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Transcriptional Changes in Bifidobacterium bifidum Involved in Synergistic Multispecies Biofilms

Abstract

Bifidobacterium bifidum is part of the core microbiota of healthy infant guts where it may form biofilms on epithelial cells, mucosa, and food particles in the gut lumen. Little is known about transcriptional changes in B. bifidum engaged in synergistic multispecies biofilms with ecologically relevant species of the human gut. Recently, we reported prevalence of synergism in mixed-species biofilms formed by the human gut microbiota. This study represents a comparative gene expression analysis of B. bifidum when grown in a single-species biofilm and in two multispecies biofilm consortia with Bifidobacterium longum subsp. infantis, Bacteroides ovatus, and Parabacteroides distasonis in order to identify genes involved in this adaptive process in mixed biofilms and the influence on its metabolic and functional traits. Changes up to 58% and 43% in its genome were found when it grew in three- and four-species biofilm consortia, respectively. Upregulation of genes of B. bifidum involved in carbohydrate metabolism (particularly the galE gene), quorum sensing (luxS and pfs), and amino acid metabolism (especially branched chain amino acids) in both multispecies biofilms, compared to single-species biofilms, suggest that they may be contributing factors for the observed synergistic biofilm production when B. bifidum coexists with other species in a biofilm.

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Data Availability

Raw sequencing reads generated from this study are deposited at the NCBI sequence read archive (SRA) in a Bioproject (PRJNA736549) under accession numbers SRR14839360 (R1), SRR14839359 (R2), and SRR14839348 (R3) for three replicates of single-species biofilms of Bifidobacterium bifidum, SRR14839349 (R1), SRR14839350 (R2), and SRR14839347 (R3) for all replicates of three species biofilms (ABC), and SRR14839346 (R1), SRR14839345 (R2), and SRR14839344 (R3) for all replicates of the four-species biofilm (ABCD).

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Acknowledgements

We are thankful to Novogene (China) for RNA sequencing.

Funding

The research was funded by the National Nature Science Foundation of China (31871774, 31820103010), the Fundamental Research Funds for the Central Universities (JUSRP51903B), 111 project (BP0719028), International Cooperation Fund Pool Project of Jiangsu Industrial Technology Research Institute, the collaborative innovation center of food safety and quality control in Jiangsu Province, and the National First-class Discipline Program of Food Science and Technology (JUFSTR20180102).

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FAS and WL designed the study and FAS conducted all experiments. ZJX, ZH, and WC approved and supervised the project and provided all facilities for execution of the work.

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Correspondence to Hao Zhang.

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The authors declare no competing interests.

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Sadiq, F.A., Wenwei, L., Wei, C. et al. Transcriptional Changes in Bifidobacterium bifidum Involved in Synergistic Multispecies Biofilms. Microb Ecol (2021). https://doi.org/10.1007/s00248-021-01904-7

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Keywords

  • Multispecies biofilms
  • Synergism
  • Gut microbes
  • Bifidobacteria
  • Bacterial interaction