Page 56 - Read Online

Kleerebezem et al. Microbiome Res Rep 2024;3:46 https://dx.doi.org/10.20517/mrr.2024.48 Page 3 of 14

chain fraction of the FOS product used (mono-, di- and tri-saccharides; fructose, sucrose, and 1-kestose,
respectively), analogous to what has been observed for other FosE-lacking strains of this species [12,13] . These
considerations leave it undecided whether the synbiotic used in this study should be regarded as a
complementary or synergistic synbiotic mixture. Moreover, due to the lack of single-constituent control
interventions, it remains to be established whether the administration of only L. plantarum ATCC202195
(i.e., without FOS co-administration) could achieve the same health impacts.

In the section below, we will review some of the work performed with L. plantarum as an exemplary case for
the design of strain-specific synergistic synbiotics and the exploration of their capacity to (selectively)
enhance the intestinal fitness of L. plantarum.

DESIGNING SYNERGISTIC SYNBIOTICS
Strain-specific synergistic synbiotics for L. plantarum
Strains of the species L. plantarum have long been recognized as excellent probiotic candidates [14-17] . The
species has a very wide ecological distribution ranging from the GI tract of humans and animals to decaying
[18]
plant materials and fermented and non-fermented food products . L. plantarum WCFS1, a single isolate of
strain NCIMB8826, is among the most documented and extensively studied L. plantarum strains and has
been instrumental in our understanding of the lifestyle of this species. The L. plantarum WCFS1 genome
[19]
was the first genome of the lactobacilli to be published and has since then been extensively analyzed,
[22]
including a comprehensive overview of its predicted secretome [20,21] , a genome-scale metabolic model , and
a reconstruction of its regulatory network . The availability of these tools rendered the WCFS1 strain a
[23]
useful model for in-depth investigation of the molecular mechanisms that underlie probiotic function in
[25]
[24]
lactobacilli . More recently, comparative genomics of 54 L. plantarum strains (later expanded to 611
genomes ) revealed a large pan-genome (> 7,000 orthologous groups), which did not approach saturation
[26]
(i.e., also not with 611 genomes ), indicating that the genomic diversity of the species was still substantially
[26]
larger than the 7,000 orthologous groups found in the 54 strains , which was expanded to more than
[25]
[26]
20,000 genes in 611 strains . These findings agreed with the ecological flexibility and nomadic lifestyle of
L. plantarum [25,27] .
The genotypic and phenotypic diversity of L. plantarum strains is strongly reflected by the highly strain-
specific carbohydrate utilization gene-repertoires, which is reflected by an array of genomic “lifestyle”
islands that contain genes annotated as carbohydrate utilization cassettes, which appear to be clustered close
to the origin of replication. Interestingly, no correlation between the diversity in these cassettes and the
niche of isolation of these strains could be detected [18,25,28] . These strain-specific carbohydrate utilization gene
repertoires offer an attractive starting point for the development of strain-specific synbiotics. Therefore, we
developed a synbiotic matchmaking approach in our lab to identify prebiotic substrates that could
differentially be utilized for growth by a panel of 77 L. plantarum strains . Substantial variations in
[29]
prebiotic utilization capacity were detected among the 77 strains for galacto-oligosaccharides (GOS) and
isomalto-oligosaccharides (IMOS), whereas only a single strain (L. plantarum Lp900) isolated from ogi, a
fermented sorghum pudding from Nigeria, was able to effectively utilize short- and long-chain fructo-
oligosaccharides (FOS and inulin, respectively) . Notably, it is well-established that the substrates that
[29]
supported variable growth of the L. plantarum strains (i.e., GOS and IMOS) encompass a variety of distinct
saccharide constituents that vary in degree of polymerization (DP) and glycosidic linkages [30,31] . Refinement
of the matchmaking approach by determination of the strain-specific utilization capacity of individual GOS
and IMOS constituents was able to explain the observed variations in the overall utilization (growth) of
these prebiotics, which through gene-trait matching could be linked to specific L. plantarum genes that are
involved in the metabolization of these IMOS and GOS constituents [29,32] . Similarly, the single L. plantarum