Mick Watson
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View article: Methanogenesis inhibition remodels microbial fermentation and stimulates acetogenesis in ruminants
Methanogenesis inhibition remodels microbial fermentation and stimulates acetogenesis in ruminants Open
Rumen microbiota enable ruminants to grow on fibrous plant materials, but also produce methane, driving 5% of global greenhouse gas emissions and leading to a loss of gross energy content. Methanogenesis inhibitors such as 3-nitrooxypropan…
View article: The selective culture and enrichment of major rumen bacteria on three distinct anaerobic culture media
The selective culture and enrichment of major rumen bacteria on three distinct anaerobic culture media Open
Ruminants play an important part in global food security, but also emit methane, which contributes to global warming. Rumen microbes strongly influence the energy retention efficiency from the host’s plant-based diet and produce methane as…
View article: Precision biotics enhance growth performance in broiler chickens by selectively modifying their intestinal microbiome to better respond to enteric challenges
Precision biotics enhance growth performance in broiler chickens by selectively modifying their intestinal microbiome to better respond to enteric challenges Open
Precision biotics (PB) are innovative feed additives designed to influence key metabolic pathways in the microbiome, particularly those involved in short-chain fatty acid (SCFA) production. These SCFAs are crucial for the healthy developme…
View article: Direct Democracy and Its Potential for Advancing Human Rights in the United States
Direct Democracy and Its Potential for Advancing Human Rights in the United States Open
View article: Predator-Prey Q-Learning Based Collaborative Coverage Path Planning for Swarm Robotics
Predator-Prey Q-Learning Based Collaborative Coverage Path Planning for Swarm Robotics Open
Coverage Path Planning (CPP) is an effective approach to let intelligent robots cover an area by finding feasible paths through the environment. In this paper, we focus on using reinforcement learning to learn about a given environment and…
View article: In vitro validation of colon delivery of vitamin B2 through a food grade multi-unit particle system
In vitro validation of colon delivery of vitamin B2 through a food grade multi-unit particle system Open
Colon target delivery of active ingredients is frequently applied in pharmaceutical products. However, in functional food and beverage applications, dietary supplements, and medical nutrition, formats targeting colonic delivery to improve …
View article: Temporal stability of the rumen microbiome and its longitudinal associations with performance traits in beef cattle
Temporal stability of the rumen microbiome and its longitudinal associations with performance traits in beef cattle Open
View article: Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota
Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota Open
The chicken immune system and microbiota play vital roles in maintaining gut homeostasis and protecting against pathogens. In mammals, XCR1+ conventional dendritic cells (cDCs) are located in the gut-draining lymph nodes and play a major r…
View article: The selective culture and enrichment of major rumen bacteria on three distinct anaerobic culture media
The selective culture and enrichment of major rumen bacteria on three distinct anaerobic culture media Open
Ruminants play an important part in global food security, but also emit methane which contributes to global warming. Microbes in the rumen strongly influence the energy retention efficiency from the host’s plant-based diet and produce meth…
View article: Methanogenesis inhibition remodels microbial fermentation and stimulates acetogenesis in ruminants
Methanogenesis inhibition remodels microbial fermentation and stimulates acetogenesis in ruminants Open
Rumen microbiota enable ruminants to grow on fibrous plant materials but also produce methane, driving 5% of global greenhouse gas emissions and leading to a loss of gross energy content. Methanogenesis inhibitors such as 3-nitrooxypropano…
View article: Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota
Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota Open
The chicken immune system and microbiota play vital roles in maintaining gut homeostasis and protecting against pathogens. In mammals, XCR1+ conventional dendritic cells (cDCs) are located in the gut-draining lymph nodes and play a major r…
View article: Including microbiome information in a multi-trait genomic evaluation: a case study on longitudinal growth performance in beef cattle
Including microbiome information in a multi-trait genomic evaluation: a case study on longitudinal growth performance in beef cattle Open
View article: KOunt: a reproducible KEGG orthologue abundance workflow
KOunt: a reproducible KEGG orthologue abundance workflow Open
Summary Accurate gene prediction is essential for successful metagenome analysis. We present KOunt, a Snakemake pipeline, that precisely quantifies KEGG orthologue abundance. Availability and implementation KOunt is available on GitHub: ht…
View article: A comparison of single-coverage and multi-coverage metagenomic binning reveals extensive hidden contamination
A comparison of single-coverage and multi-coverage metagenomic binning reveals extensive hidden contamination Open
View article: KOunt – A reproducible KEGG orthologue abundance workflow
KOunt – A reproducible KEGG orthologue abundance workflow Open
Summary Accurate gene prediction is essential for successful metagenome analysis. We present KOunt, a Snake-make pipeline, that precisely quantifies KEGG orthologue abundance. Availability and implementation KOunt is available on GitHub: h…
View article: nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing
nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing Open
Motivation Iso-Seq RNA long-read sequencing enables the identification of full-length transcripts and isoforms, removing the need for complex analysis such as transcriptome assembly. However, the raw sequencing data need to be processed in…
View article: High throughput analysis of <scp>MHC</scp> class I and class <scp>II</scp> diversity of Zambian indigenous cattle populations
High throughput analysis of <span>MHC</span> class I and class <span>II</span> diversity of Zambian indigenous cattle populations Open
The classical MHC class I and class II molecules play key roles in determining the antigenic‐specificity of CD8+ and CD4+ T‐cell responses—as such characterisation of the repertoire of MHCI and MHCII allelic diversity is fundamental to our…
View article: 550. Extensive functional genomics information from early developmental time points for pig and chicken
550. Extensive functional genomics information from early developmental time points for pig and chicken Open
International audience
View article: 93. Novel recombinant measles virus vaccine prevents measles virus disease in rhesus macaques
93. Novel recombinant measles virus vaccine prevents measles virus disease in rhesus macaques Open
Background Measles-Mumps-Rubella (MMR) is an effective live-virus vaccine against measles virus (MeV). However, use of MMR is limited by its inability to boost MeV immunity, lack of immunogenicity in infants, and contraindication in pregna…
View article: Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome
Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome Open
View article: Correction: Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions
Correction: Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions Open
View article: Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions
Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions Open
View article: Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome
Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome Open
Microbiome analysis is quickly moving towards high-throughput methods such as metagenomic sequencing. Accurate taxonomic classification of metagenomic data relies on reference sequence databases, and their associated taxonomy. However, for…
View article: Bovine host genome acts on rumen microbiome function linked to methane emissions
Bovine host genome acts on rumen microbiome function linked to methane emissions Open
View article: Additional file 2 of Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome
Additional file 2 of Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome Open
Additional file 2: Table S3 A list of the Hungate genome files used to create the simulated data. Shown in the table are the Hungate genome files used to create the simulated data. They are separated into the complete (single-contig) and d…
View article: Additional file 2 of Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions
Additional file 2 of Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions Open
Additional file 2: Table S1. Microbial gene abundances in rumen microbiome (analyzed after an additive log-ratio transformation) with significant host genomic effects referred to as host-specific functional core microbiome (HGFC). Table S2…
View article: Effect of cecal microbiota transplantation between different broiler breeds on the chick flora in the first week of life
Effect of cecal microbiota transplantation between different broiler breeds on the chick flora in the first week of life Open
View article: Jaagsiekte sheep retrovirus infection induces changes in microRNA expression in the ovine lung
Jaagsiekte sheep retrovirus infection induces changes in microRNA expression in the ovine lung Open
Ovine pulmonary adenocarcinoma (OPA) is an infectious neoplastic lung disease of sheep caused by jaagsiekte sheep retrovirus. OPA is an important veterinary problem and is also a valuable large animal model for human lung adenocarcinoma. J…
View article: Bovine host genome acts on specific metabolism, communication and genetic processes of rumen microbes host-genomically linked to methane emissions
Bovine host genome acts on specific metabolism, communication and genetic processes of rumen microbes host-genomically linked to methane emissions Open
Whereas recent studies in different species showed that the host genome shapes the microbial community profile, our new research strategy revealed substantial host genomic control of comprehensive functional microbial processes in the rume…
View article: Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture
Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture Open
Background The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal ex…