The Temporal Dynamics of Rumen Microbiota in Early Weaned Lambs

Weaning affects the development of ruminal bacteria in lambs during early life. However, the temporal dynamics of rumen microbiota in early weaned lambs is unknown compared to conventionally weaned lambs. In this study, one group was reared with their dams (control, CON) and conventionally weaned at 49 days (d), while the other lambs were weaned at 21 d (early weaning, EW) using starter. Rumen microbial samples collected at 26, 35, and 63 d were used for next-generation sequencing. Here, we found that the abundance and diversity of rumen microbiota in EW were significantly lower at 26 and 35 d than the CON. Linear discriminant analysis Effect Size (LEfSe) analysis was performed to identify the signature microbiota for EW at these three ages. At 26 d, Prevotella 7, Syntrophococcus, Sharpea, Dialister, Pseudoscardovia, and Megasphaera in the rumen of the EW group had greater relative abundances. At 35 d, the Lachnospiraceae_NK3A20_group was enriched in CON. On 63 d, Erysipelotrichaceae_UCG-002 was abundant in EW. Syntrophococcus and Megaspheaera in EW lambs were abundant at 26 and 35 d, but kept similar to CON at 63 d. The relative abundance of Erysipelotrichaceae_UCG-002 at all-time points was consistently higher in the EW group. In conclusion, early weaning led to a significant decrease in rumen microbiota richness and diversity in the short term. The changes in rumen microbiota are associated with the persistence of weaning stress. The temporal dynamics of relative abundances of Syntrophococcus, Megasphaera, and Ruminococcaceae_UCG-014 reflect the weaning stress over a short period and rumen recovery after early weaning.

Exploring the Ruminal Microbial Community Associated with Fat Deposition in Lambs

Microbial communities of the sheep rumen have been studied extensively; however, their involvement in the regulation of fat deposition is unknown. Herein, we aimed to identify the correlations among fat deposition-related phenotypes and the effect of microbiota on changes in body fat accumulation. The rumen microbiota of 141 lambs was profiled by 16S ribosomal RNA sequencing, and the volatile fatty acids’ (VFAs’) concentrations were quantified by gas chromatography. Subsequently, the animals were grouped according to body mass index (BMI) to compare the microbiota of the rumen among the sheep with different fat deposition levels. Results further revealed differences in terms of the species abundance, diversity, and microbial composition between sheep with different fat deposition levels. Linear discriminant analysis (LDA) Effect Size (LEfSe) analysis and Random Forest (RF) regression analysis identified changes in 29 ruminal bacteria, which may be the main driver for different fat deposition.

Bioprospecting of cow's ruminal microbiota from a slaughterhouse in Ambarawa, Central Java, Indonesia

Murwani R, Sibero MT, Silitonga PRA, Ambariyanto A. 2021. Bioprospecting of cow's ruminal microbiota from a slaughterhouse in Ambarawa, Central Java, Indonesia. Biodiversitas 22: 5030-5038. Ruminal microorganisms play essential roles in maintaining ruminant health. However, most studies focused only on ruminal lactic acid bacteria (LAB), although other ruminal microorganisms might have biological properties for biotechnological purposes. Therefore, the current study aimed to isolate ruminal bacteria (LAB and non-LAB) and fungi from ruminal material and conducted a bioprospecting study to understand their ability to produce antibacterial compounds and polysaccharide-degrading enzymes. The ruminal bacteria were isolated on MRS and ISP4 agar, while PDA was used to isolate the different fungi. The antibacterial property was tested against multidrug-resistant Escherichia coli and Salmonella enterica ser. Typhi. The ability to produce agarase, alginate-lyase, and carrageenase was screened. Prospective isolates were identified using DNA barcoding approach. Twelve bacteria were isolated using MRS agar, six from ISP4 agar, and four fungi from PDA. Among twelve bacteria from MRS agar, eleven were considered LAB, which consisted of Lactobacillus plantarum and Pediococcus acidilactici. Several classes of bacteria such as actinobacteria, firmicutes, ?-proteobacteria, and ?-proteobacteria were isolated during this study. In addition, three fungal classes, namely Saccharomycetes, Eurotiomycetes, and Mucoromycetes were also isolated. All bacteria from MRS agar were suggested to have potential compounds with antimicrobial activity, while all ruminal fungi exhibited potential sources of polysaccharide-degrading enzymes.

PSX-B-9 Effect of trace mineral sources in the supplement for grazing cattle on ruminal bacteria diversity

The rumen soluble Cu and Zn can affect the rumen microbial populations. This study aimed to evaluate the effect of trace mineral sources (Cu and Zn) in the supplement of grazing steers on ruminal bacteria diversity. Eight rumen cannulated Nellore steers (541 kg ± 18 kg BW) were distributed in a randomized block design in individual paddocks of Urochloa brizantha cv. Marandu. Steers were supplemented during 101 days between dry to rainy season at 5 g/kg BW with commercial supplement (25% CP) containing Cu (40 mg/ kg) and Zn (148 mg/kg) in the inorganic (Control) or hydroxy (HDX; Micronutrients Inc., IN) source. Samples of ruminal content were collected before supplementation at day 97 of experimental period and the total DNA extracted by commercial kit (Quick-DNA Fecal/Soil Microbe Miniprep). The V3/V4 regions of 16SrRNA gene was sequencing using the Illumina MiSeq, using the Quantitative Insights into Microbial Ecology (QIIME v.1.9.1) to filter reads and determine Operational Taxonomic Units (OTUs). Data were compared using an unpaired Wilcoxon test in R. A total of 293 OTUs were identified at genus level. The HDX resulted in a higher ruminal abundance of Corynebacterium 1 (P = 0.01), Prevotella 1 (P = 0.01), Lachnoclostridium 10 (P = 0.02), Lachnospiraceae AC2044 group (P = 0.03), Lachnospiraceae UCG-008 (P = 0.03), Streptococcus (P = 0.02), Ruminococcaceae UCG-010 (P = 0.01), Ruminococcaceae UCG-014 (P = 0.01), Ruminococcus 1 (P = 0.04), Coprococcus 1 (P = 0.04), Mogibacterium (P = 0.02), Selenomonas 1 (P = 0.02), Anaerovibrio (P = 0.03), Methylobacterium (P = 0.02), Treponema 2 (P = 0.02), Rikenellaceae RC9 gut group (P = 0.03), Ruminococcaceae; uncultured rumen bacterium (P = 0.02) and Eubacterium hallii group (P = 0.05), and lower abundance of Fibrobacter (P = 0.04), Butyrivibrio 2 (P = 0.05), Anaerotruncus (P = 0.03), Ruminiclostridium 5 (P = 0.03), Anaerorhabdus furcosa group (P = 0.02) and Erysipelotrichaceae UCG-004 (P = 0.01). The use of HDX in the supplement for grazing cattle between dry to rainy season increase the ruminal abundance of bacteria, mainly into Firmicutes phylum with important structural and non-structural carbohydrates degradation functions.

Characterisation of the rumen resistome in Spanish dairy cattle

Background Rumen microorganisms carry antimicrobial resistance genes which pose a threaten to animals and humans in a One Health context. In order to tackle the emergence of antimicrobial resistance it is vital to understand how they appear, their relationship with the host, how they behave as a whole in the ruminal ecosystem or how they spread to the environment or humans. We sequenced ruminal samples from 416 Holstein dairy cows in 14 Spanish farms using nanopore technology, to uncover the presence of resistance genes and their potential effect on human, animal and environmental health. Results We found 998 antimicrobial resistance genes (ARGs) in the cow rumen and studied the 25 most prevalent genes in the 14 dairy cattle farms. The most abundant ARGs were related to the use of antibiotics to treat mastitis, metritis and lameness, the most common diseases in dairy cattle. The relative abundance (RA) of bacteriophages was positively correlated to the ARGs RA. The heritability of the RA of the more abundant ARGs ranged between 0.10 (mupA) and 0.49 (tetW), similar to the heritability of the RA of microbes that carried those ARGs. Even though these genes are carried by the microorganisms, the host is partially controlling their RA by having a more suitable rumen pH, folds, or other physiological traits that promote the growth of those microorganisms. Conclusions We were able to determine the most prevalent ARGs (macB, msbA, parY, rpoB2, tetQ and TaeA) in the ruminal bacteria ecosystem. The rumen is a reservoir of ARGs, and strategies to reduce the ARG load from livestock must be pursued.

Calorimetry, physicochemical characteristics and nitrogen release from extruded urea

Our hypothesis was that extrusion of urea associated with corn may reduce N solubilization and increase the nutritional quality of this food for ruminants. We aimed to physically and chemically characterize a corn and urea mixture before and after the extrusion process. It was evaluated morphological differences by scanning electron microscopy, nitrogen solubilization, and compound mass loss by thermogravimetry. In scanning electron microscopy, extruded urea showed agglomerated and defined structures, with changes in the morphology of starch granules and urea crystals, differing from the arrangement of the corn and urea mixture. The extruded urea maintained a constant nitrogen release pattern for up to 360 min. In thermogravimetry, extruded urea presented a higher temperature to initiate mass loss, that is, the disappearance of the material with increasing temperature, but the mass loss was lower when compared to the first event of the corn and urea mixture. In conclusion the process of extrusion of urea with corn modifies the original structures of these ingredients and controls the release of nitrogen from the urea, maintaining in its formation an energy source optimizing the use of nitrogen by ruminal bacteria, because the more synchronized the release of starch (energy) and nitrogen, the better the use by ruminal microorganisms.

Diet dominates age in shaping the rumen bacteria community and function in dairy cattle

Background To understand the effects of diet and age on the rumen bacterial community and function, forty-eight dairy cattle at 1.5 (M1.5), 6 (M6), 9 (M9), 18 (M18), 23 (M23), and 27 (M27) months old were selected. The M1.5, M6, and M27 had the high protein and starch dietary, while the M9, M18, and M23 had the high fiber dietary. Fermentation profile, enzyme activity, and bacteria community in rumen fluid were measured. Results The acetate to propionate ratio (A/P) at M9, M18, and M23 (high fiber diet) was higher than other ages, and M6 was the lowest (P < 0.05). The total volatile fatty acid (TVFA) at M23 and M27 was higher than other ages (P < 0.05). The urease at M18 was lower than M1.5, M6, and M9, and the xylanase at M18 was higher than M1.5, M23, and M27 (P < 0.05). The α-diversity indexes (Ace and Chao1) of ruminal bacteria increased from M1.5 to M23, while they decreased from M23 to M27 (P < 0.05). Thirty-three bacteria were identified as biomarkers of the different groups based on the linear discriminant analysis (LDA) when the LDA score > 4. The variation partitioning approach analysis showed that the age and diet had a 7.98% and 32.49% contribution to the rumen bacteria community variation, respectively. The richness of Succinivibrionaceae_UCG-002 and Fibrobacter were positive correlated with age (r > 0.60, P < 0.01) and also positively correlated with TVFA and acetate (r > 0.50, P < 0.01). The Lachnospiraceae_AC2044_group, Pseudobutyrivibrio, and Saccharofermentans has a positive correlation (r > 0.80, P < 0.05) with diet NDF and negative correlation (r < -0.80, P < 0.05) with diet CP and starch, which were also positively correlated with the acetate and A/P (r > 0.50, P < 0.01). Conclusion These findings indicated that the quantitative effect of diet and age on the rumen bacteria were 7.98% and 32.49%, respectively. The genera of Lachnospiraceae_AC2044_group, Pseudobutyrivibrio, and Saccharofermentans could be worked as the target bacteria to modulate the rumen fermentation by diet; meanwhile, the high age-correlated bacteria such as Succinivibrionaceae_UCG-002 and Fibrobacter also should be considered when shaping the rumen function.

The Rumen Bacterial Community in Dairy Cows Is Correlated to Production Traits During Freshening Period

The rumen microbiome plays a vital role in providing nutrition to the host animal, thereby influencing ruminant production. Despite its importance, it is not fully understood how variation in the ruminal bacteria community composition influences dry matter intake (DMI), milk yield and ruminal fermentative parameters in dairy cows, especially during freshening period. Here, we hypothesized that during early lactation, high DMI cows having a different ruminal microbiota than low DMI cows, and that this difference persists over time. To test this, we enrolled 65 fresh and determinzed their DMI using an auto-feed intake recording system. Fourteen days after calving, the 10 animals with the lowest (LFI) and the 10 animals with the highest (HFI)-average DMI were selected for further analysis. Rumen fluid was collected from these two cohorts at 1 (Fresh1d) and 14 days (Fresh14d) after calving and their ruminal microbiota were assessed using 16S rRNA sequencing. Volatile fatty acid (VFA) concentrations were also quantified. Comparison of the ruminal microbiotas between Fresh1d and Fresh14d showed that Fresh14d cows had a significantly higher relative abundance of VFA—producing microbes (P &lt; 0.05), such as Prevotella_7 and Succinivibrionaceae_UCG-001. This was commensurate with the concentrations of acetate, propionate, butyrate, valerate and total VFAs, were also significantly (P &lt; 0.05) increased in Fresh14d cows. We also found that the differences in the ruminal microbiota between LFI and HFI cows was limited, but DMI significantly altered (P &lt; 0.05) the relative proportion of bacteria in the families Coriobacteriaceae, and Succinivibrionaceae. Furthermore, specific operational taxonomic units belonging to the Anaeroplasma was significantly (P &lt; 0.05) correlated with DMI and milk yield. Taking together, our findings provide a framework for future studies of freshening period cow that seek to better understand the role of the ruminal microbiota during this critical period in the lactation cycle.

RUMINAL AMMONIA AND BLOOD UREA METABOLISM IN SHEEP FED HAY WITH OR WITHOUT CONCENTRATE SUPPLEMENT

Metabolism of ruminal ammonia and blood urea was investigated in West African Dwarf ewes and wethers, fed a low quality hay with or without concentrate supplementation, using single injection of [15N] ammonium chloride (HN4Cl) or [15N] urea into the rumen and blood respectively. The percentages of 15N administered intraruminal as HN4Cl recovered in the urine, faeces and milk of the ewes were 4.3, 9.0 and 3.1, Also 32.3 and 28.7% of [15Nl urea administered into the blood were recovered in the urine of the wethers. Ruminal ammonia contributed 50.6% or protozoal-N in sheep fed hay and 14.2 78.7 and 35.0% respectively in sheep fed hay and concentrate. Also, 59.0 and 7.9% of ruminal ammonia-N was derived from blood urea of sheep fed hay and hay plus concentrate respectively. The inclusion of concentrate in the diet increased the extent of ruminal bacteria protein synthesis but not that of the protozoa, However, the contributions of ruminal ammonia to blood urea synthesis and of blood urea to ruminal ammonia were Sharply decreased in the presence of the concentrate.