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

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.

Antilisterial activity of raw sheep milk from two native Epirus breeds: Culture-dependent identification, bacteriocin gene detection and primary safety evaluation of the antagonistic LAB biota

“…Several recent studies, particularly dealing with soft acid-curd artisan Turkish cheeses, have linked the prevalence of S. lutetiensis, S. gallolyticus, S. macedonicus and S. infantarius subsp. infantarius with beneficial biotechnological and antagonistic (bacteriocin) properties and/or gene clusters in their genome ( Papadimitriou et al., 2014 ; Hill et al., 2020 ; Demirci et al., 2021 ; Özkan et al., 2021b ; Tsuda and Kodama, 2021 ; Aktas et al., 2022 ; Güley et al., 2022 ; de Oliveira et al., 2022 ). The above phylogenetic and biotechnological cheese ecology studies are emphasized because (i) the isolate S. gallolyticus KFM26 ( Table 4 ) was alternatively identified at 99.93 % similarity of its 16S rRNA gene sequence with S. pasteurianus (a Dutch strain with MK330581.1), suggesting that KFM26 is a S. gallolyticus subsp.…”

Comparative genomics of four lactic acid bacteria identified with Vitek MS (MALDI-TOF) and whole-genome sequencing

“…For whole genome sequences, OrthoANI values were calculated by EZBioCloud (Lee et al 2016 ; Yoon et al 2017 ). Biosynthetic gene clusters and bacteriocin precursor peptides were detected with antiSMASH 7 ( https://antismash.secondarymetabolites.org/#!/start , accessed on 19.01.2023) by using .fasta files selecting KnowClusterblast, SubClusterBlast, Pfam-based GO term annotation, and ActiveSiteFinder (Santos et al 2022 ). Bacteriocins were identified with BAGEL 4.0 ( http://bagel5.molgenrug.nl/ , accessed on 19.01.2023) (Alam et al 2022 ).…”

Partial characterization of a bacteriocin-like inhibitory substance produced by Streptococcus equinus C6I9, a bovine rumen isolate.

“…Naturally present ruminal bacteria are commonly capable of synthesizing antimicrobial compounds, such as bacteriocins (MANTOVANI et al, 2001;WHITFORD et al, 2001;de OLIVEIRA et al, 2022). Bacteriocins are produced by Gram-negative and Gram-positive bacteria, as well as by some strains of the Archaea domain, and they have bactericidal or bacteriostatic activity against the target cell (DARBANDI et al, 2022).…”