This repository contains the analysis code and data processing pipelines associated with the paper:
“Microbial Single-Cell Transcriptomics Links Gut Microbiota Functional States to Metabolic Remodeling in Mice”

Original scripts used in the study are organized within this directory.

This directory contains all scripts used for benchmarking the three reference genome resources and performing species identification using a Kraken2-based classifier. The included scripts cover:

FASTQ preprocessing for taxonomic classification:
Read filtering and quality control, Barcode/UMI extraction
Species classification scripts:
Batch classification of FASTQ files with the previously described Kraken2-based workflow
Parsing, summarizing, and exporting genus-level and species-level reports
Reference genome comparison utilities:
Scripts to evaluate mapping / assignment rates across the three reference sets
Scripts to compare database content FastANI-based genome similarity comparison between reference catalogs

Each script contains detailed parameters, tool versions, and instructions for execution.

This directory contains all downstream R scripts used to generate the figures in the manuscript. Each script corresponds directly to a specific figure or figure panel.

Figure 2
smClassify pipeline scripts
Community composition summaries

Figure 3
Cell clustering and dimensionality reduction
Differential gene expression analysis
KEGG pathway enrichment
Functional-cluster distribution
Species proportion analysis
Subcluster characterization

Figure 4
PLS-DA analysis
Differential metabolite analysis
Network construction and visualization
KEGG pathway mapping
Metabolite boxplots and dotplots (amino acids, bile acids, LCFA, PUL-related metabolites)

Figure 5
Analysis of community-embedded functional states
Cross-species functional complementation within the gut microbiota

Figure 6
Subpopulation analysis of M. gordoncarteri
Disrupted nitrogen- and stress-response programs linked to host nitrogen imbalance