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Page 2 of 15 Spus et al. Microbiome Res Rep 2023;2:33 https://dx.doi.org/10.20517/mrr.2023.20

lineages, thus providing experimental support for the constant-diversity dynamics model in a complex microbial
community.

Keywords: Microbial community, bacteriophage, population dynamics, starter culture

INTRODUCTION
In natural environments, bacteria rarely or never exist as a homogeneous single-strain culture but rather as
[1]
microbial consortia encompassing many strains representing different lineages of a variety of species . The
species richness and strain diversity are a function of the physico-chemical and biological conditions found
in a given habitat. However, bacteria not only interact with each other and their environment but are also
typically exposed to bacteriophage predation .
[2]
Erkus et al. characterized in detail an industrially relevant microbial community of a complex cheese starter
[3]
culture named Ur . As highlighted by Smid et al., the history of use of the Ur starter led to the
establishment of, at first glance, a simple three-species (Lactococcus lactis, Lactococcus cremoris and
Leuconostoc mesenteroides) culture . Further analysis of the Ur starter demonstrated a substantial degree of
[4]
diversity beyond the sub-species level. In fact, seven genetic lineages of Lactococcus and an eighth lineage of
Lc. mesenteroides could be distinguished by amplified fragment length polymorphism (AFLP) typing within
a representative collection of single strain isolates. Bacteriophage resistance tests with individual strains
[5]
uncovered another level of diversity among isolated strains of the Ur starter belonging to the same genetic
lineage. Interestingly, the sensitivity for lytic phages among strains belonging to the same genetic lineage
varied substantially .
[5]

In general, bacteriophages are thought to play a crucial role in controlling the abundance of bacteria in the
environment . A theoretical model explaining the role of bacteriophages in microbial communities was
[6,7]
[8]
proposed previously by Thingstad , who suggested that the “Kill-the-Winner” (KtW) principle explains
microbial diversity in aquatic microbial systems. This model explains the prevention of niche domination
by the best competitors and thus the maintenance of community diversity. Along with the principles set by
Thingstad , Rodriguez-Valera et al. introduced the constant-diversity (CD) dynamics model, where phage
[8]
predation is a driver of microbial communities’ diversity . The CD dynamics model is different from the
[9]
periodic selection (PS) dynamics model, although both models are not mutually exclusive. In the case of PS
dynamics, the fittest strain eventually dominates the niche, which leads to a clonal sweep of other less fit
strains or lineages. The clonal sweep is expected to result in lower ecosystem efficiency as indicated by
Rodriguez-Valera et al. . If PS dynamics take place in the community of a complex starter culture, it may
[9]
affect the starter’s functionality. The CD model explains the generation and maintenance of microbial
diversity in natural ecosystems where bacterial populations can interact with each other and with lytic
bacteriophages. In such habitats, nutrients are dissolved and bacterial populations are characterized by large
diversity in bacteriophage resistance. Diversity in bacteriophage resistance prevents lysis of the complete
bacterial population caused by bacteriophages due to the presence and emergence of resistant variants.
According to Rodriguez-Valera et al. not only bacterial populations in aquatic environments could follow
CD dynamics but also other communities of interacting microbes found in nature .
[9]

All natural complex systems are exposed to gradual changes in abiotic and biotic conditions. A smooth
response to such changes can be disrupted by a sudden catastrophic shift, resulting in an alternative state.
Such shifts have been observed in natural complex systems such as lakes, coral reefs, and oceans [10-12] .
Various triggers can cause these shifts, eventually leading to the loss of resilience (capacity to respond to a