduced as a separate state variable and it is supposed to degrade with a first order hydrolysis rate. With the aid of this model, the effect of fine sieves is simulated using two alternatives, by either sieving the influent or the activated sludge. The model proved to be useful for operational purposes, and illustrates the need for including cellulose as separate state variable.

Novel Insights from Comparative In Silico Analysis of Green Microalgal Cellulases

The assumption that cellulose degradation and assimilation can only be carried out by heterotrophic organisms was shattered in 2012 when it was discovered that the unicellular green alga, Chlamydomonas reinhardtii (Cr), can utilize cellulose for growth under CO₂-limiting conditions. Publications of genomes/transcriptomes of the colonial microalgae, Gonium pectorale (Gp) and Volvox carteri (Vc), between 2010⁻2016 prompted us to look for cellulase genes in these algae and to compare them to cellulases from bacteria, fungi, lower/higher plants, and invertebrate metazoans. Interestingly, algal catalytic domains (CDs), belonging to the family GH9, clustered separately and showed the highest (33⁻42%) and lowest (17⁻36%) sequence identity with respect to cellulases from invertebrate metazoans and bacteria, respectively, whereas the identity with cellulases from plants was only 27⁻33%. Based on comparative multiple alignments and homology models, the domain arrangement and active-site architecture of algal cellulases are described in detail. It was found that all algal cellulases are modular, consisting of putative novel cysteine-rich carbohydrate-binding modules (CBMs) and proline/serine-(PS) rich linkers. Two genes were found to encode a protein with a putative Ig-like domain and a cellulase with an unknown domain, respectively. A feature observed in one cellulase homolog from Gp and shared by a spinach cellulase is the existence of two CDs separated by linkers and with a C-terminal CBM. Dockerin and Fn-3-like domains, typically found in bacterial cellulases, are absent in algal enzymes. The targeted gene expression analysis shows that two Gp cellulases consisting, respectively, of a single and two CDs were upregulated upon filter paper addition to the medium.

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Rumen microbiome biology gets a boost with the release of 410 high-quality reference genomes from the Hungate1000 project.

Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B₁₂, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ∼75% of the genus-level bacterial and archaeal taxa present in the rumen.

The Ruminococci: key symbionts of the gut ecosystem

Mammalian gut microbial communities form intricate mutualisms with their hosts, which have profound implications on overall health. One group of important gut microbial mutualists are bacteria in the genus Ruminococcus, which serve to degrade and convert complex polysaccharides into a variety of nutrients for their hosts. Isolated decades ago from the bovine rumen, ruminococci have since been cultured from other ruminant and non-ruminant sources, and next-generation sequencing has further shown their distribution to be widespread in a diversity of animal hosts. While most ruminococci that have been studied are those capable of degrading cellulose, much less is known about non-cellulolytic, nonruminant-associated species, such as those found in humans. Furthermore, a mechanistic understanding of the role of Ruminococcus spp. in their respective hosts is still a work in progress. This review highlights the broad work done on species within the genus Ruminococcus with respect to their physiology, phylogenetic relatedness, and their potential impact on host health.

A global analysis of gene expression in Fibrobacter succinogenes S85 grown on cellulose and soluble sugars at different growth rates

BACKGROUND

Cellulose is the most abundant biological polymer on earth, making it an attractive substrate for the production of next-generation biofuels and commodity chemicals. However, the economics of cellulose utilization are currently unfavorable due to a lack of efficient methods for its hydrolysis. Fibrobacter succinogenes strain S85, originally isolated from the bovine rumen, is among the most actively cellulolytic mesophilic bacteria known, producing succinate as its major fermentation product. In this study, we examined the transcriptome of F. succinogenes S85 grown in continuous culture at several dilution rates on cellulose, cellobiose, or glucose to gain a system-level understanding of cellulose degradation by this bacterium.

RESULTS

Several patterns of gene expression were observed for the major cellulases produced by F. succinogenes S85. A large proportion of cellulase genes were constitutively expressed, including the gene encoding for Cel51A, the major cellulose-binding endoglucanase produced by this bacterium. Moreover, other cellulase genes displayed elevated expression during growth on cellulose relative to growth on soluble sugars. Growth rate had a strong effect on global gene expression, particularly with regard to genes predicted to encode carbohydrate-binding modules and glycoside hydrolases implicated in hemicellulose degradation. Expression of hemicellulase genes was tightly regulated, with these genes displaying elevated expression only during slow growth on soluble sugars. Clear differences in gene expression were also observed between adherent and planktonic populations within continuous cultures growing on cellulose.

CONCLUSIONS

This work emphasizes the complexity of the fiber-degrading system utilized by F. succinogenes S85, and reinforces the complementary role of hemicellulases for accessing cellulose by these bacteria. We report for the first time evidence of global differences in gene expression between adherent and planktonic populations of an anaerobic bacterium growing on cellulose at steady state during continuous cultivation. Finally, our results also highlight the importance of controlling for growth rate in investigations of gene expression.

Biochanin A improves fibre fermentation by cellulolytic bacteria

AIMS

The objective was to determine the effect of the isoflavone biochanin A (BCA) on rumen cellulolytic bacteria and consequent fermentative activity.

METHODS AND RESULTS

When bovine microbial rumen cell suspensions (n = 3) were incubated (24 h, 39°C) with ground hay, cellulolytic bacteria proliferated, short-chain fatty acids were produced and pH declined. BCA (30 μg ml^-1 ) had no effect on the number of cellulolytic bacteria or pH, but increased acetate, propionate and total SCFA production. Addition of BCA improved total digestibility when cell suspensions (n = 3) were incubated (48 h, 39°C) with ground hay, Avicel, or filter paper. Fibrobacter succinogenes S85, Ruminococcus flavefaciens 8 and Ruminococcus albus 8 were directly inhibited by BCA. Synergistic antimicrobial activity was observed with BCA and heat killed cultures of cellulolytic bacteria, but the effects were species dependent.

CONCLUSIONS

These results indicate that BCA improves fibre degradation by influencing cellulolytic bacteria competition and guild composition.

SIGNIFICANCE AND IMPACT OF THE STUDY

BCA could serve as a feed additive to improve cellulosis when cattle are consuming high-fibre diets. Future research is needed to evaluate the effect of BCA on fibre degradation and utilization in vivo.

A metagenomic approach to discover a novel β-glucosidase from bovine rumens

β-Glucosidases play an important role in biomass degradation as they hydrolyze cellobiose to glucose in a final step of cellulolysis. In particular, ruminant animals rely onβ-glucosidases from rumen microorganisms for conversion of plant cellulosic materials into glucose. In this study, we are interested in characterization of a novelβ-glucosidase from rumen microorganisms. However, most rumen microorganisms are obligate anaerobes, which require special cultivation conditions. Presently, the metagenomic techniques, which enable isolation and characterization of microbial genes directly from environmental samples, have been applied to overcome these problems. In this study, the sequence-based screening approach was successfully applied to identify a novelβ-glucosidase gene,Br2, from a bovine rumen metagenomic sample. A 1338-bp complete coding sequence ofBr2encodes a 51-kDa GH1β-glucosidase of 445 amino acid residues with 59% sequence identity to aβ-glucosidase fromCellulosilyticum ruminicolaJCM 14822. The recombinantly expressed Br2 exhibited an optimal activity at pH 6.5 and 40°C, reflecting its rumen bacterial origin, and relatively higher catalytic efficiencies toward glucoside and fucoside substrates than other glycosides, similar to many previously reported bacterialβ-glucosidases. Our sequence-based screening approach can be applied to identify other genes of interest from environmental samples.

Impact of food intake on in vivo VOC concentrations in exhaled breath assessed in a caprine animal model

Physiological processes within the body may change emitted volatile organic compound (VOC) composition, and may therefore cause confounding biological background variability in breath gas analyses. To evaluate the effect of food intake on VOC concentration patterns in exhaled breath, this study assessed the variability of VOC concentrations due to food intake in a standardized caprine animal model. VOCs in (i) alveolar breath gas samples of nine clinically healthy goats and (ii) room air samples were collected and pre-concentrated before morning feeding and repeatedly after (+60 min, +150 min, +240 min) using needle trap microextraction (NTME). Analysis of VOCs was performed by gas chromatography and mass spectrometry (GC-MS). Only VOCs with significantly higher concentrations in breath gas samples compared to room air samples were taken into consideration. Six VOCs that belonged to the chemical classes of hydrocarbons and alcohols were identified presenting significantly different concentrations before and after feeding. Selected hydrocarbons showed a concentration pattern that was characterized by an initial increase 60 min after food intake, and a subsequent gradual decrease. Results emphasize consideration of physiological effects on exhaled VOC concentrations due to food intake with respect to standardized protocols of sample collection and critical evaluation of results.

Physiological variability in volatile organic compounds (VOCs) in exhaled breath and released from faeces due to nutrition and somatic growth in a standardized caprine animal model

Physiological effects may change volatile organic compound (VOC) concentrations and may therefore act as confounding factors in the definition of VOCs as disease biomarkers. To evaluate the extent of physiological background variability, this study assessed the effects of feed composition and somatic growth on VOC patterns in a standardized large animal model. Fifteen clinically healthy goats were followed during their first year of life. VOCs present in the headspace over faeces, exhaled breath and ambient air inside the stable were repeatedly assessed in parallel with the concentrations of glucose, protein, and albumin in venous blood. VOCs were collected and analysed using solid-phase or needle-trap microextraction and gas chromatograpy together with mass spectroscopy. The concentrations of VOCs in exhaled breath and above faeces varied significantly with increasing age of the animals. The largest variations in volatiles detected in the headspace over faeces occurred with the change from milk feeding to plant-based diet. VOCs above faeces and in exhaled breath correlated significantly with blood components. Among VOCs exhaled, the strongest correlations were found between exhaled nonanal concentrations and blood concentrations of glucose and albumin. Results stress the importance of a profound knowledge of the physiological backgrounds of VOC composition before defining reliable and accurate marker sets for diagnostic purposes.

Salmonella pathogenicity and host adaptation in chicken-associated serovars

Enteric pathogens such as Salmonella enterica cause significant morbidity and mortality. S. enterica serovars are a diverse group of pathogens that have evolved to survive in a wide range of environments and across multiple hosts. S. enterica serovars such as S. Typhi, S. Dublin, and S. Gallinarum have a restricted host range, in which they are typically associated with one or a few host species, while S. Enteritidis and S. Typhimurium have broad host ranges. This review examines how S. enterica has evolved through adaptation to different host environments, especially as related to the chicken host, and continues to be an important human pathogen. Several factors impact host range, and these include the acquisition of genes via horizontal gene transfer with plasmids, transposons, and phages, which can potentially expand host range, and the loss of genes or their function, which would reduce the range of hosts that the organism can infect. S. Gallinarum, with a limited host range, has a large number of pseudogenes in its genome compared to broader-host-range serovars. S. enterica serovars such as S. Kentucky and S. Heidelberg also often have plasmids that may help them colonize poultry more efficiently. The ability to colonize different hosts also involves interactions with the host's immune system and commensal organisms that are present. Thus, the factors that impact the ability of Salmonella to colonize a particular host species, such as chickens, are complex and multifactorial, involving the host, the pathogen, and extrinsic pressures. It is the interplay of these factors which leads to the differences in host ranges that we observe today.

In vitro methane formation and carbohydrate fermentation by rumen microbes as influenced by selected rumen ciliate species

Ciliate protozoa contribute to ruminal digestion and emission of the greenhouse gas methane. Individual species of ciliates co-cultured with mixed prokaryote populations were hypothesized to utilize carbohydrate types differently. In an in vitro batch culture experiment, 0.6 g of pure cellulose or xylan was incubated for 24 h in 40-mL cultures of Entodinium caudatum, Epidinium ecaudatum, and Eudiplodinium maggii with accompanying prokaryotes. Irrespective of ciliate species, gas formation (mL) and short-chain fatty acids (SCFA) concentrations (mmol L(-1)) were higher with xylan (71; 156) than with cellulose (52; 105). Methane did not differ (7.9% of total gas). The SCFA profiles resulting from fermentation of the carbohydrates were similar before and after removing the ciliates from the mixed microbial population. However, absolute methane production (mL 24 h(-1)) was lower by 50% on average after removing E. caudatum and E. maggii. Methanogen copies were less without E. maggii, but not without E. ecaudatum. Within 3 weeks part of this difference was compensated. Butyrate proportion was higher in cultures with E. maggii and E. ecaudatum than with E. caudatum and only when fermenting xylan. In conclusion, the three ciliate species partly differed in their response to carbohydrate type and in supporting methane formation.

In situ identification of carboxymethyl cellulose-digesting bacteria in the rumen of cattle fed alfalfa or triticale

A method was developed and used to arrest and stain reducing sugars (glucose) produced by bacteria with cell-surface-associated carboxymethyl cellulase (CMCase) and endoglucanase activities (CMC bacteria) in the rumen of cows fed alfalfa or triticale. Precipitation of silver oxide on the surface of individual cells was observed using cellulolytic bacterial pure cultures with known CMCase activity and rumen mixed cultures. The CMC bacteria in the liquid and solid fractions of the rumen digesta were identified using fluorescence in situ hybridization (FISH) with currently available and newly designed oligonucleotide probes. The CMC bacteria contributed between 8.2% and 10.1% to the total bacterial cell numbers. Most of the CMC bacteria (75.2-78.5%) could be identified by FISH probing. The known cellulolytic populations Ruminococcus flavefaciens, R. albus, and Fibrobacter succinogenes constituted 44.5-53.1% of the total. Other CMC bacteria identified hybridized with the probe Clo549 (11.2-23.0%) targeting members of an uncharacterized genus in Clostridia, the probe Inc852 (8.9-10.7%) targeting members of the family Incertae Sedis III and unclassified Clostridiales, and the probe But1243 (< 1%) designed against members of genus Butyrivibrio. Different forage feeds had no marked effects on the percentage abundances of these identified CMC bacteria. All appeared to be involved in cellulose degradation in the rumen of cows fed either alfalfa or triticale.

Dietary fiber content influences soluble carbohydrate levels in ruminal fluids

The soluble carbohydrate concentration of ruminal fluid, as affected by dietary forage content (DFC) and/or ruminally undegradable intake protein content (UIPC), was determined. Four ruminally cannulated steers, in a 4 × 4 Latin square design, were offered diets containing high (75 % of DM) or low (25 % of DM) DFC and high (6 % of DM) or low (5 % of DM) UIPC, in a 2 × 2 factorial arrangement. Zinc-treated SBM was the primary UIP source. Soluble hexose concentration (145.1 μM) in ruminal fluid (RF) of steers fed low DFC diets exhibited a higher trend (P = 0.08) than that (124.5 μM) of steers fed high DFC diets. UIPC did not modulate (P = 0.54) ruminal soluble hexose concentrations. Regardless of diet, soluble hexose concentration declined immediately after feeding and did not rise until 3 h after feeding (P < 0.0001). Cellobiose (≈90 %) and glucose (≈10 %) were the major soluble hexoses present in RF. Maltose was not detected. Soluble glucose concentration (13.0 μM) was not modified by either UIPC (P = 0.40) nor DFC (P = 0.61). However, a DFC by post-prandial time interaction was detected (P = 0.02). Pentose concentrations were greater (P = 0.02) in RF of steers fed high DFC (100.2 μM) than steers fed low DFC (177.0 μM). UIPC did not influence (P = 0.35) soluble pentose concentration. The identity of soluble pentoses in ruminal fluid could not be determined. However, unsubstituted xylose and arabinose were excluded. These data indicate that: (i) soluble carbohydrate concentrations remain in ruminal fluid during digestion and fermentation; (ii) slight diurnal changes began after feeding; (iii) DFC influences the soluble carbohydrate concentration in RF; and (iv) UIPC of these diets does not affect the soluble carbohydrate concentration of RF.

Quantitative analysis of cellulose degradation and growth of cellulolytic bacteria in the rumen

Ruminant animals digest cellulose via a symbiotic relationship with ruminal microorganisms. Because feedstuffs only remain in the rumen for a short time, the rate of cellulose digestion must be very rapid. This speed is facilitated by rumination, a process that returns food to the mouth to be rechewed. By decreasing particle size, the cellulose surface area can be increased by up to 10(6)-fold. The amount of cellulose digested is then a function of two competing rates, namely the digestion rate (K(d)) and the rate of passage of solids from the rumen (K(p)). Estimation of bacterial growth on cellulose is complicated by several factors: (1) energy must be expended for maintenance and growth of the cells, (2) only adherent cells are capable of degrading cellulose and (3) adherent cells can provide nonadherent cells with cellodextrins. Additionally, when ruminants are fed large amounts of cereal grain along with fiber, ruminal pH can decrease to a point where cellulolytic bacteria no longer grow. A dynamic model based on STELLA software is presented. This model evaluates all of the major aspects of ruminal cellulose degradation: (1) ingestion, digestion and passage of feed particles, (2) maintenance and growth of cellulolytic bacteria and (3) pH effects.

Comparison of microbial community composition and activity in sulfate-reducing batch systems remediating mine drainage

Five microbial inocula were evaluated in batch tests for the ability to remediate mine drainage (MD). Dairy manure (DM), anaerobic digester sludge, substrate from the Luttrell (LUTR) and Peerless Jenny King (PJK) sulfate-reducing permeable reactive zones (SR-PRZs) and material from an MD-treatment column that had been inoculated with material from a previous MD-treatment column were compared in terms of sulfate and metal removal and pH neutralization. The microbial communities were characterized at 0, 2, 4, 9, and 14 weeks using denaturing gradient gel electrophoresis and quantitative polymerase chain reaction to quantify all bacteria and the sulfate-reducing bacteria of the genus Desulfovibrio. The cultures inoculated with the LUTR, PJK, and DM materials demonstrated significantly higher rates of sulfate and metal removal, and contained all the microorganisms associated with the desired functions of SR-PRZs (i.e., polysaccharide degradation, fermentation, and sulfate reduction) as well as a relatively high proportion of Desulfovibrio spp. These results demonstrate that inoculum influences performance and also provide insights into key aspects of inoculum composition that impact performance. This is the first systematic biomolecular examination of the relationship between microbial community composition and MD remediation capabilities.

Gene transfer events and their occurrence in selected environments

Genes encoding virulence determinants are transferred between species in many different environments. In this review we describe gene transfer events to and from different species of bacteria, from bacteria to plants, and from plants to bacteria. Examples of the setting for these transfer events include: the GI tract, the rumen, the oral cavity, and in food matrixes. As a case study, the flux of virulence factors from E.coli O157:H7 is described as an example of gene flow in the environment.

Characterization of a family 45 glycosyl hydrolase from Fibrobacter succinogenes S85

Fibrobacter succinogenes is one of the most active cellulolytic bacteria ever isolated from the rumen, but enzymes from F. succinogenes capable of hydrolyzing native (insoluble) cellulose at a rapid rate have not been identified. However, the genome sequence of F. succinogenes is now available, and it was hoped that this information would yield new insights into the mechanism of cellulose digestion. The genome has a single family 45 beta-glucanase gene, and some of the enzymes in this family have good activity against native cellulose. The gene encoding the family 45 glycosyl hydrolase from F. succinogenes S85 was cloned into Escherichia coli JM109(DE3) using pMAL-c2 as a vector. Recombinant E. coli cells produced a soluble fusion protein (MAL-F45) that was purified on a maltose affinity column and characterized. MAL-F45 was most active on carboxymethylcellulose between pH 6 and 7 and it hydrolyzed cellopentaose and cellohexaose but not cellotetraose. It also cleaved p-nitrophenyl-cellopentose into cellotriose and p-nitrophenyl-cellobiose. MAL-F45 produced cellobiose, cellotriose and cellotetraose from acid swollen cellulose and bacterial cellulose, but the rate of this hydrolysis was much too low to explain the rate of cellulose digestion by growing cultures. Because the F. succinogenes S85 genome lacks dockerin and cohesin sequences, does not encode any known processive cellulases, and most of its endoglucanase genes do not encode carbohydrate binding modules, it appears that F. succinogenes has a novel mechanism of cellulose degradation.

Effects of varying dietary protein and energy levels on the production of lactating dairy cows

Forty-five multiparous and 18 primiparous Holstein cows were fed three levels of crude protein (CP), each at three levels of neutral detergent fiber (NDF), to identify optimal dietary CP and energy. Cows were blocked by parity and days in milk into seven groups of nine and randomly assigned to an incomplete 9 x 9 Latin square trial with four, 4-wk periods. Diets were formulated from alfalfa and corn silages, high-moisture corn, soybean meal, minerals, and vitamins. Forage was 60% alfalfa and 40% corn silage on all diets; NDF contents of 36, 32, and 28% were obtained by feeding 75, 63, and 50% forage, respectively. Dietary CP contents of 15.1, 16.7, and 18.4% were obtained by replacing high-moisture corn with soybean meal. Production data were from the last 2 wk of each period. Spot fecal and urine samples were collected from 36 cows to estimate N excretion using fecal indigestible acid detergent fiber (ADF) and urinary creatinine as markers. There were no interactions (P > or = 0.08) between dietary CP and NDF for any trait; thus, effects of CP were not confounded by NDF or vice versa. Intake of DM and fat yield were lower on 15.1% CP than at higher CP. There were linear increases in milk urea and urinary N excretion and linear decreases in N efficiency with increasing CP. Increasing CP from 15.1 to 18.4% reduced milk N from 31 to 25% of dietary N, increased urinary N from 23 to 35% of dietary N, and reduced fecal N from 45 to 41% of dietary N. Decreasing NDF gave linear increases in BW gain, yield of milk, protein, true protein, lactose, and SNF, and milk/DM intake and milk N/N intake, and linear decreases in milk urea. However, fat yield was lower on 28% than 32% NDF. Reducing NDF from 36 to 28% increased purine derivative excretion by 19%, suggesting increased microbial protein. Increasing CP by adding soybean meal to diets fed cows averaging 34 kg/d of milk increased intake and fat yield but depressed N efficiency. Increasing dietary energy by reducing forage improved milk yield and efficiency and decreased excretion of environmentally labile urinary N.

Modeling ruminal digestibility of carbohydrates and microbial protein flow to the duodenum

Carbohydrates are the major source of energy for dairy cows and for microbial protein synthesis in the rumen. The prediction of ruminal carbohydrate digestibility and of the flow of microbial protein to the small intestine is difficult because of the variability among various feeds in the kinetics of digestion and passage of neutral detergent fiber and starch. Disappearance of fiber and starch in vitro or in situ and gas production in vitro have been extensively evaluated, improved, and reviewed. Similarly, markers and models to measure ruminal passage rate have been extensively researched and improved. Sources of variation and decreased accuracy for these techniques are discussed. Variation and potential errors also remain for the prediction of microbial protein flow to the duodenum using in vivo procedures. However, when in vivo results were accumulated into a database, microbial N flow to the duodenum over a wide range of conditions could be predicted accurately by intake of net energy for lactation or by dry matter intake and percentage of neutral detergent fiber in the diet. Although evaluation of feeding interactions and specific dietary limitations for microbial protein production in the rumen are possible with some models but not with this regression approach, mechanistic models need further validation and more accurate rate constants for improved accuracy over a wide range of conditions.

Diet and carcinogen alter the fecal microbial populations of rats

An analysis of viable bacterial populations enumerated on carbohydrate selective media was used to simulate the colonic environment in vitro and determine if differential media could detect significant microbial shifts due to dietary fiber source, dietary fat source, and carcinogen. Male Sprague-Dawley rats were provided with either pectin or cellulose as a fiber source, either corn or fish oil as a source of fatty acids, and injected with either azoxymethane (AOM), a gastrointestinal carcinogen, or saline in a 2 x 2 x 2 factorial design. At 6 and 10 mo of age, fresh feces were collected, homogenized in anaerobic buffer and anaerobically plated onto differential media. Diets containing pectin supported more anaerobes at 6 mo of age (P < 0.01) than diets containing cellulose. Rats injected with AOM and consuming either pectin or corn oil supported more anaerobes at 10 mo of age (P < 0.05) than rats injected with saline and consuming the same diets. Rats consuming cellulose and receiving AOM but not expressing tumors possessed larger anaerobic populations at 10 mo of age (P < 0.05) than rats consuming cellulose, injected with AOM and expressing tumors. These effects show that gastrointestinal bacterial populations, as measured by carbohydrate specific media, respond to dietary changes such as dietary fiber source, and thus may play a key role in the etiology of colon cancer.

Microorganisms and enzymes involved in the degradation of plant fiber cell walls

One of natures most important biological processes is the degradation of lignocellulosic materials to carbon dioxide, water and humic substances. This implies possibilities to use biotechnology in the pulp and paper industry and consequently, the use of microorganisms and their enzymes to replace or supplement chemical methods is gaining interest. This chapter describes the structure of wood and the main wood components, cellulose, hemicelluloses and lignins. The enzyme and enzyme mechanisms used by fungi and bacteria to modify and degrade these components are described in detail. Techniques for how to assay for these enzyme activities are also described. The possibilities for biotechnology in the pulp and paper industry and other fiber utilizing industries based on these enzymes are discussed.

Why don't ruminal bacteria digest cellulose faster?

The bacteria Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminococcus albus generally are regarded as the predominant cellulolytic microbes in the rumen. Comparison of available data from the literature reveals that these bacteria are the most actively cellulolytic of all mesophilic organisms described to date from any habitat. In light of numerous proposals to improve microbial cellulose digestion in ruminants, it is instructive to examine the characteristics of these species that contribute to their superior cellulolytic capabilities and to identify the factors that prevent them from digesting cellulose even more rapidly. As a group, these species have extreme nutritional specialization. They are able to utilize cellulose (or in some cases xylan) and its hydrolytic products as their nearly sole energy sources for growth. Moreover, each species apparently has evolved to similar maximum rates of cellulose digestion (first-order rate constants of 0.05 to 0.08 h-1). Active cellulose digestion involves adherence of cells to the fibers via a glycoprotein glycocalyx, which protects cells from protozoal grazing and cellulolytic enzymes from degradation by ruminal proteases while it retains-at least temporarily-the cellodextrin products for use by the cellulolytic bacteria. These properties result in different ecological roles for the adherent and nonadherent populations of each species, but overall provide an enormous selective advantage to these cellulolytic bacteria in the ruminal environment. However, major constraints to cellulose digestion are caused by cell-wall structure of the plant (matrix interactions among wall biopolymers and low substrate surface area) and by limited penetration of the nonmotile cellulolytic microbes into the cell lumen. Because of these constraints and the highly adapted nature of cellulose digestion by the predominant cellulolytic bacteria in the rumen, transfer of cellulolytic capabilities to noncellulolytic ruminal bacteria (e.g., by genetic engineering) that display other desirable properties offers limited opportunities to improve ruminal digestion of cellulose.

Cellulose-binding proteins of Fibrobacter succinogenes and the possible role of a 180-kDa cellulose-binding glycoprotein in adhesion to cellulose

Fibrobacter succinogenes possesses seven cellulose-binding proteins (CBPs) of 40, 45, 50, 120, 180, 220, and 240 kDa. The 120-, 180-, 220-, and 240-kDa proteins were present in the outer membrane (OM), while the 40-, 45-, 50-, and 120-kDa proteins were either periplasmic or peripheral membrane proteins. The 120-kDa CBP, which was identified as endoglucanase 2, was a major component in both the OM and periplasm. Zymogram analysis for glucanases showed that the major membrane-associated CBPs, with the exception of endoglucanase 2, lacked endoglucanase activity. Affinity-purified antibodies against the 180-kDa CBP cross-reacted strongly with numerous cell envelope proteins of higher and lower molecular mass, including the previously characterized chloride-stimulated cellobiosidase. Treatment of the 180-kDa CBP and cell envelope proteins with periodate resulted in almost complete loss of antibody binding, suggesting that they possessed a common epitope that was carbohydrate in nature. Immunogold labelling of whole cells using antibodies against the 180-kDa CBP demonstrated that either the 180-kDa CBP or related proteins with a cross-reactive epitope were located at the cell surface. These epitopes were distributed uniformly on cells not bound to cellulose but congregated on the cell surface at sites of adhesion of cells to cellulose. Antibodies to the 180-kDa protein caused 62% inhibition of binding of F. succinogenes to crystalline cellulose, which provides evidence that either the 180-kDa CBP and (or) other related cross-reactive surface proteins have a role in adhesion to cellulose.Key words: cellulose, adhesin, adhesion, binding, Fibrobacter, succinogenes, rumen.