Ilma Tapio

Natural Resources Institute Finland (Luke) · Production Systems

The European Union has set goals to diminish the use of antibiotics in animal husbandry. New legislation came into effect in January 2022, banning the practice of routinely feed farmed animals with antibiotics. This practice has been used to compensate the undertakings animal welfare management. Functional feeds contain biological-active components...

The rumen represents a dynamic microbial ecosystem where fermentation metabolites and microbial concentrations change over time in response to dietary changes. The integration of microbial genomic knowledge and dynamic modelling can enhance our system-level understanding of rumen ecosystem’s function. However, such an integration between dynamic mo...

Early-life modulation of rumen microbiota holds promise for enhancing calf growth, health, and long-term production in ruminants. However, limited attention has been given to the impact of rumen microbiota modulation on the establishment of hindgut microbiota. In this study, fecal microbiota development was examined in identical twin calves for 12...

Background Diversifying animal cultivation demands efficient genotyping for enabling genomic selection, but non-model species lack efficient genotyping solutions. The aim of this study was to optimize a genotyping-by-sequencing (GBS) double-digest RAD-sequencing (ddRAD) pipeline. Bovine data was used to automate the bioinformatic analysis. The appl...

An experiment was conducted to examine how dietary interventions reducing enteric methane (CH4) emissions influence manure CH4 emissions in biogas production (as biochemical methane potential (BMP)) or under static conditions mimicking natural manure storage conditions. Experimental treatments consisted of a factorial arrangement of high (HF: 0.65)...

For sustainable food production selection and breeding of feed efficient animals is crucial. The objective of this study was to evaluate whether multiparous dairy cows, ranked during their first lactation based on residual energy intake (REI) as efficient (low; L-REI) or inefficient (high; H-REI), differ in terms of nutrient use efficiency, methane...

The effects of grass silage and barley grain preservation methods on dairy cows were evaluated using four Nordic Red dairy cows placed in respiration chambers in a 4 × 4 Latin square. Silage was conserved using a formic acid-based product (AS) or a homofermentative lactic acid bacteria inoculant (IS), while grains were dried (DB) or crimped and ens...

The rumen represents a dynamic microbial ecosystem where fermentation metabolites and microbial concentrations change over time in response to dietary changes. The integration of microbial genomic knowledge and dynamic modelling can enhance our system-level understanding of rumen ecosystem's function. However, such an integration between dynamic mo...

Background Diversifying animal cultivation demands efficient genotyping for enabling genomic selection, but non-model species lack efficient genotyping solutions. The aim of this study was to optimize a genotyping-by-sequencing (GBS) double-digest RAD-sequencing (ddRAD) pipeline. Bovine data was used to automate the bioinformatic analysis. The appl...

Saprolegnia oomycete infection causes serious economic losses and reduces fish health in aquaculture. Genomic selection based on thousands of DNA markers is a powerful tool to improve fish traits in selective breeding programmes. Our goal was to to develop a Single Nucleotide Polymorphism (SNP) marker panel and to test its use in genomic selection...

The aim of this trial was to determine the effect of a garlic and citrus extract supplement (GCE) on the performance, rumen fermentation, methane emissions, and rumen microbiome of dairy cows. Fourteen multiparous Nordic Red cows in mid-lactation from the research herd of Luke (Jokioinen, Finland) were allocated to 7 blocks in a complete randomized...

Efficient feed utilization in dairy cows is crucial for economic and environmental reasons. The rumen microbiota plays a significant role in feed efficiency, but studies utilizing microbial data to predict host phenotype are limited. In this study, 87 primiparous Nordic Red dairy cows were ranked for feed efficiency during their early lactation bas...

Identification of bacterial communities in both the raw material and the subsequent silages provides new insights into understanding the silage fermentation process. The objective was to evaluate how different silage management factors affect silage preservation characteristics, the microbiome, and their correlations. A red clover dominated sward w...

Information about the relationships between preservation characteristics and main bacterial communities of fermented feeds can guide decision making during feed preservation and silage additive development. The objective was to evaluate fermentation quality, aerobic stability, microbial quality and bacterial profile of crimped barley grains ensiled...

Rumen microbiota modulation during the pre-weaning period has been suggested as means to affect animal performance later in life. In this follow-up study, we examined the post-weaning rumen microbiota development differences in monozygotic twin-heifers that were inoculated (T-group) or not inoculated (C-group) ( n = 4 each) with fresh adult rumen l...

New technologies related to the identification of bacterial communities in fresh forage and silage may give valuable detailed information on the best practices to produce animal feeds. The objective was to evaluate how management conditions during silage making manipulate the profile of bacterial communities and fermentation quality of grass silage...

Simple Summary Determination of BHB concentration in the second week of lactation (WK 2) may allow us to predict the fertility properties of cows and help better manage farms. BHB concentration can be considered as a predictor trait of reproduction success. High BHB concentration requires a higher amount of insemination. The season in which the cow...

Grass was ensiled using an acid-based additive (AS) or homofermentative lactic acid bacteria (IS). In addition, barley grain was either dried (DB) or crimped and ensiled (EB). The feeds were fed as total mixed rations (TMR) in a 2 × 2 factorial arrangement to 16 Nordic Red dairy cows in four replicated Latin squares. The differences in the fermenta...

The development of the functional rumen in calves involves a complex interplay between the host and host-related microbiome. Attempts to modulate rumen microbial community establishment may therefore have an impact on weaning success, calf health, and animal performance later in life. In this experiment, we aimed to elucidate how rumen liquid inocu...

Dairy cows have intense fluctuations in digestive, metabolic and hormonal systems around calving which predispose them to various disorders and health problems. The aim of the current experiment was to investigate feed and nutrient intake, rumen fermentation, rumen bacterial communities, milk production, milk fatty acid composition and plasma bioma...

Four multiparous dairy cows were used in a 4 × 4 Latin square to examine how starch level and oil mixture impact dry matter (DM) intake and digestibility, milk yield and composition, rumen fermentation, ruminal methane (CH4) emissions, and microbial diversity. Experimental treatments comprised high (HS) or low (LS) levels of starch containing 0 or...

Exogenous fibrolytic enzymes (EFE) and yeast are feed supplements that improve forage digestion in rumen, but their influences on physical reticulorumen parameters are not well studied. This study was designed to evaluate the effect of the EFE:endo-β-xylanase (37x104 U/cow/day), endocellulase (45x104 U/cow/day), endo-β-glucanase (12x104U/cow/day),...

To evaluate the trade-offs between enteric and manure CH4 emissions, four Nordic-Red cows were fed diets containing 65:35 or 35:65 grass-silage to concentrate ratio and 0 or 50 g kg‑1 rapeseed oil on a dry matter (DM) basis in a 4×4 Latin square with 21-day periods. Feed intake increased by feeding more concentrates and tended to decrease with oil...

The use of antibiotics in livestock production may trigger ecosystem disservices, including increased emissions of greenhouse gases. To evaluate this, we conducted two separate animal experiments, administering two widely used antibiotic compounds (benzylpenicillin and tetracycline) to dairy cows over a 4- or 5-day period locally and/or systemicall...

A 1000-cow study across four European countries was undertaken to understand to what extent ruminant microbiomes can be controlled by the host animal and to identify characteristics of the host rumen microbiome axis that determine productivity and methane emissions. A core rumen microbiome, phylogenetically linked and with a preserved hierarchical...

The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to breakdown plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane. Consequently, ruminants produce meat and milk,...

Four lipid supplements varying in chain length or degree of unsaturation were examined for their effects on milk yield and composition, ruminal CH4 emissions, rumen fermentation, nutrient utilization, and microbial ecology in lactating dairy cows. Five Nordic Red cows fitted with rumen cannulas were used in a 5 × 5 Latin square with five 28-d perio...

Methane emissions from ruminal fermentation contribute significantly to total anthropological greenhouse gas (GHG) emissions. New meta-omics technologies are beginning to revolutionise our understanding of the rumen microbial community structure, metabolic potential and metabolic activity. Here we explore these developments in relation to GHG emiss...

Methane emissions from ruminant livestock contribute significantly to the large environmental footprint of agriculture. The rumen is the principal source of methane, and certain features of the microbiome are associated with low/high methane phenotypes. Despite their primary role in methanogenesis, the abundance of archaea has only a weak correlati...

The ruminal microbiome, comprising large numbers of bacteria, ciliate protozoa, archaea and fungi, responds to diet and dietary additives in a complex way. The aim of this study was to investigate the benefits of increasing the depth of the community analysis in describing and explaining responses to dietary changes. Quantitative PCR, ssu rRNA ampl...

Supporting information, containing supporting methods, supporting data, and supporting references. (DOCX)

Bacterial, archaeal, protozoal and fungal evenness as measured from amplicon sequence data, in four diets. Diets are as follows: high (H) or low (L) proportion of concentrates without oil, or supplemented with SO (HSO and LSO, respectively). (TIF)

Rumen bacterial, archaeal, ciliate protozoa and fungal taxa average abundances per diet and Tukey test for pairwise comparisons (P values). (XLSX)

Graphical network representing the interactions between rumen microorganisms within L-H diet comparison. Nodes correspond to microbial taxa while green and red edges represent positive and negative partial correlations above 0.05, respectively. Microbial taxa are colored by taxonomy: archaea—gray, ciliate protozoa—blue, fungi—dark yellow, bacteria—...

Sequences of primers used for qPCR and metabarcoding amplicon sequencing. (DOCX)

Bacterial, archaeal, protozoal and fungal richness as measured from amplicon sequence data, in four diets. Diets are as follows: high (H) or low (L) proportion of concentrates without oil, or supplemented with SO (HSO and LSO, respectively). (TIF)

Graphical network representing the interactions between rumen microorganisms within L-LSO diet comparison. Nodes correspond to microbial taxa while green and red edges represent positive and negative partial correlations above 0.05, respectively. Microbial taxa are colored by taxonomy: archaea—gray, ciliate protozoa—blue, fungi—dark yellow, bacteri...

Graphical network representing the interactions between rumen microorganisms within H-HSO diet comparison. Nodes correspond to microbial taxa while green and red edges represent positive and negative partial correlations above 0.05, respectively. Microbial taxa are colored by taxonomy: archaea—gray, ciliate protozoa—blue, bacteria—white. (PDF)

The effects of supplementing high-or low-concentrate diets with sunflower oil (SO) on rumen fermentation, nutrient utilization, and ruminal methane (CH 4) emissions in lactating cows were examined. Four multiparous Nordic Red dairy cows fitted with rumen cannulae were used in a 4 × 4 Latin square with a 2 × 2 factorial arrangement of treatments and...

Background: Intravenous or ruminal infusion of lithium salt of cobalt EDTA (Co-EDTA) or cobalt-acetate alters milk fat composition in cattle, but the mechanisms involved are not known. Objective: The present study evaluated the effect of ruminal Co-EDTA infusion on milk FA composition, mammary lipid metabolism, and mammary lipogenic gene express...

Microbial community analysis was carried out on ruminal digesta obtained directly via rumen fistula and buccal fluid, regurgitated digesta (bolus) and faeces of dairy cattle to assess if non-invasive samples could be used as proxies for ruminal digesta. Samples were collected from five cows receiving grass silage based diets containing no additiona...

Supporting information, containing five Tables and two Figures. Table A. Sequences of primers used for qPCR and amplicon sequencing. Table B. Within-diet significances of sample type in qPCR analyses shown in Fig 1. Table C. Between-diet significances of qPCR analyses shown in Fig 1. Table D. Number of filtered high quality sequences and the averag...

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Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35...

Five Finnish Ayrshire cows in early lactation fitted with rumen cannulae were used in a 5×5 Latin Square with 28 d experimental periods. Treatments comprised a control diet, or the same diet supplemented with 50 g/kg diet DM of myristic acid (MA), rapeseed (RO), safflower (SO) or linseed (LO) oils. Diets were based on grass silage (0.60 diet DM), b...

The comparison of the bacterial profile of intracellular (iDNA) and extracellular DNA (eDNA) isolated from cow rumen content stored under different conditions was conducted. The influence of rumen fluid treatment (cheesecloth squeezed, centrifuged, filtered), storage temperature (RT, -80oC) and cryoprotectants (PBS-glycerol, ethanol) on quality and...

E-Mails: p.a.koolmees@uu.nl (P.A.K.); l.t.g.theunissen@uu.nl (B.T.) Abstract: Classification of cattle breeds contributes to our understanding of the history of cattle and is essential for an effective conservation of genetic diversity. Here we review the various classifications over the last two centuries and compare the most recent classification...

Identification of global livestock diversity hotspots and their importance in diversity maintenance is essential for making global conservation efforts. We screened 52 sheep breeds from the Eurasian subcontinent with 20 microsatellite markers. By estimating and weighting differently within- and between-breed genetic variation our aims were to ident...

Table S1 - Marker diversity parameters. PDF file with list of microsatellites and their chromosomal location, total number of alleles, expected unbiased heterozygosity, and estimates of within-population (f) and among-population (θ) fixation indices.

Figure S1 - Additional synthetic maps. PDF file synthetic maps for within-breed diversity and breed differentiation.

Table S3 - Breed-wise optimal contributions to a core-set for different weightings of the within-breed variation. PDF file with detailed data summarized in Table 3.

Table S4 - Distribution of core-set contributions using genetic clustering. PDF file with table similar to Table 3, but using genetic clusters instead of regional groups to categorize breeds.

Table S5 - Breeds, having equal contributions to the core set when the number of breeds conserved is fixed. PDF file with table of included breeds when the number of included breeds is fixed at 5, 10, 15 or 20.

Table S2 - Table of the name of sheep breeds, their origin, demographic status and diversity parameters. PDF file with data on per population sample size, expected heterozygosity, within-breed fixation index (f), allelic richness, and number of private alleles.

Yakutian cattle, the last remaining native cattle breed in Siberia, are well adapted to the extreme sub-arctic conditions. Nowadays only ca. 1200 purebred animals are left in Yakutia. The semen of six Yakutian bulls was stored in a cryo-bank without any pedigree documentation because of the traditional free herding style of the population. To clari...

Mean relatedness and their standard deviations of the two relatedness estimators (rQG and rW) for the four simulated relatedness categories.

Results of the shared parentage analysis.

Alignment of the variable sites in the 255 nt fragment of the cattle mtDNA control region.

Average relatedness estimates for pairwise comparisons among the six Yakutian cryo-bank bulls obtained using relatedness estimators rW , rQG and rK.

We analysed 30 autosomal microsatellites in order to clarify genetic relatedness between these bulls and provide recommendations for the use of their semen in conservation and breed management.

Quantitative trait loci (QTL) studies have indicated growth hormone receptor (GHR) as a candidate gene affecting cattle milk yield and composition. In order to characterize genetic variation at GHR in cattle, we studied European and East African breeds with different histories of selection, and Bos grunniens, Ovis aries, Sus scrofa, Bison bison and...

We investigated the genetic structure and variation of 21 populations of cattle (Bos taurus) in northern Eurasia and the neighbouring Near Eastern regions of the Balkan, the Caucasus and Ukraine employing 30 microsatellite markers. By analyses of population relationships, as well as by a Bayesian-based clustering approach, we identified a genetic d...

Northern European indigenous cattle breeds are currently endangered and at a risk of becoming extinct. We analyzed variation at 20 microsatellite loci in 23 indigenous, 3 old imported, and 9 modern commercial cattle breeds that are presently distributed in northern Europe. We measured the breeds' allelic richness and heterozygosity, and studied the...

Extinction of breeds threatens genetic diversity of livestock species. The need to conserve genetic diversity is widely accepted but involves in general two questions: (i) is the expected loss of diversity in a set of breeds within a defined future time horizon large enough to establish a conservation plan, and if so (ii) which breeds should be pri...

Abstract Extinction of breeds threatens genetic diversity of livestock species. The need to conserve genetic diversity is widely accepted but involves in general two questions: (i) is the expected loss of diversity in a set of breeds within a defined future time horizon large enough to establish a conservation plan, and if so (ii) which breeds shou...