The effect of rumen chitinolytic bacteria on cellulolytic anaerobic fungi

Effects of the supplementation of distillers' grape residues on ruminal degradability, whole tract digestibility and nitrogen metabolism in sheep

Five ruminally and duodenally cannulated Kazakh male lambs (30 ± 2.75 kg) maintained singly in a metabolic cage were used in a 5 × 5 Latin square experiment to investigate the effect of supplementing a ration with five different levels of distillers' grape residue (DGR) on ruminal degradability, whole tract digestibility and nitrogen (N) metabolism of growing lambs. The rations were isoenergetic and isonitrogenous and contained 0, 3.85, 7.70, 11.55 and 15.41% DGR (DM basis). Each experimental period lasted for 18 d: 10 d for adaptation to the dietary treatment and 8 d for faecal, urinary, ruminal and duodenal digesta sample collections. The outflow rate of ruminal digesta increased (p = 0.032) linearly with the increased level of dietary neutral detergent fibre content, caused by the supplementation of DGR. As a result, the effective degradability of dry matter and crude protein decreased significantly with the treatments. Although the dietary intake of N, duodenal flow of total N, and the endogenous N at the duodenum were not affected by experimental treatments, N fractions in the digesta were altered. Ruminal microbial N decreased (p < 0.01) linearly; in contrast, ruminal un-degradable protein increased linearly (p < 0.01) in response to the increased addition of DGR. Although there was no significant difference in faecal N among treatments, N retention was increased linearly (p = 0.014), owing to the remarkable reduction (p = 0.016) of urinary N excretion with an increasing level of DGR. The results indicate that the DGR has some potential benefits of increasing the supply of bypass protein and of improving the utilisation efficiency of N for sheep. Therefore, the supplementation of DGR in ruminant feeding is recommended at levels not exceeding 10% of the diet.

Effect of Limit-Fed Diets With Different Forage to Concentrate Ratios on Fecal Bacterial and Archaeal Community Composition in Holstein Heifers

Limit-feeding of a high concentrate diet has been proposed as an effective method for improving feed efficiency and reducing total manure output of dairy heifers; meanwhile the effects of this method on hindgut microbiota are still unclear. This study investigated the effects of a wide range of dietary forage:concentrate ratios (F:C) on the fecal composition of bacteria and archaea in heifers using next-generation sequencing. Four diets with different F:C (80:20, 60:40, 40:60, and 20:80) were limit-fed to 24 Holstein heifers, and the fecal fermentation parameters and bacterial and archaeal communities were investigated. With increasing dietary concentrate levels, the fecal dry matter output, neutral detergent fiber (NDF) content, and proportion of acetate decreased linearly (P < 0.01), while the fecal starch content and proportions of propionate, butyrate, and total branched-chain volatile fatty acids (TBCVFAs) were increased (P ≤ 0.05). An increased concentrate level linearly increased (P = 0.02) the relative abundance of Proteobacteria, and linearly decreased (P = 0.02) the relative abundance of Bacteroidetes in feces. At the genus level, the relative abundance of unclassified Ruminococcaceae and Paludibacter which may have the potential to degrade forage decreased linearly (q ≤ 0.02) with increasing dietary concentrate levels, while the relative abundance of Roseburia and Succinivibrio which may be non-fibrous carbohydrate degrading bacteria increased linearly (q ≤ 0.05). Some core microbiota operational taxonomic units (OTUs) also showed significant association with fecal VFAs, NDF, and/or acid detergent fiber (ADF) content. Meanwhile, the relative abundance of most detected taxa in archaea were similar across different F:C, and only Methanosphaera showed a linear decrease (P = 0.01) in high concentrate diets. Our study provides a better understanding of fecal fermentation parameters and microbiota under a wide range of dietary F:C. These findings support the potential for microbial manipulation by diet, which could enhance feed digestibility and relieve environmental problems associated with heifer rearing.

Sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host association

It has become increasingly clear that the composition of mammalian gut microbial communities is substantially diet driven. These microbiota form intricate mutualisms with their hosts, which have profound implications on overall health. For example, many gut microbes are involved in the conversion of host-ingested dietary polysaccharides into host-usable nutrients. One group of important gut microbial symbionts are bacteria in the genus Ruminococcus. Originally isolated from the bovine rumen, ruminococci have been found in numerous mammalian hosts, including other ruminants, and non-ruminants such as horses, pigs and humans. All ruminococci require fermentable carbohydrates for growth, and their substrate preferences appear to be based on the diet of their particular host. Most ruminococci that have been studied are those capable of degrading cellulose, much less is known about non-cellulolytic non-ruminant-associated species, and even less is known about the environmental distribution of ruminococci as a whole. Here, we capitalized on the wealth of publicly available 16S rRNA gene sequences, genomes and large-scale microbiota studies to both resolve the phylogenetic placement of described species in the genus Ruminococcus, and further demonstrate that this genus has largely unexplored diversity and a staggering host distribution. We present evidence that ruminococci are predominantly associated with herbivores and omnivores, and our data supports the hypothesis that very few ruminococci are found consistently in non-host-associated environments. This study not only helps to resolve the phylogeny of this important genus, but also provides a framework for understanding its distribution in natural systems.

Fungal lysis by a soil bacterium fermenting cellulose

Recycling of plant biomass by a community of bacteria and fungi is fundamental to carbon flow in terrestrial ecosystems. Here we report how the plant fermenting, soil bacterium Clostridium phytofermentans enhances growth on cellulose by simultaneously lysing and consuming model fungi from soil. We investigate the mechanism of fungal lysis to show that among the dozens of different glycoside hydrolases C. phytofermentans secretes on cellulose, the most highly expressed enzymes degrade fungi rather than plant substrates. These enzymes, the GH18 Cphy1799 and Cphy1800, synergize to hydrolyse chitin, a main component of the fungal cell wall. Purified enzymes inhibit fungal growth and mutants lacking either GH18 grow normally on cellulose and other plant substrates, but have a reduced ability to hydrolyse chitinous substrates and fungal hyphae. Thus, C. phytofermentans boosts growth on cellulose by lysing fungi with its most highly expressed hydrolases, highlighting the importance of fungal interactions to the ecology of cellulolytic bacteria.

The role of anaerobic gut fungi in ruminants

Anaerobic chytridiomycete fungi are found in the gastrointestinal tracts of sheep, cattle and goats, as well as in many other domesticated ruminant and nonruminant herbivores and a wide variety of wild herbivorous mammals. They are principally found associated with the fibrous plant particles of digesta and as free swimming zoospores in the fluid phase. The presence of large fungal populations in animals consuming mature pasture or diets largely composed of hay or straw together with the production of highly active fibre degrading enzymes lead to' the belief that anaerobic fungi may have a significant role to play in the assimilation of fibrous feeds by ruminants. While many early studies focused on anaerobic fungi because of their unusual biology and metabolism, the large part of subsequent research has emphasized the biotechnological potential of their cellulases, xylanases and phenolic esterases. In recent years, the extent of the contribution of anaerobic fungi to the nutrition of ruminants has also been established through studies of fungal populations in the rumen and the dietary factors which influence them, as presented in this review. Further, we discuss the evidence supporting an important contribution of anaerobic fungal populations in the rumen to feed intake and digestion of poor quality feed by domesticated ruminants. In conclusion, the review explores some different methods for manipulating fungi in the rumen for increased feed intake and digestion.

Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)

BACKGROUND

The microbiota of an animal's intestinal tract plays important roles in the animal's overall health, productivity and well-being. There is still a scarcity of information on the microbial diversity in the gut of livestock species such as cattle. The primary reason for this lack of data relates to the expense of methods needed to generate such data. Here we have utilized a bacterial tag-encoded FLX 16s rDNA amplicon pyrosequencing (bTEFAP) approach that is able to perform diversity analyses of gastrointestinal populations. bTEFAP is relatively inexpensive in terms of both time and labor due to the implementation of a novel tag priming method and an efficient bioinformatics pipeline. We have evaluated the microbiome from the feces of 20 commercial, lactating dairy cows.

RESULTS

Ubiquitous bacteria detected from the cattle feces included Clostridium, Bacteroides, Porpyhyromonas, Ruminococcus, Alistipes, Lachnospiraceae, Prevotella, Lachnospira, Enterococcus, Oscillospira, Cytophage, Anaerotruncus, and Acidaminococcus spp. Foodborne pathogenic bacteria were detected in several of the cattle, a total of 4 cows were found to be positive for Salmonella spp (tentative enterica) and 6 cows were positive for Campylobacter spp. (tentative lanienae).

CONCLUSION

Using bTEFAP we have examined the microbiota in the feces of cattle. As these methods continue to mature we will better understand the ecology of the major populations of bacteria the lower intestinal tract. This in turn will allow for a better understanding of ways in which the intestinal microbiome contributes to animal health, productivity and wellbeing.

Cellular expression of gut chitinase mRNA in the gastrointestinal tract of mice and chickens

Recently, the second mammalian chitinase, designated acidic mammalian chitinase (AMCase), has been identified in human, mouse, and cow. In contrast to the earlier identified macrophage-derived chitinase (chitotriosidase), this chitinase is richly expressed in the gastrointestinal (GI) tract, suggesting its role in digestion of chitin-containing foods as well as defense against chitin-coated microorganisms and parasites. This in situ hybridization study first revealed cellular localization of the gut-type chitinase in the mouse and chicken. In adult mice, the parotid gland, von Ebner's gland, and gastric chief cells, all of which are exocrine cells of the serous type, expressed the gut chitinase mRNA. In the chicken, oxyntico-peptic cells in glandular stomach (proventriculus) and hepatocytes expressed the chitinase mRNA. Because cattle produce the gut chitinase (chitin-binding protein b04) only in the liver, the gut chitinases in mammals and birds have three major sources of production, i.e., the salivary gland, stomach, and liver. During ontogenetic development, the expression level in the parotid gland and stomach of mice increased to the adult level before weaning, whereas in the stomach of chickens intense signals were detectable in embryos from incubation day 7.

A novel serum chitinase that is expressed in bovine liver

Chitinases are ubiquitous chitin-fragmenting hydrolases. They are synthesized by a vast array of organisms, including those not composed of chitin. Here, we describe a novel serum chitinase (chitin-binding protein b04, CBPb04), which is expressed in bovine liver. Although CBPb04 is secreted as an endocrine chitinase, it shows higher homology with human gastrointestinal tract exocrine chitinase (AMCase) than with macrophage endocrine chitinase (human chitotriosidase). This suggests that cows have a specific defense against chitin-containing microorganisms. CBPb04 mRNA is expressed in hepatocytes. This is the first report of a hepatogenic mammalian chitinase.

Chitinolytic enzymes produced by ovine rumen bacteria

Two strains of clostridia, isolated from the rumen fluid of sheep as potential antagonists toward anaerobic fungi showed a complete array of chitinolytic enzymes. Enzyme tests in cultures demonstrated endochitinase, exochitinase, N-acetyl-glucosaminidase, chitosanase and chitin deacetylase activities mainly in the extracellular fractions. In all samples, the highest was the activity of exochitinase (600-1100 nmol mL-1 h-1); the activity of endochitinase (280-500 nmol mL-1 h-1) was also significant. Chitinases were stimulated in the presence of reducing compounds and no dependence on cations was observed. In both strains different isoforms of chitinases of molar mass 36-96 kDa were detected. The chitinases from our isolates lyzed cell walls of anaerobic fungi in vitro and inhibited the activity of fungal beta-1,4-endoglucanases. Of the two bacteria examined, one was more effective in both antifungal effects.