Location: Livestock Nutrient Management Research
Project Number: 3090-31630-006-058-N
Project Type: Non-Funded Cooperative Agreement
Start Date: Nov 1, 2024
End Date: Oct 31, 2027
Objective:
1.) Perform a meta-analysis on identified 16S rRNA sequencing data in publicly available repositories using published protocol.
2.) Publish results of the meta-analysis research.
3.) Actively pursue opportunities to strengthen collaboration and its continuation.
Approach:
Literature search using Web of Science, Scopus, AGRIS, and Google Scholar will be implemented. Eligible criteria will be defined using PICO (population, intervention, comparator, and outcomes) elements. Two independent reviewers will be utilized for both the literature search and data compilation. Risk of bias will be assessed using the Cochrane Risk Bias 2.0 tool. Publicly available 16S rRNA amplicon gene sequencing data will be downloaded from NCBI Sequence Read Archive, European Nucleotide Archive or similar database using appropriate extraction methods. Data processing will be performed using QIIME2 following a standardized protocol. Meta-analyses will be performed on both alpha and beta diversity as well as taxonomic analyses. Alpha diversity metrics will be tested using a Kruskal-Wallis test with a Benjamini-Hochberg multiple testing correction. Beta diversity will be statistically tested using PERMANOVA testing with multiple test corrections. Hedge’s g standardized mean difference statistic will be used to calculate fixed and random effects model estimates using a 95% confidence interval. Heterogeneity between studies will be assessed using the I2 statistic. Potential publication bias will be further assessed using Begg’s correlation test and Egger’s regression test. The GRADE approach will be used to assess the certainty of evidence. The following work could be used to enhance livestock management techniques for improved productivity. Access to SCINet computing clusters will be requested for the cooperator.