mNFE: microbiome network flow entropy for detecting pre-disease states of type 1 diabetes

ABSTRACT

In the development of Type 1 diabetes (T1D), there are critical states just before drastic changes, and identifying these pre-disease states may predict T1D or provide crucial early-warning signals. Unlike gene expression data, gut microbiome data can be collected noninvasively from stool samples. Gut microbiome sequencing data contain different levels of phylogenetic information that can be utilized to detect the tipping point or critical state in a reliable manner, thereby providing accurate and effective early-warning signals. However, it is still difficult to detect the critical state of T1D based on gut microbiome data due to generally non-significant differences between healthy and critical states. To address this problem, we proposed a new method – microbiome network flow entropy (mNFE) based on a single sample from each individual – for detecting the critical state before seroconversion and abrupt transitions of T1D at various taxonomic levels. The numerical simulation validated the robustness of mNFE under different noise levels. Furthermore, based on real datasets, mNFE successfully identified the critical states and their dynamic network biomarkers (DNBs) at different taxonomic levels. In addition, we found some high-frequency species, which are closely related to the unique clinical characteristics of autoantibodies at the four levels, and identified some non-differential ‘dark species’ play important roles during the T1D progression. mNFE can robustly and effectively detect the pre-disease states at various taxonomic levels and identify the corresponding DNBs with only a single sample for each individual. Therefore, our mNFE method provides a new approach not only for T1D pre-disease diagnosis or preventative treatment but also for preventative medicine of other diseases by gut microbiome.

KEYWORDS:

• Tipping point
• dynamic network biomarker (DNB)
• gut microbiome
• Type 1 diabetes (T1D)
• network flow entropy (NFE)

Disclosure statement

No potential conflict of interest was reported by the author(s).

Availability of data and materials

Metagenomic sequencing data of T1D³³ can be downloaded from https://diabimmune.broadinstitute.org/diabimmune/(NCBI BioProject ID: PRJNA231909). To ensure reproducible results, the original code is available at https://github.com/G-R-0/mNFE.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19490976.2024.2327349

Additional information

Funding

This work was supported by the National Natural Science Foundation of China (Nos. T2350003,T2341007, 31930022, 12131020), National Key R&D Program of China (No. 2022YFA1004800), Strategic Priority Research Program of the Chinese Academy of Sciences (No. XDB38040400), Special Fund for Science and Technology Innovation Strategy of Guangdong Province (Nos 2021B0909050004, 2021B0909060002), the Young Backbone Teacher Funding Scheme of Henan (No. 2019GGJS079), Key Research and Development and Promotion Special Program of Henan Province (No. 212102310988), JST Moonshot R&D (No. JPMJMS2021) and Deutsche Forschungsgemeinschaft (No. 390713860).