Maximum depth sequencing reveals an ON/OFF replication slippage switch and apparent in vivo selection for bifidobacterial pilus expression

Christophe Penno, Mary O’Connell Motherway, Yuan Fu, Virag Sharma, Fiona Crispie, Paul D. Cotter, Benoit Houeix, Lokesh Joshi, Francesca Bottacini, Aoife O’Dwyer, Gary Loughran, John F. Atkins, Douwe van Sinderen*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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The human gut microbiome, of which the genus Bifidobacterium is a prevalent and abundant member, is thought to sustain and enhance human health. Several surface-exposed structures, including so-called sortase-dependent pili, represent important bifidobacterial gut colonization factors. Here we show that expression of two sortase-dependent pilus clusters of the prototype Bifidobacterium breve UCC2003 depends on replication slippage at an intragenic G-tract, equivalents of which are present in various members of the Bifidobacterium genus. The nature and extent of this slippage is modulated by the host environment. Involvement of such sortase-dependent pilus clusters in microbe-host interactions, including bacterial attachment to the gut epithelial cells, has been shown previously and is corroborated here for one case. Using a Maximum Depth Sequencing strategy aimed at excluding PCR and sequencing errors introduced by DNA polymerase reagents, specific G-tract sequences in B. breve UCC2003 reveal a range of G-tract lengths whose plasticity within the population is functionally utilized. Interestingly, replication slippage is shown to be modulated under in vivo conditions in a murine model. This in vivo modulation causes an enrichment of a G-tract length which appears to allow biosynthesis of these sortase-dependent pili. This work provides the first example of productive replication slippage influenced by in vivo conditions. It highlights the potential for microdiversity generation in "beneficial" gut commensals.

Original languageEnglish
Article number9576
Number of pages17
JournalScientific Reports
Issue number1
Early online date10 Jun 2022
Publication statusPublished - 01 Dec 2022


  • Animals
  • Bifidobacterium breve/metabolism
  • Bifidobacterium/genetics
  • Fimbriae, Bacterial/genetics
  • Gastrointestinal Microbiome/genetics
  • Host Microbial Interactions
  • Humans
  • Mice


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