Rumen fermentation and microbiota in Shami goats fed on condensed tannins or herbal mixture.

BACKGROUND: Phytochemical compounds can modify the rumen microbiome and improve rumen fermentation. This study evaluated the impact of supplementation with tannin and an herbal mixture containing ginger (Zingiber officinale), garlic (Allium sativum), Artemisia (Artemisia vulgaris), and turmeric (Curcuma longa) on the rumen fermentation and microbiota, and histology of rumen tissue of goats. Eighteen Shami male goats were divided into three groups (n = 6): non-supplemented animals fed the basal diet (C, control); animals fed basal diet and supplemented with condensed tannin (T); and animals fed basal diet and supplemented with herbal mixture (HM). Each animal received a basal diet composed of Alfalfa hay and a concentrate feed mixture. RESULTS: Group HM revealed higher (P < 0.05) rumen pH, total volatile fatty acids (VFA), acetic, propionic, isobutyric, butyric, isovaleric, and valeric. Principal Co-ordinate analysis (PCoA) showed that rumen microbial communities in the control group and supplemented groups were distinct. The supplementation increased (P < 0.05) the relative abundances of phylum Bacteroidota and Proteobacteria and declined (P < 0.05) Firmicutes and Fibrobacterota. Additionally, the dominant genus Prevotella and Rikenellaceae RC9 gut group were increased (P < 0.05) and the family Ruminococcaceae was declined (P < 0.05) due to the supplementation. The supplementation decreased (P < 0.05) the archaeal genus Methanobrevibacter and increased (P < 0.05) Candidatus Methanomethylophilus. Tannin supplementation in T group shortened the rumen papillae. CONCLUSIONS: The results revealed that the herbal mixture might be used to alter the rumen microbiota to improve rumen fermentation.

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.

New insights into the genetic predisposition of brucellosis and its effect on the gut and vaginal microbiota in goats.

Goats contribute significantly to the global food security and industry. They constitute a main supplier of meat and milk for large proportions of people in Egypt and worldwide. Brucellosis is a zoonotic infectious disease that causes a significant economic loss in animal production. A case-control genome-wide association analysis (GWAS) was conducted using the infectious status of the animal as a phenotype. The does that showed abortion during the last third period of pregnancy and which were positive to both rose bengal plate and serum tube agglutination tests, were considered as cases. Otherwise, they were considered as controls. All animals were genotyped using the Illumina 65KSNP BeadChip. Additionally, the diversity and composition of vaginal and fecal microbiota in cases and controls were investigated using PCR-amplicone sequencing of the V4 region of 16S rDNA. After applying quality control criteria, 35,818 markers and 66 does were available for the GWAS test. The GWAS revealed a significantly associated SNP (P = 5.01 × 10-7) located on Caprine chromosome 15 at 29 megabases. Four other markers surpassed the proposed threshold (P = 2.5 × 10-5). Additionally, fourteen genomic regions accounted for more than 0.1% of the variance explained by all genome windows. Corresponding markers were located within or in close vicinity to several candidate genes, such as ARRB1, RELT, ATG16L2, IGSF21, UBR4, ULK1, DCN, MAPB1, NAIP, CD26, IFIH1, NDFIP2, DOK4, MAF, IL2RB, USP18, ARID5A, ZAP70, CNTN5, PIK3AP1, DNTT, BLNK, and NHLRC3. These genes play important roles in the regulation of immune responses to the infections through several biological pathways. Similar vaginal bacterial community was observed in both cases and controls while the fecal bacterial composition and diversity differed between the groups (P < 0.05). Faeces from the control does showed a higher relative abundance of the phylum Bacteroidota compared to cases (P < 0.05), while the latter showed more Firmicutes, Spirochaetota, Planctomycetota, and Proteobacteria. On the genus level, the control does exhibited higher abundances of Rikenellaceae RC9 gut group and Christensenellaceae R-7 group (P < 0.05), while the infected does revealed higher Bacteroides, Alistipes, and Prevotellaceae UCG-003 (P < 0.05). This information increases our understanding of the genetics of the susceptibility to Brucella in goats and may be useful in breeding programs and selection schemes that aim at controlling the disease in livestock.

Response of rumen fermentation and microbiota to dietary supplementation of sodium selenite and bio-nanostructured selenium in lactating Barki sheep.

Dietary selenium (Se) sources affects the structure of the rumen microbial community and rumen fermentation. This study evaluated the effects of sodium selenite (SS) and bio-nanostructured selenium (SeNSM) on rumen fermentation and structure of rumen microbial community of lactating Barki ewes. Twenty one lactating Barki ewes were assigned into three groups based on their body weight and milk yield. The experiment lasted for 50 days, whenever, the control group was fed basal diet; group SS received basal diets plus sodium selenite as inorganic source of Se; and group SeNSM received basal diet plus organic selenium bio-nanostructured. Ruminal pH and volatile Fatty Acids (VFA) was lower (P < 0.05) in SeNSM group compared to control. Principle Coordinate Analysis separated the microbial communities into three clusters based on feeding treatment. The bacterial community was dominated by phylum Bacteroidetes and Firmicutes that were affected (P < 0.05) by Se sources. Specifically Bacteriodetes was higher (P < 0.05) in SS and SeNSM groups; and Firmicutes was higher (P < 0.05) in the control group. Moreover, the predominant bacterial genera were Prevotella, Rikenellaceae RC9 gut group, Unclassified_Bacteroidales, which were higher (P < 0.05) in SeNSM group. The methanogenic community belonged to phylum Euryarchaeota and was significantly decreased (P < 0.05) by Se supplementation. Principal component analysis based on rumen fermentation parameters, and relative abundances of bacteria and methanogens revealed three distinct clusters. These findings suggest that Se supplementation affected the relative abundances of dominant bacterial groups, declined rumen methanogens and SeNSM supplementation showed some positive impacts on some fibrolytic bacteria.

Genome-wide landscape of runs of homozygosity and differentiation across Egyptian goat breeds.

Understanding the genomic features of livestock is essential for successful breeding programs and conservation. This information is scarce for local goat breeds in Egypt. In the current study, genomic regions with selection signatures were identified as well as runs of homozygosity (ROH), genomic inbreeding coefficients (FROH) and fixation index (FST) were detected in Egyptian Nubian, Damascus, Barki and Boer goat breeds. A total of 46,268 SNP markers and 337 animals were available for the genomic analyses. On average, 145.44, 42.02, 87.90 and 126.95 ROHs were detected per individual in the autosomal genome of the respective breeds. The mean accumulative ROH lengths ranged from 46.5 Mb in Damascus to 360 Mb in Egyptian Nubian. The short ROH segments (< 2 Mb) were most frequent in all breeds, while the longest ROH segments (> 16 Mb) were exclusively found in the Egyptian Nubian. The highest average FROH was observed in Egyptian Nubian (~ 0.12) followed by Boer (~ 0.11), while the lowest FROH was found in Damascus (~ 0.05) and Barki breed (~ 0.03). The estimated mean FST was 0.14 (Egyptian Nubian and Boer), 0.077 (Egyptian Nubian and Barki), 0.075 (Egyptian Nubian and Damascus), 0.071 (Barki and Boer), 0.064 (Damascus and Boer), and 0.015 (Damascus and Barki), for each pair of breeds. Interestingly, multiple SNPs that accounted for high FST values were observed on chromosome 6 in regions harboring ALPK1 and KCNIP4. Genomic regions overlapping both FST and ROH harbor genes related to immunity (IL4R, PHF23, GABARAP, GPS2, and CD68), reproduction (SPATA2L, TNFSF12, TMEM95, and RNF17), embryonic development (TCF25 and SOX15) and adaptation (MC1R, KDR, and KIT), suggesting potential genetic adaptations to local environmental conditions. Our results contribute to the understanding of the genetic architecture of different goat breeds and may provide valuable information for effective preservation and breeding programs of local goat breeds in Egypt.

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.

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.

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.

Effect of olive and date palm by-products on rumen methanogenic community in Barki sheep.

Rumen methanogens prevent the accumulation of fermentation gases in the rumen and generate methane that increases global warming and represents a loss in animals' gross energy. Non-traditional feed resources such as the by-products of date palm (Phoenix dactylifera) and olive (Olea europaea) trees have received attention to be used in animal feeding. This study evaluated the impact of non-traditional feed resources including olive cake (OC), discarded dates (DD), and date palm frond (DPF) in sheep diet on rumen fermentation, diversity and relative abundance of rumen methanogens. Nine adult rams were assigned to three equal groups and fed three diets: traditional concentrates mixture (S1); non-traditional concentrate mixture (S2) based on DD and OC; and (S3) composed of the same S2 concentrate supplemented with DPF as a roughage part. The results showed that rumen pH was higher with S3 diet than the other two diets. However, the S1 diet showed the highest values of total volatile fatty acids (TVFA) and rumen ammonia. In addition, the proportions of acetic and butyric acids were increased, whereas propionic acid declined in S2 and S3 compared to the S1 diet. Rumen methanogens were dominated by Methanobrevibacter that showed a numeric decline by including DD, OC, and DPF in the animal diets. Principal component analysis (PCA) based on rumen fermentation parameters and relative abundances of methanogens genera showed three distinct clusters. Also, positive and negative correlations were revealed between methanogens genera and rumen metabolites. This study expands the knowledge regarding the effect of agricultural byproducts on rumen fermentation and the methanogenic community.

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.

Fibrolytic rumen bacteria of camel and sheep and their applications in the bioconversion of barley straw to soluble sugars for biofuel production.

Lignocellulosic biomass such as barley straw is a renewable and sustainable alternative to traditional feeds and could be used as bioenergy sources; however, low hydrolysis rate reduces the fermentation efficiency. Understanding the degradation and colonization of barley straw by rumen bacteria is the key step to improve the utilization of barley straw in animal feeding or biofuel production. This study evaluated the hydrolysis of barley straw as a result of the inoculation by rumen fluid of camel and sheep. Ground barley straw was incubated anaerobically with rumen inocula from three fistulated camels (FC) and three fistulated sheep (FR) for a period of 72 h. The source of rumen inoculum did not affect the disappearance of dry matter (DMD), neutral detergent fiber (NDFD). Group FR showed higher production of glucose, xylose, and gas; while higher ethanol production was associated with cellulosic hydrolysates obtained from FC group. The diversity and structure of bacterial communities attached to barley straw was investigated by Illumina Mi-Seq sequencing of V4-V5 region of 16S rRNA genes. The bacterial community was dominated by phylum Firmicutes and Bacteroidetes. The dominant genera were RC9_gut_group, Ruminococcus, Saccharofermentans, Butyrivibrio, Succiniclasticum, Selenomonas, and Streptococcus, indicating the important role of these genera in lignocellulose fermentation in the rumen. Group FR showed higher RC9_gut_group and group FC revealed higher Ruminococcus, Saccharofermentans, and Butyrivibrio. Higher enzymes activities (cellulase and xylanase) were associated with group FC. Thus, bacterial communities in camel and sheep have a great potential to improve the utilization lignocellulosic material in animal feeding and the production of biofuel and 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.

Lignocelluloytic activities and composition of bacterial community in the camel rumen.

The camel is well-adapted to utilize the poor-quality forages in the harsh desert conditions as the camel rumen sustains fibrolytic microorganisms, mainly bacteria that are capable of breaking down the lignocellulosic biomass efficiently. Exploring the composition of the bacterial community in the rumen of the camel and quantifying their cellulolytic and xylanolytic activities could lead to understanding and improving fiber fermentation and discovering novel sources of cellulases and xylanases. In this study, Illumina MiSeq sequencing of the V4 region on 16S rRNA was applied to identify the bacterial and archaeal communities in the rumen of three camels fed wheat straw and broom corn. Furthermore, rumen samples were inoculated into bacterial media enriched with xylan and different cellulose sources, including filter paper (FP), wheat straw (WS), and alfalfa hay (AH) to assess the ability of rumen bacteria to produce endo-cellulase and endo-xylanase at different fermentation intervals. The results revealed that the phylum Bacteroidetes dominated the bacterial community and Candidatus Methanomethylophilus dominated the archaeal community. Also, most of the bacterial community has fibrolytic potential and the dominant bacterial genera were Prevotella, RC9_gut_group, Butyrivibrio, Ruminococcus, Fibrobacteres, and Treponema. The highest xylanase production (884.8 mU/mL) was observed at 7 days. The highest cellulase production (1049.5 mU/mL) was observed when rumen samples were incubated with Alfalfa hay for 7 days.

Comparative analysis of the metabolically active microbial communities in the rumen of dromedary camels under different feeding systems using total rRNA sequencing.

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.