DOI: 10.5281/zenodo.17470369
title: gut pathogens in 482 stroke patients

description: 1. Data sourceThis dataset was generated by the Department of Neurology  of Nanfang Hospital, Yanling Hospital, and Zhujiang Hospital of Southern Medical University in China. Consecutive patients admitted with a primary diagnosis of acute ischaemic stroke (AIS, ICD-10 code I63) were enrolled prospectively between February 2014 and December 2020. The study was approved by the Ethics Committee of each participating centre (ChiCTR-ROC-17011567, registered on 2017-06-05 00:00:00). Written informed consent was obtained from every participant or their legal proxy.
2. Sample collection & storageWithin 48 h of hospital admission, a single faecal specimen was self-collected with a sterile spoon. Samples were immediately placed into 5 ml DNA/RNA Shield faecal collection tubes (Zymo Research, USA), transported at 2–8 °C to the central laboratory within 4 h, and stored at –80 °C until DNA extraction.

3. DNA extraction and sequencingFecal samples collected within 48 hours of admission were frozen at -80°C within two hours of collection. DNA extraction and amplification of the bacterial 16S rRNA gene V4 region via polymerase chain reaction (PCR), and subsequent sequencing were performed according to protocols outlined in our previous reports. Microbiota analysis was conducted using QIIME (version 1.9.1), with samples normalized to 8000 sequences. The association between infection-related pathogens and GIB was estimated by identifying differentially abundant taxa. First, a targeted classification was applied to detect common pathogens, which were classified as present if at least one read was detected; otherwise, they were classified as absent. Operational taxonomic units (OTUs) identifiers were assigned to specific pathogens at the lowest possible hierarchical levels (genus level for Acinetobacter, Klebsiella, Staphylococcus, Pseudomonas, and Enterococcus). Second, the relative abundance of these specific pathogens within gut microbiota was analyzed.

4. Taxonomic variables providedThe Excel file contains relative abundances (dimensionless, range 0–1) of six potential enteric pathogens that have been repeatedly associated with gut barrier dysfunction and systemic inflammation:





Klebsiella




Staphylococcus




Pseudomonas




Acinetobacter




Streptococcus




Enterococcus



These genera were extracted from the rarefied genus-level table and normalised by the total bacterial reads of each sample. Values <0.000 001 are shown as 0.000 000 1 (1 × 10⁻⁷) for technical reasons but should be treated as zero.

5. Clinical variables





Patient_ID: unique study identifier (anonymised)




GIB_group: classification of overt_GIB, occult_GIB or non_GIB based on endoscopy and/or faecal occult blood testing within 7 days of admission




age: years




gender: 1 = male, 0 = female




NIHSS1: baseline National Institutes of Health Stroke Scale (0–42)




Smoke_history: 1 = ever/former/current, 0 = never




alcohol_history: 1 = regular drinker, 0 = never/occasional




diabetes_history, hyperlipidaemia_history, hypertension_history: 1 = yes, 0 = no




mRS_90day: modified Rankin Scale at 90 days (0–6)




MACES_1year: major adverse cardiovascular events within 12 months (1 = event, 0 = no event)



6. Missing dataFor 42 patients the 1-year follow-up MACES could not be obtained (marked as blank). A small number of genus values are blank when the ASV was completely absent after rarefaction; these should be interpreted as zero relative abundance.



7. Software & code availability
Statistical analyses were performed using SPSS version 24 (IBM SPSS, Chicago, IL), and the raw demultiplexed FASTQ reads will be deposited in a separate Zenodo entry (DOI to be linked) under the same project umbrella.

8. Data reuseThe dataset is released under CC-BY 4.0. Users are requested to cite:“Gut pathogen relative abundance in acute ischaemic stroke and its association with occult gastrointestinal bleeding and clinical outcomes, multi-centre prospective study 2014-2020” (2025). Zenodo.

For any questions please contact the corresponding author: yinj@smu.edu.cn.