SPLANG—a synthetic poisson-lognormal-based abundance and network generative model for microbial interaction inference algorithms

• Published in: Scientific reports Vol. 14; no. 1; pp. 25099 - 14
• Main Authors: Qian, Weicheng, Stanley, Kevin G., Aziz, Zohaib, Aziz, Umair, Siciliano, Steven D.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 23.10.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114/2397; 631/326/2565/855; 704/158/2463; Abundance; Algorithms; Bacteria - genetics; Bacteria - metabolism; Humanities and Social Sciences; Introduced species; Microbial Interactions; Microbiota; multidisciplinary; Poisson Distribution; Science; Science (multidisciplinary)
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-76513-8

Microbes are pervasive and their interaction with each other and the environment can impact fields as diverse as health and agriculture. While network inference and related algorithms that use abundance data from pyrosequencing can infer microbial interaction networks, the ambiguity surrounding the actual underlying networks hampers the validation of these algorithms. This study introduces a generative model to synthesize both the underlying interactive network and observable abundance data, serving as a test bed for the existing and future network inference algorithms. We tested our generative model with four typical network inference algorithms; our results suggest that none of these algorithms demonstrate adequate accuracy for inferring ecologies of non-commensalistic species, either mutualistic or competitive. We further explored the potential for predictability by combining existing algorithms with an oracle algorithm built by fusing the results of several existing algorithms. The oracle algorithm reveals promising improvements in predictability, although it falls short when applied to networks characterized by dense interspecies taxa interactions. Our work underscores the need for the continued development and validation of algorithms to unravel the intricacies of microbial interaction networks.