Biology subjects

Stopnisek, N.

Publications and source records attributed to Stopnisek, N..

10 recordsLinked to original sources

bioRxiv2026

Distinct types of gut dysbiosis and oral-gut microbial signatures differentiate C. difficile, Campylobacter, and Salmonella infections: a cross-sectional study

Gastrointestinal bacterial infections are associated with substantial perturbations of the gut microbiota, yet most microbiome studies have examined individual pathogens in isolation, limiting identification of shared and pathogen-specific microbial signatures across enteric infections. We performed a comparative analysis of fecal microbiota profiles from 586 stool samples using 16S rRNA gene sequencing, encompassing infections caused by Clostridioides difficile, Campylobacter spp., and Salmonella spp., alongside viral gastroenteritis, diagnostic-negative samples, and healthy controls. Fecal calprotectin concentrations were measured in a subset of samples to assess intestinal inflammation. Comparative analyses revealed two major dysbiotic configurations among bacterial enteric infections. C. difficile infection was characterized by an Enterococcus-dominated community structure, whereas Campylobacter and Salmonella infections were associated with enrichment of a tightly correlated consortium of oral-associated taxa, including Streptococcus, Granulicatella, and Haemophilus. These taxa were among the most informative features in an XGBoost machine-learning classifier, which accurately discriminated bacterial infection types from one another and from viral infections and healthy-associated microbiota profiles (macro F1 score = 0.74). In contrast, expansion of Enterobacteriaceae represented a shared, non-specific signature of intestinal disturbance and was associated with elevated fecal calprotectin concentrations. Together, these findings demonstrate that bacterial enteric infections are associated with distinct microbiota configurations that distinguish pathogen-specific signatures from general infection-related dysbiosis. The enrichment of oral-associated taxa in Campylobacter and Salmonella infections suggests a potential role for the oral-gut microbial axis in bacterial gastroenteritis and provides a foundation for future mechanistic studies and the development of microbiota-informed diagnostic, preventive, and therapeutic strategies. Author SummaryBacterial infections of the intestine can cause severe diarrhea and inflammation, but their effects on the community of microbes living in the gut are not fully understood. Most previous studies have focused on a single disease-causing organism, making it difficult to determine which microbiome changes are shared across infections and which are specific to particular pathogens. In this study, we compared gut microbiota profiles from people infected with Clostridioides difficile, Campylobacter, or Salmonella, and examined these alongside samples from individuals with viral gastroenteritis, diagnostic-negative diarrhea, and healthy controls. We found that bacterial enteric infections were associated with two distinct patterns of microbiome disruption. C. difficile infection was linked to an overgrowth of Enterococcus, whereas Campylobacter and Salmonella infections were characterized by increased levels of several bacterial groups that are commonly found in the mouth. In contrast, expansion of Enterobacteriaceae was observed across different infections and appeared to reflect general intestinal disturbance rather than a specific pathogen. Our findings identify microbial signatures that distinguish different bacterial infections and suggest that bacteria originating from the oral cavity may play an important role in some forms of gastroenteritis. These results provide a foundation for future studies aimed at understanding how microbial communities influence intestinal infection and recovery.

microbiology↗

bioRxiv2024

Insights into Diversity, Host-Range, and Temporal Stability of Bacteroides and Phocaeicola Prophages

BackgroundPhages are critical components of the gut microbiome, influencing bacterial composition and function as predators, parasites, and modulators of bacterial phenotypes. Prophages, integrated forms of these phages, are prevalent in many bacterial genomes and play a role in bacterial adaptation and evolution. However, the diversity and stability of prophages within gut commensals, particularly in the genera Bacteroides and Phocaeicola, remain underexplored. This study aims to screen and characterize prophages in these genera, providing insights into their diversity, host range, and temporal dynamics in the human gut. ResultsUsing a combination of three bioinformatic tools--Cenote-Taker 3, Vibrant, and PHASTER--we conducted a comprehensive analysis of prophages in Bacteroides and Phocaeicola. Cenote-Taker 3 identified the most diverse set of prophages, with significant overlaps observed between the tools. After clustering high-quality prophages, we identified 22 unique viral operational taxonomic units (vOTUs). Notably, comparisons between prophages identified in isolated bacterial genomes, metaviromes, and large public gut virome databases revealed a broader host range than initially observed in single isolates. Certain prophages were consistent across time points and individuals, suggesting temporal stability. All identified prophages belonged to the Caudoviricetes class and contained genes related to antibiotic resistance, toxin production, and metabolic processes. ConclusionsThe combined use of multiple prophage detection tools allowed for a more comprehensive assessment of prophage diversity in Bacteroides and Phocaeicola. The identified prophages were not only prevalent but also exhibited broad host ranges and temporal stability. The presence of antibiotic resistance and toxin genes suggests that these prophages may significantly influence bacterial community structure and function in the gut, with potential implications for human health. These findings highlight the importance of using diverse detection tools to accurately assess prophage diversity and dynamics.

microbiology↗

bioRxiv2023

Gut metabolite L-lactate supports Campylobacter jejuni population expansion during acute infection

How the microaerobic pathogen Campylobacter jejuni establishes its niche and expands in the gut lumen during infection is poorly understood. Using six-week-old ferrets as a natural disease model, we examined this aspect of C. jejuni pathogenicity. Unlike mice, which require significant genetic or physiological manipulation to become colonized with C. jejuni, ferrets are readily infected without the need to disarm the immune system or alter the gut microbiota. Disease after C. jejuni infection in ferrets reflects closely how human C. jejuni infection proceeds. Rapid growth of C. jejuni and associated intestinal inflammation was observed within two-three days of infection. We observed pathophysiological changes that were noted by cryptic hyperplasia through the induction of tissue repair systems, accumulation of undifferentiated amplifying cells on the colon surface, and instability of HIF-1 in colonocytes, which indicated increased epithelial oxygenation. Metabolomic analysis demonstrated that lactate levels in colon content were elevated in infected animals. A C. jejuni mutant lacking lctP, which encodes an L-lactate transporter, was significantly decreased for colonization during infection. Lactate also influences adhesion and invasion by C. jejuni to a colon carcinoma cell line (HCT116). The oxygenation required for expression of lactate transporter (lctP) led to discovery of a putative thiol based redox switch regulator (LctR) that may repress lctP transcription under anaerobic conditions. Our work provides new insights into the pathogenicity of C. jejuni. SignificanceThere is a gap in knowledge about the mechanisms by which C. jejuni populations expand during infection. Using an animal model which accurately reflects human infection without the need to alter the host microbiome or the immune system prior to infection, we explored pathophysiological alterations of the gut after C. jejuni infection. Our study identified the gut metabolite L-lactate as playing an important role as a growth substrate for C. jejuni during acute infection. We identified a DNA binding protein, LctR, that binds to the lctP promoter and may repress lctP expression, resulting in decreased lactate transport under low oxygen levels. This work provides new insights about C. jejuni pathogenicity.

microbiology↗

bioRxiv2021

Disentangling the genetic basis of rhizosphere microbiome assembly in tomato

Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, 16S amplicon and metagenomic features of the rhizosphere microbiome were mapped as quantitative traits of a recombinant inbred line population of a cross between wild and domesticated tomato. Gene content analysis of prioritized tomato QTLs suggested a genetic basis for differential recruitment of various rhizobacterial lineages, including a Streptomyces-associated 6.31-Mbp region harboring tomato domestication sweeps and encoding, among others, the iron regulator FIT and the aquaporin SlTIP2.3. Within metagenome-assembled genomes of the rhizobacterial lineages Streptomyces and Cellvibrio, we identified microbial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associated with either modern or wild tomato QTLs. Integrating microbiomics and quantitative plant genetics pinpointed putative plant and reciprocal microbial traits underlying microbiome assembly, thereby providing the first step towards plant-microbiome breeding programs.

microbiology↗

bioRxiv2021

Endophytic microbiome variation at the level of a single plant seed

Like other plant compartments, the seed harbors a microbiome. The members of the seed microbiome are the first to colonize a germinating seedling, and they initiate the trajectory of microbiome assembly for the next plant generation. Therefore, the members of the seed microbiome are important for the dynamics of plant microbiome assembly and the vertical transmission of potentially beneficial symbionts. However, it remains challenging to assess the microbiome at the individual seed level (and, therefore, for the future individual plant) due to low endophytic microbial biomass, seed exudates that can select for particular members, and high plant and plastid contamination of resulting reads. Here, we report a protocol for extracting metagenomic DNA from an individual seed (common bean, Phaseolus vulgaris L.) with minimal disruption of host tissue, which we expect to be generalizable to other medium-and large-seed plant species. We applied this protocol to quantify the 16S rRNA V4 and ITS2 amplicon composition and variability for individual seeds harvested from replicate common bean plants grown under standard, controlled conditions to maintain health. Using metagenomic DNA extractions from individual seeds, we compared seed-to-seed, pod-to-pod, and plant-to-plant microbiomes, and found highest microbiome variability at the plant level. This suggests that several seeds from the same plant could be pooled for microbiome assessment, given experimental designs that apply treatments at the maternal plant level. This study adds protocols and insights to the growing toolkit of approaches to understand the plant-microbiome engagements that support the health of agricultural and environmental ecosystems.

microbiology↗

bioRxiv2021

Genome-centric analyses of seasonal phyllosphere microbiome activities in perennial crops

Plants and microorganisms form beneficial associations. Understanding plant-microbe interactions will inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify key leaf microbiome members on field-grown switchgrass and miscanthus, and quantify their activities for switchgrass over two growing seasons. We integrate metagenome and metatranscriptome sequencing from 192 leaf samples collected over key time points in crop phenology. We curated 40 focal metagenome-assembled-genomes (MAGs) and conservatively focus analysis on transcript recruitment to medium and high-quality MAGs that were <10% contaminated and >50% complete. Classes represented by these MAGs (Actinomycetia, Alpha- and Gamma-Proteobacteria, and Bacteroidota) were active and had seasonal dynamics in key functions, including enrichments in transcripts for of short chain dehydrogenase, molybdopterin oxioreductase, and polyketide cyclase in the late season. The majority of MAGs had activated stress-associated pathways, including trehalose metabolism, indole acetic acid degradation, betaine biosynthesis, and reactive oxygen species degradation, suggesting direct engagement with the host environment. We also detected seasonally activated biosynthetic pathways for terpenes (carotenoid and isoprenoids), and for various non-ribosomal peptide pathways that were poorly annotated. Overall, this study overcame laboratory and bioinformatic challenges associated with field-based leaf metatranscriptome analysis to inform potential key activities of these phyllosphere populations. These activities collectively support that leaf-associated bacterial populations are seasonally dynamic, responsive to host cues and interactively engage in feedbacks with the plant.

microbiology↗

bioRxiv2020

Synergistic epistasis enhances cooperativity of mutualistic interspecies interactions

Frequent fluctuations in sulfate availability rendered syntrophic interactions between the sulfate reducing bacterium Desulfovibrio vulgaris (Dv) and the methanogenic archaeon Methanococcus maripaludis (Mm) unsustainable. By contrast, prolonged laboratory evolution in obligate syntrophy conditions improved the productivity of this community but at the expense of erosion of sulfate respiration (SR). Hence, we sought to understand the evolutionary trajectories that could both increase the productivity of syntrophic interactions and sustain SR. We combined a temporal and combinatorial survey of mutations accumulated over 1000 generations of 9 independently-evolved communities with analysis of the genotypic structure for one community down to the single-cell level. We discovered a high level of parallelism across communities despite considerable variance in their evolutionary trajectories and the perseverance of a rare SR+ Dv lineage within many evolution lines. An in-depth investigation revealed that synergistic epistasis across Dv and Mm genotypes had enhanced cooperativity within SR- and SR+ assemblages, allowing their co-existence as r- and K-strategists, respectively.

evolutionary biology↗

bioRxiv2020

Discovery of a spatially and temporally persistent core microbiome of the common bean rhizosphere

Plants recruit soil microbes that provide nutrients, promote growth and protect against pathogens1-3. However, the full potential of microbial communities for supporting plant health and agriculture is unrealized4-6, in part because rhizosphere members key for plant health are difficult to prioritize7. Microbes that ubiquitously associate with a plant species across large spatial scales and varied soil conditions provide a practical starting point for discovering beneficial members7. Here, we quantified the structures of bacterial/archaeal and fungal communities in the common bean rhizosphere (Phaseolus vulgaris), and assessed its core membership across space and time. To assess a spatial core, two divergent bean genotypes were grown in field conditions across five major growing regions in the United States, and then also compared to eight genotypes grown in Colombian soil. To assess a temporal core, we conducted a time course of rhizosphere and rhizoplane microbiome members over bean development in the field. Surprisingly, there were 48 persistent bacterial taxa that were detected in all samples, inclusive of U.S. and Colombian-grown beans and over plant development, suggesting cosmopolitan enrichment and time-independence. Neutral models of abundance-occupancy relationships and co-occurrence networks show that many of these core taxa are deterministically selected and likely in intimate relationships with the plant. Many of the core taxa were yet-uncultured and affiliated with Proteobacteria; these taxa are prime targets in support of translational plant-microbiome management. More generally, this work reveals that core members of the plant microbiome can have both broad ranges and temporal persistence with their host, suggesting intimate, albeit possibly opportunistic, interactions.

microbiology↗

bioRxiv2019

Cross-continental biogeography of the common bean rhizosphere microbiome reveals a persistent core membership

The full potential of managing microbial communities to support plant health is yet-unrealized, in part because it remains difficult to ascertain which members are most important for the plant. However, microbes that consistently associate with a plant species across varied field conditions and over plant development likely engage with the host or host environment. Here, we applied abundance-occupancy concepts from macroecology to quantify the core membership of bacterial/archaeal and fungal communities in the rhizosphere of the common bean (Phaseolus vulgaris). Our study investigated the microbiome membership that persisted over multiple dimensions important for plant agriculture, including major growing regions, plant development, annual plantings, and divergent genotypes, and also included re-analysis of public data. We found 48 core bacterial taxa that were consistently detected in all samples, inclusive of all datasets and dimensions. This suggests reliable enrichment of these taxa to the plant environment and time-independence of their association with the plant. More generally, this work provides a robust approach for systematically prioritizing core microbiome memberships in any host or system.

microbiology↗

bioRxiv2018

Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops

Perennial grasses are promising feedstocks for biofuel production. The phyllosphere (aerial surfaces) of these cellulosic crops provide a sizable surface area of microbial habitation. Leaf microbial communities may benefit the host plant, have consequence for biomass deconstruction, and interact with foliar pathogens. Here, we characterized the origins, diversity, and assembly of bacterial and archaeal communities of two perennial cellulosic feedstocks: switchgrass (Panicum virgatum L.) and miscanthus (Miscanthus x giganteus). We used 16S rRNA gene sequencing to assess microbiome structure on leaves and soils, following crop phenology every three weeks from pre-emergence through senescence for one miscanthus growing season and two consecutive switchgrass seasons. We found abundant and persistent core leaf taxa that originated in soil but were adapted for life on the leaf, rather than vagabonds that randomly disperse from air or soil. Seasonal and host-specific assembly suggested a functional relationship between the phyllosphere microbiomes and plants. This foundational knowledge advances goals to leverage native microbiomes to promote crop wellness and productivity in the field, and specifically in support of biofuels agriculture.

microbiology↗