This page has only limited features, please log in for full access.
The aim of this trial was to assess the effect of feeding a concentrate including cold-pressed rapeseed cake (CPRC) on productive performance, milk quality and its sensory properties, ruminal biohydrogenation, and bacterial communities. Eighteen cows were paired, and two experimental diets (control vs. CPRC) were distributed within the pair. Concentrates were iso-energetic and iso-proteic and contained similar amounts of fat. The average days in milk, milk yield, and body weight of the animals were (mean ± SD) 172 ± 112 d, 585 ± 26 kg, and 25.4 ± 6.2 kg/d, respectively. The experiment lasted for 10 wk. Feeding CPRC resulted in lower ruminal saturated (p < 0.001) and higher monounsaturated (p = 0.002) fatty acids. Feeding CPRC increased Ruminococcus, Prevotella, and Entodinium but decreased Blautia; p-75-a5; undefined genera within orders Clostridiaceae and RF39 and within families Christensenellaceae, Lachnospiracease, and Ruminococcaceae; and fungi from the phylum neocallimastigomycota. The milk fatty acid profile was characterized by a lower n6:n3 ratio (p = 0.028). Feeding CPRC did not affect the milk yield, milk quality, or fat corrected milk (p > 0.05). Feeding CPRC improved the overall milk acceptability (p = 0.047). In conclusion, CPRC affected some microbial taxa, modified the biohydrogenation process, and improved the milk fatty acid profile and consumer acceptance without detrimental effects on milk production and composition.
Idoia Goiri; Izaro Zubiria; Jose Luís Lavín; Hanen Benhissi; Raquel Atxaerandio; Roberto Ruiz; Nerea Mandaluniz; Aser García-Rodríguez. Evaluating the Inclusion of Cold-Pressed Rapeseed Cake in the Concentrate for Dairy Cows upon Ruminal Biohydrogenation Process, Ruminal Microbial Community and Milk Production and Acceptability. Animals 2021, 11, 2553 .
AMA StyleIdoia Goiri, Izaro Zubiria, Jose Luís Lavín, Hanen Benhissi, Raquel Atxaerandio, Roberto Ruiz, Nerea Mandaluniz, Aser García-Rodríguez. Evaluating the Inclusion of Cold-Pressed Rapeseed Cake in the Concentrate for Dairy Cows upon Ruminal Biohydrogenation Process, Ruminal Microbial Community and Milk Production and Acceptability. Animals. 2021; 11 (9):2553.
Chicago/Turabian StyleIdoia Goiri; Izaro Zubiria; Jose Luís Lavín; Hanen Benhissi; Raquel Atxaerandio; Roberto Ruiz; Nerea Mandaluniz; Aser García-Rodríguez. 2021. "Evaluating the Inclusion of Cold-Pressed Rapeseed Cake in the Concentrate for Dairy Cows upon Ruminal Biohydrogenation Process, Ruminal Microbial Community and Milk Production and Acceptability." Animals 11, no. 9: 2553.
Alejandro Saborío-Montero; Adrían López-García; Mónica Gutiérrez-Rivas; Raquel Atxaerandio; Idoia Goiri; Aser García-Rodriguez; José A. Jiménez-Montero; Carmen González; Javier Tamames; Fernando Puente-Sánchez; Luis Varona; Magdalena Serrano; Cristina Ovilo; Oscar González-Recio. A dimensional reduction approach to modulate the core ruminal microbiome associated with methane emissions via selective breeding. Journal of Dairy Science 2021, 104, 8135 -8151.
AMA StyleAlejandro Saborío-Montero, Adrían López-García, Mónica Gutiérrez-Rivas, Raquel Atxaerandio, Idoia Goiri, Aser García-Rodriguez, José A. Jiménez-Montero, Carmen González, Javier Tamames, Fernando Puente-Sánchez, Luis Varona, Magdalena Serrano, Cristina Ovilo, Oscar González-Recio. A dimensional reduction approach to modulate the core ruminal microbiome associated with methane emissions via selective breeding. Journal of Dairy Science. 2021; 104 (7):8135-8151.
Chicago/Turabian StyleAlejandro Saborío-Montero; Adrían López-García; Mónica Gutiérrez-Rivas; Raquel Atxaerandio; Idoia Goiri; Aser García-Rodriguez; José A. Jiménez-Montero; Carmen González; Javier Tamames; Fernando Puente-Sánchez; Luis Varona; Magdalena Serrano; Cristina Ovilo; Oscar González-Recio. 2021. "A dimensional reduction approach to modulate the core ruminal microbiome associated with methane emissions via selective breeding." Journal of Dairy Science 104, no. 7: 8135-8151.
Antimicrobial and antioxidant properties of spent coffee grounds (SCG) make them a potential ingredient in a diet for ruminants. This study investigated the effects of SCG on rumen microbiota. For 51 days, 36 dairy ewes were assigned to the experimental treatments (0, 30, 50, and 100 g SCG/kg). Ruminal samples were collected on day 50. DNA was extracted and subjected to paired-end Illumina sequencing of the V3-V4 hypervariable region of the 16S rRNA genes. Bioinformatic analyses were performed using QIIME (v.1.9.0). SCG increased dose-dependently bacterial diversity and altered bacterial structure. Further, 60, 78, and 449 operational taxonomic unit (OUT) were different between control and 30, 50 and 100 g/kg SCG groups, respectively. Higher differences were observed between the control and 100 g/kg SCG group, where OTU of the genera Treponema, CF231, Butyrivibrio, BF331, Anaeroplasma, Blautia, Fibrobacter, and Clostridium were enriched with SCG. Correlations between volatile fatty acids (VFA) and bacterial taxa were sparser in the SCG groups and had little overlap. Certain bacterial taxa presented different signs of the correlation with VFA in SCG and control groups, but Butyrivibrio and Blautia consistently correlated with branched-chain VFA in all groups. SCG induced shifts in the ruminal bacterial community and altered the correlation networks among bacterial taxa and ruminal VFA.
Idoia Goiri; Xabier Díaz De Otálora; Roberto Ruiz; Jagoba Rey; Raquel Atxaerandio; Jose Luis Lavín; David San Martin; Mikel Orive; Bruno Iñarra; Jaime Zufia; Jabi Urkiza; Aser García-Rodríguez. Spent Coffee Grounds Alter Bacterial Communities in Latxa Dairy Ewes. Microorganisms 2020, 8, 1961 .
AMA StyleIdoia Goiri, Xabier Díaz De Otálora, Roberto Ruiz, Jagoba Rey, Raquel Atxaerandio, Jose Luis Lavín, David San Martin, Mikel Orive, Bruno Iñarra, Jaime Zufia, Jabi Urkiza, Aser García-Rodríguez. Spent Coffee Grounds Alter Bacterial Communities in Latxa Dairy Ewes. Microorganisms. 2020; 8 (12):1961.
Chicago/Turabian StyleIdoia Goiri; Xabier Díaz De Otálora; Roberto Ruiz; Jagoba Rey; Raquel Atxaerandio; Jose Luis Lavín; David San Martin; Mikel Orive; Bruno Iñarra; Jaime Zufia; Jabi Urkiza; Aser García-Rodríguez. 2020. "Spent Coffee Grounds Alter Bacterial Communities in Latxa Dairy Ewes." Microorganisms 8, no. 12: 1961.
Records of methane emissions from 1,501 cows on 14 commercial farms in 4 regions of Spain were collected from May 2018 to June 2019. Methane concentrations (MeC) were measured using a nondispersive infrared methane detector installed within the feed bin of the automatic milking system during 14- to 21-d periods. Rumination time (RT; min/d) was collected using collars with a tag that registered time (minutes) spent eating and ruminating. The means of MeC and methane production (MeP) were 1,254.28 ppm and 182.49 g/d, respectively; mean RT was 473.38 min/d. Variance components for MeC, MeP, and RT were estimated with REML using pedigree and genomic information in a single-step model. Heritabilities for MeC and MeP were 0.11 and 0.12, respectively. Rumination time showed a slightly larger heritability estimate (0.17). The genetic correlation between MeP and MeC was high (>0.95), suggesting that selection on either trait would lead to a positive correlated response on the other. Negative correlations were estimated between RT and MeC (-0.24 ± 0.38) and MeP (-0.43 ± 0.35). Methane concentration and MeP had slightly positive correlations with milk yield (0.17 ± 0.39 and 0.21 ± 0.36), protein percentage (0.08 ± 0.32 and 0.30 ± 0.45), protein yield (0.22 ± 0.41 and 0.31 ± 0.35), fat percentage (0.02 ± 0.40 and 0.27 ± 0.36), and fat yield (0.27 ± 0.28 and 0.29 ± 0.28) from bivariate analyses. Rumination time had positive correlations with milk yield (0.41 ± 0.75) and protein yield (0.26 ± 0.57) and negative correlations with fat yield (-0.45 ± 0.32), protein percentage (-0.15 ± 0.38), and fat percentage (-0.40 ± 0.47). A positive approximated genetic correlation was estimated between fertility and MeC (0.10 ± 0.05) and MeP (0.18 ± 0.05), resulting in slightly higher CH4 production when selecting for better fertility [days open estimated breeding values (EBV) are expressed with mean 100 and SD 10, inversely related to days from calving to conception; that is, greater days open EBV implies better fertility]. Positive correlations were also estimated for stature with MeC and MeP (0.30 ± 0.04 and 0.43 ± 0.04, respectively). Other type traits (chest width, udder depth, angularity, and capacity) were positively correlated with methane traits, possibly because of higher milk yield and higher feed intake from these animals. Rumination time showed positive EBV correlations with production traits and type traits, and negative correlations with somatic cell count and body condition score. Based on the genetic correlations and heritabilities estimated in this study, methane is measurable and heritable, and estimates of genetic correlations suggest no strong opposition to current breeding objectives in Spanish Holsteins.
J. López-Paredes; I. Goiri; R. Atxaerandio; A. García-Rodríguez; E. Ugarte; J.A. Jiménez-Montero; R. Alenda; O. González-Recio. Mitigation of greenhouse gases in dairy cattle via genetic selection: 1. Genetic parameters of direct methane using noninvasive methods and proxies of methane. Journal of Dairy Science 2020, 103, 7199 -7209.
AMA StyleJ. López-Paredes, I. Goiri, R. Atxaerandio, A. García-Rodríguez, E. Ugarte, J.A. Jiménez-Montero, R. Alenda, O. González-Recio. Mitigation of greenhouse gases in dairy cattle via genetic selection: 1. Genetic parameters of direct methane using noninvasive methods and proxies of methane. Journal of Dairy Science. 2020; 103 (8):7199-7209.
Chicago/Turabian StyleJ. López-Paredes; I. Goiri; R. Atxaerandio; A. García-Rodríguez; E. Ugarte; J.A. Jiménez-Montero; R. Alenda; O. González-Recio. 2020. "Mitigation of greenhouse gases in dairy cattle via genetic selection: 1. Genetic parameters of direct methane using noninvasive methods and proxies of methane." Journal of Dairy Science 103, no. 8: 7199-7209.
Spent coffee grounds (SCG) represent one of the main residues derived from restoration and hostelry. The aim of this study was to evaluate the effect of SCG, included in the concentrate at different concentrations (0, 30, 50 and 100 g/kg), on milk yield and quality, feeding behaviour, dry matter intake, apparent digestibility and ruminal short chain fatty acid profile. In this trial of 51 days of duration, 48 Latxa dairy ewes were used. The ewes were blocked in quartets according to milk yield (1918 ± 287 g) and days in milk (35.7 ± 8.9 days). All of the concentrates were formulated to be isoenergetic (1.01 UFL), isoproteic (166 g/kg), isofat (76 g/kg) and to meet the production needs. The concentrate was given in two doses of 450 g of dry matter during the morning and afternoon milkings, and fescue hay was offered ad libitum. Milk production was recorded and samples were taken for fat, protein and lactose composition analysis. Dry matter intake and apparent dry matter digestibility were estimated using two markers, and feeding behaviour data was recorded. Increasing doses of SCG in the concentrate up to 100 g/kg resulted in a linear (P < 0.001) increase in the rumen of the isovaleric and isobutyric acid contents which could explain the observed quadratic response (P < 0.001) in milk yield and a linear increase (P < 0.001) in milk protein. A linear increase (P < 0.001) in milk fat was found which could be explained by the observed linear increase (P < 0.001) in ruminal acetic and butyric acid contents. Increasing doses of SCG in the concentrate linearly decreased ruminal (P < 0.001) propionic acid content, resulting in a concomitant linear increase (P < 0.001) in acetic:propionic ratio. Furthermore, no differences were found in intake, apparent dry matter digestibility and feeding behaviour. In conclusion, inclusion of SCG up to 100 g/kg in the concentrate modified ruminal fermentation pattern towards an increase in isoacids and acetic and butyric acid contents in the rumen with a concomitant improvement in milk production and composition without impairing feeding behaviour or apparent digestibility.
X. Díaz de Otálora; R. Ruiz; I. Goiri; J. Rey; Raquel Atxaerandio; David San Martin; M. Orive; Bruno Iñarra; J. Zufia; J. Urkiza; Aser Garcia. valorisation of spent coffee grounds as functional feed ingredient improves productive performance of Latxa dairy ewes. Animal Feed Science and Technology 2020, 264, 114461 .
AMA StyleX. Díaz de Otálora, R. Ruiz, I. Goiri, J. Rey, Raquel Atxaerandio, David San Martin, M. Orive, Bruno Iñarra, J. Zufia, J. Urkiza, Aser Garcia. valorisation of spent coffee grounds as functional feed ingredient improves productive performance of Latxa dairy ewes. Animal Feed Science and Technology. 2020; 264 ():114461.
Chicago/Turabian StyleX. Díaz de Otálora; R. Ruiz; I. Goiri; J. Rey; Raquel Atxaerandio; David San Martin; M. Orive; Bruno Iñarra; J. Zufia; J. Urkiza; Aser Garcia. 2020. "valorisation of spent coffee grounds as functional feed ingredient improves productive performance of Latxa dairy ewes." Animal Feed Science and Technology 264, no. : 114461.
EU countries are the most important worldwide coffee consumers with about 2.52 million tons. Coffee processing and consumption lead to substantial amounts of residues, mainly coffee silver skin and spent coffee grounds (SCG) as follows: 1 kg of coffee generates around 2 kg of wet SCG. Around 46% of this total SCG generation is landfilled with the subsequent soil, water and air pollution. So, an alternative solution for large SCG volumes currently sent to landfills is necessary. Livestock products are projected to increase up to by 70% by 2050. Many of the ingredients in the diets of EU livestock are sourced from imported raw materials from the Americas: mainly soybeans, etc. This deficit presents already a risk to social, economic and environmental progress in Europe due to the increasing scarcity of global resources. Hence, the inclusion of biowaste in animal feed is necessary to lead to additional benefits for animal feed sector: availability of environmentally friendly ingredient sources and decrease of dependence on foreign sources. This study demonstrates that coffee spent ground stands as a potential alternative ingredient in dairy cattle due to their availability in Europe, their nutritional characteristics and the results of the growing trials with animals: feeding of 5% SCG in the concentrate did not affect milk yields or fat contents and only a negligible decrease in crude protein (by 1.8%). This is because SCG was formulated as a functional ingredient in the concentrate and therefore would not impair animal performance.
D. San Martin; M. Orive; Bruno Iñarra; Aser Garcia; I. Goiri; Raquel Atxaerandio; J. Urkiza; J. Zufía. Spent coffee ground as second-generation feedstuff for dairy cattle. Biomass Conversion and Biorefinery 2020, 11, 589 -599.
AMA StyleD. San Martin, M. Orive, Bruno Iñarra, Aser Garcia, I. Goiri, Raquel Atxaerandio, J. Urkiza, J. Zufía. Spent coffee ground as second-generation feedstuff for dairy cattle. Biomass Conversion and Biorefinery. 2020; 11 (2):589-599.
Chicago/Turabian StyleD. San Martin; M. Orive; Bruno Iñarra; Aser Garcia; I. Goiri; Raquel Atxaerandio; J. Urkiza; J. Zufía. 2020. "Spent coffee ground as second-generation feedstuff for dairy cattle." Biomass Conversion and Biorefinery 11, no. 2: 589-599.
Cold-pressed sunflower cake (CPSC) is a cheap by-product of oil-manufacturing. Supplementing diets with CPSC, rich in fat and linoleic acid, could be an effective tool for increasing healthy fatty acids (FA) in milk. To test this hypothesis, 10 cows were used in a crossover design with two experimental diets fed during two 63-day periods. Cows' milk production was recorded and samples were taken for fat, protein, lactose, and for FA composition analysis. Dry matter intake (DMI) and dry matter apparent digestibility (DMD) were estimated using two markers. Milk acceptance test was carried out. CPSC decreased milk C12:0 (10%, p = 0.023) and C16:0 (5%, p = 0.035) and increased C18:1 cis-12 (37%, p = 0.006), C18:1 trans-11 (32%, p = 0.005), C18:2 cis-9 cis-12 (13%, p = 0.004), and cis-9 trans-11 CLA (35%, p = 0.004). CPSC increased total trans-monounsaturated FA (21%, p = 0.003), total CLA (31%, p = 0.007), and PUFA:SFA ratio (18%, p = 0.006). CPSC did not affect milk production, DMD, DMI and milk composition, but reduced fat yield (9%, p = 0.013) and FCM (7%, p = 0.013). CPSC improved milk overall acceptability. In conclusion, CPSC could modify milk FA profile without a detrimental effect on digestibility, production performance, or milk acceptance.
Idoia Goiri; Izaro Zubiria; Hanen Benhissi; Raquel Atxaerandio; Roberto Ruiz; Nerea Mandaluniz; Aser Garcia-Rodriguez. Use of Cold-Pressed Sunflower Cake in the Concentrate as a Low-Input Local Strategy to Modify the Milk Fatty Acid Profile of Dairy Cows. Animals 2019, 9, 803 .
AMA StyleIdoia Goiri, Izaro Zubiria, Hanen Benhissi, Raquel Atxaerandio, Roberto Ruiz, Nerea Mandaluniz, Aser Garcia-Rodriguez. Use of Cold-Pressed Sunflower Cake in the Concentrate as a Low-Input Local Strategy to Modify the Milk Fatty Acid Profile of Dairy Cows. Animals. 2019; 9 (10):803.
Chicago/Turabian StyleIdoia Goiri; Izaro Zubiria; Hanen Benhissi; Raquel Atxaerandio; Roberto Ruiz; Nerea Mandaluniz; Aser Garcia-Rodriguez. 2019. "Use of Cold-Pressed Sunflower Cake in the Concentrate as a Low-Input Local Strategy to Modify the Milk Fatty Acid Profile of Dairy Cows." Animals 9, no. 10: 803.
Cold-pressed sunflower cake (CPSC), by-product of oil-manufacturing, has high crude fat and linoleic acid concentrations, being a promising supplement to modulate rumen fatty acid (FA) profile. This trial studied CPSC effects on ruminal fermentation, biohydrogenation and the bacterial community in dairy cows. Ten cows were used in a crossover design with two experimental diets and fed during two 63-day periods. The cows were group fed forage ad libitum and the concentrate individually. The concentrates, control and CPSC, were isoenergetic, isoproteic and isofat. The ruminal samples collected at the end of each experimental period were analyzed for short-chain fatty acid, FA and DNA sequencing. CPSC decreased butyrate molar proportion (4%, p = 0.005). CPSC decreased C16:0 (28%, p < 0.001) and increased C18:0 (14%, p < 0.001) and total monounsaturated FA, especially C18:1 trans-11 (13%, p = 0.023). The total purine derivative excretion tended to be greater (5%, p = 0.05) with CPSC, resulting in a 6% greater daily microbial N flow. CPSC did not affect the diversity indices but increased the relative abundances of Treponema and Coprococcus, and decreased Enterococcus, Ruminococcus and Succinivibrio. In conclusion, the changes in ruminal fermentation and the FA profile were not associated with changes in microbial diversity or abundance of dominant populations, however, they might be associated with less abundant genera.
Izaro Zubiria; Aser Garcia-Rodriguez; Raquel Atxaerandio; Roberto Ruiz; Hanen Benhissi; Nerea Mandaluniz; Jose Luis Lavín; Leticia Abecia; Idoia Goiri; Garcia- Rodriguez; Ruiz. Effect of Feeding Cold-Pressed Sunflower Cake on Ruminal Fermentation, Lipid Metabolism and Bacterial Community in Dairy Cows. Animals 2019, 9, 755 .
AMA StyleIzaro Zubiria, Aser Garcia-Rodriguez, Raquel Atxaerandio, Roberto Ruiz, Hanen Benhissi, Nerea Mandaluniz, Jose Luis Lavín, Leticia Abecia, Idoia Goiri, Garcia- Rodriguez, Ruiz. Effect of Feeding Cold-Pressed Sunflower Cake on Ruminal Fermentation, Lipid Metabolism and Bacterial Community in Dairy Cows. Animals. 2019; 9 (10):755.
Chicago/Turabian StyleIzaro Zubiria; Aser Garcia-Rodriguez; Raquel Atxaerandio; Roberto Ruiz; Hanen Benhissi; Nerea Mandaluniz; Jose Luis Lavín; Leticia Abecia; Idoia Goiri; Garcia- Rodriguez; Ruiz. 2019. "Effect of Feeding Cold-Pressed Sunflower Cake on Ruminal Fermentation, Lipid Metabolism and Bacterial Community in Dairy Cows." Animals 9, no. 10: 755.
The advent of metagenomics in animal breeding poses the challenge of statistically modelling the relationship between the microbiome, the host genetics and relevant complex traits. A set of structural equation models (SEMs) of a recursive type within a Markov chain Monte Carlo (MCMC) framework was proposed here to jointly analyse the host–metagenome–phenotype relationship. A non‐recursive bivariate model was set as benchmark to compare the recursive model. The relative abundance of rumen microbes (RA), methane concentration (CH4) and the host genetics was used as a case of study. Data were from 337 Holstein cows from 12 herds in the north and north‐west of Spain. Microbial composition from each cow was obtained from whole metagenome sequencing of ruminal content samples using a MinION device from Oxford Nanopore Technologies. Methane concentration was measured with Guardian® NG infrared gas monitor from Edinburgh Sensors during cow's visits to the milking automated system. A quarterly average from the methane eructation peaks for each cow was computed and used as phenotype for CH4. Heritability of CH4 was estimated at 0.12 ± 0.01 in both the recursive and bivariate models. Likewise, heritability estimates for the relative abundance of the taxa overlapped between models and ranged between 0.08 and 0.48. Genetic correlations between the microbial composition and CH4 ranged from −0.76 to 0.65 in the non‐recursive bivariate model and from −0.68 to 0.69 in the recursive model. Regardless of the statistical model used, positive genetic correlations with methane were estimated consistently for the seven genera pertaining to the Ciliophora phylum, as well as for those genera belonging to the Euryarchaeota (Methanobrevibacter sp.), Chytridiomycota (Neocallimastix sp.) and Fibrobacteres (Fibrobacter sp.) phyla. These results suggest that rumen's whole metagenome recursively regulates methane emissions in dairy cows and that both CH4 and the microbiota compositions are partially controlled by the host genotype.
Alejandro Saborío‐Montero; Mónica Gutiérrez‐Rivas; Aser García‐Rodríguez; Raquel Atxaerandio; Idoia Goiri; Evangelina López De Maturana; José Antonio Jiménez‐Montero; Rafael Alenda; Oscar González‐Recio. Structural equation models to disentangle the biological relationship between microbiota and complex traits: Methane production in dairy cattle as a case of study. Journal of Animal Breeding and Genetics 2019, 137, 36 -48.
AMA StyleAlejandro Saborío‐Montero, Mónica Gutiérrez‐Rivas, Aser García‐Rodríguez, Raquel Atxaerandio, Idoia Goiri, Evangelina López De Maturana, José Antonio Jiménez‐Montero, Rafael Alenda, Oscar González‐Recio. Structural equation models to disentangle the biological relationship between microbiota and complex traits: Methane production in dairy cattle as a case of study. Journal of Animal Breeding and Genetics. 2019; 137 (1):36-48.
Chicago/Turabian StyleAlejandro Saborío‐Montero; Mónica Gutiérrez‐Rivas; Aser García‐Rodríguez; Raquel Atxaerandio; Idoia Goiri; Evangelina López De Maturana; José Antonio Jiménez‐Montero; Rafael Alenda; Oscar González‐Recio. 2019. "Structural equation models to disentangle the biological relationship between microbiota and complex traits: Methane production in dairy cattle as a case of study." Journal of Animal Breeding and Genetics 137, no. 1: 36-48.
The aim of this trial was to study the agreement between the non-dispersive infrared methane analyzer (NDIR) method and the hand held laser methane detector (LMD). Methane (CH4) was measured simultaneously with the two devices totaling 164 paired measurements. The repeatability of the CH4 concentration was greater with the NDIR (0.42) than for the LMD (0.23). However, for the number of peaks, repeatability of the LMD was greater (0.20 vs. 0.14, respectively). Correlation was moderately high and positive for CH4 concentration (0.73 and 0.74, respectively) and number of peaks (0.72 and 0.72, respectively), and the repeated measures correlation and the individual-level correlation were high (0.98 and 0.94, respectively). A moderate concordance correlation coefficient was observed for the CH4 concentration (0.62) and for the number of peaks (0.66). A moderate-high coefficient of individual agreement for the CH4 concentration (0.83) and the number of peaks (0.77) were observed. However, CH4 concentrations population means and all variance components differed between instruments. In conclusion, methane concentration measurements obtained by means of NDIR and LMD cannot be used interchangeably. The joint use of both methods could be considered for genetic selection purposes or for mitigation strategies only if sources of disagreement, which result in different between-subject and within-subject variabilities, are identified and corrected for.
Jagoba Rey; Raquel Atxaerandio; Roberto Ruiz; Eva Ugarte; Oscar González-Recio; Aser Garcia-Rodriguez; Idoia Goiri; Rey; Ruiz; González- Recio; Garcia- Rodriguez. Comparison Between Non-Invasive Methane Measurement Techniques in Cattle. Animals 2019, 9, 563 .
AMA StyleJagoba Rey, Raquel Atxaerandio, Roberto Ruiz, Eva Ugarte, Oscar González-Recio, Aser Garcia-Rodriguez, Idoia Goiri, Rey, Ruiz, González- Recio, Garcia- Rodriguez. Comparison Between Non-Invasive Methane Measurement Techniques in Cattle. Animals. 2019; 9 (8):563.
Chicago/Turabian StyleJagoba Rey; Raquel Atxaerandio; Roberto Ruiz; Eva Ugarte; Oscar González-Recio; Aser Garcia-Rodriguez; Idoia Goiri; Rey; Ruiz; González- Recio; Garcia- Rodriguez. 2019. "Comparison Between Non-Invasive Methane Measurement Techniques in Cattle." Animals 9, no. 8: 563.
Diet has an essential influence in the establishment of the cecum microbial communities in poultry, so its supplementation with safe additives, such as probiotics, prebiotics, and synbiotics might improve animal health and performance. This study showed the ceca microbiome modulations of laying hens, after feeding with dry whey powder as prebiotics, Pediococcus acidilactici as probiotics, and the combination of both as synbiotics. A clear grouping of the samples induced per diet was observed (p < 0.05). Operational taxonomic units (OTUs) identified as Olsenella spp., and Lactobacillus crispatus increased their abundance in prebiotic and synbiotic treatments. A core of the main functions was shared between all metagenomes (45.5%), although the genes encoding for the metabolism of butanoate, propanoate, inositol phosphate, and galactose were more abundant in the prebiotic diet. The results indicated that dietary induced-changes in microbial composition did not imply a disturbance in the principal biological roles, while the specific functions were affected.
Carolina Pineda-Quiroga; Daniel Borda Molina; Diego Chaves-Moreno; Roberto Ruiz; Raquel Atxaerandio; Amélia Camarinha-Silva; Aser García-Rodríguez. Microbial and Functional Profile of the Ceca from Laying Hens Affected by Feeding Prebiotics, Probiotics, and Synbiotics. Microorganisms 2019, 7, 123 .
AMA StyleCarolina Pineda-Quiroga, Daniel Borda Molina, Diego Chaves-Moreno, Roberto Ruiz, Raquel Atxaerandio, Amélia Camarinha-Silva, Aser García-Rodríguez. Microbial and Functional Profile of the Ceca from Laying Hens Affected by Feeding Prebiotics, Probiotics, and Synbiotics. Microorganisms. 2019; 7 (5):123.
Chicago/Turabian StyleCarolina Pineda-Quiroga; Daniel Borda Molina; Diego Chaves-Moreno; Roberto Ruiz; Raquel Atxaerandio; Amélia Camarinha-Silva; Aser García-Rodríguez. 2019. "Microbial and Functional Profile of the Ceca from Laying Hens Affected by Feeding Prebiotics, Probiotics, and Synbiotics." Microorganisms 7, no. 5: 123.
A lactation study was carried out utilizing 72 ewes in a 2 × 3 factorial arrangement involving two forages: Tall fescue (FES) and sainfoin (SAIN) hays; and 3 concentrates, which contained hydrogenated prilled palm fat (CTR), cold-pressed sunflower cake (SUN) or cold-pressed rapeseed cake (RPS) as fat sources. Ewes were divided into 6 equilibrated groups of 12 ewes each, according to milk yield and days in milk. Concentrates were offered individually and forage was group fed ad libitum. Milk yield was daily recorded; individual samples of milk were taken for fat, protein, lactose and for fatty acid (FA) composition analysis. Dry matter intake (DMI) and organic matter apparent digestibility (OMD) were estimated using two markers. Feeding behaviour was recorded for 48 h. Blood samples were collected for non-esterified fatty acids, blood urea nitrogen and IGF-1 determinations. Curd acceptance test was carried out using a non-trained sensory panel using a 10-point line scale for the attributes of appearance, flavour, odour, texture and overall acceptability. Milk yield and composition were analysed using the MIXED procedure for repeated measures with fixed effects of concentrate, forage and week, their interaction and the initial record measured at week 0 as covariate, and day and ewe as random effects. Total, hay and concentrate DMI, OMD, plasma metabolites and milk FA profile were analysed using the GLM procedure. Feeding behaviour and sensorial data were analysed using the previous statistical model but without including a covariate. SUN reduced milk total saturated fatty acids (SFA) compared to CTR with both forages, while RPS only reduced SFA with SAIN. Polyunsaturated FA were increased with both cakes and SAIN. SUN increased n-6:n-3 ratio compared to CTR (+54%) and RPS (+62%), and SAIN reduced this ratio compared to FES (-27%). SUN reduced milk index of atherogenicity compared to CTR (up to -33%) with both forages, while RPS reduced (up to -31%) this index only with SAIN. Concentrate did not affect milk production, digestibility and intake, but SAIN increased these traits together with plasma IGF-1. Neither concentrate nor forage affected curd acceptance traits. Healthier milk can be obtained with cakes. Nevertheless the forage used in the ration seems to be of great importance. Neither cakes nor SAIN had a detrimental effect on digestibility, production performance or curd acceptance in lactating ewes.
A. Pascual; C. Pineda-Quiroga; I. Goiri; R. Atxaerandio; R. Ruiz; A. García-Rodríguez. Effects of feeding UFA-rich cold-pressed oilseed cakes and sainfoin on dairy ewes’ milk fatty acid profile and curd sensory properties. Small Ruminant Research 2019, 175, 96 -103.
AMA StyleA. Pascual, C. Pineda-Quiroga, I. Goiri, R. Atxaerandio, R. Ruiz, A. García-Rodríguez. Effects of feeding UFA-rich cold-pressed oilseed cakes and sainfoin on dairy ewes’ milk fatty acid profile and curd sensory properties. Small Ruminant Research. 2019; 175 ():96-103.
Chicago/Turabian StyleA. Pascual; C. Pineda-Quiroga; I. Goiri; R. Atxaerandio; R. Ruiz; A. García-Rodríguez. 2019. "Effects of feeding UFA-rich cold-pressed oilseed cakes and sainfoin on dairy ewes’ milk fatty acid profile and curd sensory properties." Small Ruminant Research 175, no. : 96-103.
Background: Microbiome studies need to analyze massive sequencing data, which requires the use of sophisticated bioinformatics pipelines. Up to date, several tools are available, although the literature is scarce on studies that compare the performance of different bioinformatics pipelines on rumen microbiota when 16S rRNA amplicons are analyzed. The impact of the pipeline on the outcome of the results is also unknown, mainly in terms of the output from studies using these tools as an intermediate phenotype (pseudophenotypes). This study compares two commonly used software (Quantitative Insights Into Microbial Ecology) (QIIME) and mothur, and two microbial gene data bases (GreenGenes and SILVA) for 16S rRNA gene analysis, using metagenome read data collected from rumen content of a cohort of dairy cows. Results: We compared the relative abundance (RA) of the identified OTUs at the genus level. Both tools presented a high degree of agreement at identifying the most abundant genera: Bifidobacterium, Butyrivibrio, Methanobrevibacter, Prevotella, and Succiniclasticum (RA > 1%), regardless the database. There were no statistical differences between mothur and QIIME (P > 0.05) at estimating the overall RA of the most abundant (RA > 10%) genera, either using SILVA or GreenGenes. However, differences were found at RA < 10% (P < 0.05) when using GreenGenes as database, with mothur assigning OTUs to a larger number of genera and in larger RA for these less frequent microorganisms. With this database mothur resulted in larger richness (P < 0.05), more favorable rarefaction curves and a larger analytic sensitivity. These differences caused significant and relevant differences between tools at identifying the dissimilarity of microbiotas between pairs of animals. However, these differences were attenuated, but not erased, when SILVA was used as the reference database. Conclusion: The findings showed that the SILVA database seemed a preferred reference dataset for classifying OTUs from rumen microbiota. If this database was used, both QIIME and mothur produced comparable richness and diversity, and also in the RA of most common rumen microbes. However, important differences were found for less common microorganisms which impacted on the beta diversity calculated between pipelines. This may have relevant implications at studying global rumen microbiota.
Adrián López-García; Carolina Pineda-Quiroga; Raquel Atxaerandio; Adrian Pérez; Itziar Hernández; Aser García-Rodríguez; Oscar González-Recio. Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences. Frontiers in Microbiology 2018, 9, 3010 .
AMA StyleAdrián López-García, Carolina Pineda-Quiroga, Raquel Atxaerandio, Adrian Pérez, Itziar Hernández, Aser García-Rodríguez, Oscar González-Recio. Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences. Frontiers in Microbiology. 2018; 9 ():3010.
Chicago/Turabian StyleAdrián López-García; Carolina Pineda-Quiroga; Raquel Atxaerandio; Adrian Pérez; Itziar Hernández; Aser García-Rodríguez; Oscar González-Recio. 2018. "Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences." Frontiers in Microbiology 9, no. : 3010.
This study aimed to evaluate whether the host genotype exerts any genetic control on the microbiome composition of the rumen in cattle. Microbial DNA was extracted from 18 samples of ruminal content from 2 breeds (Holstein and Brown Swiss). Reads were processed using mothur (https://www.mothur.org/) in 16S and 18S rRNA gene-based analyses. Then, reads were classified at the genus clade, resulting in 3,579 operational taxonomic units (OTU) aligned against the 16S database and 184 OTU aligned against the 18S database. After filtering on relative abundance (>0.1%) and penetrance (95%), 25 OTU were selected for the analyses (17 bacteria, 1 archaea, and 7 ciliates). Association with the genetic background of the host animal based on the principal components of a genomic relationship matrix based on single nucleotide polymorphism markers was analyzed using Bayesian methods. Fifty percent of the bacteria and archaea genera were associated with the host genetic background, including Butyrivibrio, Prevotella, Paraprevotella, and Methanobrevibacter as main genera. Forty-three percent of the ciliates analyzed were also associated with the genetic background of the host. In total, 48% of microbes were associated with the host genetic background. The results in this study support the hypothesis and provide some evidence that there exists a host genetic component in cattle that can partially regulate the composition of the microbiome.
O. Gonzalez-Recio; I. Zubiria; A. García-Rodríguez; A. Hurtado; R. Atxaerandio. Short communication: Signs of host genetic regulation in the microbiome composition in 2 dairy breeds: Holstein and Brown Swiss. Journal of Dairy Science 2018, 101, 2285 -2292.
AMA StyleO. Gonzalez-Recio, I. Zubiria, A. García-Rodríguez, A. Hurtado, R. Atxaerandio. Short communication: Signs of host genetic regulation in the microbiome composition in 2 dairy breeds: Holstein and Brown Swiss. Journal of Dairy Science. 2018; 101 (3):2285-2292.
Chicago/Turabian StyleO. Gonzalez-Recio; I. Zubiria; A. García-Rodríguez; A. Hurtado; R. Atxaerandio. 2018. "Short communication: Signs of host genetic regulation in the microbiome composition in 2 dairy breeds: Holstein and Brown Swiss." Journal of Dairy Science 101, no. 3: 2285-2292.
Dietary interventions are a common practice in the poultry industry to promote optimal performance and health of animals. Here, we aim at assessing the influence of supplementing broiler diets with dry whey powder (DWP) and whey protein concentrate (WPC) on nutrient coefficient of apparent ileal digestibility (CAID) and productive performance. Cecal microbiota composition was also determined using Illumina amplicon sequencing. Dietary treatments were control diet (no supplementation of DWP or WPC), 60-DWP (60 g/kg of DWP), and 80-WPC (80 g/kg of WPC). One-day-old male broilers were randomly assigned to one of three treatments, and housed in floor pens. In Trial 1, 90 1-day-old chicks were allocated to three pens/treatment, with 10 birds/pen, during 21 days for CAID evaluation. Diet 60-DWP increased Ca CAID (P=0.041), while diet 80-WPC improved Ca and P CAID (PPPP=0.048 for ADG), and during the entire feeding period (PPP=0.048), when compared to control diet. At day 42, cecal microbial communities of chickens that were fed with 60-DWP and 80-WPC differed from those fed with control diet (R=0.776, P=0.008; and R=0.740, P=0.008, respectively). The abundance of Bacteroides fragilis, Bacteroides spp., Escherichia coli/Shigella flexneri and Megamonas furniformis increased when 60-DWP and 80-WPC diets were offered, while the presence of Helicobacter pullorum decreased. Lactobacillus salivarius consistently increased in chickens with better feed conversion ratio, which were those fed with 60-DWP. The results obtained in the present study indicate that growth of chickens is improved by DWP and WPC supplementation because of a higher mineral digestibility, increased feed intake and modulation of cecal microbiota communities.
C. Pineda-Quiroga; Amélia Camarinha Silva; Daniel Borda Molina; Raquel Atxaerandio; R. Ruiz; Aser Garcia. Feeding broilers with dry whey powder and whey protein concentrate affected productive performance, ileal digestibility of nutrients and cecal microbiota community. Animal 2018, 12, 692 -700.
AMA StyleC. Pineda-Quiroga, Amélia Camarinha Silva, Daniel Borda Molina, Raquel Atxaerandio, R. Ruiz, Aser Garcia. Feeding broilers with dry whey powder and whey protein concentrate affected productive performance, ileal digestibility of nutrients and cecal microbiota community. Animal. 2018; 12 (4):692-700.
Chicago/Turabian StyleC. Pineda-Quiroga; Amélia Camarinha Silva; Daniel Borda Molina; Raquel Atxaerandio; R. Ruiz; Aser Garcia. 2018. "Feeding broilers with dry whey powder and whey protein concentrate affected productive performance, ileal digestibility of nutrients and cecal microbiota community." Animal 12, no. 4: 692-700.
Carolina Pineda-Quiroga; Amélia Camarinha-Silva; Raquel Atxaerandio; Roberto Ruiz; Aser García-Rodríguez. Changes in broiler performance, duodenal histomorphometry, and caeca microbiota composition in response to wheat-barley based diets supplemented with non-antibiotic additives. Animal Feed Science and Technology 2017, 234, 1 -9.
AMA StyleCarolina Pineda-Quiroga, Amélia Camarinha-Silva, Raquel Atxaerandio, Roberto Ruiz, Aser García-Rodríguez. Changes in broiler performance, duodenal histomorphometry, and caeca microbiota composition in response to wheat-barley based diets supplemented with non-antibiotic additives. Animal Feed Science and Technology. 2017; 234 ():1-9.
Chicago/Turabian StyleCarolina Pineda-Quiroga; Amélia Camarinha-Silva; Raquel Atxaerandio; Roberto Ruiz; Aser García-Rodríguez. 2017. "Changes in broiler performance, duodenal histomorphometry, and caeca microbiota composition in response to wheat-barley based diets supplemented with non-antibiotic additives." Animal Feed Science and Technology 234, no. : 1-9.
C. Pineda-Quiroga; Raquel Atxaerandio; R. Ruiz; A. García-Rodríguez. Effects of dry whey powder alone or combined with calcium butyrate on productive performance, duodenal morphometry, nutrient digestibility, and ceca bacteria counts of broiler chickens. Livestock Science 2017, 206, 65 -70.
AMA StyleC. Pineda-Quiroga, Raquel Atxaerandio, R. Ruiz, A. García-Rodríguez. Effects of dry whey powder alone or combined with calcium butyrate on productive performance, duodenal morphometry, nutrient digestibility, and ceca bacteria counts of broiler chickens. Livestock Science. 2017; 206 ():65-70.
Chicago/Turabian StyleC. Pineda-Quiroga; Raquel Atxaerandio; R. Ruiz; A. García-Rodríguez. 2017. "Effects of dry whey powder alone or combined with calcium butyrate on productive performance, duodenal morphometry, nutrient digestibility, and ceca bacteria counts of broiler chickens." Livestock Science 206, no. : 65-70.
C. Pineda-Quiroga; Raquel Atxaerandio; I. Zubiria; I. Gonzalez-Pozuelo; A. Hurtado; R. Ruiz; Aser Garcia. Productive performance and cecal microbial counts of floor housed laying hens supplemented with dry whey powder alone or combined with Pediococcus acidilactici in the late phase of production. Livestock Science 2017, 195, 9 -12.
AMA StyleC. Pineda-Quiroga, Raquel Atxaerandio, I. Zubiria, I. Gonzalez-Pozuelo, A. Hurtado, R. Ruiz, Aser Garcia. Productive performance and cecal microbial counts of floor housed laying hens supplemented with dry whey powder alone or combined with Pediococcus acidilactici in the late phase of production. Livestock Science. 2017; 195 ():9-12.
Chicago/Turabian StyleC. Pineda-Quiroga; Raquel Atxaerandio; I. Zubiria; I. Gonzalez-Pozuelo; A. Hurtado; R. Ruiz; Aser Garcia. 2017. "Productive performance and cecal microbial counts of floor housed laying hens supplemented with dry whey powder alone or combined with Pediococcus acidilactici in the late phase of production." Livestock Science 195, no. : 9-12.
Background Bovine viral diarrhoea virus (BVDV) is a member of the genus Pestivirus that belongs to the family Flaviviridae. BVDV is found worldwide in cattle population and causes significant economic losses to the dairy and beef industries. Two distinct genotypes of BVDV exist: BVDV type 1 (BVDV-1) and BVDV type 2 (BVDV-2). Objective: The aim of the present study was to investigate retrospectively the presence of BVDV-2 in Spain. Results With this objective, 47 blood samples that had tested positive in an ELISA for BVDV antigen were selected. Samples had been submitted by practitioners to the Diagnostic Service of NEIKER. The 18 herds of origin were all located in the northern half of Spain. BVDV positive samples were genotyped by reverse transcription-PCR. BVDV-1 was detected with the highest frequency (46/47), in contrast to BVDV-2 (2/47). In one blood sample, both pestivirus genotypes, BVDV-1 and BVDV-2, were detected. Sequencing of a viral genomic region, 5′ untranslated region, confirmed the identity of the BVDV-2 isolate. Conclusions So far as the authors know, this is the first reported presence of BVDV-2 in cattle herds in Spain. This finding may have important implications for the epidemiology, diagnosis and control of BVDV infection in the country.
Gorka Aduriz; Raquel Atxaerandio; Nekane Cortabarria. First detection of bovine viral diarrhoea virus type 2 in cattle in Spain. Veterinary Record Open 2015, 2, e000110 .
AMA StyleGorka Aduriz, Raquel Atxaerandio, Nekane Cortabarria. First detection of bovine viral diarrhoea virus type 2 in cattle in Spain. Veterinary Record Open. 2015; 2 (1):e000110.
Chicago/Turabian StyleGorka Aduriz; Raquel Atxaerandio; Nekane Cortabarria. 2015. "First detection of bovine viral diarrhoea virus type 2 in cattle in Spain." Veterinary Record Open 2, no. 1: e000110.
Yersiniosis is a zoonotic disease reported worldwide. Culture and PCR based protocols are the most common used methods for detection of pathogenic Yersinia species in animal samples. PCR sensitivity could be increased by an initial enrichment step. This step is particularly useful in surveillance programs, where PCR is applied to samples from asymptomatic animals. The aim of this study was to evaluate the improvement in pathogenic Yersinia species detection using a suitable enrichment method prior to the real time PCR (rtPCR). Nine different enrichment protocols were evaluated including six different broth mediums (CASO, ITC, PSB, PBS, PBSMSB and PBSSSB).
Maialen Arrausi-Subiza; Jose Carlos Ibabe; Raquel Atxaerandio; Ramon A Juste; Marta Barral. Evaluation of different enrichment methods for pathogenic Yersiniaspecies detection by real time PCR. BMC Veterinary Research 2014, 10, 192 -192.
AMA StyleMaialen Arrausi-Subiza, Jose Carlos Ibabe, Raquel Atxaerandio, Ramon A Juste, Marta Barral. Evaluation of different enrichment methods for pathogenic Yersiniaspecies detection by real time PCR. BMC Veterinary Research. 2014; 10 (1):192-192.
Chicago/Turabian StyleMaialen Arrausi-Subiza; Jose Carlos Ibabe; Raquel Atxaerandio; Ramon A Juste; Marta Barral. 2014. "Evaluation of different enrichment methods for pathogenic Yersiniaspecies detection by real time PCR." BMC Veterinary Research 10, no. 1: 192-192.