| 1. |
- Lembrechts, Jonas J., et al.
(author)
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SoilTemp : A global database of near-surface temperature
- 2020
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In: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 26:11, s. 6616-6629
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Journal article (peer-reviewed)abstract
- Current analyses and predictions of spatially explicit patterns and processes in ecology most often rely on climate data interpolated from standardized weather stations. This interpolated climate data represents long-term average thermal conditions at coarse spatial resolutions only. Hence, many climate-forcing factors that operate at fine spatiotemporal resolutions are overlooked. This is particularly important in relation to effects of observation height (e.g. vegetation, snow and soil characteristics) and in habitats varying in their exposure to radiation, moisture and wind (e.g. topography, radiative forcing or cold-air pooling). Since organisms living close to the ground relate more strongly to these microclimatic conditions than to free-air temperatures, microclimatic ground and near-surface data are needed to provide realistic forecasts of the fate of such organisms under anthropogenic climate change, as well as of the functioning of the ecosystems they live in. To fill this critical gap, we highlight a call for temperature time series submissions to SoilTemp, a geospatial database initiative compiling soil and near-surface temperature data from all over the world. Currently, this database contains time series from 7,538 temperature sensors from 51 countries across all key biomes. The database will pave the way toward an improved global understanding of microclimate and bridge the gap between the available climate data and the climate at fine spatiotemporal resolutions relevant to most organisms and ecosystem processes.
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| 2. |
- Dahlberg, Josef, et al.
(author)
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Absence of changes in the milk microbiota during Escherichia coli endotoxin induced experimental bovine mastitis
- 2023
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In: Veterinary research (Print). - : BioMed Central (BMC). - 0928-4249 .- 1297-9716. ; 54
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Journal article (peer-reviewed)abstract
- Changes in the milk microbiota during the course of mastitis are due to the nature of a sporadic occurring disease difficult to study. In this study we experimentally induced mastitis by infusion of Escherichia coli endotoxins in one udder quarter each of nine healthy lactating dairy cows and assessed the bacteriological dynamics and the milk microbiota at four time points before and eight time points after infusion. As control, saline was infused in one udder quarter each of additionally nine healthy cows that followed the same sampling protocol. The milk microbiota was assessed by sequencing of the 16 S rRNA gene and a range of positive and negative controls were included for methodological evaluation. Two different data filtration models were used to identify and cure data from contaminating taxa. Endotoxin infused quarters responded with transient clinical signs of inflammation and increased SCC while no response was observed in the control cows. In the milk microbiota data no response to inflammation was identified. The data analysis of the milk microbiota was largely hampered by laboratory and reagent contamination. Application of the filtration models caused a marked reduction in data but did not reveal any associations with the inflammatory reaction. Our results indicate that the microbiota in milk from healthy cows is unaffected by inflammation.
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| 3. |
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| 4. |
- Dahlberg, Josef
(author)
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Bovine milk microbiota - methods matter
- 2019
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Doctoral thesis (other academic/artistic)abstract
- The idea of a bacterial community, a microbiota, in milk with the purpose of inoculating the offspring's intestine for a better start in life is very appealing from an evolutionary perspective. The overall purpose of this thesis was to investigate if such bacterial community exists in bovine milk from healthy individuals and to describe factors that affect the microbiota. Sequencing of the 16S rRNA gene was used for studying the microbiota. This method permits the identification of all bacteria present in a sample. Bacterial culturing according to mastitis diagnostics routines were included for reference and inflammatory status was followed by milk somatic cell count. Three animal experiments were performed with the aims of describing variations in the milk microbiota due to milk sampling technique, milk fraction, over time and during Escherichia coli endotoxin induced mastitis. Additionally, the microbiota in milk samples collected directly from the udder quarter were compared to that found on the skin of the teat end and in the teat canal, as well as in udder quarter composite milk collected from the milking machine. The results showed that udder quarter composite milk cannot be used as a representative sample to study the microbiota in the udder as the composition of the microbiota in these samples differed significantly from the microbiota in milk collected directly from the teat. Moreover, the microbiota found on the teat end and in the teat canal differed significantly from the microbiota in milk. Despite a careful and sterile handling of samples throughout the whole analytical process, contamination of the sequencing data proved to be a major contributor to the microbiota data in two of the included studies. A correlation between bacterial biomass and impact of contamination was found, showing that the problem increased with low concentration of bacteria in a sample. The degree of contamination of the sequencing data prohibited conclusions on the variation of microbiota over time and during Escherichia coli endotoxin induced mastitis. The overall conclusion is that contamination, from sample processing, had such a substantial effect on the data that the presence of a microbiota in milk from healthy individuals could not be evaluated.
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| 5. |
- Dahlberg, Josef, et al.
(author)
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Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination
- 2019
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In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 14
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Journal article (peer-reviewed)abstract
- Discoveries of bacterial communities in environments that previously have been described as sterile have in recent years radically challenged the view of these environments. In this study we aimed to use 16S rRNA sequencing to describe the composition and temporal stability of the bacterial microbiota in bovine milk from healthy udder quarters, an environment previously believed to be sterile. Sequencing of the 16S rRNA gene is a technique commonly used to describe bacterial composition and diversity in various environments. With the increased use of 16S rRNA gene sequencing, awareness of methodological pitfalls such as biases and contamination has increased although not in equal amount. Evaluation of the composition and temporal stability of the microbiota in 288 milk samples was largely hampered by background contamination, despite careful and aseptic sample processing. Sequencing of no template control samples, positive control samples, with defined levels of bacteria, and 288 milk samples with various levels of bacterial growth, revealed that the data was influenced by contaminating taxa, primarily Methylobacterium. We observed an increasing impact of contamination with decreasing microbial biomass where the contaminating taxa became dominant in samples with less than 10 4 bacterial cells per mL. By applying a contamination filtration on the sequence data, the amount of sequences was substantially reduced but only a minor impact on number of identified taxa and by culture known endogenous taxa was observed. This suggests that data filtration can be useful for identifying biologically relevant associations in milk microbiota data.
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| 6. |
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| 7. |
- Dahlberg, Josef, et al.
(author)
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Microbiota of bovine milk, teat skin, and teat canal: Similarity and variation due to sampling technique and milk fraction
- 2020
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In: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 103, s. 7322-7330
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Journal article (peer-reviewed)abstract
- The aim of this study was to evaluate the effect of sampling technique and milk fraction on bovine milk microbiota data and to compare the microbiota in milk to microbiota on the teat end and in the teat canal. Representative milk samples are highly important for assessment of bacteriological findings and microbiota in milk. Samples were obtained from 5 healthy lactating dairy cows at udder quarter level during 1 milking. Swab samples from the teat. end and teat canal, and milk samples collected using different techniques and in different milk fractions were included. Milk was collected by hand stripping and through a teat canal cannula before and after machine milking, through a trans-teat wall needle aspirate after milking, and from udder quarter composite milk. The microbiota of the samples was analyzed with sequencing of the V1-V3 region of the 16S rRNA gene. In addition, somatic cell counts and bacterial cultivability were analyzed in the milk samples. Microbiota data were analyzed using multivariate methods, and differences between samples were tested using analysis of similarity (ANOSIM). Differences between samples were further explored via individual studies of the 10 most abundant genera. The microbiota on the teat end, in the teat canal, and in udder quarter composite milk, collected using a milking machine, differed in composition from the microbiota in milk collected directly from the udder quarter. No differences in milk microbiota composition were detected between hand-stripped milk samples, milk samples taken through a teat canal cannula, or milk samples taken as a trans-teat wall needle aspirate before or after milking. We conclude that for aseptic milk samples collected directly from the lactating udder quarter, sampling technique or milk fraction has minor effect on the microbiota composition.
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| 8. |
- Danielsson, Rebecca, et al.
(author)
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Compound- and context-dependent effects of antibiotics on greenhouse gas emissions from livestock
- 2019
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In: Royal Society Open Science. - : The Royal Society. - 2054-5703. ; 6
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Journal article (peer-reviewed)abstract
- 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 systemically. We then recorded enteric methane production, total gas production from dung decomposing under aerobic versus anaerobic conditions, prokaryotic community composition in rumen and dung, and accompanying changes in nutrient intake, rumen fermentation, and digestibility resulting from antibiotic administration. The focal antibiotics had no detectable effect on gas emissions from enteric fermentation or dung in aerobic conditions, while they decreased total gas production from anaerobic dung. Microbiome-level effects of benzylpenicillin proved markedly different from those previously recorded for tetracycline in dung, and did not differ by the mode of administration (local or systemic). Antibiotic effects on gas production differed substantially between dung maintained under aerobic versus anaerobic conditions and between compounds. These findings demonstrate compound- and context-dependent impacts of antibiotics on methane emissions and underlying processes, and highlight the need for a global synthesis of data on agricultural antibiotic use before understanding their climatic impacts.
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| 9. |
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| 10. |
- Johnzon, Carl-Fredrik, et al.
(author)
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The Effect of Lipopolysaccharide-Induced Experimental Bovine Mastitis on Clinical Parameters, Inflammatory Markers, and the Metabolome : A Kinetic Approach
- 2018
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In: Frontiers in Immunology. - : FRONTIERS MEDIA SA. - 1664-3224. ; 9
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Journal article (peer-reviewed)abstract
- Mastitis is an inflammatory condition of the mammary tissue and represents a major problem for the dairy industry worldwide. The present study was undertaken to study how experimentally induced acute bovine mastitis affects inflammatory parameters and changes in the metabolome. To this end, we induced experimental mastitis in nine cows by intramammary infusion of 100 pg purified Escherichia call lipopolysaccharide (LPS) followed by kinetic assessments of cytokine responses (by enzyme-linked immunosorbent assay), changes in the metabolome (assessed by nuclear magnetic resonance), clinical parameters (heat, local pain perception, redness, swelling, rectal temperature, clot formation, and color changes in the milk), and milk somatic cell counts, at several time points post LPS infusion. Intramammary LPS infusion induced clinical signs of mastitis, which started from 2 h post infusion and had returned to normal levels within 24-72 h. Milk changes were seen with a delay compared with the clinical signs and persisted for a longer time. In parallel, induction of IL-6 and TNF-alpha were seen in milk, and there was also a transient elevation of plasma IL-6 whereas plasma TNF-alpha was not significantly elevated. In addition, a robust increase in CCL2 was seen in the milk of LPS-infused cows, whereas G-CSF, CXCL1, and histamine in milk were unaffected. By using a metabolomics approach, a transient increase of plasma lactose was seen in LPS-induced cows. In plasma, significant reductions in ketone bodies (3-hydroxybutyrate and acetoacetate) and decreased levels of short-chain fatty acids, known to be major products released from the gut microbiota, were observed after LPS infusion; a profound reduction of plasma citrate was also seen. Intramammary LPS infusion also caused major changes in the milk metabolome, although with a delay in comparison with plasma, including a reduction of lactose. We conclude that the LPS-induced acute mastitis rapidly affects the plasma metabolome and cytokine induction with similar kinetics as the development of the clinical signs, whereas the corresponding effects in milk occurred with a delay.
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| 11. |
- Lembrechts, Jonas J., et al.
(author)
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Global maps of soil temperature
- 2022
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In: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 28:9, s. 3110-3144
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Journal article (peer-reviewed)abstract
- Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0–5 and 5–15cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world's major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean=3.0±2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6±2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (−0.7±2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications.
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