Biology subjects

Somerville, V.

Publications and source records attributed to Somerville, V..

13 recordsLinked to original sources

bioRxiv2026

Uncovering novel phage defense systems through genomic island analysis in Streptococcus thermophilus

Bacteria encode diverse antiviral defense systems, yet the evolutionary reservoirs that generate this immune innovation remain poorly defined. Although genomic context has been instrumental in discovering defense systems, genomic islands (GIs), variable chromosomal regions enriched in defense genes and proteins of unknown function, have not been systematically explored as sources of new bacterial immunity. Here, using comparative genomics of Streptococcus thermophilus, we identified 30 defense-associated GIs displaying extensive accessory gene diversity. Investigation of candidate loci from three GIs uncovered 15 previously uncharacterized antiviral systems, including 10 with novel architectures or features, revealing the potential within even a small subset of GIs. Several systems were not located near known defense genes, highlighting that GI-based discovery complements the traditional guilt-by-association approach, revealing systems that would otherwise remain undetected. Together, our findings establish GIs as reservoirs of antiviral innovation and provide a framework for uncovering the diversity of bacterial immune systems.

microbiology↗

bioRxiv2026

Predictable adaptive evolution of a phage endolysin through substrate recognition optimization

Bacteriophages release progeny by producing endolysins that degrade the bacterial cell wall. While the frequent horizontal transfer of endolysins suggests substantial evolutionary plasticity, the mechanisms by which these enzymes adapt to new phage-host contexts remain poorly understood. Here, we investigated the evolutionary dynamics and structural mechanisms governing endolysin adaptation following experimental evolution of a chimeric phage generated via heterologous endolysin exchange between phages infecting different hosts. Using replicate experimental evolution and time-resolved PacBio sequencing, we identified a dominant, highly reproducible adaptive trajectory characterized by the stepwise fixation of three key mutations. This constrained mutational order correlated with incremental gains in enzymatic activity, reflecting a rugged yet predictable fitness landscape. High-resolution structural analyses revealed that these substitutions lie exclusively outside the catalytic site; instead, they enhance substrate recognition through electrostatic tuning, optimized hydrophobic packing, and local conformational refinement, resulting in significantly higher binding affinity. While the adaptive trajectory was largely conserved, one replicate followed an alternative path, highlighting the interplay between selection and historical contingency. Adaptation was further shaped by a functional trade-off, whereby increased lytic activity on the novel host was accompanied by reduced activity on the ancestral host, consistent with antagonistic pleiotropy. Genome-wide sequencing additionally identified a compensatory mutation in a lytic transglycosylase, suggesting coordinated evolution of the broader lysis machinery. Together, these results demonstrate that endolysins evolve through reproducible adaptive walks constrained by structure, selection, and trade-offs, providing a mechanistic framework for understanding enzyme evolution and informing rational protein engineering.

evolutionary biology↗

bioRxiv2026

Microbial community dynamics in a traditional Swiss mountain cheese over 142 years of cheesemaking

The history of cheesemaking is deeply intertwined with the evolution of microbial communities, from spontaneous fermentation to modern, standardized practices. Despite centuries of refinement, the most profound shifts in cheese production occurred in the last century, driven by advances in microbiology and production technologies. These changes have shaped the bacterial and viral communities within cheese, yet the specific impacts remain underexplored. Using shotgun metagenomics and 16S rRNA gene amplicon sequencing approaches, we examined microbial community changes in Raclette du Valais, a traditional Swiss cheese, using preserved cheese wheels from 1875 to 2017 from the same alpine dairy in Switzerland. Our results reveal that significant shifts in microbial community composition coincide with changes in production practices. Notably, the oldest cheese harbored a distinct bacterial community, dominated by Lactiplantibacillus paraplantarum, Streptococcus thermophilus, Pseudolactococcus laudensis, and taxa commonly associated with the gut environment, indicative of spontaneous fermentation and the use of calf stomach for milk coagulation. Functionally, we can also track the rise and fall of antibiotic resistance genes mirroring their use. Furthermore, we found that domestication of lactic acid bacteria predates the studied period, and that bacteriophage genera detected in 1875 are representatives of those commonly found in modern cheesemaking. These findings highlight how microbial communities have adapted to changing production methods and how human intervention, through practices like antibiotic use in animal husbandry, has influenced these ecosystems in remote alpine cheesemaking. Significance StatementCheesemaking relies on complex microbial ecosystems shaped by long-standing human practices, yet how these communities responded to the modernization of food production has remained largely unknown. By analyzing DNA preserved in historical cheese wheels from a single alpine dairy, we examine microbial community changes across a key technological transition. We show that modernization impacted bacterial composition and functional potential, that cheese microbiomes record the rise of agricultural antibiotic use, and that major cheese-associated phages and domesticated starter bacteria were already established over a century ago. These findings demonstrate that historical cheeses preserve long-term microbial records and offer a glimpse how changes in food production practices shape fermented-food microbiomes.

microbiology↗

bioRxiv2025

ReCycled: A Tool to Reset the Start of Circular Bacterial Chromosomes

Summary (two sentences)For many publicly available bacterial genomes the chromosome start is not set at the replication initiation protein. This is a burden for comparative genomics studies as the synteny between such genomes cannot readily be assessed. Here, we present ReCycled, a tool for identifying and resetting the start of circular bacterial chromosomes. Availability and implementationFreely available on GitHub at https://github.com/Freevini/ReCycled under the GPL-3.0 license. Runs on all tested GNU/Linux systems. ContactVincent Somerville, vincent@somerville.earth Supplementary InformationThe analyses, scripts and data to test the different pipelines are deposited online on zenodo (10.5281/zenodo.15170502).

bioinformatics↗

bioRxiv2025

Strain-level and phenotypic stability contrasts with plasmid and phage variability in water kefir communities

Microbial communities can change in response to top-down factors, such as phages, and bottom-up factors, such as nutrient availability. Previous studies have successfully investigated bacterial species-level dynamics, but diversity and interactions beyond the species-level is usually lacking. Traditional fermented foods, such as water kefir, provide ideal systems to study ecological and evolutionary dynamics beyond the species-level, as they are simple and trackable systems that are cultivated in non-sterile, nutrient-rich environments which foster microbial growth and invasion. Despite the central role of only a few lactic acid bacteria for fermentation, little is known about the genomic diversity and dynamics of these community members over time. Within the framework of a graduate course, 35 students propagated water kefir across several generations under different nutrient conditions and in different households to study microbial responses over time. We found that water kefir communities were generally stable at the species-level, with only rare bacterial species replaced over long timescales (more than 2 years). While we observed little strain-level diversity with few strain replacements over long timescales, closely related strains exhibited variation in accessory gene content, often encoded on plasmids, particularly those involved in ecologically meaningful functions such as sugar utilization pathways and phage defense systems. We hypothesise that these genomic variations could reflect the adaptations of strains to different sugars and phages. Consistent with this, we observed a diverse array of phages, many likely originating from the unique household environments. By documenting the genomic landscape of microbial species, strains, plasmids, and phages, this study advances our understanding of the diversity and dynamics of microbial communities in fermented foods. Furthermore, our course material is publicly available and offers a blueprint for bridging the gap between teaching and research, inspiring the next generation of scientists to unravel the complexities of microbial ecosystems. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/640646v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@56db6borg.highwire.dtl.DTLVardef@5f6dc6org.highwire.dtl.DTLVardef@11fff14org.highwire.dtl.DTLVardef@1a37a9f_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Genomic and phenotypic imprints of microbial domestication on cheese starter cultures

Domestication - the artificial selection of wild species to obtain variants with traits of human interest- was integral to the rise of civilization. During the neolithic, the oversupply of food enabled by the domestication of crop plants and farm animals was associated with the invention of food preservation strategies through microbial fermentation. However, it remains unclear whether fermented food microbes show similar signs of domestication by humans like plants or animals. Only a few eukaroytic have been studied so far in this respect (e.g., yeasts used in mantou or wine), whereas little is known for bacteria. Here, we tested if cheese starter cultures harbour typical hallmarks of domestication by characterising over 100 community samples and over 100 individual strains isolated from historical and modern traditional Swiss cheese starter cultures. We find that cheese starter cultures have low genetic diversity both at the species and strain-level and are taxonomically and phenotypically stable. Our analyses further suggest that the evolutionary origin of the bacteria in cheese starter cultures coincided with the start of cheesemaking as reported from archeological records. Finally, we find evidence for ongoing genome decay and pseudogenization via transposon insertion related to a reduction of their niche breadth. These characteristics suggest that cheese starter cultures were domesticated by humans before knowing about microbes, potentially starting as early as the neolithics Future work documenting the prevalence of these hallmarks across diverse fermented food systems and geographic regions will be key to unveiling the joint history of humanity with fermented food microbes.

microbiology↗

bioRxiv2023

Dairy practices select for thermostable endolysins in phages

Endolysins are phage lytic enzymes that degrade the bacterial cell wall to release phage progeny. We found that the diversity of endolysins is unsuspectedly low and dominated by a single structural type in distinct phages that infect Streptococcus thermophilus. Through X-ray crystallography, we discovered that this type of endolysin contains a highly conserved calcium-binding motif in its cell wall binding domain. Inactivation of the motif in the purified endolysin or in the phage genome revealed its key role in stabilizing the enzyme under conditions that mimic the cheesemaking process, including at elevated temperatures. Fermented dairy products such as yogurt and cheeses are incubated or cooked at higher temperatures and require the addition of thermophilic lactic acid bacteria such as S. thermophilus to drive milk fermentation. It appears that dairy practices have influenced the genetic signatures of streptococcal phages by selecting for thermostable endolysins, which in turn have limited their diversity.

microbiology↗

bioRxiv2022

Deep divergence and genomic diversification of gut symbionts of neotropical stingless bees

Social bees harbor conserved gut microbiota that may have been acquired in a common ancestor of social bees and subsequently co-diversified with their hosts. However, most of this knowledge is based on studies on the gut microbiota of honey bees and bumble bees. Much less is known about the gut microbiota of the third and most diverse group of social bees, the stingless bees. Specifically, the absence of genomic data from their microbiota presents an important knowledge gap in understanding the evolution and functional diversity of the social bee microbiota. Here we combined community profiling with culturing and genome sequencing of gut bacteria from six neotropical stingless bee species from Brazil. Phylogenomic analyses show that most stingless bee gut isolates form deep-branching sister clades of core members of the honey bee and bumble bee gut microbiota with conserved functional capabilities, confirming the common ancestry and ecology of their microbiota. However, our bacterial phylogenies were not congruent with those of the host indicating that the evolution of the social bee gut microbiota was not driven by strict co-diversification, but included host switches and independent symbiont gain and losses. Finally, as reported for the honey bee and bumble bee microbiota, we find substantial genomic divergence among strains of stingless bee gut bacteria suggesting adaptation to different host species and glycan niches. Our study offers first insights into the genomic diversity of the stingless bee microbiota, and highlights the need for broader samplings to understand the evolution of the social bee gut microbiota. ImportanceStingless bees are the most diverse group of the corbiculate bees and represent important pollinator species throughout the tropics and subtropics. They harbor specialized microbial communities in their gut that are related to those found in honey bees and bumble bees and that are likely important for bee health. Few bacteria have been cultured from the gut of stingless bees which has prevented characterization of their genomic diversity and functional potential. Here, we established cultures of major community members of the gut microbiota of six stingless bee species and sequenced their genomes. We find that most stingless bee isolates belong to novel bacterial species distantly related to those found in honey bees and bumble bees and encoding similar functional capabilities. Our study offers a new perspective on the evolution of the social bee gut microbiota and presents the basis to characterize the symbiotic relationships between gut bacteria and stingless bees.

microbiology↗

bioRxiv2022

Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities

Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such diversity is maintained because the effective immune system of a bacterial species is the one distributed across all strains present in the community. However, only few studies have analyzed the distribution of bacterial defense systems at the community-level, mostly focusing on CRISPR and comparing samples from complex environments. Here, we studied 2778 bacterial genomes and 158 metagenomes from cheese-associated communities, which are dominated by a few bacterial taxa and occur in relatively stable environments. We find that nearly identical strains of cheese-associated bacteria contain diverse and highly variable arsenals of innate and adaptive (i.e CRISPR-Cas) immunity suggesting rapid turnover of defense mechanisms in these communities. CRISPR spacer abundance correlated with the abundance of matching target sequences across the metagenomes providing evidence that the identified defense repertoires are functional and under selection. While these characteristics align with the pan-immunity model, the detected CRISPR spacers only covered a subset of the phages previously identified in cheese, suggesting that CRISPR does not provide complete immunity against all phages, and that the innate immune mechanisms may have complementary roles. Our findings show that the evolution of bacterial defense mechanisms is a highly dynamic process and highlight that experimentally tractable, low complexity communities such as those found in cheese, can help to understand ecological and molecular processes underlying phage-defense system relationships. ImportanceBacteria are constantly exposed to phage predation and hence harbor highly diverse defense arsenals. According to the pan-immunity hypothesis the effective immune system of a bacterial species is not the one encoded in a single genome but in the entire community. However, few studies have investigated how defense systems are distributed within communities. Here, we carried out (meta)genomic analyses of bacterial communities used in cheesemaking. These are tractable communities of biotechnological interest which house few bacterial species and are exposed to high phage pressure. In line with the pan-immunity hypothesis, we find that nearly identical strains of cheese-associated bacteria contain highly variable arsenals of innate and adaptive immunity. We provide evidence for the functional importance of this diversity, and reveal that CRISPR alone does not provide complete immunity against all phages. Our findings can have implications for the design of robust synthetic communities used in biotechnology and the food industry.

microbiology↗

bioRxiv2021

Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures

Undefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by repeated propagation in closed and highly controlled environments over centuries. This makes them interesting for understanding eco-evolutionary dynamics governing microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to an important Swiss cheese starter culture and analyzed historical and experimental samples reflecting 82 years of starter culture propagation. We found that the bacterial community is highly stable and dominated by only a few coexisting strains of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Genome sequencing, metabolomics analysis, and co-culturing experiments of 43 isolates show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large and diverse repertoire of matching CRISPR spacers. Our findings show that functionally equivalent strains can coexist in domesticated microbial communities and highlight an important role of bacteria-phage interactions that are different from kill-the-winner dynamics.

microbiology↗

bioRxiv2020

An integrated model system to gain mechanistic insights into biofilm formation and antimicrobial resistance development in Pseudomonas aeruginosa MPAO1

Pseudomonas aeruginosa MPAO1 is the parental strain of the widely utilized transposon mutant collection for this important clinical pathogen. Here, we validate a model system to identify genes involved in biofilm growth and antibiotic resistance. Our model employs a genomics-driven workflow to assemble the complete MPAO1 genome, identify unique and conserved genes by comparative genomics with the PAO1 reference strain and missed genes by proteogenomics. Among over 200 unique MPAO1 genes, we identified six general essential genes that were overlooked when mapping public Tn-seq datasets against PAO1, including an antitoxin. Genomic data were integrated with phenotypic data from an experimental workflow using a user-friendly, soft lithography-based microfluidic flow chamber for biofilm growth. Experiments conducted across three laboratories delivered reproducible data on P. aeruginosa biofilms and validated both known and novel genes involved in biofilm growth and antibiotic resistance identified in screens of the mutant collection. Differential protein expression data from planktonic cells versus biofilm confirmed upregulation of candidates known to affect biofilm formation, of structural and secreted proteins of type six secretion systems, and provided proteogenomic evidence for some missed MPAO1 genes. This integrated, broadly applicable model promises to improve the mechanistic understanding of biofilm formation, antimicrobial tolerance and resistance evolution.

systems biology↗

bioRxiv2018

Long read-based de novo assembly of low complex metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system

BackgroundComplete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly of an isolated bacterial strain is in most cases straightforward, more informative data about co-existing bacteria as well as synergistic and antagonistic effects can be obtained from a direct analysis of microbial communities. However, the complexity of metagenomic samples represents a major challenge. While third generation sequencing technologies have been suggested to enable finished metagenome-assembled-genomes, to our knowledge, the complete genome assembly of all dominant strains in a microbiome sample has not been shown so far. Natural whey starter cultures (NWCs) are used in the production of cheese and represent low complex microbiomes. Previous studies of Swiss Gruyere and selected Italian hard cheeses, mostly based on amplicon-based metagenomics, concurred that three species generally pre-dominate: Streptococcus thermophilus, Lactobacillus helveticus and Lactobacillus delbrueckii.\n\nResultsTwo NWCs from Swiss Gruyere producers were subjected to whole metagenome shotgun sequencing using Pacific Biosciences Sequel, Oxford Nanopore Technologies MinION and Illumina MiSeq platforms. We achieved the complete assembly of all dominant bacterial genomes from these low complex NWCs, which was corroborated by a 16S rRNA based amplicon survey. Moreover, two distinct L. helveticus strains were successfully co-assembled from the same sample. Besides bacterial genomes, we could also assemble several bacterial plasmids as well as phages and a corresponding prophage. Biologically relevant insights could be uncovered by linking the plasmids and phages to their respective host genomes using DNA methylation motifs on the plasmids and by matching prokaryotic CRISPR spacers with the corresponding protospacers on the phages. These results could only be achieved by employing third generation, long-read sequencing data able to span intragenomic as well as intergenomic repeats.\n\nConclusionsHere, we demonstrate the feasibility of complete de novo genome assembly of all dominant strains from low complex NWCs based on whole metagenomics shotgun sequencing data. This allowed to gain novel biological insights and is a fundamental basis for subsequent systems-wide omic analyses, functional profiling and phenotype to genotype analysis of specific microbial communities.

genomics↗

bioRxiv2018

SPECIES-SPECIFIC ROOT MICROBIOTA DYNAMICS IN RESPONSE TO PLANT-AVAILABLE PHOSPHORUS

O_LIPhosphorus (P) is a limiting element for plant growth. Several root microbes, including arbuscular mycorrhizal fungi (AMF), have the capacity to improve plant nutrition and their abundance is known to depend on P fertility. However, how complex root-associated bacterial and fungal communities respond to changes in P availability remains ill-defined.\nC_LIO_LIWe manipulated the availability of soil P in pots and compared the root microbiota of non-mycorrhizal Arabidopsis with mycorrhizal Petunia plants. Root bacteria and fungi were profiled using ribosomal operon gene fragment sequencing, we searched for P sensitive microbes and tested whether a P sensitive core microbiome could be identified.\nC_LIO_LIRoot microbiota composition varied substantially by P availability. A P sensitive core microbiome was not identified as different bacterial and fungal groups responded to low-P conditions in Arabidopsis and Petunia. P sensitive microbes included Mortierellomycotina in Arabidopsis, while these were AMF and their symbiotic endobacteria in Petunia. Of note, their P-dependent root colonization was reliably quantified by sequencing.\nC_LIO_LIThe species-specific root microbiota dynamics suggest that Arabidopsis and Petunia evolved different microbial associations under the selection pressure of low P availability. This implies that the development of microbial products that improve P availability requires the consideration of host-species specificity.\nC_LI

plant biology↗