Whole-Genome Sequencing and Comparative Genomic Analysis of Antimicrobial Producing Streptococcus lutetiensis from the Rumen.

Isabela Maria Fernandes De Oliveira,Sofia Magalhães Moreira,Christopher J Creevey,Fernanda Godoy-Santos,Linda Boniface Oyama,Sharon Ann Huws,Hilário Cuquetto Mantovani,Rodrigo Gonçalves Dias

doi:10.3390/microorganisms10030551

Isabela Maria Fernandes De Oliveira, Sofia Magalhães Moreira + Show 6 more

Open Access

https://doi.org/10.3390/microorganisms10030551

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Abstract

Antimicrobial peptides (AMPs) can efficiently control different microbial pathogens and show the potential to be applied in clinical practice and livestock production. In this work, the aim was to isolate AMP-producing ruminal streptococci and to characterize their genetic features through whole-genome sequencing. We cultured 463 bacterial isolates from the rumen of Nelore bulls, 81 of which were phenotypically classified as being Streptococcaceae. Five isolates with broad-range activity were genome sequenced and confirmed as being Streptococcus lutetiensis. The genetic features linked to their antimicrobial activity or adaptation to the rumen environment were characterized through comparative genomics. The genome of S. lutetiensis UFV80 harbored a putative CRISPR-Cas9 system (Type IIA). Computational tools were used to discover novel biosynthetic clusters linked to the production of bacteriocins. All bacterial genomes harbored genetic clusters related to the biosynthesis of class I and class II bacteriocins. SDS-PAGE confirmed the results obtained in silico and demonstrated that the class II bacteriocins predicted in the genomes of three S. lutetiensis strains had identical molecular mass (5197 Da). These results demonstrate that ruminal bacteria of the Streptococcus bovis/equinus complex represent a promising source of novel antimicrobial peptides.

Highlights

The rumen ecosystem is colonized by a diverse microbial community, composed mainly of commensal anaerobic bacteria, archaea, protozoa, fungi, and viruses that are essential to the rumen function and the nutrition of the host [1]
We identified conserved biosynthetic gene clusters (BGCs) associated with the production of class II bacteriocins and demonstrated that the ruminal Streptococcus lutetiensis are potential producers of these antimicrobial peptides (AMPs)
The genomic analyses performed revealed that the precursor peptides of the ruminal isolates showed a high sequence identity with ubericin A, an AMP produced by a strain of Streptococcus uberis associated with bovine mastitis

Summary

Introduction

The rumen ecosystem is colonized by a diverse microbial community, composed mainly of commensal anaerobic bacteria, archaea, protozoa, fungi, and viruses that are essential to the rumen function and the nutrition of the host [1]. The capacity of rumen bacteria to produce antimicrobial compounds enhances their response to competitive challenges, enables occupancy of an ecological niche, and improves survival within this complex microbial community [6]. Previous studies indicated that the genera Ruminococcus [7], Butyrivibrio [8], Enterococcus [9], and Streptococcus [10,11] are frequently associated with the production of antimicrobial peptides [12,13]. The methods used for prospecting such molecules encompass both traditional culture-based approaches [14] as well as in silico analyses of biosynthetic gene clusters (BGCs) in rumen bacterial genomes using computational tools [6,12]. In a previous in silico study, we demonstrated that lanthipeptide BGCs are distributed

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