Source: National Institutes of Health

Source: National Institutes of Health

Nasopharyngeal Microbiome Diversity Changes over Time in Children with Asthma

Professor Keith Crandall, Director of the Computational Biology Institute, and faculty member Dr. Marcos Perez-Losada have been published in PLOS One, along with collaborators from the Children’s National Medical Center and the Universidade do Porto in Portugal. The article, “Nasopharyngeal microbiome diversity changes over time in children with asthma,” focuses on the composition and temporal dynamics of microbiotas from children and adolescents. The team made use of NGS technology to characterize the nasopharyngeal microbiomes of asthmatics children and adolescents (6 to 18 years) to determine their stability over time. 

Screen Shot 2017-01-10 at 8.05.18 AM.png


Keith Crandall

Freshwater crayfishes (sometimes called “crawfish” and by a wide variety of common and/or local names (Hart, 1994)) are a taxonomically diverse group with over 640 described species worldwide (Crandall and Buhay, 2008). Crayfishes are a monophyletic group that is a sister group to the clawed lobsters (Nephropoidea Dana, 1852) (Crandall et al., 2000). Crayfishes are classified into two superfamilies, Astacoidea Latreille, 1802 (Northern Hemisphere) consisting of two families (Cambaridae Hobbs, 1942 and Astacidae Latreille, 1802), and Parastacoidea Huxley, 1879 (Southern Hemisphere) with a single family, Parastacidae Huxley, 1879 (see Hobbs, 1974). Some of the groups are in need of a complete taxonomic reworking and there have been a number of more recent studies that can aid in appropriate assignments (Fratini et al., 2005; Larson et al., 2016). The separation of these superfamilies represent

Heat map of 79 genes with a log-fold-change ≥3 between asthmatics and controls.

Heat map of 79 genes with a log-fold-change ≥3 between asthmatics and controls.

Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma

Marcos Pérez-Losada, Eduardo Castro-Nallar, Matthew L. Bendall, Robert J. Freishtat, Keith A. Crandall

High-throughput sequencing (HTS) analysis of microbial communities from the respiratory airways has heavily relied on the 16S rRNA gene. Given the intrinsic limitations of this approach, airway microbiome research has focused on assessing bacterial composition during health and disease, and its variation in relation to clinical and environmental factors, or other microbiomes. Consequently, very little effort has been dedicated to describing the functional characteristics of the airway microbiota and even less to explore the microbe-host interactions. Here we present a simultaneous assessment of microbiome and host functional diversity and host-microbe interactions from the same RNA-seq experiment, while accounting for variation in clinical metadata.


Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children

Marcos Pérez-Losada, Keith A. Crandall, Robert J. Freishtat

The nasopharynx is a reservoir for pathogens associated with respiratory illnesses, such as asthma. Next-generation sequencing (NGS) has been used to characterize the nasopharyngeal microbiome during health and disease. Most studies so far have surveyed the nasopharynx as a whole; however, less is known about spatial variation (biogeography) in nasal microenvironments and how sampling techniques may capture that microbial diversity.


Fish-T1K (Transcriptomes of 1,000 Fishes) Project: large-scale transcriptome data for fish evolution studies

Ying Sun, Yu Huang, Xiaofeng Li, Carole C. Baldwin, Zhuocheng Zhou, Zhixiang Yan, Keith A. Crandall, Yong Zhang, Xiaomeng Zhao, Min Wang, Alex Wong, Chao Fang, Xinhui Zhang, Hai Huang, Jose V. Lopez, Kirk Kilfoyle, Yong Zhang, Guillermo Ortí, Byrappa Venkatesh,   and Qiong Shi

Ray-finned fishes (Actinopterygii) represent more than 50 % of extant vertebrates and are of great evolutionary, ecologic and economic significance, but they are relatively underrepresented in ‘omics studies. Increased availability of transcriptome data for these species will allow researchers to better understand changes in gene expression, and to carry out functional analyses. An international project known as the “Transcriptomes of 1,000 Fishes” (Fish-T1K) project has been established to generate RNA-seq transcriptome sequences for 1,000 diverse species of ray-finned fishes. The first phase of this project has produced transcriptomes from more than 180 ray-finned fishes, representing 142 species and covering 51 orders and 109 families. Here we provide an overview of the goals of this project and the work done so far.