Composition of bacterial and archaeal communities in the rumen of dromedary camel using cDNA-amplicon sequencing

Molecular detection of ruminal micro-flora and micro-fauna in Saudi Arabian camels: Effects of season and region

This study investigated and explored the availability of micro-flora and micro-fauna in the ruminal contents of Arabian camel (Camelus dromedarius) from three different regions in Saudi Arabia along with two seasons. Samples were prepared and tested by conventional polymerase chain reaction (PCR). This study confirmed that the bacterial flora were dominating over other microbes. Different results of the availability of each microbe in each region and season were statistically analyzed and discussed. There was no significant effect of season on the micro-flora or micro-fauna however, the location revealed a positive effect with Ruminococcus flavefaciens (p < 0 0.03) in the eastern region. This study was the first to investigate the abundance of micro-flora and micro-fauna in the ruminal contents of camels of Saudi Arabia. This study underscores the significance of camel ruminal micro-flora and micro-fauna abundance, highlighting their correlation with both seasonality and geographic location. This exploration enhances our comprehension of camel rumination and digestion processes. The initial identification of these microbial communities serves as a foundational step, laying the groundwork for future in-depth investigations into camel digestibility and nutritional requirements.

Multi-omics revealed the effects of dietary energy levels on the rumen microbiota and metabolites in yaks under house-feeding conditions

Yak (Bos grunniens) is a unique large ruminant species in the Qinghai-Tibetan Plateau (QTP). Changing the energy levels of their rations can significantly improve their growth performance. Therefore, studying the effects of dietary energy levels on the rumen microflora and metabolites of yak is crucial for enhancing the development of the yak industry. Currently, there is a lack of understanding regarding the impact of feeding energy diets on rumen fermentation parameters, microbial functions, and metabolites. This study was designed to determine the appropriate energy level for feeding yak. Three test diets with metabolizable energy levels of 7.57 MJ/kg, 9.44 MJ/kg, and 11.9 MJ/kg were used and the concentration of volatile fatty acids (VFA) in rumen fluid was measured. The microbial communities, functions, and metabolites in yaks were studied by 16S rRNA sequencing, metagenome, and LC-MS non-targeted metabolomics to investigate the relationships among rumen fermentation parameters, microbial diversity, and metabolites. Ration energy levels significantly affect total VFA, acetate, propionate, butyrate, iso-valerate, valerate, and acetate/propionate (p < 0.05). At the phylum level, the dominant phyla in all three treatment groups were Bacteroidota, Firmicutes, and Actinobacteriota. At the genus level, the abundance of the unclassified_o__Bacteroidales, norank_f_Muribaculaceae, Lachnospiraceae_NK4A136_group, and Family _XIII_AD3011_group showed significant differences (p < 0.05) and were significantly correlated with differential metabolites screened for phosphatidylcholine [PC(16:0/0:0), PC(18:3/0:0)], uridine 3'-monophosphate, and adenosine monophosphate, etc. CAZymes family analysis showed that GHs and CEs differed significantly among the three groups. In addition, differential metabolites were mainly enriched in the pathways of lipid metabolism, nucleotide metabolism, and biosynthesis of other secondary metabolites, and the concentrations of differential metabolites were correlated with microbial abundance. In summary, this study analyzed the effects of ration energy levels on rumen microorganisms and metabolites of yaks and their relationships. The results provided a scientific basis for the selection of dietary energy for yaks in the house feeding period in the future.

Composition of the rumen archaeal community of growing camels fed different concentrate levels

Understanding the rumen fermentation and methanogenic community in camels fed intensively is critical for optimizing rumen fermentation, improving feed efficiency, and lowering methane emissions. Using Illumina MiSeq sequencing, quantitative real-time PCR, and high-performance liquid chromatography, this study evaluates the influence of different concentrate supplement levels in the diet on rumen fermentation as well as the diversity and structure of the rumen methanogenic community for growing dromedary camels. Twelve growing camels were divided into three groups and given three levels of concentrate supplement, 0.7% (C1), 1% (C2), and 1.3% (C3) based on their body weight. All animals were fed alfalfa hay ad libitum. The levels of total volatile fatty acid, rumen ammonia, and methanogen copy number were unaffected by the supplementation level. Increasing the concentrate supplement level increased the proportion of propionic acid while decreasing the proportion of acetic acid. Increasing the level of concentrate in the diet had no effect on alpha diversity metrics or beta diversity of rumen methanogens. Methanobrevibacter and Methanosphaera predominated the methanogenic community and were declined as concentrate supplement level increased. This study sheds new light on the effect of concentrate supplement level in growing camels' diet on rumen fermentation and methanogenic community, which could help in the development of a strategy that aimed to reduce methane emissions and enhance feed efficiency.

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

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

Changes in the bacterial community colonizing extracted and non-extracted tannin-rich plants in the rumen of dromedary camels

Leguminous trees and saltbushes provide potential alternatives to conventional feeds to overcome feed deficiency in arid and semi-arid countries. However, these plants are rich in antinutritional factors that have adverse effects on rumen microbiota and the host- animal. Some rumen microbiota detoxifies plants' secondary metabolites; thus, understanding plant-microbe interaction in the rumen could improve the plants' utilization. This study investigated the bacterial colonization and degradation of non-extracted and extracted tanniniferous plants: Atriplex halimus, Acacia saligna, and Leucaena leucocephala, in the rumen of three fistulated camels at 6 and 12 hours. The results showed that these plants have high nutritional value and tannins contents. The rumen degradation and microbial diversity of plant-attached bacteria varied according to plant type and phenols' extraction. Atriplex and leucaena showed higher microbial diversity at 6 and 12h, respectively. Bacteroidetes and Firmicutes were the main bacterial phyla, and the main genera were Prevotella, RC9_gut_group, Butyrivibrio that overrepresented in non-extracted plants (P<0.05). Fibrobacteres and Anaerovibrio showed sensitivity to plant toxins and Ruminococcus attached to plants with lower tannins. Several bacterial genera in the camel rumen have the potential to resist antinutritional factors in fodder plants, which could be used to improve the performance of grazing animals.

Sex Differences in Fecal Microbiome Composition and Function of Dromedary Camels in Saudi Arabia

The gastrointestinal microbiome plays a significant role in diet digestion and the energy production of its host. Several factors that affect the gastrointestinal microbiota composition were studied in camels. Yet, the impact of sex on the gastrointestinal bacteriome of camels remains unexplored to date. In this perspective, the fecal microbiome community composition from dromedary camels was determined in 10 male and 10 female samples using the 16S rRNA amplicon, in order to estimate if this was influenced by sex. The core microbiome in females contained 284 bacterial OTUs and one archaeal OUT, whereas in males, it contained 279 bacterial OTUs and one archaeal OTU. In females, Bacteroidetes and Spirochaetes were significantly more abundant than in male camels, whereas Lentisphaerae and Euryarchaeota were significantly abundant in males. According to Principal Coordinate Analysis and UPGMA clustering, grouping with respect to sex was observed. The functional prediction results showed differences such as energy production and conversion, and that the cell wall/membrane/envelope were enriched in female camels. The fecal microbiome of male camels was rich in amino acid, lipid transport and metabolism.

Effect of barley straw and Egyptian clover hay on the rumen fermentation and structure and fibrolytic activities of rumen bacteria in dromedary camel

Background and Aim

Understanding the regulations of rumen microbiota and their fibrolytic capabilities under different forages are essential to improve rumen fermentation and animal feed efficiency. This study aimed to evaluate the changes in the rumen fermentation and the structure and fibrolytic activities of rumen bacteria in camels fed barley straw and Egyptian clover hay.

Materials and Methods

Three fistulated camels were fed a diet containing barley straw for 30 days; then transitioned to a diet containing Egyptian clover hay for 30 days. In addition, bacterial media enriched with xylan and different cellulose sources, namely, filter paper, wheat straw, and alfalfa hay, were used to evaluate the ability of camel rumen bacteria to produce xylanase and cellulase enzymes.

Results

The camel group fed Egyptian clover hay showed higher crude protein intake, rumen ammonia, total volatile fatty acids, and acetic acid. Moreover, the camel group fed barley straw showed higher neutral detergent fiber intake, rumen pH, and propionic and butyric acids. Principal component analysis showed that bacterial communities were separated based on the forage type. Forage type affected the composition of rumen bacteria and most of the bacterial community was assigned to phylum Bacteroidetes and Firmicutes. Egyptian clover hay diet increased the proportions of genus Prevotella and Ruminococcus; while fed barley straw diet increased the Butyrivibrio, RC9_gut_group, and Fibrobacteres. The bacterial culture of the Egyptian clover hay fed group produced the greatest xylanase and the bacterial culture of the barley straw fed group produced the maximum cellulase.

Conclusion

Egyptian clover hay is recommended to feed camels in intensive production. Moreover, the bacterial community in the camel rumen is a promising source of lignocellulolytic enzymes.

Rumen bacterial community profile and fermentation in Barki sheep fed olive cake and date palm byproducts

Rumen bacteria make the greatest contribution to rumen fermentation that enables the host animal to utilize the ingested feeds. Agro-industrial byproducts (AIP) such as olive cake (OC) and date palm byproducts (discarded dates (DD), and date palm fronds (DPF)) represent a practical solution to the deficiency in common feed resources. In this study, thirty-six growing Barki lambs were divided into three groups to evaluate the effect of untraditional diets including the AIP on the growth performance. Subsequently, nine adult Barki rams were used to evaluate the effect of experimental diets on rumen fermentation and rumen bacteria. Three rations were used: common concentrate mixture (S1), common untraditional concentrate mixture including OC and DD (S2), and the same concentrate mixture in S2 supplemented with roughage as DPF enriched with 15% molasses (S3). The animals in S2 group showed higher dry matter intake (DMI) and lower relative growth rate (RGR) as compared to the animals in S1 group. However, the animals in S3 group were the lowest in DMI but achieved RGR by about 87.6% of that in the S1 group. Rumen pH, acetic and butyric acids were more prevalent in animals of S3 group and rumen ammonia (NH3-N), total volatile fatty acids (TVFA), propionic acid were higher in S1. Rumen enzymes activities were higher in S1 group followed by S3 and S2. The bacterial population was more prevalent in S1 and microbial diversity was higher in the S3 group. Principal coordinate analysis revealed clusters associated with diet type and the relative abundance of bacteria varied between sheep groups. The bacterial community was dominated by phylum Bacteroidetes and Firmicutes; whereas, Prevotella, Ruminococcus, and Butyrivibrio were the dominant genera. Results indicate that diet S3 supplemented by OC, DD, and DPF could replace the conventional feed mixture.

Characterizing rumen microbiota and CAZyme profile of Indian dromedary camel (Camelus dromedarius) in response to different roughages

In dromedary camels, which are pseudo-ruminants, rumen or C1 section of stomach is the main compartment involved in fiber degradation, as in true ruminants. However, as camels are adapted to the harsh and scarce grazing conditions of desert, their ruminal microbiota makes an interesting target of study. The present study was undertaken to generate the rumen microbial profile of Indian camel using 16S rRNA amplicon and shotgun metagenomics. The camels were fed three diets differing in the source of roughage. The comparative metagenomic analysis revealed greater proportions of significant differences between two fractions of rumen content followed by diet associated differences. Significant differences were also observed in the rumen microbiota collected at different time-points of the feeding trial. However, fraction related differences were more highlighted as compared to diet dependent changes in microbial profile from shotgun metagenomics data. Further, 16 genera were identified as part of the core rumen microbiome of Indian camels. Moreover, glycoside hydrolases were observed to be the most abundant among all Carbohydrate-Active enzymes and were dominated by GH2, GH3, GH13 and GH43. In all, this study describes the camel rumen microbiota under different dietary conditions with focus on taxonomic, functional, and Carbohydrate-Active enzymes profiles.

Bacterial community analysis on the different mucosal immune inductive sites of gastrointestinal tract in Bactrian camels

The microbial communities colonize the mucosal immune inductive sites could be captured by hosts, which could initiate the mucosal immune responses. The aggregated lymphoid nodule area (ALNA) and the ileal Payer's patches (PPs) in Bactrian camels are both the mucosal immune inductive sites of the gastrointestinal tract. Here, the bacteria community associated with the ALNA and ileal PPs were analyzed using of 16S rDNA-Illumina Miseq sequencing. The mutual dominant bacterial phyla at the two sites were the Bacteroidetes, Firmicutes, Verrucomicrobia and Proteobacteria, and the mutual dominant genus in both sits was Prevotella. The abundances of the Fibrobacter, Campylobacter and RFP12 were all higher in ALNA than in ileal PPs. While, the abundances of the 5-7N15, Clostridium, and Escherichia were all higher in ileal PPs than in ALNA. The results suggested that the host's intestinal microenvironment is selective for the symbiotic bacteria colonizing the corresponding sites, on the contrary, the symbiotic bacteria could impact on the physiological functions of this local site. In ALNA and ileal PPs of Bactrian camel, the bacteria which colonized different immune inductive sites have the potential to stimulate different immune responses, which is the result of the mutual selection and adaptation between microbial communities and their host.