Biology subjects

Fofanov, V.

Publications and source records attributed to Fofanov, V..

7 recordsLinked to original sources

bioRxiv2026

MetaTracer: A nucleotide alignment-based framework for high-resolution taxonomic and transcript assignment in metatranscriptomic data

SummaryMetaTracer is a nucleotide alignment-based tool for metatranscriptomic analysis of complex bacterial communities that assigns sequence reads to both taxonomic groups and expressed genes in a single pass. Full nucleotide-level alignment improves accuracy relative to k-mer-based classifiers and preserves species-level resolution that is often lost in protein-based approaches. By retaining alignment coordinates and mapping reads directly to annotated genomic features, MetaTracer enables direct attribution of gene expression to specific microbial species. On simulated datasets, MetaTracer achieves high accuracy for both taxonomic and gene assignment. Applied to real dental plaque metatranscriptomic datasets, MetaTracer resolves species-specific transcriptional activity and detects reproducible differences in microbial gene expression between children with early childhood caries and healthy controls. Availability and implementationMetaTracer is implemented as a Python-based workflow wrapper (metatracer v0.1.0) that depends on the mtsv-tools core engine (v2.1.0), which is written in Rust. The required functionality is supported by the v2.1.0 release of mtsv-tools. Both packages are open source under the MIT license and are available at github.com/FofanovLab/metatracer and github.com/FofanovLab/mtsv-tools. Versioned releases are archived at Zenodo (DOI: 10.5281/zenodo.18665766 and DOI: 10.5281/zenodo.18718002). Installation is supported via Bioconda. ContactViacheslav.Fofanov@nau.edu

bioinformatics↗

bioRxiv2025

Biological Drivers of Early Childhood Caries in Preschool Children of Northern Arizona and Hawaii

Early childhood caries (ECC) is the most prevalent chronic childhood disease, disproportionately affecting children from specific racial/ethnic groups. While ECC is a multifactorial disease influenced by demographic, behavioral, and environmental factors, it is also widely associated with the presence of Streptococcus mutans in the oral microbiome. To better understand the interplay between demographic and microbial factors and ECC risk, we collected saliva samples from 408 preschool children aged 1-6 years, including 266 from northern Arizona and 142 from Hawaii, representing racially and geographically diverse populations. Logistic regression showed that the odds of developing ECC increased 80.09% with each year of age, and that compared to White children, the odds were significantly higher for Native Hawaiian/Pacific Islander (330.94%), Native American (282.35%), and Hispanic (245.22%) children. Oral S. mutans colonization increased odds by 360.49%. The S. mutans-positive samples were genotyped using a multiplexed targeted amplicon sequencing assay. Phylogenetic analysis showed high genetic diversity in S. mutans between and within populations, with no geographic clustering. Some S. mutans clades were associated with up to a 33-fold increase in ECC odds. Only Native Hawaiian/Pacific Islander children were more likely to carry S. mutans strains from higher-risk clades. Markers associated with high risk S. mutans strains were identified in genes involved in carbohydrate metabolism, pH regulation, and biofilm formation. This study underscores the multifaceted nature of ECC, linking demographic disparities with strain-specific features of S. mutans and identifies new genetic markers that may play a role in S. mutans virulence.

microbiology↗

bioRxiv2024

Population sequencing for diversity and transmission analyses

Genomic diversity in a pathogen population is the foundation for evolution and adaptations in virulence, drug resistance, pathogenesis, and immune evasion. Characterizing, analyzing, and understanding population-level diversity is also essential for epidemiological and forensic tracking of sources and revealing detailed pathways of transmission and spread. For bacteria, culturing, isolating, and sequencing the large number of individual colonies required to adequately sample diversity can be prohibitively time-consuming and expensive. While sequencing directly from a mixed population will show variants among reads, they cannot be linked to reveal allele combinations associated with particular traits or phylogenetic inheritance patterns. Here, we describe the theory and method of how population sequencing directly from a mixed sample can be used in conjunction with sequencing a very small number of colonies to describe the phylogenetic diversity of a population without haplotype reconstruction. To demonstrate the utility of population sequencing in capturing phylogenetic diversity, we compared isogenic clones to population sequences of Burkholderia pseudomallei from the sputum of a single patient. We also analyzed population sequences of Staphylococcus aureus derived from different people and different body sites. Sequencing results confirm our ability to capture and characterize phylogenetic diversity in our samples. Our analyses of B. pseudomallei populations led to the surprising discovery that the pathogen population is highly structured in sputum, suggesting that for some pathogens, sputum sampling may preserve structuring in the lungs and thus present a non-invasive alternative to understanding colonization, movement, and pathogen/host interactions. Our analyses of S. aureus samples show how comparing phylogenetic diversity across populations can reveal directionality of transmission between hosts and across body sites, demonstrating the power and utility for characterizing the spread of disease and identification of reservoirs at the finest levels. We anticipate that population sequencing and analysis can be broadly applied to accelerate research in a broad range of fields reliant on a foundational understanding of population diversity. Author SummaryThe ability to characterize diversity in a single bacterial population (i.e., a single host or even a single body site) is critical for understanding adaptation and evolution, with far-reaching implications on disease treatment and prevention that include revealing patterns of spread and persistence. While the scientific community has made great strides in sequencing methods to characterize single colonies and entire communities, there is a dearth of studies at the population level. This is because 1) the need to culture and sequence a sufficiently representative number of isogenic colonies is prohibitive, and 2) the theoretical foundation for characterizing a population by sequencing a single sample (as is done for microbiome and metagenomic analyses) has not been developed. Here, we introduce this theoretical foundation and validate its applicability by characterizing a lung infection caused by Burkholderia pseudomallei. We also demonstrate the utility of this method in determining the directionality of spread of Staphylococcus aureus between people and across body sites within the same host (a level of spatial resolution that has not been previously performed). We anticipate that this work will open the door to a host of new studies and discoveries across a diverse set of microbiological fields.

evolutionary biology↗

bioRxiv2021

Rapid response of nitrogen cycling gene transcription to labile carbon amendments in a soil microbial community

Episodic inputs of labile carbon (C) to soil can rapidly stimulate nitrogen (N) immobilization by soil microorganisms. However, the transcriptional patterns that underlie this process remain unclear. In order to better understand the regulation of N cycling in soil microbial communities, we conducted a 48 h laboratory incubation with an agricultural soil where we stimulated the uptake of inorganic N by amending the soil with glucose. We analyzed the metagenome and metatranscriptome of the microbial communities at four timepoints that corresponded with changes in N availability. The relative abundances of genes remained largely unchanged throughout the incubation. In contrast, glucose addition rapidly increased transcription of genes encoding for ammonium and nitrate transporters, enzymes responsible for N assimilation into biomass, and genes associated with the N regulatory network. This upregulation coincided with an increase in transcripts associated with glucose breakdown and oxoglutarate production, demonstrating a connection between C and N metabolism. When concentrations of ammonium were low, we observed a transient upregulation of genes associated with the nitrogen fixing enzyme nitrogenase. Transcripts for nitrification and denitrification were downregulated throughout the incubation, suggesting that dissimilatory transformations of N may be suppressed in response to labile C inputs in these soils. These results demonstrate that soil microbial communities can respond rapidly to changes in C availability by drastically altering the transcription of N cycling genes. IMPORTANCEA large portion of activity in soil microbial communities occurs in short time frames in response to an increase in C availability, affecting the biogeochemical cycling of nitrogen. These changes are of particular importance as nitrogen represents both a limiting nutrient for terrestrial plants as well as a potential pollutant. However, we lack a full understanding of the short-term effects of labile carbon inputs on the metabolism of microbes living in soil. Here, we found that soil microbial communities responded to labile carbon addition by rapidly transcribing genes encoding proteins and enzymes responsible for inorganic nitrogen acquisition, including nitrogen fixation. This work demonstrates that soil microbial communities respond within hours to carbon inputs through altered gene expression. These insights are essential for improved understanding of the microbial processes governing soil organic matter production, decomposition, and nutrient cycling in natural and agricultural ecosystems.

microbiology↗

bioRxiv2020

Sample pooling methods for efficient pathogen screening: Practical implications

Due to the large number of negative tests, individually screening large populations for rare pathogens can be wasteful and expensive. Sample pooling methods improve the efficiency of large-scale pathogen screening campaigns by reducing the number of tests and reagents required to accurately categorize positive and negative individuals. Such methods rely on group testing theory which mainly focuses on minimizing the total number of tests; however, many other practical concerns and tradeoffs must be considered when choosing an appropriate method for a given set of circumstances. Here we use computational simulations to determine how several theoretical approaches compare in terms of (a) the number of tests, to minimize costs and save reagents, (b) the number of sequential steps, to reduce the time it takes to complete the assay, (c) the number of samples per pool, to avoid the limits of detection, (d) simplicity, to reduce the risk of human error, and (e) robustness, to poor estimates of the number of positive samples. We found that established methods often perform very well in one area but very poorly in others. Therefore, we introduce and validate a new method which performs fairly well across each of the above criteria making it a good general use approach.

molecular biology↗

bioRxiv2020

Phylogenetic Analysis of St. Louis Encephalitis Virus within Two Southwestern United State Counties: a case for a bulk introduction event into the southwest United States

St. Louis Encephalitis Virus (SLEV) has been seasonally detected within the Culex spp. populations within Maricopa County, Arizona and Coachella Valley, California since an outbreak in Maricopa County in 2015. Previous work revealed that the outbreak was caused by an importation of SLEV genotype III, which had only been detected within Argentina in prior years. However, little is known about when the importation occurred or the population dynamics since its arrival into the southwestern United States. In this study, we wanted to determine if the annual detection of SLEV in Maricopa and Riverside counties is due to enzootic cycling or new importations. To address this question, we analyzed 143 SLEV genomes (138 sequenced as part of this study) using the Bayesian phylogenetic analysis software, BEAST, to estimate the date of arrival into the American Southwest and characterize the underlying population structure of SLEV. Phylogenetic clustering showed that SLEV variants circulating in Arizona and California form two distinct populations with little evidence of transmission among the two populations since the onset of the outbreak. Interestingly, the SLEV variants in Coachella Valley appear to be annually imported from a nearby source, whereas the Arizona population is locally sourced each year. Finally, the earliest representatives of SLEV genotype III in the southwestern US formed a polytomy that includes both California and Arizona samples. We propose that the initial outbreak could have resulted from an introductory population of SLEV, perhaps in one or more bird flocks migrating north in 2013, rather than a single variant introduced by one bird.

bioinformatics↗

bioRxiv2020

Megafauna decline have reduced pathogen dispersal which may have increased emergent infectious diseases

The Late Quaternary extinctions of megafauna (defined as animal species >44.5 kg) reduced the dispersal of seeds and nutrients, and likely also microbes and parasites. Here we use body-mass based scaling and range maps for extinct and extant mammal species to show that these extinctions led to an almost seven-fold reduction in the movement of gut-transported microbes, such as Escherichia coli (3.3 km2/day to 0.5 km2/day). Similarly, the extinctions led to a seven-fold reduction in the mean home ranges of vector-borne pathogens (7.8 km2 to 1.1 km2). To understand the impact of this, we created an individual-based model where an order of magnitude decrease in home range increased maximum aggregated microbial mutations 4-fold after 20,000 years. We hypothesize that pathogen speciation and hence endemism increased with isolation, as global dispersal distances decreased through a mechanism similar to the theory of island biogeography. To investigate if such an effect could be found, we analysed where 145 zoonotic diseases have emerged in human populations and found quantitative estimates of reduced dispersal of ectoparasites and fecal pathogens significantly improved our ability to predict the locations of outbreaks (increasing variance explained by 8%). There are limitations to this analysis which we discuss in detail, but if further studies support these results, they broadly suggest that reduced pathogen dispersal following megafauna extinctions may have increased the emergence of zoonotic pathogens moving into human populations.

ecology↗