A novel approach to differential expression analysis of co-occurrence networks for small-sampled microbiome data

TL;DR

This paper introduces a specialized graph-based method for inferring meaningful co-occurrence networks from small-sample microbiome data, enabling biological insights despite data sparsity and complexity.

Contribution

It presents a novel graph theoretic approach tailored for small datasets, including filtering and enrichment techniques, applicable to microbiome and multi-omics data.

Findings

Inferred networks reveal disease progression-related changes in microbiome interactions.

Identified persistent microbiome sub-networks across different disease stages.

Demonstrated biologically meaningful insights from purely statistical network analysis.

Abstract

Graph-based machine learning methods are useful tools in the identification and prediction of variation in genetic data. In particular, the comprehension of phenotypic effects at the cellular level is an accelerating research area in pharmacogenomics. In this article, a novel graph theoretic approach is proposed to infer a co-occurrence network from 16S microbiome data. The approach is specialised to handle datasets containing a small number of samples. Small datasets exacerbate the significant challenges faced by biological data, which exhibit properties such as sparsity, compositionality, and complexity of interactions. Methodologies are also proposed to enrich and statistically filter the inferred networks. The utility of the proposed method lies in that it extracts an informative network from small sampled data that is not only feature-rich, but also biologically meaningful and statistically significant. Although specialised for small data sets, which are abundant, it can be generally applied to any small-sampled dataset, and can also be extended to integrate multi-omics data. The proposed methodology is tested on a data set of chickens vaccinated against and challenged by the protozoan parasite Eimeria tenella. The raw genetic reads are processed, and networks inferred to describe the ecosystems of the chicken intestines under three different stages of disease progression. Analysis of the expression of network features derive biologically intuitive conclusions from purely statistical methods. For example, there is a clear evolution in the distribution of node features in line with the progression of the disease. The distributions also reveal clusters of species interacting mutualistically and parasitically, as expected. Moreover, a specific sub-network is found to persist through all experimental conditions, representative of a persistent microbiome.