In-depth diversity analysis of the bacterial community resident in the camel rumen

A metagenomic analysis of the camel rumen's microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation

BACKGROUND

The diverse microbiome present in the rumen of ruminant animals facilitates the digestion of plant-based fiber. In this study, a shotgun metagenomic analysis of the microbes adhering to plant fiber in the camel rumen was undertaken to identify the key species contributing to lignocellulose degradation and short chain volatile fatty acids (VFA) fermentation.

RESULTS

The density of genes in the metagenome encoding glycoside hydrolases was estimated to be 25 per Mbp of assembled DNA, which is significantly greater than what has been reported in other sourced metagenomes, including cow rumen. There was also a substantial representation of sequences encoding scaffoldins, dockerins and cohesins, indicating the potential for cellulosome-mediated lignocellulose degradation. Binning of the assembled metagenome has enabled the definition of 65 high-quality genome bins which showed high diversity for lignocellulose degrading enzymes. Species associated to Bacteroidetes showed a high proportion of genes for debranching and oligosaccharide degrading enzymes, while those belonging to Firmicutes and Fibrobacteres were rich in cellulases and hemicellulases and thus these lineages were probably the key for ensuring the degradation of lignocellulose. The presence of many "polysaccharide utilization loci" (PULs) in Bacteroidetes genomes indicates their broad substrate specificity and high potential carbohydrate degradation ability. An analysis of VFA biosynthesis pathways showed that genes required for the synthesis of acetate were present in a range of species, except for Elusimicrobiota and Euryarchaeota. The production of propionate, exclusively via the succinate pathway, was carried out by species belonging to the phyla Bacteroidetes, Firmicutes, Spirochaetes and Fibrobacteres. Butyrate was generated via the butyrylCoA: acetate CoA-transferase pathway by Bacteroidetes and Lentisphaerae species, but generally via the butyrate kinase pathway by Firmicutes species.

CONCLUSION

The analysis confirmed the camel rumen's microbiome as a dense and yet largely untapped source of enzymes with the potential to be used in a range of biotechnological processes including biofuel, fine chemicals and food processing industries.

Enhancing the Resolution of Rumen Microbial Classification from Metatranscriptomic Data Using Kraken and Mothur

The advent of next generation sequencing and bioinformatics tools have greatly advanced our knowledge about the phylogenetic diversity and ecological role of microbes inhabiting the mammalian gut. However, there is a lack of information on the evaluation of these computational tools in the context of the rumen microbiome as these programs have mostly been benchmarked on real or simulated datasets generated from human studies. In this study, we compared the outcomes of two methods, Kraken (mRNA based) and a pipeline developed in-house based on Mothur (16S rRNA based), to assess the taxonomic profiles (bacteria and archaea) of rumen microbial communities using total RNA sequencing of rumen fluid collected from 12 cattle with differing feed conversion ratios (FCR). Both approaches revealed a similar phyla distribution of the most abundant taxa, with Bacteroidetes, Firmicutes, and Proteobacteria accounting for approximately 80% of total bacterial abundance. For bacterial taxa, although 69 genera were commonly detected by both methods, an additional 159 genera were exclusively identified by Kraken. Kraken detected 423 species, while Mothur was not able to assign bacterial sequences to the species level. For archaea, both methods generated similar results only for the abundance of Methanomassiliicoccaceae (previously referred as RCC), which comprised more than 65% of the total archaeal families. Taxon R4-41B was exclusively identified by Mothur in the rumen of feed efficient bulls, whereas Kraken uniquely identified Methanococcaceae in inefficient bulls. Although Kraken enhanced the microbial classification at the species level, identification of bacteria or archaea in the rumen is limited due to a lack of reference genomes for the rumen microbiome. The findings from this study suggest that the development of the combined pipelines using Mothur and Kraken is needed for a more inclusive and representative classification of microbiomes.

Purification and characterization of deoxyribonuclease from small intestine of camel Camelus dromedarius

The chromatography of deoxyribonuclease (DNase) from small intestine of camel Camelus dromedarius by DEAE-Sepharose separated three isoforms DNase 1, DNase 2 and DNase 3. The DNase 3 was purified to homogeneity by chromatography on Sephacryl S-200. The molecular weight of DNase 3 was 30 kDa using gel filtration and SDS-PAGE. The pH optimum of DNase 3 was reported at 7.0 using Tris-HCl buffer. The temperature optimum of DNase 3 was found to be 50 °C. The enzyme was stable up to 50 °C for one h incubation. The Km value was 28.5 µg DNA, where this low value indicated the high affinity of enzyme toward DNA as substrate. No activity of DNase 3 was determined in the absence of metal cations. Mg2+ and Ca2+ caused significant enhancement in the enzyme activity by 90 and 75%, respectively. The mixture of Mg2+ and Ca2+ caused 100% of enzyme activity. Ni2+, Co2+, Ba2+, Zn2+ and Cd2+ showed very strong inhibitory effect on enzyme activity. In conclusion, the characterization of DNase 3 indicated that the enzyme is considered as a member of DNase I family. The low Km value of the DNA suggested that the high digestion of DNA of camel forage by small intestine DNase 3.

Development of a bifunctional xylanase-cellulase chimera with enhanced activity on rice and barley straws using a modular xylanase and an endoglucanase procured from camel rumen metagenome

The camel rumen metagenome is an untapped source of glycoside hydrolases. In this study, novel genes encoding for a modular xylanase (XylC) and a cellulase (CelC) were isolated from a camel rumen metagenome and expressed in Escherichia coli BL21 (DE3). XylC with xylanase (Xyn), CBM, and carbohydrate esterase (CE) domains was characterized as a β-1,4-endoxylanase with remarkable catalytic activity on oat-spelt xylan (K cat = 2919 ± 57 s-1). The implication of XylC's modular structure in its high catalytic activity was analyzed by truncation and fusion construction with CelC. The resulting fusions including Cel-CBM, Cel-CBM-CE, and Xyn-CBM-Cel showed remarkable enhancement in CMCase activity with K cat values of 742 ± 12, 1289 ± 34.5, and 2799 ± 51 s-1 compared to CelC with a K cat of 422 ± 3.5 s-1. It was also shown that the bifunctional Xyn-CBM-Cel with synergistic xylanase/cellulase activities was more efficient than XylC and CelC in hydrolysis of rice and barley straws.

The dynamics of the bacterial communities developed in maize silage

Ensilage provides an effective means of conserving summer‐grown green forage to supply as winter feed to ruminants. The fermentation process involved in the ensilage process relies on lactic acid bacteria (LAB). Here, 16S ribosomal DNA amplicon pyrosequencing was used to follow the dynamic behaviour of the LAB community during the ensilage of maize biomass, with a view to identify the key species involved in the process. The biomass used for ensilage was a single‐cross maize hybrid, harvested at the milk‐line stage. The crop was grown at three contrasting locations. Aspects of the physico‐chemical composition of the material and the LAB species present were sampled at 0, 3, 6, 14, 21 and 32 days after ensilage was initiated. In all three cases, members of the Leuconostocaceae family dominated the epiphytic bacterial community, notably Leuconostoc and Weissella, but some variation was noted in the abundance of certain Leuconostocaceae and Lactobacillaceae species, as well as that of some Acetobacteraceae, Enterobacteriaceae and Moraxellaceae species. The constellation of the microbiome which developed during the ensilage process differed markedly from that of the epiphytic one, with Lactobacillaceae, particularly Lactobacillus and Pediococcus spp. dominating. The abundance of heterofermentative Leuconostocaceae spp. in the epiphytic community and the extent of the transition from hetero‐ to homo‐fermentation during the initial ensilage period are important factors in determining silage quality.

Effects of various weaning times on growth performance, rumen fermentation and microbial population of yellow cattle calves

Objective

This study was conducted to investigate the effects of weaning times on the growth performance, rumen fermentation and microbial communities of yellow cattle calves.

Methods

Eighteen calves were assigned to a conventional management group that was normally weaned (NW, n = 3) or to early weaned (EW) group where calves were weaned when the feed intake of solid feed (starter) reached 500 g (EW₅₀₀, n = 5), 750 g (EW₇₅₀, n = 5), or 1,000 g (EW_1,000, n = 5).

Results

Compared with NW, the EW treatments increased average daily gain (p<0.05). The calves in EW₇₅₀ had a higher (p<0.05) starter intake than those in EW_1,000 from wk 9 to the end of the trial. The concentrations of total volatile fatty acids in EW₇₅₀ were greater than in NW and EW_1,000 (p<0.05). The EW treatments decreased the percentage of acetate (p<0.05). The endogenous enzyme activities of the rumen were increased by EW (p<0.05). EW had no effect on the number of total bacteria (p>0.05), but changes in bacterial composition were found.

Conclusion

From the present study, it is inferred that EW is beneficial for rumen fermentation, and weaning when the feed intake of the starter reached 750 g showed much better results.

Functional gene profiling through metaRNAseq approach reveals diet-dependent variation in rumen microbiota of buffalo (Bubalus bubalis)

Recent advances in next generation sequencing technology have enabled analysis of complex microbial community from genome to transcriptome level. In the present study, metatranscriptomic approach was applied to elucidate functionally active bacteria and their biological processes in rumen of buffalo (Bubalus bubalis) adapted to different dietary treatments. Buffaloes were adapted to a diet containing 50:50, 75:25 and 100:0 forage to concentrate ratio, each for 6 weeks, before ruminal content sample collection. Metatranscriptomes from rumen fiber adherent and fiber-free active bacteria were sequenced using Ion Torrent PGM platform followed by annotation using MG-RAST server and CAZYmes (Carbohydrate active enzymes) analysis toolkit. In all the samples Bacteroidetes was the most abundant phylum followed by Firmicutes. Functional analysis using KEGG Orthology database revealed Metabolism as the most abundant category at level 1 within which Carbohydrate metabolism was dominating. Diet treatments also exerted significant differences in proportion of enzymes involved in metabolic pathways for VFA production. Carbohydrate Active Enzyme(CAZy) analysis revealed the abundance of genes encoding glycoside hydrolases with the highest representation of GH13 CAZy family in all the samples. The findings provide an overview of the activities occurring in the rumen as well as active bacterial population and the changes occurring through different dietary treatments.

Maintaining stability of the rumen ecosystem is associated with changes of microbial composition and epithelial TLR signaling

We used the goat as a model to study the effects of rumen microbial composition and epithelial TLR signaling on maintaining rumen stability during exogenous butyrate interference. Six cannulated goats received a rapid intraruminal infusion of 0.1 mol/L potassium phosphate buffer with (BT, n = 3) or without (CO, n = 3) 0.3 g/kg·BW·day sodium butyrate for 28 days. The ruminal pH and the concentration of total SCFA were not affected by the interference. 16S rRNA gene amplicon sequencing revealed a change in microbial composition after the butyrate infusion. LEfSe analysis showed a shift of the biomarker species from butyrate‐producing bacteria to acetate‐and propionate‐producing bacteria. Quantitative PCR‐based comparisons showed that significant increases in TLR2, TLR5, and MyD88 expression were accompanied by a significant decrease in IL‐1β and IFN‐γ expression in the ruminal epithelium. Constrained correlation analysis showed that the relative abundance of Roseburia was positively correlated with the expression of TLR5. Taken together, our study shows that microbial composition plays an important role in maintaining the stability of the microbial ecosystem in rumen, and indicates that the microbe‐TLR‐cytokine axis was involved in maintaining the stability of the gastrointestinal ecosystem.

New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11

Ruminants have co-evolved with their gastrointestinal microbial communities that digest plant materials to provide energy for the host. Some arctic and boreal ruminants have already shown to be vulnerable to dietary shifts caused by changing climate, yet we know little about the metabolic capacity of the ruminant microbiome in these animals. Here, we use meta-omics approaches to sample rumen fluid microbial communities from Alaskan moose foraging along a seasonal lignocellulose gradient. Winter diets with increased hemicellulose and lignin strongly enriched for BS11, a Bacteroidetes family lacking cultivated or genomically sampled representatives. We show that BS11 are cosmopolitan host-associated bacteria prevalent in gastrointestinal tracts of ruminants and other mammals. Metagenomic reconstruction yielded the first four BS11 genomes; phylogenetically resolving two genera within this previously taxonomically undefined family. Genome-enabled metabolic analyses uncovered multiple pathways for fermenting hemicellulose monomeric sugars to short-chain fatty acids (SCFA), metabolites vital for ruminant energy. Active hemicellulosic sugar fermentation and SCFA production was validated by shotgun proteomics and rumen metabolites, illuminating the role BS11 have in carbon transformations within the rumen. Our results also highlight the currently unknown metabolic potential residing in the rumen that may be vital for sustaining host energy in response to a changing vegetative environment.

Microbial community profiles of the jejunum from steers differing in feed efficiency

Research regarding the association between the microbial community and host feed efficiency in cattle has primarily focused on the rumen. However, the various microbial populations within the gastrointestinal tract as a whole are critical to the overall well-being of the host and need to be examined when determining the interplay between host and nonhost factors affecting feed efficiency. The objective of this study was to characterize the microbial communities of the jejunum among steers differing in feed efficiency. Within 2 contemporary groups of steers, individual ADFI and ADG were determined from animals fed the same diet. At the end of each feeding period, steers were ranked based on their standardized distance from the bivariate mean (ADG and ADFI). Four steers with the greatest deviation within each Cartesian quadrant were sampled ( = 16/group; 2 groups). Bacterial 16S rRNA gene amplicons were sequenced from the jejunum content using next-generation sequencing technology. The phylum Firmicutes accounted for up to 90% of the populations within all samples and was dominated by the families Clostridiaceae and Ruminococcaceae. UniFrac principal coordinate analyses did not indicate any separation of microbial communities within the jejunum based on feed efficiency phenotype, and no significant changes were indicated by bacterial diversity or richness metrics. The relative abundances of microbial populations and operational taxonomic units did reveal significant differences between feed efficiency groups ( < 0.05), including the phylum Proteobacteria ( = 0.030); the families Lachnospiraceae ( = 0.035), Coriobacteriaceae ( = 0.012), and Sphingomonadaceae ( = 0.035); and the genera ( = 0.019), ( = 0.018), and ( = 0.022). The study identified jejunal microbial associations with feed efficiency, ADG, and ADFI. This study suggests the association of the jejunum microbial community as a factor influencing feed efficiency at the 16S level.

An Update on the Status of Current Research on the Mammalian Microbiome

The microbiome refers to the thousands of microbial species that inhabit a specific host or environment. Extensive microbiome surveys have been conducted for soils, the built environment, and our oceans. In addition, extensive studies of the human microbiome have revealed significant microbial diversity across all body sites and have hinted at new opportunities for diagnostic and therapeutic approaches to addressing human health and disease. Mammals in general are known to hold a complicated mix of species within their gastrointestinal tracts, including virus, archaea, bacteria, and fungi. These microbial species present beneficial aspects to the host species through the production of vitamins, metabolism of plant structural compounds and sugars, and education of the immune system. In addition to a vast number of studies on humans, studies of the mammalian microbiome have been performed, with several publications on a variety of animal species currently available. These have included studies on the microbiome of companion animals, animals used for research, and animals used for agricultural and food purposes, and various human/animal models.

Comparison of Fecal Microbiota of Mongolian and Thoroughbred Horses by High-throughput Sequencing of the V4 Region of the 16S rRNA Gene

The hindgut of horses is an anaerobic fermentative chamber for a complex and dynamic microbial population, which plays a critical role in health and energy requirements. Research on the gut microbiota of Mongolian horses has not been reported until now as far as we know. Mongolian horse is a major local breed in China. We performed high-throughput sequencing of the 16S rRNA genes V4 hypervariable regions from gut fecal material to characterize the gut microbiota of Mongolian horses and compare them to the microbiota in Thoroughbred horses. Fourteen Mongolian and 19 Thoroughbred horses were used in the study. A total of 593,678 sequence reads were obtained from 33 samples analyzed, which were found to belong to 16 phyla and 75 genera. The bacterial community compositions were similar for the two breeds. Firmicutes (56% in Mongolian horses and 53% in Thoroughbred horses) and Bacteroidetes (33% and 32% respectively) were the most abundant and predominant phyla followed by Spirochaete, Verrucomicrobia, Proteobacteria, and Fibrobacteres. Of these 16 phyla, five (Synergistetes, Planctomycetes, Proteobacteria, TM7, and Chloroflexi) were significantly different (p<0.05) between the two breeds. At the genus level, Treponema was the most abundant genus (43% in Mongolian horses vs 29% in Thoroughbred horses), followed by Ruminococcus, Roseburia, Pseudobutyrivibrio, and Anaeroplasma, which were detected in higher distribution proportion in Mongolian horses than in Thoroughbred horses. In contrast, Oscillibacter, Fibrobacter, Methanocorpusculum, and Succinivibrio levels were lower in Mongolian horses. Among 75 genera, 30 genera were significantly different (p<0.05) between the two breeds. We found that the environment was one of very important factors that influenced horse gut microbiota. These findings provide novel information about the gut microbiota of Mongolian horses and a foundation for future investigations of gut bacterial factors that may influence the development and progression of gastrointestinal disease in horses.