BackgroundDescribing the microbial populations present in small grain silage and understanding their changes during ensiling is of interest for improving the nutrient value of these important forage crops. Barley, oat and triticale forages as well as an intercropped mixture of the 3 crops were harvested and ensiled in mini silos for a period of 90 days, followed by 14 days of aerobic exposure. Changes in fermentation characteristics and nutritive value were assessed in terminal silages and bacterial and fungal communities during ensiling and aerobic exposure were described using 16S and 18S rDNA sequencing, respectively.ResultsAll small grain silages exhibited chemical traits that were associated with well ensiled forages, such as low pH value (4.09 ± 0.28) and high levels of lactic acid (59.8 ± 14.59 mg/g DM). The number of microbial core genome operational taxonomic units (OTUs) decreased with time of ensiling. Taxonomic bacterial community profiles were dominated by the Lactobacillales after fermentation, with a notable increase in Bacillales as a result of aerobic exposure. Diversity of the fungal core microbiome was shown to also be reduced during ensiling. Operational taxonomic units assigned to filamentous fungi were found in the core microbiome at ensiling and after aerobic exposure, whereas the Saccharomycetales were the dominate yeast population after 90 days of ensiling and aerobic exposure. Bacterial and fungal orders typically associated with silage spoilage were identified in the core microbiome after aerobic exposure.ConclusionNext Generation Sequencing was successfully used to describe bacterial communities and the first record of fungal communities throughout the process of ensiling and utilization. Adequately describing the microbial ecology of silages could lead to improved ensiling practices and the selection of silage inoculants that act synergistically with the natural forage microbiome.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-017-0947-0) contains supplementary material, which is available to authorized users.

Breakdown of plant biomass in rumen depends on interactions between bacteria, archaea, fungi, and protozoa; however, the majority of studies of the microbiome of ruminants, including the few studies of the rumen of camels, only studied one of these microbial groups. In this study, we applied total rRNA sequencing to identify active microbial communities in 22 solid and liquid rumen samples from 11 camels. These camels were reared at three stations that use different feeding systems: clover, hay and wheat straw (G1), fresh clover (G2), and wheat straw (G3). Bacteria dominated the libraries of sequence reads generated from all rumen samples, followed by protozoa, archaea, and fungi respectively. Firmicutes, Thermoplasmatales, Diplodinium, and Neocallimastix dominated bacterial, archaeal, protozoal and fungal communities, respectively in all samples. Libraries generated from camels reared at facility G2, where they were fed fresh clover, showed the highest alpha diversity. Principal co-ordinate analysis and linear discriminate analysis showed clusters associated with facility/feed and the relative abundance of microbes varied between liquid and solid fractions. This provides preliminary evidence that bacteria dominate the microbial communities of the camel rumen and these communities differ significantly between populations of domesticated camels.

Future growth in demand for meat and milk, and the socioeconomic and environmental challenges that farmers face, represent a “grand challenge for humanity”. Improving the digestibility of crop residues such as straw could enhance the sustainability of ruminant production systems. Here, we investigated if transfer of rumen contents from bison to cattle could alter the rumen microbiome and enhance total tract digestibility of a barley straw-based diet. Beef heifers were adapted to the diet for 28 days prior to the experiment. After 46 days, ~70 percent of rumen contents were removed from each heifer and replaced with mixed rumen contents collected immediately after slaughter from 32 bison. This procedure was repeated 14 days later. Intake, chewing activity, total tract digestibility, ruminal passage rate, ruminal fermentation, and the bacterial and protozoal communities were examined before the first and after the second transfer. Overall, inoculation with bison rumen contents successfully altered the cattle rumen microbiome and metabolism, and increased protein digestibility and nitrogen retention, but did not alter fiber digestibility.

This study was performed to investigate the initial colonization of metabolically active methanogens and subsequent changes in four fractions: the rumen solid-phase (RS), liquid-phase (RL), protozoa-associated (RP), and epithelium-associated (RE) from 1 to 60 d after birth, and manipulate methanogen community by early weaning on 40 d and supplementing rhubarb from 40 to 60 d in black goats. The RNA-based real-time quantitative PCR and 16S rRNA amplicon sequencing were employed to indicate the metabolically active methanogens. Results showed that active methanogens colonized in RL and RE on 1 d after birth. RP and RE contained the highest and lowest density of methanogens, respectively. Methanobrevibacter, Candidatus Methanomethylophilus, and Methanosphaera were the top three genera. The methanogen communities before weaning differed from those post weaning and the structure of the methanogen community in RE was distinct from those in the other three fractions. The discrepancies in the distribution of methanogens across four fractions, and various fluctuations in abundances among four fractions according to age were observed. The addition of rhubarb significantly (P < 0.05) reduced the abundances of Methanimicrococcus spp. in four fractions on 50 d, but did not change the methanogen community composition on 60 d.

The objective of this present study was to explore the initial establishment of metabolically active bacteria and subsequent evolution in four fractions: rumen solid-phase (RS), liquid-phase (RL), protozoa-associated (RP), and epithelium-associated (RE) through early weaning and supplementing rhubarb root powder in 7 different age groups (1, 10, 20, 38, 41, 50, and 60 d) during rumen development. Results of the 16S rRNA sequencing based on RNA isolated from the four fractions revealed that the potentially active bacterial microbiota in four fractions were dominated by the phyla Proteobacteria, Firmicutes, and Bacteroidetes regardless of different ages. An age-dependent increment of Chao 1 richness was observed in the fractions of RL and RE. The principal coordinate analysis (PCoA) indicated that samples in four fractions all clustered based on different age groups, and the structure of the bacterial community in RE was distinct from those in other three fractions. The abundances of Proteobacteria decreased significantly (P < 0.05) with age, while increases in the abundances of Firmicutes and Bacteroidetes were noted. At the genus level, the abundance of the predominant genus Mannheimia in the Proteobacteria phylum decreased significantly (P < 0.05) after 1 d, while the genera Quinella, Prevotella, Fretibacterium, Ruminococcus, Lachnospiraceae NK3A20 group, and Atopobium underwent different manners of increases and dominated the bacterial microbiota across four fractions. Variations of the distributions of some specific bacterial genera across fractions were observed, and supplementation of rhubarb affected the relative abundance of various genera of bacteria.