Leveraging the vast genetic diversity within microbiomes offers unparalleled insights into complex phenotypes, yet the task of accurately predicting and understanding such traits from genomic data remains challenging. We propose a framework taking advantage of existing large models for gene vectorization to predict habitat specificity from entire microbial genome sequences. Based on our model, we develop attribution techniques to elucidate gene interaction effects that drive microbial adaptation to diverse environments. We train and validate our approach on a large dataset of high quality microbiome genomes from different habitats. We not only demonstrate solid predictive performance, but also how sequence-level information of entire genomes allows us to identify gene associations underlying complex phenotypes. Our attribution recovers known important interaction networks and proposes new candidates for experimental follow up.

The number of published metagenome assemblies is rapidly growing due to advances in sequencing technologies. However, sequencing errors, variable coverage, repetitive genomic regions, and other factors can produce misassemblies, which are challenging to detect for taxonomically novel genomic data. Assembly errors can affect all downstream analyses of the assemblies. Accuracy for the state of the art in reference-free misassembly prediction does not exceed an AUPRC of 0.57, and it is not clear how well these models generalize to real-world data. Here, we present the Residual neural network for Misassembled Contig identification (ResMiCo), a deep learning approach for reference-free identification of misassembled contigs. To develop ResMiCo, we first generated a training dataset of unprecedented size and complexity that can be used for further benchmarking and developments in the field. Through rigorous validation, we show that ResMiCo is substantially more accurate than the state of the art, and the model is robust to novel taxonomic diversity and varying assembly methods. ResMiCo estimated 7% misassembled contigs per metagenome across multiple real-world datasets. We demonstrate how ResMiCo can be used to optimize metagenome assembly hyperparameters to improve accuracy, instead of optimizing solely for contiguity. The accuracy, robustness, and ease-of-use of ResMiCo make the tool suitable for general quality control of metagenome assemblies and assembly methodology optimization.

Tree ensemble machine learning models are increasingly used in microbiome science as they are compatible with the compositional, high-dimensional, and sparse structure of sequence-based microbiome data. While such models are often good at predicting phenotypes based on microbiome data, they only yield limited insights into how microbial taxa may be associated. We developed endoR, a method to interpret tree ensemble models. First, endoR simplifies the fitted model into a decision ensemble. Then, it extracts information on the importance of individual features and their pairwise interactions, displaying them as an interpretable network. Both the endoR network and importance scores provide insights into how features, and interactions between them, contribute to the predictive performance of the fitted model. Adjustable regularization and bootstrapping help reduce the complexity and ensure that only essential parts of the model are retained. We assessed endoR on both simulated and real metagenomic data. We found endoR to have comparable accuracy to other common approaches while easing and enhancing model interpretation. Using endoR, we also confirmed published results on gut microbiome differences between cirrhotic and healthy individuals. Finally, we utilized endoR to explore associations between human gut methanogens and microbiome components. Indeed, these hydrogen consumers are expected to interact with fermenting bacteria in a complex syntrophic network. Specifically, we analyzed a global metagenome dataset of 2203 individuals and confirmed the previously reported association between Methanobacteriaceae and Christensenellales. Additionally, we observed that Methanobacteriaceae are associated with a network of hydrogen-producing bacteria. Our method accurately captures how tree ensembles use features and interactions between them to predict a response. As demonstrated by our applications, the resultant visualizations and summary outputs facilitate model interpretation and enable the generation of novel hypotheses about complex systems.

SUMMARY: Taxonomic and functional information from microbial communities can be efficiently obtained by metagenome profiling, which requires databases of genes and genomes to which sequence reads are mapped. However, the databases that accompany metagenome profilers are not updated at a pace that matches the increase in available microbial genomes, and unifying database content across metagenome profiling tools can be cumbersome. To address this, we developed Struo, a modular pipeline that automatizes the acquisition of genomes from public repositories and the construction of custom databases for multiple metagenome profilers. The use of custom databases that broadly represent the known microbial diversity by incorporating novel genomes results in a substantial increase in mappability of reads in synthetic and real metagenome datasets. AVAILABILITY AND IMPLEMENTATION: Source code available for download at https://github.com/leylabmpi/Struo. Custom genome taxonomy database databases available at http://ftp.tue.mpg.de/ebio/projects/struo/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: Methodological advances in metagenome assembly are rapidly increasing in the number of published metagenome assemblies. However, identifying misassemblies is challenging due to a lack of closely related reference genomes that can act as pseudo ground truth. Existing reference-free methods are no longer maintained, can make strong assumptions that may not hold across a diversity of research projects, and have not been validated on large-scale metagenome assemblies. RESULTS: We present DeepMAsED, a deep learning approach for identifying misassembled contigs without the need for reference genomes. Moreover, we provide an in silico pipeline for generating large-scale, realistic metagenome assemblies for comprehensive model training and testing. DeepMAsED accuracy substantially exceeds the state-of-the-art when applied to large and complex metagenome assemblies. Our model estimates a 1% contig misassembly rate in two recent large-scale metagenome assembly publications. CONCLUSIONS: DeepMAsED accurately identifies misassemblies in metagenome-assembled contigs from a broad diversity of bacteria and archaea without the need for reference genomes or strong modeling assumptions. Running DeepMAsED is straight-forward, as well as is model re-training with our dataset generation pipeline. Therefore, DeepMAsED is a flexible misassembly classifier that can be applied to a wide range of metagenome assembly projects. AVAILABILITY AND IMPLEMENTATION: DeepMAsED is available from GitHub at https://github.com/leylabmpi/DeepMAsED. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.