Benjamin J Ridenhour

Benjamin J Ridenhour
University of Idaho | UID · Department of Biological Sciences

PhD

About

141
Publications
6,845
Reads
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1,984
Citations
Additional affiliations
July 2010 - present
University of Notre Dame
Position
  • Professor (Assistant)
July 2008 - July 2010
Centers for Disease Control and Prevention
Position
  • Epidemiologist
July 2006 - July 2008
University of Idaho
Position
  • PostDoc Position

Publications

Publications (141)
Article
Full-text available
Early public health strategies to prevent the spread of COVID-19 in the United States relied on non-pharmaceutical interventions (NPIs) as vaccines and therapeutic treatments were not yet available. Implementation of NPIs, primarily social distancing and mask wearing, varied widely between communities within the US due to variable government mandat...
Preprint
Self-transmissible multidrug resistance (MDR) plasmids are a major health concern because they can spread antibiotic resistance to pathogens. Even though most pathogens form biofilms, little is known about how MDR plasmids persist and evolve in biofilms. We hypothesize that (i) biofilms act as refugia of MDR plasmids by retaining them in the absenc...
Article
Full-text available
Gastrointestinal disease (GI) is the most common illness in pre-weaned dairy calves. Studies have associated the fecal microbiome composition with health status, but it remains unclear how the microbiome changes across different levels of GI disease and breeds. Our objective was to associate the clinical symptoms of GI disease with the fecal microb...
Preprint
Full-text available
Early public health strategies to prevent the spread of COVID-19 in the United States relied on non-pharmaceutical interventions (NPIs) as vaccines and therapeutic treatments were not yet available. Implementation of NPIs, primarily social distancing and mask wearing, varied widely between communities within the US due to variable government mandat...
Article
Full-text available
Population dynamic models can be used in conjunction with time series of species abundances to infer interactions. Understanding microbial interactions is a prerequisite for numerous goals in microbiome research, including predicting how populations change over time, determining how manipulations of microbiomes affect dynamics and designing synthet...
Article
Full-text available
Respiratory viruses from diverse families cocirculate in human populations and are frequently detected within the same host. Although clinical studies suggest that infection by multiple different respiratory viruses may alter disease severity, animal models in which we can control the doses, timing, and strains of coinfecting viruses are critical t...
Preprint
Microbial communities are widely studied using high-throughput sequencing techniques, such as 16S rRNA gene sequencing. These techniques have attracted biologists as they offer powerful tools to explore microbial communities and investigate their patterns of diversity in biological and biomedical samples at remarkable resolution. However, the accur...
Preprint
Full-text available
The El Tor biotype of Vibrio cholerae is responsible for perpetuating the longest cholera pandemic in recorded history (1961-current). The genomic islands VSP-1 and -2 are two understudied genetic features that distinguish El Tor from previous pandemics. To understand their utility, we calculated the co-occurrence of VSP genes across bacterial geno...
Preprint
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Understanding the evolutionary dynamics of microbial communities is a key step towards the goal of predicting and manipulating microbiomes to promote beneficial states. While interactions within microbiomes and between microbes and their environment collectively determine the community composition and population dynamics, we are often concerned wit...
Preprint
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Coinfection by unrelated viruses in the respiratory tract is common and can result in changes in disease severity compared to infection by individual virus strains. We have previously shown that inoculation of mice with rhinovirus (RV) two days prior to inoculation with a lethal dose of influenza A virus (PR8), provides complete protection against...
Article
Full-text available
Background Vaccination complacency occurs when perceived risks of vaccine-preventable diseases are sufficiently low so that vaccination is no longer perceived as a necessary precaution. Disease outbreaks can once again increase perceptions of risk, thereby decrease vaccine complacency, and in turn decrease vaccine hesitancy. It is not well understo...
Preprint
Full-text available
The impacts of disease on host vital rates can be clearly demonstrated using longitudinal studies, but these studies can be expensive and logistically challenging. We examined the utility of hidden variable models to infer the individual effects of disease, caused by infection, from population-level measurements of survival and fecundity when longi...
Article
Full-text available
While microbiologists often make the simplifying assumption that genotype determines phenotype in a given environment, it is becoming increasingly apparent that phenotypic heterogeneity (in which one genotype generates multiple phenotypes simultaneously even in a uniform environment) is common in many microbial populations. The importance of phenot...
Article
Full-text available
Premature birth and its complications are the largest contributors to infant death in the United States and globally. A short cervical length and the depletion of Lactobacillus species are known risk factors for preterm birth. However, in many resource-poor areas of the world, the technology to test for their occurrence is unavailable, and pregnant...
Article
Purpose The purpose of this study was to characterize the composition of vaginal bacterial communities in a cohort of black adolescent women and to determine how the species composition of these communities correlates with levels of estradiol, glycogen, and stress. Methods Twenty-one black adolescent women were sampled longitudinally. The composit...
Article
Full-text available
For decades hormone therapy (HT) has been prescribed to treat the symptoms of menopause, such as vaginal dryness, itching and burning. Here we sought to compare the vaginal microbiomes of postmenopausal women who received low dose estrogen therapy to those of premenopausal and postmenopausal women, and to do so in conjunction with assessing the all...
Preprint
Full-text available
While microbiologists often make the simplifying assumption that genotype determines phenotype in a given environment, it is becoming increasingly apparent that phenotypic heterogeneity (in which one genotype generates multiple phenotypes simultaneously even in a uniform environment) is common in many microbial populations. The importance of phenot...
Article
Full-text available
Motivated by questions in biology, we investigate the stability of equilibria of the dynamical system x′ = P(t) ∇f(x) which arise as critical points of f, under the assumption that P(t) is positive semidefinite. It is shown that the condition∫∞ λ1(P(t)) dt = ∞1, where λ(P(t)) is the smallest eigenvalue of P(t), plays a key role in guaranteeing unif...
Preprint
Full-text available
Background Population dynamic models can be used in conjunction with time series of species abundances to infer interactions. Understanding microbial interactions is a prerequisite for numerous goals in microbiome research; predicting how populations change over time, determining how manipulations of microbiomes affect dynamics, and designing synth...
Chapter
The evolutionary forces that create and maintain the awesome diversity observed in microbial communities and populations are not well understood. For the most part, previous studies on microbial evolution have been done using model species that are grown in well-mixed homogenous environments in which cells experience continuous or episodic periods...
Article
Full-text available
Background Estimation of influenza vaccine effectiveness (VE) among older adults at high risk of serious complications of influenza infection is challenging. These challenges include identifying and adjusting for potential confounders. The rarity of documented influenza deaths, even among individuals at greatest risk, makes VE assessment for this o...
Article
As sequencing technologies have advanced, the amount of information regarding the composition of bacterial communities from various environments (for example, skin or soil) has grown exponentially. To date, most work has focused on cataloging taxa present in samples and determining whether the distribution of taxa shifts with exogenous covariates....
Article
Full-text available
The severity of respiratory viral infections is partially determined by the cellular response mounted by infected lung epithelial cells. Disease prevention and treatment is dependent on our understanding of the shared and unique responses elicited by diverse viruses, yet few studies compare host responses to viruses from different families while co...
Data
RT-qPCR validation of candidate genes. LA4 cells were inoculated with virus using the same MOI’s as for the microarray study and RNA was extracted at 24 h post-infection using Trizol (Ambion). RNA was converted to cDNA using random hexamers and SuperScript VILO (Invitrogen). Five genes with differential expression by microarray analysis were valida...
Data
Signature genes for PR8. These genes were significantly different in PR8 infection compared to mock, RV, and MHV. (XLSX)
Data
Signature genes for RV. These genes were significantly different in RV infection compared to mock, PR8, and MHV. (XLSX)
Data
Genes whose expression was significantly up-regulated by all three viruses compared to mock-inoculated cells. These genes were from the center of the Venn diagram in Fig 2A. (XLSX)
Data
Evaluation of LA4 cell susceptibility to infection by MHV, RV, and PR8. LA4 cells were inoculated with (A) 3 PFU/cell MHV, (C) 3 TCID50/cell RV, or (E) 1 PFU/cell PR8, or were mock inoculated (B, D, F). Cells were fixed in 4% formaldehyde and permeabilized with Triton X100. (A, B) MHV infection was evaluated using a monoclonal antibody that recogni...
Data
Differential expression of type I interferon-induced genes. Genes with significantly up-regulated expression compared to mock at 24 h (see Fig 2) were used to query the Interferome v.2.01 database. Interferon-regulated genes were divided into functional groups and heat maps were generated using log2-fold change values for each virus at 24 h compare...
Data
Genes whose expression was significantly down-regulated by all three viruses compared to mock-inoculated cells. These genes were from the center of the Venn diagram in Fig 2B. (XLSX)
Data
Signature genes for MHV. These genes were significantly different in MHV infection compared to mock, RV, and PR8. (XLSX)
Data
Genes up-regulated by RV in both murine and human cells. These genes were identified to be up-regulated in our study by RV1B in murine cells and also were found by Chen et al. (23) to be up-regulated by RV1B in human cells. (XLSX)
Article
Full-text available
The emergence and spread of antibiotic resistance is a crisis in health care today. Antibiotic resistance is often horizontally transferred to susceptible bacteria by means of multi-drug resistance plasmids that may or may not persist in the absence of antibiotics. Because bacterial pathogens often grow as biofilms, there is a need to better unders...
Preprint
Full-text available
The emergence and spread of antibiotic resistance is a crisis in health care today. Antibiotic resistance is often horizontally transferred to susceptible bacteria by means of multi-drug resistance plasmids that may or may not persist in the absence of antibiotics. Because bacterial pathogens often grow as biofilms, there is a need to better unders...
Article
Plasmids are extrachromosomal DNA molecules that can potentially be transferred horizontally as well as vertically in bacterial lineages. Plasmids have been shown to code for numerous bacterial phenotypes, the most concerning of which is resistance to commonly used antibiotics. Plasmid-mediated transfer of drug resistance genes has notably led to t...
Article
Coevolution plays a key role in shaping the biodiversity on Earth. Coevolution is commonly defined as reciprocal evolutionary changes brought about by interactions between species, implying that interacting species impose selection on each other. The covariance between fitness and trait value determines the strength of natural selection. Thus, to u...
Article
Full-text available
The spread of infectious diseases can be impacted by human behavior, and behavioral decisions often depend implicitly on a planning horizon—the time in the future over which options are weighed. We investigate the effects of planning horizons on epidemic dynamics. We developed an epidemiological agent-based model (along with an ODE analog) to explo...
Article
Motivated by questions in biology, we investigate the stability of equilibria of the dynamical system $\mathbf{x}^{\prime}=P(t)\nabla f(x)$ which arise as critical points of $f$, under the assumption that $P(t)$ is positive semi-definite. It is shown that the condition $\int^{\infty}\lambda_{1}(P(t))~dt=\infty$, where $\lambda_{1}(P(t))$ is the sma...
Preprint
Full-text available
Human behavior can change the spread of infectious disease. There is limited understanding of how the time in the future over which individuals make a behavioral decision, their planning horizon, affects epidemic dynamics. We developed an agent-based model (along with an ODE analog) to explore the decision-making of self-interested individuals on a...
Article
Full-text available
Cryptic species pairs including white-footed mice, Peromyscus leucopus, and deer mice, Peromyscus maniculatus, are difficult to identify using morphological and laboratory techniques. To improve rapid and accurate determination of these species, we developed an assay reliant on differences in PCR-product melt curves (MCA). We differentiated 235 P....
Article
Full-text available
Whirling Disease (WD), a severe and widespread disease of salmonids, is caused by the myxosporean parasite Myxobolus cerebralis. It is further characterized by a unique two-host life cycle, utilizing the oligochaete Tubifex tubifex as an intermediate host. M. cerebralis is an invasive species that has been affecting populations in the United States...
Article
Ecological studies of communities have become increasingly focused on the role of genetics. These studies often conclude that genetics and evolution play an important role in community structure and function. For instance, studies have shown that the structure of insect communities associated with a host plant is heritable and therefore can potenti...
Article
We assessed public health use of R0, the basic reproduction number, which estimates the speed at which a disease is capable of spreading in a population. These estimates are of great public health interest, as evidenced during the 2009 influenza A (H1N1) virus pandemic. We reviewed methods commonly used to estimate R0, examined their practical util...
Article
Full-text available
Estimates of the effectiveness of influenza vaccines in older adults may be biased because of difficulties identifying and adjusting for confounders of the vaccine-outcome association. We estimated vaccine effectiveness for prevention of serious influenza complications among older persons by using methods to account for underlying differences in ri...
Article
Full-text available
Pandemic and seasonal infectious diseases such as influenza may have serious negative health and economic consequences. Certain non-pharmaceutical intervention strategies--including school closures--can be implemented rapidly as a first line of defense against spread. Such interventions attempt to reduce the effective number of contacts between ind...
Article
Interactions, antagonistic or mutualistic, can exert selection on plant traits. We explored the role of Hadena bicruris, a pollinating seed predator, as a selective agent on its host, the dioecious plant Silene latifolia. We exposed females from artificial-selection lines (many, small flowers (SF) vs. few, large flowers (LF)) to this moth. Infestat...
Article
Full-text available
Studying the correlation between traits of interacting species has long been a popular approach for identifying putative cases of coevolution. More recently, such approaches have been used as a means to evaluate support for the geographic mosaic theory of coevolution. Here we examine the utility of these approaches, using mathematical and computati...
Article
Full-text available
In species across taxa, offspring have means to influence parental investment (PI). PI thus evolves as an interacting phenotype and indirect genetic effects may strongly affect the co-evolutionary dynamics of offspring and parental behaviors. Evolutionary theory focused on explaining how exaggerated offspring solicitation can be understood as resol...
Article
Full-text available
David K. Shay and Benjamin Ridenhour discuss a modeling study predicting that stockpiling a secondary antiviral for use early in a flu pandemic can forestall resistance to the primary stockpiled drug.
Conference Paper
Background/Question/Methods Linking evolutionary processes to community dynamics has become a major research topic in recent years. Clearly, just as genes determine the fitness of an individual, the success or failure of an individual within a community is dependent on genetics. Likewise, the success or failure of a species within a community depe...
Article
Parasites are ubiquitous and have well-documented ecological consequences. In contrast, the extent to which parasites drive phenotypic evolution in hosts remains obscure. We use a recently developed statistical technique--selective source analysis--to analyse the strength of phenotypic selection acting on floral traits in the plant Heuchera grossul...
Article
We investigated spatially variable selection in Ambystoma tigrinum virus (ATV) which causes frequent and geographically widespread epizootics of the tiger salamander, Ambystoma tigrinum. To test for evidence of selection, we sequenced several coding and noncoding regions from virus strains isolated from epizootics throughout western North America....