Biology subjects

Chouhan, K.

Publications and source records attributed to Chouhan, K..

3 recordsLinked to original sources

bioRxiv2026

NANOTAXI: A Shiny-Based GUI for Real-Time Classification and Analysis of 16S rRNA Nanopore Reads

Real-time taxonomic classification of nanopore amplicon sequencing data enables rapid insights into microbial communities, with applications in clinical diagnostics, environmental monitoring, and outbreak surveillance. However, bridging the gap between long-read data and interpretable results often requires specialised bioinformatics expertise. There remains a need for integrated, user-friendly software that combines live data acquisition with downstream microbiome analysis. Here we present NANOTAXI, a fully automated Shiny-based GUI for the classification of barcoded 16S rRNA gene sequences generated by Oxford Nanopore sequencing. The platform supports four taxonomic classifiers, integrated with five reference databases, enabling flexible selection of classification strategies based on user requirements and available computational resources. In addition to real-time monitoring, NANOTAXI performs cohort-level analyses, including alpha and beta diversity, ordination, differential abundance testing, and functional inference using PICRUSt2. Validation using barcoded synthetic communities comprising pooled genomic DNA from clinically relevant bacterial species and the ZymoBIOMICS mock community demonstrated that NANOTAXI generated biologically coherent taxonomic and functional profiles. Benchmarking revealed clear trade-offs between computational performance and taxonomic specificity. Emu provided the lowest observed species-level false-positive rate, whereas Kraken2 offered the fastest classification and enabled continuous near-real-time monitoring across all tested databases. NANOTAXI is open source and freely available at https://github.com/Nirmal2310/NANOTAXI under the GPL version 3 license.

bioinformatics↗

bioRxiv2025

Primer Blind Spots: Underrepresentation of ESKAPE Pathogens from Developing Regions in 16S rRNA Targeted Sequencing

Targeted 16S rRNA sequencing is stalwart of microbial profiling and diagnostics, but its reliance on some "universal" primers introduces bias. In this in-silico study, we investigated how well these primers capture ESKAPE pathogens by screening multiple databases and found that a considerable fraction showed suboptimal primer binding, suggesting that amplification and identification may be compromised. Notably, these strains were disproportionately associated with isolates from developing countries, underscoring the risk of primer bias in global surveillance.

bioinformatics↗

bioRxiv2025

Nutritional iron deficiency elicits profound rewiring of red pulp macrophage functions via high FPN and SYK-mediated signaling

Iron deficiency is the most common nutritional disorder worldwide, yet how individual cell types adjust to iron scarcity remains unclear. Splenic red pulp macrophages (RPMs) are essential for systemic iron homeostasis. They manage exceptionally high iron flux by recycling aged red blood cells through erythrophagocytosis, a specialized form of efferocytosis. However, how RPMs adapt their clearance and metabolic programs to iron deficiency remains unexplored. Here, we show that RPMs from mildly anemic, iron-deficient mice exhibit enhanced erythrophagocytic capacity. Proteomic profiling and flow cytometry revealed expansion and activation of lysosomal and mitochondrial networks, accompanied by elevated mitochondrial respiration. This metabolic rewiring and the increase in erythrophagocytosis depended on branched-chain amino acid (BCAA) catabolism. These responses were distinct from alternative macrophage activation states and absent in liver and peritoneal macrophages. Mechanistically, the low hepcidin-high ferroportin axis and SYK kinase activity emerged as drivers of this functional rewiring. Pharmacological inhibition of SYK or BCAA catabolism blunted iron-deficiency-induced erythrophagocytic and mitochondrial adaptations of RPMs. Together, these findings reveal a non-canonical metabolic reprogramming of RPMs that enhances their specialized clearance functions during systemic iron scarcity, raising possiblity that similar signaling circuits may operate in other efferocytic macrophage subsets under altered ferroportin-SYK axis activity.

cell biology↗