Biology subjects

Jakimowicz, M.

Publications and source records attributed to Jakimowicz, M..

3 recordsLinked to original sources

bioRxiv2026

From variants to networks: resolving low SNP overlap in dairy cattle meta-analysis through multi-level functional mapping

The objective of this study was to perform a systematic review and multi-level meta-analysis of genome-wide association studies (GWAS) for functional traits in dairy cattle, focusing on calving performance and udder health. We hypothesized that despite the limited replication of individual SNPs across independent studies, functionally related variants would converge on common genes, biological pathways, and genomic regions. Following a systematic literature search and a two-stage filtering process, we extracted data from 20 independent articles covering seven traits: direct and maternal calving ease, direct and maternal stillbirth, clinical mastitis, somatic cell count, and somatic cell score. We first conducted a conventional SNP-level meta-analysis, which demonstrated minimal variant overlap across studies, preventing the detection of significant pooled effects. To resolve this low overlap, we mapped the associated variants to higher organizational levels, including genes, proteins, KEGG and Reactome pathways, and quantitative trait loci (QTL), and combined the statistical evidence using Fishers method. This multi-level functional mapping revealed significant biological convergence. At the gene level, we identified shared genes such as CCDC170 linking maternal calving ease and maternal stillbirth, while DCK, TMPRSS11F, and SLC4A4 were significant for udder health traits. Pathway-level meta-analysis highlighted major functional networks, demonstrating that mastitis-related traits were strongly associated with immune response, signal transduction, and cellular stress pathways, whereas maternal calving traits were dominated by endocrine and calcium signaling. Furthermore, our cross-trait overlap analysis identified 35 shared pathways and 30 shared QTL, reflecting a common biological architecture connecting calving difficulties and mastitis susceptibility. Notably, the innate immune system and signal transduction pathways consistently overlapped across multiple functional traits. In conclusion, conventional SNP-level meta-analysis has limited utility for integrating dairy cattle GWAS due to insufficient cross-study marker overlap. Moving from individual variants toward higher-order functional units effectively reveals reproducible genetic signals and functional convergence. The identified genes, biological pathways, and genomic regions offer valuable insights that can be leveraged as biological priors to improve genomic prediction models for dairy cattle health and reproduction.

genetics↗

bioRxiv2025

Supplementation with effective microorganisms in earthen ponds affects common carp growth but not overall microbial communities

Probiotics are increasingly explored in aquaculture to enhance fish health and growth without leaving harmful residues. However, their efficacy in real-world pond environments remains poorly understood. Here, we conducted a 103-day field experiment to assess the effects of two effective microorganisms commercial products supplementations on microbial communities and growth performance of common carp (Cyprinus carpio). Effective microorganisms were added both to feed and directly to pond water. Microbial diversity was analysed using 16S rRNA and whole-genome shotgun sequencing across three environments - water (three time points), sediment (two time points) and fish intestine (one time point) - from 25 experimental ponds. Bioinformatics processing involved QIIME2 and MG-TK pipeline with taxonomic classification based on the SILVA database. The results showed that although supplemented bacterial families did not establish significantly in pond environments, fish exposed to specific effective microorganisms treatments exhibited improved growth metrics. These findings suggest that effective microorganisms can enhance carp growth in aquaculture without significantly altering resident microbial communities, offering a promising residue-free alternative to traditional additives.

microbiology↗

bioRxiv2024

The impact of probiotic supplementation with effective microorganisms on water and gut microbiome of the Common carp

The efficacy of probiotic products in aquaculture covers multiple aspects that act directly on fish, such as improving resistance to fungal, bacterial, and viral infections, reproduction, feed efficiency, and overall growth performance, or indirectly through improved water quality. In our experiment, the application of two commercial water and two commercial food EM supplements was tested for their effect on water and the intestinal microbiome of common carp (Cyprinus carpio), as well as on carp growth performance. Probiotic supplementation did not result in a clear pattern of changes in overall microbial diversity or in the modification of the abundance of single genera. However, its effect was clearly manifested by an increase in the final weight of the fish. The most consistent alteration was the significant increase in Lactococcus abundance in the intestinal microbiome community compared to the control observed in both experimental setups. We conclude that the positive effect of Lactococcus on growth performance can be achieved by feed supplementation, which allows the increased abundance of Lactococcus in the fish intestine, which has a positive impact on glucose absorption and metabolism already demonstrated in the literature.

microbiology↗