Microbial interactions shape spatial organisation and transcriptional responses in a model mixed-species biofilm

Sadiq, Faizan Ahmed ORCID: https://orcid.org/0000-0003-1596-4155, Yang, Nan, Goeteyn, Jenten, De Reu, Koen, Heyndrickx, Marc and Burmølle, Mette 2026. Microbial interactions shape spatial organisation and transcriptional responses in a model mixed-species biofilm. Microbial Ecology 89 (1) , 65. 10.1007/s00248-026-02701-w

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Abstract

Dynamic social interactions within bacterial biofilms drive distinct spatial organisation and transcriptional responses. Here, we combine fluorescence in situ hybridisation (FISH), confocal laser scanning microscopy (CLSM), and RNA sequencing (RNA-Seq) to investigate a model three-species biofilm community derived from a dairy pasteuriser, comprising Stenotrophomonas rhizophila, Microbacterium lacticum, and Bacillus licheniformis. CLSM revealed species-specific biovolume dynamics and stratified 3D structures over 24 h, with S. rhizophila as the dominant species and M. lacticum exhibiting the lowest abundance yet playing an essential role as the initial coloniser. Spatial patterns reflected known pairwise interactions – commensalism, exploitation, and neutral interaction. Transcriptomic profiling of S. rhizophila revealed extensive gene expression changes in dual-species biofilms with M. lacticum, including upregulation of genes related to flagellar motility, nutrient acquisition, energy metabolism, and TonB-dependent transport. In contrast, co-culture with B. licheniformis induced minimal transcriptional changes in S. rhizophila, consistent with a neutral interaction among the two. Our findings demonstrate how interspecies interactions govern both spatial topology and functional specialisation in mixed-species biofilms which is of relevance to microbial ecology, industrial biofilm control, and the targeting of keystone biofilm species.

Item Type:	Article
Date Type:	Published Online
Status:	Published
Schools:	Schools > Dentistry
Additional Information:	License information from Publisher: LICENSE 1: URL: http://creativecommons.org/licenses/by/4.0/, Type: open-access
Publisher:	Springer
ISSN:	0095-3628
Date of First Compliant Deposit:	10 March 2026
Date of Acceptance:	11 January 2026
Last Modified:	10 Mar 2026 16:15
URI:	https://orca.cardiff.ac.uk/id/eprint/185665

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