Modulation of the gut microbiota by prebiotic fibres and bacteriocins

The gut microbiota is considered an organ that co-develops with the host throughout its life. The composition and metabolic activities of the gut microbiota are subject to a complex interplay between the host genetics and environmental factors, such as lifestyle, diet, stress and antimicrobials. It is evident that certain prebiotics, and antimicrobials produced by lactic acid bacteria (LAB), can shape the composition of the gut microbiota and its metabolic activities to promote host health and/or prevent diseases. In this review, we aim to give an overview of the impact of prebiotic fibres, and bacteriocins from LAB, on the gut microbiota and its activities, which affect the physiology and health of the host. These represent two different mechanisms in modulating the gut microbiota, the first involving exploitative competition by which the growth of beneficial bacteria is promoted and the latter involving interference competition by which the growth of pathogens and other unwanted bacteria is prevented. For interference competition in the gut, bacteriocins offer special advantages over traditional antibiotics, in that they can be designed to act towards specific unwanted bacteria and other pathogens, without any remarkable collateral effects on beneficial microbes sharing the same niche

Resistance to the bacteriocin LCN972 as deciphered by genome sequencing

Trabajo presentado en el 7th Congress of European Microbiologists (FEMS 2017), celebrado en Valencia (España), del 9 al 13 de julio de 2017[Backgrounds] In view of the current threat of antibiotic resistance, new antimicrobials with low risk of resistance development are demanded. Lcn972 is a lactococcal bacteriocin that inhibits septum formation in dividing target cells by binding to the cell wall precursor lipid II. Moreover, it has a species-specific spectrum of activity, making Lcn972 an attractive template to develop or improve existing antibiotics. [Objectives] Our aim was to identify mutations underlying resistance to Lcn972. [Methods] Whole-genome sequencing (WGS) of the sensitive Lactococcus lactis MG1614 (MIC=10 AU/ml) and two Lcn972-resistant (Lcn972R) derivatives D1 and D1-20 with MICs of > 320 AU/ml and 80 AU/ml, respectively, was performed using the Illumina MiSeq platform and Rapid Annotation Subsystem Technology (RAST) server. Sequence reads were assembled with SPAdes 3.1.0. CONTIGuator and Mauve software tools were used for contigs mapping and comparison over the reference genome. [Conclusions] Two previously identified mutations in L. lactis D1 and D1-20 were mapped and confirmed by WGS: 1) a 22.6-kbp deletion enclosing genes involved in maltose metabolism, the two component system (TCS) F and the phage infection protein (Pip), and 2) insertion of IS981 that activates the promoter of llmg_2447 coding for a putative anti-ECF sigma factor. Additionally, a new mutation was identified, entailing insertion of IS905 in the promoter of the operon llmg_0186_celB that specifies the IIC component of the cellobiose phosphotransferase PTS system. The insertion took place between the putative -35 and -10 promoter regions and the consequences, in terms of promoter activity, are currently under investigation.Peer reviewe

The Potential of Class II Bacteriocins to Modify Gut Microbiota to Improve Host Health.

Production of bacteriocins is a potential probiotic feature of many lactic acid bacteria (LAB) as it can help prevent the growth of pathogens in gut environments. However, knowledge on bacteriocin producers in situ and their function in the gut of healthy animals is still limited. In this study, we investigated five bacteriocin-producing strains of LAB and their isogenic non-producing mutants for probiotic values. The LAB bacteriocins, sakacin A (SakA), pediocin PA-1 (PedPA-1), enterocins P, Q and L50 (enterocins), plantaricins EF and JK (plantaricins) and garvicin ML (GarML), are all class II bacteriocins, but they differ greatly from each other in terms of inhibition spectrum and physicochemical properties. The strains were supplemented to mice through drinking water and changes on the gut microbiota composition were interpreted using 16S rRNA gene analysis. In general, we observed that overall structure of the gut microbiota remained largely unaffected by the treatments. However, at lower taxonomic levels, some transient but advantageous changes were observed. Some potentially problematic bacteria were inhibited (e.g., Staphylococcus by enterocins, Enterococcaceae by GarML, and Clostridium by plantaricins) and the proportion of LAB was increased in the presence of SakA-, plantaricins- and GarML-producing bacteria. Moreover, the treatment with GarML-producing bacteria co-occurred with decreased triglyceride levels in the host mice. Taken together, our results indicate that several of these bacteriocin producers have potential probiotic properties at diverse levels as they promote favorable changes in the host without major disturbance in gut microbiota, which is important for normal gut functioning

Resistance to the Bacteriocin Lcn972 Deciphered by Genome Sequencing

In view of the current threat of antibiotic resistance, new antimicrobials with low risk of resistance development are demanded. Lcn972 is a lactococcal bacteriocin that inhibits septum formation by binding to the cell wall precursor lipid II in Lactococcus. It has a species-specific spectrum of activity, making Lcn972 an attractive template to develop or improve existing antibiotics. The aim of this work was to identify mutations present in the Lcn972-resistant clone Lactococcus cremoris D1-20, previously evolved from the sensitive strain L. cremoris MG1614. Whole-genome sequencing and comparison over the reference genome L. cremoris MG1363 identified several unexpected mutations in the parental strain MG1614, likely selected during in-house propagation. In the Lcn972R clone, two previously identified mutations were mapped and confirmed. Additionally, another transposition event deregulating cellobiose uptake was identified along with three point mutations of unknown consequences for Lcn972 resistance. Two new independent evolution experiments exposing L. cremoris MG1614 to Lcn972 revealed transposition of IS981 into the LLMG_RS12285 locus as the predominant mutation selected by Lcn972. This event occurs early during evolution and was found in 100% of the evolved clones, while other mutations were not selected. Therefore, activation of LLMG_RS12285 coding for a putative anti-ECF (extra-cytoplasmic function) sigma factor is regarded as the main Lcn972 resistance factor in L. cremoris MG1614

Average weights of mice in the same treatment cage over time.

<p>‘(+)’ represents bacteriocin producer cage while ‘(-)’ represents bacteriocin non-producer cage. Significance degree is represented with stars; p<0.05 with one star (*); p <0.01 with two stars (**); p <0.001 with three stars (***).</p

Bacteriocin-producing LAB in the fecal samples of mice at the end of the treatment period.

<p>Representative plates from bacteriocin activity assay were shown for each treatment. ‘(+)’ represents bacteriocin producer treatment, while ‘(-)’ represents isogenic non-producer treatment. The clear zones around the colonies indicate bacteriocin production. The indicator strains used in the assay are: <i>E</i>. <i>faecium</i> P21 (LMG 2783) for SakA and PedPA-1, <i>P</i>. <i>damnosus</i> (LMG 3397) for enterocins, <i>L</i>. <i>plantarum</i> 965 (LMG 2003) for plantaricins, and <i>L</i>. <i>lactis</i> IL1403 (LMG2705) for GarML treatments.</p

Comparison of bacteria composition of treatments.

<p>Principle coordinate analysis (PCoA) plot was generated based on the calculated distances in an unweighted UniFrac matrix. Samples were grouped by color in terms of treatment group they belong to (see legend). (For statistics see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0164036#pone.0164036.s007" target="_blank">S4 Table</a>).</p

Correlation network of relative abundances of OTUs at day 14 and serum levels.

<p>The correlations were calculated using Pearson’s correlation in CoNet and the significant ones (P < 0.05) were shown on the network. All serum values are shown by one color (grey) while OTUs belonging to different families are represented by different colors (see legend). Positive correlations are displayed with green edges and negative correlations with red edges. OTUs on the nodes were represented with OTU numbers or genus names they belong to and serum values were labelled as Trig: triglycerides, HDL: high-density lipoprotein, Chol: total cholesterol and LDL: low-density lipoprotein.</p

Changes in relative abundance of LAB and bacteriocin-targeted bacterial groups at genus level during treatment and post-treatment periods.

<p>Changes in relative abundances of genera in treatments, obtained with respect to time 0, were compared to that in CON. Significance degree is represented as following: P < 0.1 with dot (.); P < 0.05 with one star (*); P < 0.01 with two stars (**).</p