Cultivation-dependent techniques, computational analyses and genome-scale metabolic models show widespread amino acid auxotrophies, suggesting that soil microorganisms exist within integrated ecologic...

Genome-scale metabolic models (GSMMs) are important aids towards system-level understanding of the metabolic physiology of the gut microbes and for rational microbiome engineering. While large-scale r...

The advent of highly accurate structure prediction techniques such as AlphaFold3 is driving an unprecedented expansion of protein structure databases. This rapid growth creates an urgent demand for novel search tools, as even the current fastest available methods like Foldseek face significant limitations in sensitivity and scalability when confronted with these massive repositories. To meet this challenge, we have developed SSAlign, a protein structure retrieval tool that leverages protein language models to jointly encode sequence and structural information, and adopts a two-stage alignment strategy optimized with multi-GPU and multi-process parallelization. On large-scale datasets such as AFDB50, SSAlign outpaces Foldseek by two to three orders of magnitude in search speed, offering unmatched scalability for high-throughput structural analysis. Compared to Foldseek, SSAlign retrieves substantially more high-quality matches on Swiss-Prot and achieves marked performance improvements on SCOPe40, with relative AUC increases of +20.2% at the family level and +33.3% at the superfamily level, demonstrating significantly enhanced sensitivity and recall. In sum, SSAlign achieves TM-align-comparable accuracy with Foldseek-surpassing speed and coverage, offering an efficient, sensitive, and scalable solution for large-scale structural biology and structure-based drug discovery. ### Competing Interest Statement The authors have declared no competing interest. National Natural Science Foundation of China, 62172172 Hubei Provincial Natural Science Foundation of China, 2025AFB159 The Postdoctoral Fellowship Program of CPSF, GZC20240545

Aligning genomes into common coordinates is central to pangenome construction, though computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) help to frame and solve the multiple...

Abstract. Anthropogenic perturbations to the nitrogen cycle, primarily through use of synthetic fertilizers, is driving an unprecedented increase in the em

Cross-feeding, a phenomenon in which organisms share metabolites, is frequently observed in microbial communities across the natural world. One of the most common forms is waste-product cross-feeding,...

Media optimization using machine learning increased flaviolin production in Pseudomonas putida, generating counter-intuitive media recipes.

In this Perspective, Deiner, Gibbons and colleagues describe the current strengths and limitations of microbial community-scale metabolic models in microbiome research.

This study quantifies and values the carbon stored in the ocean due to biological processes. With uptake in the order of 2.8 Gt per year, valued at around US$1 trillion annually (at a carbon price of ...

A multi-omics approach reveals host–microbiome interactions in aging in mice.

Background The gut microbiome functions as a metabolic organ, producing numerous enzymes that influence host health; however, their substrates and metabolites remain largely unknown. Results We presen...

The development of sustainable biotechnological processes requires a transition from the traditional fermentation of refined substrates towards the valorization of waste materials such as lignocellulo...

We provide guidance on the planning, execution and description of statistical analyses in microbiome studies.

Many microorganisms are refractory to laboratory cultivation. One possible explanation, known as the great plate count anomaly, is metabolic dependencies among community members. However, systematic s...

Assessing more than 12,000 metagenomic samples from across the world using computational approaches, the authors determined interactions between species that co-colonize or co-exclude Enterobacteriace...

A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler