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Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.
Nat Commun
January 2025
Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
As next-generation sequencing technologies produce deeper genome coverages at lower costs, there is a critical need for reliable computational host DNA removal in metagenomic data. We find that insufficient host filtration using prior human genome references can introduce false sex biases and inadvertently permit flow-through of host-specific DNA during bioinformatic analyses, which could be exploited for individual identification. To address these issues, we introduce and benchmark three host filtration methods of varying throughput, with concomitant applications across low biomass samples such as skin and high microbial biomass datasets including fecal samples.
View Article and Find Full Text PDFPrecision Psychobiotics for Gut-Brain Axis Health: Advancing the Discovery Pipelines to Deliver Mechanistic Pathways and Proven Health Efficacy.
Microb Biotechnol
January 2025
Fonterra Microbiome Research Centre, University College Cork, Cork, Ireland.
Advancing microbiome-gut-brain axis science requires systematic, rational and translational approaches to bridge the critical knowledge gaps currently preventing full exploitation of the gut microbiome as a tractable therapeutic target for gastrointestinal, mental and brain health. Current research is still marked by many open questions that undermine widespread application to humans. For example, the lack of mechanistic understanding of probiotic effects means it remains unclear why even apparently closely related strains exhibit different effects in vivo.
View Article and Find Full Text PDFPopulation dynamics modeling reveals that myeloid bias involves both HSC differentiation and progenitor proliferation biases.
Blood
December 2024
UCLA Signaling Systems Laboratory, Los Angeles, California, United States.
Aging and chronic inflammation are associated with overabundant myeloid-primed multipotent progenitors (MPPs) amongst hematopoietic stem and progenitor cells (HSPCs). While HSC differentiation bias has been considered a primary cause of myeloid bias, whether it is sufficient has not been quantitatively evaluated. Here, we analyzed bone marrow data from the IκB- (Nfkbia+/-Nfkbib-/-Nfkbie-/-) mouse model of inflammation with elevated NFκB activity, which shows increased myeloid-biased MPPs.
View Article and Find Full Text PDFOptimizing Drug Selection in Children with Multiple Sclerosis: What Do We Know and What Remains Unanswered?
Paediatr Drugs
December 2024
Division of Neurology, Department of Pediatrics, The Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada.
Pediatric-onset multiple sclerosis (POMS) refers to multiple sclerosis with onset before 18 years of age. It is characterized by a more inflammatory course, more frequent clinical relapses, and a greater number of magnetic resonance imaging (MRI) lesions compared with adult-onset MS (AOMS), leading to significant impacts on both disability progression and cognitive outcomes in affected individuals. Managing POMS presents distinct challenges due to the unique needs of pediatric patients and the limited number of disease-modifying therapies (DMTs) approved for pediatric use.
View Article and Find Full Text PDFPrimes a Multilayered Transcriptional Defense Response to the Nematode spp. in Tomato.
Int J Mol Sci
November 2024
Facultad de Ciencias Agropecuarias, Universidad de Caldas, Calle 65 No. 26-10, Manizales 170003, Caldas, Colombia.
Article Synopsis
- Meloidogyne nematodes cause significant damage to crops like tomatoes, while certain beneficial bacteria can help protect plants from various pathogens.
- The study focused on understanding the molecular responses in tomato plants to the nematode and bacteria, using RNA sequencing to analyze how the plants reacted to each agent individually and together.
- Results showed that many more genes were activated than repressed, particularly those related to defense mechanisms, lipid metabolism, and carbohydrate processing, indicating a strong defense response in the plants, especially when both microorganisms were present.
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