Keith A. Crandall

George Washington University | GW · Department of Biostatistics and Bioinformatics

Persons with cystic fibrosis (PwCF) suffer from pulmonary exacerbations (PEx) related in part to lung infection. While higher microbial diversity is associated with higher lung function, the data on the impact of short-term antibiotics on changes in microbial diversity is conflicting. Further, Prevotella secretes beta-lactamases, which may influenc...

Introduction Pulmonary exacerbations (PEx) in persons with cystic fibrosis (CF) are primarily related to acute or chronic inflammation associated with bacterial lung infections, which may be caused by several bacteria that activate similar bacterial genes and produce similar by-products. The goal of our study was to perform a stratified functional...

Aim: Ongoing research in the urinary disease field suggests that a subset of patients with bladder pain and incontinence may have an infection as the cause of those clinical features, which may be difficult to diagnose by standard testing. Shotgun metagenomics sequencing (smNGS) provides a comprehensive way to identify infectious agents, namely, vi...

Background: Molecular epidemiological approaches provide opportunities to characterize HIV transmission dynamics. We analyzed HIV sequences and virus load (VL) results obtained during routine clinical care, and individual's zip-code location to determine utility of this approach. Methods: HIV-1 pol sequences aligned using ClustalW were subtyped...

The distributional patterns of the species of the South American freshwater crayfishes of the family Parastacidae were analysed using panbiogeographical track analyses to identify targeted regions of crayfish biodiversity for understanding biogeographical patterns. Two generalized tracks were identified using the track analysis approach: (1) Urugua...

For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood, and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7,600 species representing a striking diversity of morphology and ecology, including repeated adaptation to...

Fecal microbiota transplantation (FMT) is a promising therapeutic modality for the treatment and prevention of metabolic disease. We previously conducted a double-blind, randomized, placebo-controlled pilot trial of FMT in obese metabolically healthy patients in which we found that FMT enhanced gut bacterial bile acid metabolism and delayed the dev...

During the COVID-19 Delta variant surge, the CLAIRE cross-sectional study sampled saliva from 120 hospitalized patients, 116 of them with a positive COVID-19 PCR test. Patients received antibiotics upon admission due to possible secondary bacterial infections, with patients at risk of sepsis receiving more potent antibiotics. The saliva samples wer...

The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group of animals on earth, containing over 80% of animal species. It has been the subject of several recent phylogenomic analyses, but despite analyzing hundreds of genes, relationships within Pancrustacea show a notable lack of stability. Here, the phylogeny is estima...

Freshwater crayfishes are a large group (670+ species) of decapod crustaceans widely distributed around the world with the exception of Africa and the Indian subcontinent (Crandall and DeGrave 2017). There is, however, an endemic freshwater crayfish genus, Astacoides, found on Madagascar. This fact has puzzled zoogeographers for years (Hobbs 1988)...

Background Cystic fibrosis (CF) is characterized by recurrent pulmonary exacerbations (PEx) and lung function decline. PEx are frequently treated with antibiotics. However, little is known about the cumulative effects of antibiotics on the airway microbiome of persons with CF over time. The purpose of this study was to evaluate changes in the micro...

Rhizosphere microbial communities exert critical roles in plant health, nutrient cycling, and soil fertility. Despite the essential functions conferred by microbes, the source and acquisition of the rhizosphere are not entirely clear. Therefore, we investigated microbial community diversity and potential source using the only two native Antarctic p...

Winemaking is a well-known process comprising several steps to produce must and wine. Grape marc is a byproduct of wine production that can be vermicomposted and used as organic fertiliser. Grape marc vermicompost has a richer and more stable microbiome than grape marc alone and when added to the soil of vineyards it can improve grape production an...

Host evolutionary history is a key factor shaping the earthworm cast microbiome, although its effect can be shadowed by the earthworm's diet. To untangle dietary from taxon effects, we raised nine earthworm species on a uniform diet of cow manure and compared cast microbiome across species while controlling for diet. Our results showed that, under...

Most experiments studying bacterial microbiomes rely on the PCR amplification of all or part of the gene for the 16S rRNA subunit, which serves as a biomarker for identifying and quantifying the various taxa present in a microbiome sample. Several computational methods exist for analyzing 16S amplicon-based metagenomics. However, the most-used bioi...

Winemaking is a well-known process that includes several steps in the production of grape must and wine. Grape marc, or bagasse, is a byproduct of wine production that can be vermicomposted and used as organic fertilizer. Grape marc vermicompost has microbial communities that are richer and more stable than grape marc alone, and its addition to a v...

Proteins are direct products of the genome and metabolites are functional products of interactions between the host and other factors such as environment, disease state, clinical information, etc. Omics data, including proteins and metabolites, are useful in characterizing biological processes underlying COVID-19 along with patient data and clinica...

Elimination of human immunodeficiency virus (HIV) reservoirs is a critical endpoint to eradicate HIV. One therapeutic intervention against latent HIV is “shock and kill.” This strategy is based on the transcriptional activation of latent HIV with a latency-reversing agent (LRA) with the consequent killing of the reactivated cell by either the cytop...

Background Mastitis pathogenesis involves a wide range of opportunistic and apparently resident microorganims including bacteria, viruses and archaea. In dairy animals, microbes reside in the host, interact with environment and evade the host immune system, providing a potential for host-tropism to favor mastitis pathogenesis. To understand the hos...

CRF47_BF is a circulating recombinant form (CRF) of the human immunodeficiency virus type 1 (HIV-1), the etiological agent of AIDS. CRF47_BF represents one of 19 CRFx_BFs and has a geographic focus in Spain, where it was first identified in 2010. Since its discovery, CRF47_BF has expanded considerably in Spain, predominantly through heterosexual co...

Earthworms heavily modify the soil microbiome as it passes throughout their guts. However, there are no detailed studies describing changes in the composition, structure and diversity of soil microbiomes during gut transit and once they are released back to the soil as casts. To address this knowledge gap, we used 16S rRNA next-generation sequencin...

The study of microbial communities or microbiotas in animals and environments is important because of their impact in a broad range of industrial applications, diseases and ecological roles. High throughput sequencing (HTS) is the best strategy to characterize microbial composition and function. Microbial profiles can be obtained either by shotgun...

During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated the development of testing methods and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid...

Importance: Prior observational studies suggest that aspirin use may be associated with reduced mortality in high-risk hospitalized patients with COVID-19, but aspirin's efficacy in patients with moderate COVID-19 is not well studied. Objective: To assess whether early aspirin use is associated with lower odds of in-hospital mortality in patient...

Background The barnacles are a group of >2,000 species that have fascinated biologists, including Darwin, for centuries. Their lifestyles are extremely diverse, from free-swimming larvae to sessile adults, and even root-like endoparasites. Barnacles also cause hundreds of millions of dollars of losses annually due to biofouling. However, genomic re...

CRF47_BF is a circulating recombinant form (CRF) of the human immunodeficiency virus type 1 (HIV-1), the etiological agent of AIDS. CRF47_BF represents one of 19 CRFx_BFs and has a geographic focus in Spain, where it was first identified in 2010. Since its discovery, CRF47_BF has expanded considerably in Spain, predominantly through heterosexual co...

Supporting data for the manuscript "Chromosome-level genome assembly, annotation, and phylogenomics of the gooseneck barnacle Pollicipes pollicipes" https://doi.org/10.1093/gigascience/giac021 This includes the genome sequence and annotation (from NCBI) as well as all BUSCO results, alignments, phylogenetic trees, read counts, and differential gen...

Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the con...

November 2020 marked 2 y since the launch of the Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across all aspects of the EBP roadmap, as outlined in the 2018 article describing the project’s goals, strategies, and challenges (1). The launch phas...

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific commun...

The taxonomy of North American crayfishes has recently experienced a boom in interest as these crustaceans have become increasingly imperiled. Improving taxonomic resolution can inform and facilitate conservation efforts but has proven challenging for crayfishes due to the limited number of molecular tools available to resolve species complexes and...

The purpose of the meeting described in this review was to decide how best to ensure the sustainability of the Network for Integrating Bioinformatics into Life Science Education (NIBLSE; pronounced “nibbles”). Biology research today generates large and complex datasets, and the analysis of these datasets is becoming increasingly critical to progres...

The microbiota of the nasopharyngeal tract (NT) play a role in host immunity against respiratory infectious diseases. However, scant information is available on interactions of SARS-CoV-2 with the nasopharyngeal microbiome. This study characterizes the effects of SARS-CoV-2 infection on human nasopharyngeal microbiomes and their relevant metabolic...

The microbiota of the nasopharyngeal tract (NT) play a role in host immunity against respiratory infectious diseases. However, scant information is available on interactions of SARS-CoV-2 with the nasopharyngeal microbiome. This study characterizes the effects of SARS-CoV-2 infection on human nasopharyngeal microbiomes and their relevant metabolic...

SARS-CoV-2 (CoV) is the etiological agent of the COVID-19 pandemic and evolves to evade both host immune systems and intervention strategies. We divided the CoV genome into 29 constituent regions and applied novel analytical approaches to identify associations between CoV genomic features and epidemiological metadata. Our results show that nonstruc...

Proteins are direct products of the genome and metabolites are functional products of interactions between the host and other factors such as environment, disease state, clinical information, etc. Omics data, including proteins and metabolites, are useful in characterizing biological processes underlying COVID-19 along with patient data and clinica...

Elimination of latent HIV reservoirs is a critical endpoint to eradicate HIV. One therapeutic intervention against latent HIV is ‘shock and kill’. This strategy is based on the transcriptional activation of latent HIV with a Latency-Reversing Agent (LRA) with the consequent killing of the reactivated cell by either the cytopathic effect of HIV or t...

Background Evidence of whether people living with HIV are at elevated risk of adverse COVID-19 outcomes is inconclusive. We aimed to investigate this association using the population-based National COVID Cohort Collaborative (N3C) data in the USA. Methods We included all adult (aged ≥18 years) COVID-19 cases with any health-care encounter from 54...

SARS‐CoV‐2 is evolved into eight fundamental clades where four (G, GH, GR, and GV) are globally prevalent in 2020. To explain plausible epistatic effects of the signature co‐occurring mutations of these circulating clades on viral replication and transmission fitness, we proposed a hypothetical model using in silico approach. Molecular docking and...

The Copepoda is a clade of pancrustaceans containing 14,485 species that are extremely varied in their morphology and lifestyle. Not only do copepods dominate marine plankton and sediment communities and make up a sizeable component of the freshwater plankton, but over 6,000 species are symbiotically associated with every major phylum of marine met...

Presented is an account of the crayfish genus Creaserinus Hobbs, 1973 for Texas, based on materials gathered during a 13-year survey of the state. Home to Texas are six members of the genus, including C. hedgpethi (Hobbs, 1948) stat. rev., n. comb., which is resurrected from the synonymy of C. fodiens; and five species new to science described here...

Wastewater treatment plants produce hundreds of million tons of sewage sludge every year all over the world. Vermicomposting is well established worldwide and has been successful at processing sewage sludge, which can contribute to alleviate the severe environmental problems caused by its disposal. Here, we utilized 16S and ITS rRNA high-throughput...

Introgression is an important biological process affecting at least 10% of the extant species in the animal kingdom. Introgression significantly impacts inference of phylogenetic species relationships where a strictly binary tree model cannot adequately explain reticulate net-like species relationships. Here we use phylogenomic approaches to unders...

Background Individuals with immune dysfunction, including people with HIV (PWH) or solid organ transplant recipients (SOT), might have worse outcomes from COVID-19. We compared odds of COVID-19 outcomes between patients with and without immune dysfunction. Methods We evaluated data from the National COVID-19 Cohort Collaborative (N3C), a multicente...

Background: The role of anaerobic organisms in the cystic fibrosis (CF) lung microbiome is unclear. Our objectives were to investigate the effect of broad (BS) versus narrow (NS) spectrum antianaerobic antibiotic activity on lung microbiome diversity and pulmonary function, hypothesizing that BS antibiotics would cause greater change in microbiome...

Importance The National COVID Cohort Collaborative (N3C) is a centralized, harmonized, high-granularity electronic health record repository that is the largest, most representative COVID-19 cohort to date. This multicenter data set can support robust evidence-based development of predictive and diagnostic tools and inform clinical care and policy....

Background/Aims: ALDH2 (Aldehyde dehydrogenase 2) is associated with multiple human diseases including cancers, Asian flush syndrome (deficiencies affect 35%-40% of East Asians), and alcoholic liver disease. Yet, oncogenic mechanisms and pathways that ALDH2 interacts with remain unclear. Previously we have demonstrated that TGF-β-deficient mutants...

Wastewater treatment plants produce hundreds of million tons of sewage sludge every year all over the world. Vermicomposting is well established worldwide and has been successful in processing sewage sludge, which can contribute to alleviate the severe environmental problems caused by their disposal. Here, we utilized 16S and ITS rRNA high-throughp...

Cystic fibrosis (CF) is a chronic lung disease characterized by acute pulmonary exacerbations (PExs) that are frequently treated with antibiotics. The impact of antibiotics on airway microbial diversity remains a critical knowledge gap. We sought to define the association between beta-lactam pharmacokinetic (PK) and pharmacodynamic target attainmen...

In response to the COVID-19 outbreak, scientists and medical researchers are capturing a wide range of host responses, symptoms and lingering postrecovery problems within the human population. These variable clinical manifestations suggest differences in influential factors, such as innate and adaptive host immunity, existing or underlying health c...

The 2019 novel coronavirus (SARS-CoV-2) is the etiological agent of the COVID-19 pandemic and evolves to evade both host immune systems and intervention strategies. To diminish the short-term and long-term impacts of coronavirus (CoV), we investigated CoV differences at the nucleotide and protein level and CoV genomic variation associated with epid...

Motivation The discovery of biologically interpretable and clinically actionable communities in heterogeneous omics data is a necessary first step towards deriving mechanistic insights into complex biological phenomena. Here we present a novel clustering approach, omeClust, for community detection in omics profiles by simultaneously incorporating s...

Human endogenous retroviruses (HERV) have been implicated in a variety of diseases including cancers. Recent research implicates HERVs in epigenetic gene regulation. Here we utilize a recently developed bioinformatics tool for identifying HERV expression at the locus-specific level to identify differential expression of HERVs in matched tumor-norma...

Background The SARS-CoV-2 primarily enters into the human body through nasopharyngeal tract (NT) and is the etiological agent of COVID-19. The microbiota of the NT may play a role in host immunity against respiratory infectious diseases. However, scant information is available on interactions of SARS-CoV-2 with the nasopharyngeal microbiome. To she...