Jacob Agerbo Rasmussen
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View article: A bacterial and viral genome catalogue from Atlantic salmon highlights diverse gut microbiome compositions at pre- and post-smolt life stages
A bacterial and viral genome catalogue from Atlantic salmon highlights diverse gut microbiome compositions at pre- and post-smolt life stages Open
Resolving the microbiome of the Atlantic salmon Salmo salar gut is challenged by a low microbial diversity often dominated by one or two species of bacteria, and high levels of host contamination in sequencing data. Nevertheless, existing …
View article: Possible origins of kombucha in spontaneous fermentation
Possible origins of kombucha in spontaneous fermentation Open
Although the microbial composition and functional attributes of kombucha have been extensively studied, the origins and mechanisms of the formation of their biofilm (Symbiotic Culture of Bacteria and Yeasts, or SCOBY) remain speculative. B…
View article: Early-life <i>Helicobacter pylori</i> infection worsens metabolic state in mice receiving a high-fat diet
Early-life <i>Helicobacter pylori</i> infection worsens metabolic state in mice receiving a high-fat diet Open
Perturbations to the early life microbial colonization of humans alter the development of the host immune system and can cause increased weight gain. We hypothesized that establishing early-life infection with H. pylori , a symbiotic bacte…
View article: Advanced airborne eDNA sampling allows robust spatiotemporal characterisation of vertebrate communities
Advanced airborne eDNA sampling allows robust spatiotemporal characterisation of vertebrate communities Open
Effective biodiversity survey methods are crucial for monitoring ecosystems threatened by climatic fluctuations and anthropogenic pressures. Here we advance methods for the collection of a novel source of biodiversity data - airborne envir…
View article: HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production
HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production Open
The HoloFood project used a hologenomic approach to understand the impact of host–microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to nove…
View article: Growth and metabolic performance of house fly and black soldier fly larvae differ across densities and waste-based growth substrates
Growth and metabolic performance of house fly and black soldier fly larvae differ across densities and waste-based growth substrates Open
Large scale production of insect larvae is considered a sustainable way to upcycle various organic waste- and by-products into more valuable food and feed products. The sustainability of insect larvae production depends on the substrates a…
View article: Intestinal microbial profiles of wild Alaskan rainbow trout (Oncorhynchus mykiss) characterized by 16S rRNA amplicon data
Intestinal microbial profiles of wild Alaskan rainbow trout (Oncorhynchus mykiss) characterized by 16S rRNA amplicon data Open
Rainbow trout (Oncorhynchus mykiss) is a dominant aquaculture species of the Salmonidae family, native only to the North Pacific. Recently, the gut microbiome has been shown to reflect the health status and responses to environmenta…
View article: A practical introduction to holo-omics
A practical introduction to holo-omics Open
View article: Ancient reindeer mitogenomes reveal island-hopping colonisation of the Arctic archipelagos
Ancient reindeer mitogenomes reveal island-hopping colonisation of the Arctic archipelagos Open
View article: Host–gut microbiota interactions shape parasite infections in farmed Atlantic salmon
Host–gut microbiota interactions shape parasite infections in farmed Atlantic salmon Open
Studying host–microbiota interactions through the perspective of the hologenome is gaining interest across all life sciences. Intestinal parasite infections are a huge burden on human and animal health; however, there are few studies inves…
View article: Distinctive mitogenomic lineages within populations of white-tailed eagles (Haliaeetus albicilla)
Distinctive mitogenomic lineages within populations of white-tailed eagles (Haliaeetus albicilla) Open
Using whole mitochondrial DNA sequences from 89 white-tailed eagles (Haliaeetus albicilla) sampled from Iceland, Greenland, Norway, Denmark and Estonia between 1990-2018, we investigate the mitogenomic variation within and between countrie…
View article: A zebrafish model to elucidate the impact of host genes on the microbiota
A zebrafish model to elucidate the impact of host genes on the microbiota Open
Every host species and organism provides a unique environmental niche contributing to the overall diversity of microbial ecosystems from the intestine of an animal to the oceans and forests of our planet. The study of host–microbiota inter…
View article: Succession of microbial community composition and secondary metabolism during marine biofilm development
Succession of microbial community composition and secondary metabolism during marine biofilm development Open
In nature, secondary metabolites mediate interactions between microorganisms residing in complex microbial communities. However, the degree to which community dynamics can be linked to secondary metabolite potential remains largely unknown…
View article: The Salmon Microbial Genome Atlas enables novel insights into bacteria-host interactions via functional mapping
The Salmon Microbial Genome Atlas enables novel insights into bacteria-host interactions via functional mapping Open
The essential role of the gut microbiota for host health and nutrition is well established for many terrestrial animals, while its importance for fish and particularly Atlantic salmon is unclear. Here, we present the Salmon Microbial Genom…
View article: An ethnographic framework for identifying dog sledding in the archaeological record
An ethnographic framework for identifying dog sledding in the archaeological record Open
For at least 9000 years dogs have been pulling sleds across the Arctic, facilitating subsistence strategies and migrations. Despite the enduring presence of dogs in the Arctic there is an absence of comprehensive studies of the material cu…
View article: Adaptation to the High-Arctic island environment despite long-term reduced genetic variation in Svalbard reindeer
Adaptation to the High-Arctic island environment despite long-term reduced genetic variation in Svalbard reindeer Open
View article: Exploring the microbial diversity of novel misos with metagenomics
Exploring the microbial diversity of novel misos with metagenomics Open
Interest in fermented foods, especially plant-based ones, has increased considerably in the last decade. Miso-a Japanese paste traditionally fermented with soybeans, salt, and kōji (Aspergillus oryzae grown on grains or beans)-has gained a…
View article: Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon
Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon Open
Animals and their associated microbiota share long evolutionary histories. Both host genotype and associated microbiota influence phenotypes such as growth and disease resilience. We applied a hologenomic approach to explore the relationsh…
View article: Genome-resolving metagenomics reveals wild western capercaillies (Tetrao urogallus) as avian hosts for antibiotic-resistance bacteria and their interactions with the gut-virome community
Genome-resolving metagenomics reveals wild western capercaillies (Tetrao urogallus) as avian hosts for antibiotic-resistance bacteria and their interactions with the gut-virome community Open
The gut microbiome is a critical component of avian health, influencing nutrient uptake and immune functions. While the gut microbiomes of agriculturally important birds have been studied, the microbiomes of wild birds still need to be exp…
View article: Co-diversification of an intestinal <i>Mycoplasma</i> and its salmonid host
Co-diversification of an intestinal <i>Mycoplasma</i> and its salmonid host Open
Understanding the evolutionary relationships between a host and its intestinal resident bacteria can transform how we understand adaptive phenotypic traits. The interplay between hosts and their resident bacteria inevitably affects the int…
View article: Genomic diversity and differentiation between island and mainland populations of white‐tailed eagles (<i>Haliaeetus albicilla</i>)
Genomic diversity and differentiation between island and mainland populations of white‐tailed eagles (<i>Haliaeetus albicilla</i>) Open
Divergence in the face of high dispersal capabilities is a documented but poorly understood phenomenon. The white‐tailed eagle ( Haliaeetus albicilla ) has a large geographic dispersal capability and should theoretically be able to maintai…
View article: Genome-Resolving Metagenomics Reveals Wild Western Capercaillies (Tetrao Urogallus) as Avian Hosts for Antibiotic-Resistance Bacteria and its Interactions with the Gut-Virome Community
Genome-Resolving Metagenomics Reveals Wild Western Capercaillies (Tetrao Urogallus) as Avian Hosts for Antibiotic-Resistance Bacteria and its Interactions with the Gut-Virome Community Open
View article: An Ethnographic Framework for Identifying Dog Sledding in the Archaeological Record
An Ethnographic Framework for Identifying Dog Sledding in the Archaeological Record Open
View article: Exploring the Microbial Diversity of Novel Misos with Metagenomics
Exploring the Microbial Diversity of Novel Misos with Metagenomics Open
View article: Genomic diversity and differentiation between island and mainland populations of White-tailed Eagles (Haliaeetus albicilla)
Genomic diversity and differentiation between island and mainland populations of White-tailed Eagles (Haliaeetus albicilla) Open
Divergence in the face of high dispersal capabilities is a documented but poorly understood phenomenon. The white-tailed eagle (Haliaeetus albicilla) has a large geographic dispersal capability and should theoretically be able to maintain …
View article: Genomic evidence refutes the hypothesis that the Bornean banteng is a distinct species
Genomic evidence refutes the hypothesis that the Bornean banteng is a distinct species Open
The banteng ( Bos javanicus ) is an endangered species within the wild Asian Bos complex, that has traditionally been subdivided into three geographically isolated subspecies based on (i) mainland Southeast Asia ( B. j. birmanicus ), (ii) …
View article: A strategic model of a host–microbe–microbe system reveals the importance of a joint host–microbe immune response to combat stress-induced gut dysbiosis
A strategic model of a host–microbe–microbe system reveals the importance of a joint host–microbe immune response to combat stress-induced gut dysbiosis Open
Microbiomes provide key ecological functions to their host; however, most host-associated microbiomes are too complicated to allow a model of essential host–microbe–microbe interactions. The intestinal microbiota of salmonids may offer a s…
View article: Hologenomic insights demonstrate co-evolution between an intestinal Mycoplasma and its salmonid host
Hologenomic insights demonstrate co-evolution between an intestinal Mycoplasma and its salmonid host Open
The study of co-evolution between host and microbes has the potential to transform how we understand evolutionary adaptations, yet genuine co-evolutionary relationships are challenging to show. The host's intestinal environment shapes the …
View article: <scp>Rhizosphere</scp><scp>bacterial communities differ among traditional maize landraces</scp>
<span>Rhizosphere</span><span>bacterial communities differ among traditional maize landraces</span> Open
The plant‐associated microbiome has been shown to vary considerably between species and across environmental gradients. The effects of genomic variation on the microbiome within single species are less clearly understood, with results ofte…
View article: Microbiome “Inception”: an Intestinal Cestode Shapes a Hierarchy of Microbial Communities Nested within the Host
Microbiome “Inception”: an Intestinal Cestode Shapes a Hierarchy of Microbial Communities Nested within the Host Open
The importance of the parasite microbiome is gaining recognition. Of particular concern is understanding how these parasite microbiomes influence host-parasite interactions and parasite interactions with the vertebrate host microbiome as p…