[HTML][HTML] Biobased short chain fatty acid production-Exploring microbial community dynamics and metabolic networks through kinetic and microbial modeling …

M Atasoy, WT Scott Jr, A Regueira… - Biotechnology …, 2024 - Elsevier
In recent years, there has been growing interest in harnessing anaerobic digestion
technology for resource recovery from waste streams. This approach has evolved beyond its …

Agricultural practices influence soil microbiome assembly and interactions at different depths identified by machine learning

Y Mo, R Bier, X Li, M Daniels, A Smith, L Yu… - Communications …, 2024 - nature.com
Agricultural practices affect soil microbes which are critical to soil health and sustainable
agriculture. To understand prokaryotic and fungal assembly under agricultural practices, we …

Identifying keystone species in microbial communities using deep learning

XW Wang, Z Sun, H Jia, S Michel-Mata… - Nature Ecology & …, 2024 - nature.com
Previous studies suggested that microbial communities can harbour keystone species
whose removal can cause a dramatic shift in microbiome structure and functioning. Yet, an …

Metagenomic and machine learning-aided identification of biomarkers driving distinctive Cd accumulation features in the root-associated microbiome of two rice …

Z Cheng, Q Zheng, J Shi, Y He, X Yang… - Isme …, 2023 - academic.oup.com
Develo** low-cadmium (Cd) rice cultivars has emerged as a promising avenue for food
safety in Cd-contaminated farmlands. The root-associated microbiomes of rice have been …

Recurrent neural networks enable design of multifunctional synthetic human gut microbiome dynamics

M Baranwal, RL Clark, J Thompson, Z Sun, AO Hero… - Elife, 2022 - elifesciences.org
Predicting the dynamics and functions of microbiomes constructed from the bottom-up is a
key challenge in exploiting them to our benefit. Current models based on ecological theory …

[HTML][HTML] Algal community structure prediction by machine learning

M Liu, Y Huang, J Hu, J He, X **ao - Environmental Science and …, 2023 - Elsevier
The algal community structure is vital for aquatic management. However, the complicated
environmental and biological processes make modeling challenging. To cope with this …

Deep learning in microbiome analysis: a comprehensive review of neural network models

P Przymus, K Rykaczewski, A Martín-Segura… - Frontiers in …, 2025 - frontiersin.org
Microbiome research, the study of microbial communities in diverse environments, has seen
significant advances due to the integration of deep learning (DL) methods. These …

Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes

S Arya, AB George, JP O'Dwyer - Proceedings of the …, 2023 - National Acad Sciences
Microbiome engineering offers the potential to leverage microbial communities to improve
outcomes in human health, agriculture, and climate. To translate this potential into reality, it …

Learning beyond-pairwise interactions enables the bottom–up prediction of microbial community structure

H Ishizawa, Y Tashiro, D Inoue… - Proceedings of the …, 2024 - National Acad Sciences
Understanding the assembly of multispecies microbial communities represents a significant
challenge in ecology and has wide applications in agriculture, wastewater treatment, and …

Evaluation of microbial and organic metabolite characteristics in fermented tobacco from different grades by comprehensive microbiomes and chemometrics analysis

M Zhang, D Guo, H Wang, G Wu, Y Shi, T Zheng… - Industrial Crops and …, 2024 - Elsevier
The microbial and organic metabolite characteristics of different grades of fermented filler
tobacco leaves (FTLs) have a direct impact on the quality of the finished cigars. This study …