Biology subjects

Ansorge, R.

Publications and source records attributed to Ansorge, R..

8 recordsLinked to original sources

bioRxiv2026

The effects of bacteriophage cocktail treatment on healthy gut microbiota: an in vitro human colon model study

The human gut microbiome is a complex community that plays an important role in health, where perturbations can result in dysbiosis and disease. Bacteriophages (phages) can provide treatment for bacterial gastrointestinal disease, and commercial preparations such as the Intesti bacteriophage cocktail can be taken orally to target bacterial pathogens. However, interactions between these phages and the native gut microbiota are understudied. To investigate the impact of phage treatment, we used simulated gut models seeded with healthy donor microbiota from three individuals, sequenced the DNA, and analysed the bacterial and viral portion from samples obtained over time. Each donor had a unique bacterial composition which diverged with time. When comparing phage treated to control samples, we observed that Escherichia coli abundance accounted for the largest portion of bacterial community variance and was more associated with the controls. The lower abundance in phage treated samples may have resulted from the lytic action of phages from the cocktail. Additionally, our analyses of the viral portion revealed a phage bloom exclusive to phage treated samples. A highly abundant phage in this bloom was matched with the Intesti bacteriophage cocktail, showed similarity to Enterobacteria phage phi92, and provided evidence of productive infection within the model. While we did observe fluctuations in relative abundance of additional viral sequences in the presence of the phage cocktail, these changes were often transient. Furthermore, we detected only slight differences to typical members of the virome, and low numbers of active prophages. Our experiments suggest that the phage cocktail had minimal interruption to the native gut microbiota within the model. Impact statementBacteriophages are increasingly investigated and tested for their efficacy in treating infections and are a key component in fight against antimicrobial resistant bacterial infections. Because of their specificity, it has become almost a dogma to state that they do not alter the gut microbiome. We have now tested this in an in vitro study using a commercially available cocktail and real human faecal microbiota. We show minimal effects on the composition of the healthy microbiota with an individual-specific effect on Escherichia coli caused by productive infection of one phage in the cocktail.

microbiology↗

bioRxiv2023

Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease

There is strong interest in exploring the potential of the gut microbiome for Parkinsons disease (PD) diagnosis and treatment. However, a consensus on the microbiome features associated with PD and a multi-study assessment of their diagnostic value is lacking. Here, we present a machine learning meta-analysis of PD microbiome studies of unprecedented scale (including 4,490 samples). Within most studies, microbiome-based machine learning models could accurately classify PD patients. However, models were study-specific and did not generalise well across other studies. By training models on multiple datasets, we could improve their general applicability and disease specificity as assessed against microbiomes from other neurodegenerative diseases. Meta-analysis of shotgun metagenomes moreover delineated PD-associated microbial pathways potentially contributing to the deterioration of gut health and favouring the translocation of pathogenic molecules along the gut-brain axis. Strikingly, diverse microbial pathways for the biotransformation of solvents and pesticides were enriched in PD. These results align with the epidemiological evidence that exposure to these molecules increases PD risk and raise the question of whether gut microbial metabolism modulates their toxicity. Taken together, we offer the most comprehensive overview to date about the PD gut microbiome and provide future reference for its diagnostic and functional potential.

microbiology↗

bioRxiv2021

Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium

In obligate symbioses, partner fidelity plays a central role in maintaining the association over evolutionary time. Fidelity has been well studied in hosts with only a few symbionts, but little is known about how fidelity is maintained in obligate associations with multiple co-occurring symbionts. Here, we show that partner fidelity varies from strict to absent in a gutless marine annelid and its consortium of co-occurring symbionts that provide it with nutrition. We sequenced the metagenomes of 80 Olavius algarvensis individuals from the Mediterranean, and compared host mitochondrial and symbiont phylogenies based on single nucleotide polymorphisms across genomes, using a low-coverage sequencing approach that has not yet been applied to microbial community analyses. Fidelity was strongest for the two chemoautotrophic, sulphur-oxidizing symbionts that dominated the microbial consortium in all host individuals. In contrast, fidelity was only intermediate to absent in the sulphate-reducing and spirochaetal symbionts, which occurred in lower abundance and were not always present in all host individuals. We propose that variable degrees of fidelity are advantageous for these hosts by allowing the faithful transmission of their nutritionally most important symbionts and flexibility in the acquisition of other symbionts that promote ecological plasticity in the acquisition of environmental resources.

microbiology↗

bioRxiv2020

The hidden pangenome: comparative genomics reveals pervasive diversity in symbiotic and free-living sulfur-oxidizing bacteria

Sulfur-oxidizing Thioglobaceae, often referred to as SUP05 and Arctic96BD clades, are widespread and common to hydrothermal vents and oxygen minimum zones. They impact global biogeochemical cycles and exhibit a variety of host-associated and free-living lifestyles. The evolutionary driving forces that led to the versatility, adoption of multiple lifestyles and global success of this family are largely unknown. Here, we perform an in-depth comparative genomic analysis using all available and newly generated Thioglobaceae genomes. Gene content variation was common, throughout taxonomic ranks and lifestyles. We uncovered a pool of variable genes within most Thioglobaceae populations in single environmental samples and we referred to this as the hidden pangenome. The hidden pangenome is often overlooked in comparative genomic studies and our results indicate a much higher intra-specific diversity within environmental bacterial populations than previously thought. Our results show that core-community functions are different from species core genomes suggesting that core functions across populations are divided among the intra-specific members within a population. Defense mechanisms against foreign DNA and phages were enriched in symbiotic lineages, indicating an increased exchange of genetic material in symbioses. Our study suggests that genomic plasticity and frequent exchange of genetic material drives the global success of this family by increasing its evolvability in a heterogeneous environment.

microbiology↗

bioRxiv2020

Deep-sea mussels from a hybrid zone on the Mid-Atlantic Ridge host genetically indistinguishable symbionts

The composition and diversity of animal microbiomes is shaped by a variety of factors, many of them interacting, such as host traits, the environment, and biogeography. Hybrid zones, in which the ranges of two host species meet and hybrids are found, provide natural experiments for determining the drivers of microbiome communities, but have not been well studied in marine environments. Here, we analysed the composition of the symbiont community in two deep-sea, Bathymodiolus mussel species along their known distribution range at hydrothermal vents on the Mid-Atlantic Ridge, with a focus on the hybrid zone where they interbreed. In-depth metagenomic analyses of the sulphur-oxidising symbionts of 30 mussels from the hybrid zone, at a resolution of single nucleotide polymorphism analyses of [~]2500 orthologous genes, revealed that parental and hybrid mussels have genetically indistinguishable symbionts. While host genetics does not appear to affect symbiont composition in these mussels, geographic location of the mussels on the Mid-Atlantic Ridge explained 45 % of symbiont genetic variability based on redundancy analyses. We hypothesize that geographic structuring of the free-living symbiont population plays a major role in driving the composition of the microbiome in these deep-sea mussels.

microbiology↗

bioRxiv2019

Horizontal acquisition followed by expansion and diversification of toxin-related genes in deep-sea bivalve symbionts

Deep-sea bathymodioline mussels gain their nutrition from intracellular bacterial symbionts. Their sulfur-oxidizing (SOX) symbionts were recently shown to encode abundant toxin-related genes (TRGs) in their genomes, which may play a role in beneficial host-microbe interactions. Here, we compared TRGs in the genomes of SOX symbionts from 10 bathymodioline mussel and two sponge species to better understand their potential functions and evolutionary origins. Despite the close phylogenetic relatedness of these symbionts, the number and classes of encoded toxins varied greatly between host species. One of the TRG classes, YDs, has experienced gene expansions multiple times, suggesting that these genes are under adaptive selection. Some symbiont genomes contained secretion systems, which can play a role in host-microbe interactions. Both TRGs and secretion systems had a heterogeneous distribution, suggesting that these closely related bacteria have acquired different molecular mechanisms for interacting with the same family of animal hosts, possibly through convergent evolution.

microbiology↗

bioRxiv2019

Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated

Eukaryotes are habitats for bacterial organisms where the host colonization and dispersal among individual hosts have consequences for the bacterial ecology and evolution. Vertical symbiont transmission leads to geographic isolation of the microbial population and consequently to genetic isolation of microbiotas from individual hosts. In contrast, the extent of geographic and genetic isolation of horizontally transmitted microbiota is poorly characterized. Here we show that chemosynthetic symbionts of individual Bathymodiolus brooksi mussels constitute genetically isolated populations. The reconstruction of core genome-wide strain sequences from high-resolution metagenomes revealed distinct phylogenetic clades. Nucleotide diversity and strain composition vary along the mussel lifespan and individual hosts show a high degree of genetic isolation. Our results suggest that the uptake of environmental bacteria is a restricted process in B. brooksi, where self-infection of the gill tissue results in serial founder effects during symbiont evolution. We conclude that bacterial colonization dynamics over the host life-cycle is thus an important determinant of population structure and genome evolution of horizontally transmitted symbionts.

microbiology↗

bioRxiv2019

Diversity matters: Deep-sea mussels harbor multiple symbiont strains

Genetic diversity of closely-related free-living microbes is widespread and underpins ecosystem functioning, but most evolutionary theories predict that it destabilizes intimate mutualisms. Indeed, symbiont strain diversity has long assumed to be restricted in intracellular bacteria associated with animals. Here, we sequenced the metagenomes and metatranscriptomes of 18 Bathymodiolus mussel individuals from four species, covering their known distribution range at deep-sea hydrothermal vents in the Atlantic. We show that as many as 16 strains of intracellular, sulfur-oxidizing symbionts coexist in individual Bathymodiolus mussels. Co-occurring symbiont strains differed extensively in key metabolic functions, such as the use of energy and nutrient sources, electron acceptors and viral defense mechanisms. Most strain-specific genes were expressed, highlighting their adaptive potential. We show that fine-scale diversity is pervasive in Bathymodiolus symbionts, and hypothesize that it may be widespread in low-cost symbioses where the environment, not the host, feeds the symbionts.

microbiology↗