Biology subjects

Shamash, M.

Publications and source records attributed to Shamash, M..

8 recordsLinked to original sources

bioRxiv2026

The Microbiota Dictates Vendor-Derived Differences in a Murine Clostridioides difficile Infection Model

Clostridioides difficile infection (CDI) is the leading cause of healthcare-associated infectious diarrhea and remains a major burden to healthcare systems worldwide. The development of novel therapeutics for CDI requires robust and reproducible preclinical models. However, the microbiota has emerged as a major source of variability in animal studies. Here, we found that genetically similar mice obtained from two commercial vendors, Jackson Laboratory (JAX) and Charles River Laboratories (CRL), exhibited marked differences in susceptibility to CDI, with JAX mice developing fulminant disease and CRL mice remaining resistant. Using full-length 16S rRNA gene sequencing, we show that JAX and CRL mice harboured distinct gut microbiota, and that cohousing susceptible JAX mice with resistant CRL mice was sufficient to shift the JAX microbiota toward the CRL community structure and confer resistance to CDI. Differential abundance analysis identified taxa distinguishing resistant and susceptible mice, providing candidates for future mechanistic investigation. These findings demonstrate that vendor-derived variation in the gut microbiota drives differential susceptibility to CDI in mice, and that this phenotype is transferable via cohousing, highlighting the importance of accounting for the microbiota when designing and interpreting animal models of infectious disease.

microbiology↗

bioRxiv2026

A human microbiota-associated mouse model of early-life malnutrition reveals persistent microbiome immaturity and limited response to fecal viral transplantation

Malnutrition is a leading cause of child mortality worldwide and has long-lasting health and socio-economic consequences. Studies have established causal links between the gut microbiota and childhood malnutrition, with key microbial signatures including delayed microbiome development and an enrichment of bacterial pathogens. While current dietary interventions improve growth and developmental outcomes, post-therapy regression to an immature microbial state is common. Fecal virome transplants (FVTs) represent a promising approach to reshape gut microbial communities, yet their therapeutic potential in early life remains poorly described. In this work, we established a diet-inducible human microbiota-associated (HMA) mouse model of early-life stunting, where malnourished pups were 35% lighter and 25% shorter than healthy controls. We developed a predictive model to quantify gut bacteriome development, identifying Enterococcus and Clostridium as primary drivers of healthy maturation. Our model revealed that the malnourished HMA mouse gut remains significantly immature compared to healthy controls and decoupled from the mouse's chronological age. While a successful FVT from a healthy donor induced targeted changes in specific bacterial taxa, including a significant increase in Enterococcus species, it did not rescue physical growth or lead to broad community-level shifts. In contrast, a failed FVT from a different healthy donor revealed a significant mismatch between the donor virome and recipient bacteriome, indicating niche incompatibility that limits FVT efficacy. Our work establishes a robust human microbiota-associated mouse model for studying maturation of the gut in early life, suggesting that FVT alone is insufficient to reproducibly reshape the malnourished gut. These findings highlight the need for synergistic strategies, combining viral interventions with nutritional supplementation for maximum therapeutic effect.

microbiology↗

bioRxiv2026

The infant gut virome assembles rapidly and predictably over the first three years of life

Assembly of the gut microbiota in infancy is an important health determinant, yet the viral component, the virome, remains poorly described. Here, we conduct a meta-analysis of 12 infant cohorts across 8 countries to model gut virome development over the first three years of life. Our results revealed distinct diversity patterns, where viral richness increased significantly over the first eight months of life alongside a loss of community evenness. We define virome developmental velocity, the rate of change between sequential samples, which significantly decreased over time. This was mirrored by community-wide convergence, as infant viromes became more similar with age. Functionally, the transition to a stable state involved a significant decrease in extracellular temperate phages and shifts in phage-encoded auxiliary metabolic genes, which can modulate host metabolism. Our work provides a baseline characterization of gut virome development, marked by a conserved successional trajectory, providing a framework to identify disease-associated perturbations.

bioinformatics↗

bioRxiv2024

Improving gut virome comparisons using predicted phage host information

The human gut virome is predominantly made up of bacteriophages (phages), viruses that infect bacteria. Metagenomic studies have revealed that phages in the gut are highly individual specific and dynamic. These features make it challenging to perform meaningful cross-study comparisons. While several taxonomy frameworks exist to group phages and improve these comparisons, these strategies provide little insight into the potential effects phages have on their bacterial hosts. Here, we propose the use of predicted phage host families (PHFs) as a functionally relevant, higher rank unit of phage taxonomy to improve these cross-study analyses. We first show that bioinformatic predictions of phage hosts are accurate at the host family level by measuring their concordance to Hi-C sequencing-based predictions in human and mouse fecal samples. Next, using phage host family predictions, we determined that PHFs reduce intra- and interindividual ecological distances compared to viral contigs in a previously published cohort of 10 healthy individuals, while simultaneously improving longitudinal virome stability. Lastly, by reanalyzing a previously published metagenomics dataset with > 1,000 samples, we determined that PHFs are prevalent across individuals and can aid in the detection of inflammatory bowel disease-specific virome signatures. Overall, our analyses support the use of predicted phage hosts in reducing between-sample distances and providing a biologically relevant framework for making between-sample virome comparisons.

bioinformatics↗

bioRxiv2024

Optimization of an improved, time-saving, and scalable, protocol for the extraction of DNA from diverse viromes

IntroductionThe virome, composed of viruses inhabiting diverse ecosystems, significantly influences microbial community dynamics and host health. The phenol-chloroform DNA extraction protocol for viromes, though effective, is time-intensive and requires the use of multiple toxic chemicals. MethodsThis study introduces a streamlined, scalable protocol for DNA extraction using a commercially-available kit as an alternative, assessing its performance against the phenol-chloroform method across human fecal, mouse fecal, and soil samples. ResultsNo significant differences in virome diversity or community composition were seen between methods. Most viral operational taxonomic units (vOTUs) were common to both methods, with only a small percentage unique to either approach. Alpha- and beta-diversity analyses showed no significant impact of the extraction method on virome composition, confirming the kits efficacy and versatility. ConclusionsWhile the kit approach offers benefits like reduced toxicity and increased throughput, it has limitations such as higher costs and potential issues reliably capturing low-abundance taxa. This protocol provides a viable option for large-scale virome studies, although the phenol-chloroform approach may still be preferable for specific sample types.

microbiology↗

bioRxiv2024

Prevalent human gut Enterocloster spp. produce urolithin A from its dietary precursor using a molybdenum-dependent dehydroxylase

Urolithin A (uroA) is a polyphenol derived from the multi-step metabolism of dietary ellagitannins by the human gut microbiota that can affect host health by stimulating mitophagy. Most individuals harbor a microbiota capable of uroA production; however, the mechanisms underlying the dehydroxylation of its catechol-containing dietary precursor (uroC) are unknown. Here, we use a combination of untargeted bacterial transcriptomics, proteomics, and comparative genomics to uncover an inducible uroC dehydroxylase (ucd) operon in Enterocloster spp. We show that Enterocloster spp. are sensitive to iron chelation by uroC, and dehydroxylation to uroA rescues growth by disrupting the iron-binding catechol. Importantly, only microbiota samples actively transcribing ucd could produce uroA, establishing ucd-containing Enterocloster spp. as keystone urolithin metabolizers. Overall, this work identifies Enterocloster spp. and the ucd operon as main contributors to uroA production and establishes a multi-omics framework to further our mechanistic understanding of polyphenol metabolism by the human gut microbiota.

microbiology↗

bioRxiv2021

OnePetri: accelerating common bacteriophage Petri dish assays with computer vision

IntroductionBacteriophage plaque enumeration is a critical step in a wide array of protocols. The current gold standard for plaque enumeration on Petri dishes is through manual counting. This approach is time-intensive, has low-throughput, is limited to Petri dishes which have a countable number of plaques, and can have variable results upon recount due to human error. MethodsWe present OnePetri, a collection of trained machine learning models and open-source mobile application for the rapid enumeration of bacteriophage plaques on circular Petri dishes. ResultsWhen compared against the current gold standard of manual counting, OnePetri was significantly faster, with minimal error. Compared against two other similar tools, Plaque Size Tool and CFU.AI, OnePetri had higher plaque recall and reduced detection times on most test images. ConclusionsThe OnePetri application can rapidly enumerate phage plaques on circular Petri dishes with high precision and recall.

bioinformatics↗

bioRxiv2021

Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates severity of DSS-colitis

Inflammatory bowel diseases (IBDs) including Crohns disease (CD) and ulcerative colitis (UC) are characterized by chronic and debilitating gut inflammation. Altered bacterial communities of the intestine are strongly associated with IBD initiation and progression. The gut virome, which is primarily composed of bacterial viruses (bacteriophages, phages) is thought to be an important factor regulating and shaping microbial communities in the gut. While alterations in the gut virome have been observed in IBD patients, the contribution of these viruses to alterations in the bacterial community and heightened inflammatory responses associated with IBD patients remains largely unknown. Here, we performed in vivo microbial cross-infection experiments to follow the effects of fecal virus-like particles (VLPs) isolated from UC patients and healthy controls on bacterial diversity and severity of experimental colitis in human microbiota-associated (HMA) mice. Shotgun metagenomics confirmed that several phages were transferred to HMA mice, resulting in treatment-specific alterations in the gut virome. VLPs from healthy and UC patients also shifted gut bacterial diversity of these mice, an effect that was amplified during experimental colitis. VLPs isolated from UC patients specifically altered the relative abundance of several bacterial taxa previously implicated in IBD progression. Additionally, UC VLP administration heightened colitis severity in HMA mice, as indicated by shortened colon length and increased pro-inflammatory cytokine production. Importantly, this effect was dependent on intact VLPs. Our findings build on recent literature indicating that phages are dynamic regulators of bacterial communities in the gut and implicate the intestinal virome in modulating intestinal inflammation and disease.

microbiology↗