Oregano Essential Oils Promote Rumen Digestive Ability by Modulating Epithelial Development and Microbiota Composition in Beef Cattle.
TL;DR: In this article, the effects of oregano essential oils (OEO) on the rumen digestive ability using multi-omics sequencing techniques were explored, and it was found that OEO supplementation increased the ruminant digestive ability by modulating epithelial development and microbiota composition.
Abstract: This study aimed to explore the effects of oregano essential oils (OEO) on the rumen digestive ability using multi-omics sequencing techniques. Twenty-seven castrated Pingliang red cattle were randomly separated into three groups (3 cattle/pen; n = 9) and fed on a daily basal diet supplemented with 0 (Con group), 130 mg (L group), and 260 mg (H group) OEO. The finishing trial lasted for 390 days, and all cattle were slaughtered to collect rumen tissue and content samples. We found that the rumen papillae length in the H group was higher than in the Con group. Amylase concentrations were decreased in the H group than the Con group, whereas the β-glucosidase and cellulase concentrations increased. Compared to the Con group, the relative abundance of propionate and butyrate in the H group was significantly higher. Higher relative abundance of Parabacteroides distasonis and Bacteroides thetaiotaomicron were observed with increasing OEO concentration. The function of rumen microbiota was enriched in the GH43_17 family, mainly encoding xylanase. Besides, metabolites, including heparin, pantetheine, sorbic acid, aspirin, and farnesene concentrations increased with increasing OEO dose. A positive correlation was observed between Parabacteroides distasonis, Bacteroides thetaiotaomicron, and β-glucosidase, cellulase and propionate. The abundance of Parabacteroides distasonis and Parabacteroides_sp._CAG:409 were positively correlated with sorbic acid and farnesene. In summary, OEO supplementation increased the rumen digestive ability by modulating epithelial development and microbiota composition in beef cattle. This study provides a comprehensive insight into the OEO application as an alternative strategy to improve ruminant health production.
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TL;DR: In this paper , the effects of EOs on rumen fermentation, blood metabolites, growth performance and meat quality of beef cattle through a meta-analysis were evaluated. But, the results showed that EOs did not affect pH, color (L* a* and b*), or chemical composition (p > 0.05).
Abstract: The objective of this study was to see how dietary supplementation with essential oils (EOs) affected rumen fermentation, blood metabolites, growth performance and meat quality of beef cattle through a meta-analysis. In addition, a simulation analysis was conducted to evaluate the effects of EOs on the economic and environmental impact of beef production. Data were extracted from 34 peer-reviewed studies and analyzed using random-effects statistical models to assess the weighted mean difference (WMD) between control and EOs treatments. Dietary supplementation of EOs increased (p < 0.01) dry matter intake (WMD = 0.209 kg/d), final body weight (WMD = 12.843 kg), daily weight gain (WMD = 0.087 kg/d), feed efficiency (WMD = 0.004 kg/kg), hot carcass weight (WMD = 5.45 kg), and Longissimus dorsi muscle area (WMD = 3.48 cm2). Lower (p < 0.05) ruminal concentration of ammonia nitrogen (WMD = −1.18 mg/dL), acetate (WMD = −4.37 mol/100 mol) and total protozoa (WMD = −2.17 × 105/mL), and higher concentration of propionate (WMD = 0.878 mol/100 mol, p < 0.001) were observed in response to EOs supplementation. Serum urea concentration (WMD = −1.35 mg/dL, p = 0.026) and haptoglobin (WMD = −39.67 μg/mL, p = 0.031) were lower in cattle supplemented with EOs. In meat, EOs supplementation reduced (p < 0.001) cooking loss (WMD = −61.765 g/kg), shear force (WMD = −0.211 kgf/cm2), and malondialdehyde content (WMD = −0.040 mg/kg), but did not affect pH, color (L* a* and b*), or chemical composition (p > 0.05). Simulation analysis showed that EOs increased economic income by 1.44% and reduced the environmental footprint by 0.83%. In conclusion, dietary supplementation of EOs improves productive performance and rumen fermentation, while increasing the economic profitability and reducing the environmental impact of beef cattle. In addition, supplementation with EOs improves beef tenderness and oxidative stability.
11 citations
TL;DR: LAGS was effective in treating overall IBS symptoms, together with an improvement in the gut microbiota profile, especially for the IBS mixed subtype.
Abstract: Geraniol is an acyclic monoterpene alcohol with well-known anti-inflammatory and antimicrobial properties which has shown eubiotic activity towards gut microbiota (GM) in patients with irritable bowel syndrome (IBS). Methods: Fifty-six IBS patients diagnosed according to Rome III criteria were enrolled in an interventional, prospective, multicentric, randomized, double-blinded, placebo-controlled trial. In the treatment arm, patients received a low-absorbable geraniol food supplement (LAGS) once daily for four weeks. Results: Patients treated with LAGS showed a significant reduction in their IBS symptoms severity score (IBS-SSS) compared to the placebo (195 vs. 265, p = 0.001). The rate of responders according to IBS-SSS (reduction ≥ 50 points) was significantly higher in the geraniol vs placebo group (52.0% vs. 16.7%, p = 0.009) mainly due to the IBS mixed subtype. There were notable differences in the microbiota composition after geraniol administration, particularly a significant decrease in a genus of Ruminococcaceae, Oscillospira (p = 0.01), a decreasing trend for the Erysipelotrichaceae and Clostridiaceae families (p = 0.1), and an increasing trend for other Ruminococcaceae taxa, specifically Faecalibacterium (p = 0.09). The main circulating proinflammatory cytokines showed no differences between placebo and geraniol arms. Conclusion: LAGS was effective in treating overall IBS symptoms, together with an improvement in the gut microbiota profile, especially for the IBS mixed subtype.
3 citations
TL;DR: In this article , the effects of dietary supplementation of a polyherbal additive (PA) containing hydrolyzable tannins, flavonoids, and essential oils on productive performance, dietary energetics, carcass and meat characteristics, and blood metabolites of lambs in their finishing phase were evaluated.
Abstract: The objective of this study was to evaluate the effects of dietary supplementation of a polyherbal additive (PA) containing hydrolyzable tannins, flavonoids, and essential oils on productive performance, dietary energetics, carcass and meat characteristics, and blood metabolites of lambs in their finishing phase. Twenty-eight Pelibuey × Katahdin lambs (20.52 ± 0.88 kg body weight (BW)) were housed in individual pens and assigned to four treatments (n = 7) with different doses of PA: 0 (CON), 1 (PA1), 2 (PA2), and 3 (PA3) g of PA kg−1 of DM for 56 days. Compared to the CON, lambs in PA1 treatment had higher average daily gain (p = 0.03), higher dietary energy utilization (p = 0.01), greater backfat thickness (p = 0.02), greater Longissimus dorsi muscle area (p = 0.01), and better feed conversion ratio (p = 0.02). PA supplementation did not affect (p > 0.05) dry matter intake, carcass yield, biometric measures, and meat chemical composition. All hematological and most of the blood biochemical parameters were similar in lambs of all treatments (p > 0.05). However, compared to the CON, lambs assigned to the PA3 treatment had lower serum urea concentration (p = 0.05) and higher serum albumin concentration (p = 0.03). In conclusion, low doses of PA could be used as a growth promoter in finishing lambs without affecting dry matter intake, carcass yield, meat chemical composition, and health status of the lambs. However, more in vivo research is needed to better understand the impact of bioactive compounds from PA used on productivity, metabolism, and health status of finishing lambs.
3 citations
TL;DR: In this paper , the effects of essential oils (EO) extracts star anise (Illicium verum), citronella (Cymbopogon winterianus), clove bud (Eugenia caryophyllus), staigeriana eucalyptus (Eucaliaptus staige), globulus euclyptus, ginger (Zingiber officinale), ho wood (Cinnamomum camphora), melaleuca (Melaleuca alternifolia), oregano (Origanum vulgare) and white thyme (Thymus vulgaris) on in vitro methane emissions from four rumen-cannulated Nellore cattle grazing a tropical grass pasture as inoculum donors.
Abstract: There is increasing pressure to identify natural feed additives to mitigate methane emissions from livestock systems. Our objective was to investigate the effects of essential oils (EO) extracts star anise (Illicium verum), citronella (Cymbopogon winterianus), clove bud (Eugenia caryophyllus), staigeriana eucalyptus (Eucalyptus staigeriana), globulus eucalyptus (Eucalyptus globulus), ginger (Zingiber officinale), ho wood (Cinnamomum camphora), melaleuca (Melaleuca alternifolia), oregano (Origanum vulgare) and white thyme (Thymus vulgaris) on in vitro methane emissions from four rumen-cannulated Nellore cattle grazing a tropical grass pasture as inoculum donors. The semi-automated gas production technique was used to assess total gas production, dry matter degradability, partitioning factor, ammoniacal nitrogen, short-chain fatty acids and methane production. All essential oils were tested in four doses (0, 50, 250 and 500 mg/L) in a randomized block design, arranged with four blocks, 10 treatments, four doses and two replicates. Within our study, oregano and white Thyme EO reduced net methane production at 250 mg/L, without affecting substrate degradation. Essential oils from oregano and white thyme have the potential to modify ruminal fermentation and suppress rumen methanogenesis without negative effects on feed digestibility, indicating promise as alternatives to ionophores for methane reduction in beef cattle.
3 citations
TL;DR: Yeast products (YP) are commonly used as rumen regulators, but their mechanisms of action are still unclear as mentioned in this paper , however, they have been shown to improve rumen fermentation parameters, change the activity of rumen digestive enzymes and reduce the concentration of abnormal metabolites.
Abstract: Simple Summary Increasing the proportion of concentrate in the diet is a common strategy to improve the performance of ruminants. However, this may lead to abnormal rumen fermentation, which is a threat to animal health. As a green feed additive, yeast product (YP) is often used to regulate rumen fermentation and maintain animal health, but its mechanism of action on ruminants is unclear. This study was conducted to investigate the effects of YP (yeast culture + yeast live cells) on rumen fermentation parameters, abnormal metabolites and microbiota in sheep. Our findings suggest that YP can improve rumen fermentation parameters, change the activity of rumen digestive enzymes and reduce the concentration of abnormal metabolites. In addition, we found that YP significantly changed the relative abundance of microorganisms attached to rumen feed particles and affected microbial function. This study provides new insights into the regulation mechanism of feed additives on rumen fermentation and improves our understanding of YP on rumen fermentation regulation. Abstract Yeast products (YP) are commonly used as rumen regulators, but their mechanisms of action are still unclear. Based on our previous studies, we questioned whether yeast products would have an impact on rumen solid-associated (SA) and liquid-associated (LA) microorganisms and alter rumen fermentation patterns. Thirty 3-month-old male sheep weighing 19.27 ± 0.45 kg were selected and randomized into three groups for 60 days: (1) basal diet group (CON group), (2) basal diet add 20 g YP per day (low YP, LYP group) and (3) basal diet add 40 g YP per day (high YP, HYP group). The results demonstrated that the addition of YP increased rumen cellulase activity, butyrate and total volatile fatty acid (TVFA) concentrations (p < 0.05), while it decreased rumen amylase activity and abnormal metabolites, such as lactate, lipopolysaccharides (LPS) and histamine (HIS) (p < 0.05). Metagenomic analysis of rumen microorganisms in three groups revealed that YP mainly influenced the microbial profiles of the SA system. YP increased the relative abundance of R. flavefaciens and decreased methanogens in the SA system (p < 0.05). With the addition of YP, the abundance of only a few lactate-producing bacteria increased in the SA system, including Streptococcus and Lactobacillus (p < 0.05). However, almost all lactate-utilizing bacteria increased in the LA system, including Megasphaera, Selenomonas, Fusobacterium and Veillonella (p < 0.05). In addition, YP increased the abundance of certain GHs family members, including GH43 and GH98 (p < 0.05), but decreased the abundance of some KEGG metabolic pathways involved in starch and sucrose metabolism, biosynthesis of antibiotics and purine metabolism, among others. In conclusion, the addition of YP to high-concentrate diets can change the abundance of major functional microbiota in the rumen, especially in the solid fraction, which in turn affects rumen fermentation patterns and improves rumen digestibility.
1 citations
References
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TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Abstract: The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
70,111 citations
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Abstract: Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals.
Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ~10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package.
Availability: http://maq.sourceforge.net
Contact: [email protected]
43,862 citations
TL;DR: Fastp is developed as an ultra‐fast FASTQ preprocessor with useful quality control and data‐filtering features that can perform quality control, adapter trimming, quality filtering, per‐read quality pruning and many other operations with a single scan of the FAST Q data.
Abstract: Motivation Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient. Results We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2-5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools. Availability and implementation The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.
7,461 citations
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TL;DR: A new CD-HIT program accelerated with a novel parallelization strategy and some other techniques to allow efficient clustering of such datasets to reduce sequence redundancy and improve the performance of other sequence analyses is developed.
Abstract: Summary: CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. In response to the rapid increase in the amount of sequencing data produced by the next-generation sequencing technologies, we have developed a new CD-HIT program accelerated with a novel parallelization strategy and some other techniques to allow efficient clustering of such datasets. Our tests demonstrated very good speedup derived from the parallelization for up to ~24 cores and a quasi-linear speedup for up to ~8 cores. The enhanced CD-HIT is capable of handling very large datasets in much shorter time than previous versions.
Availability: http://cd-hit.org.
Contact: [email protected]
Supplementary information:Supplementary data are available at Bioinformatics online.
5,959 citations
TL;DR: MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner and generated a three-time larger assembly, with longer contig N50 and average contig length.
Abstract: Summary: MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252Gbps in 44.1 hours and 99.6 hours on a single computing node with and without a GPU, respectively. MEGAHIT assembles the data as a whole, i.e., no pre-processing like partitioning and normalization was needed. When compared with previous methods (Chikhi and Rizk, 2012; Howe, et al., 2014) on assembling the soil data, MEGAHIT generated a 3-time larger assembly, with longer contig N50 and average contig length; furthermore, 55.8% of the reads were aligned to the assembly, giving a 4-fold improvement . Availability: The source code of MEGAHIT is freely available at https://github.com/voutcn/megahit under GPLv3 license. Contact: rb@l3-bioinfo.com, twlam@cs.hku.hk
3,634 citations