Works (54)

Updated: June 1st, 2024 04:43

2024 journal article

Gardnerella diversity and ecology in pregnancy and preterm birth

MSystems.

By: H. Berman n, D. Goltsman*, M. Anderson n, D. Relman* & B. Callahan n

Ed(s): E. Cope

Source: ORCID
Added: May 22, 2024

2024 journal article

Impact of florfenicol dosing regimen on the phenotypic and genotypic resistance of enteric bacteria in steers

SCIENTIFIC REPORTS, 14(1).

By: J. Halleran n, H. Sylvester n, M. Jacob n, B. Callahan n, R. Baynes n & D. Foster n

Sources: Web Of Science, NC State University Libraries
Added: April 8, 2024

2024 article

Serovar-level identification of bacterial foodborne pathogens from full-length 16S rRNA gene sequencing

Grinevich, D., Harden, L., Thakur, S., & Callahan, B. (2024, February 6). (M. G. I. Langille, Ed.). MSYSTEMS, Vol. 2.

By: D. Grinevich n, L. Harden n, S. Thakur n & B. Callahan n

Ed(s): M. Langille

author keywords: serotyping; food-borne pathogens; Salmonella; Escherichia coli; 16S rRNA; long-read sequencing
TL;DR: A new computational technology is developed that allows the important foodborne pathogens Escherichia coli and Salmonella enterica to be serotyped (a subspecies level classification) from sequencing of a single-marker gene, and the 16S rRNA gene often used to surveil bacterial communities. (via Semantic Scholar)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 7, 2024

2024 journal article

Standards for fecal microbiota transplant: Tools and therapeutic advances

BIOLOGICALS, 86.

By: I. Belotserkovsky, L. Stabryla*, M. Hunter*, J. Allegretti*, B. Callahan n, P. Carlson*, P. Daschner*, M. Goudarzi ...

author keywords: Fecal microbiota standards; FMT; Standards; Live biotherapeutic product (LBP); Measurement bias; Safety; Efficacy; Stability
Sources: Web Of Science, NC State University Libraries
Added: May 20, 2024

2024 journal article

The development of non-destructive sampling methods of parchment skins for genetic species identification

PLOS ONE, 19(3).

By: M. Scheible n, T. Stinson n, M. Breen n, B. Callahan n, R. Thomas n & K. Meiklejohn n

Ed(s): A. Shakoori

TL;DR: A workflow for enriching the mitochondrial genome (mtGenome), generating next-generation sequencing reads to permit species identification, and providing interpretation guidance is defined, defining a workflow for enriching the mitochondrial genome, generating next-generation sequencing reads to permit species identification, and providing interpretation guidance. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: March 22, 2024

2023 article

A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses

Hakimzadeh, A., Abdala Asbun, A., Albanese, D., Bernard, M., Buchner, D., Callahan, B., … Anslan, S. (2023, August 7). MOLECULAR ECOLOGY RESOURCES, Vol. 8.

author keywords: amplicon data analysis; bioinformatics; environmental DNA; metabarcoding; pipeline; review
TL;DR: This review outlines the input data requirements, supported operating systems and particular attributes of thirty-two amplicon processing pipelines of metabarcoding data analysis tools and pipelines with the goal of helping users to select a pipeline for their metabarcode projects. (via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
14. Life Below Water (Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 28, 2023

2023 journal article

Evaluation of SARS-CoV-2 identification methods through surveillance of companion animals in SARS-CoV-2-positive homes in North Carolina, March to December 2020

PEERJ, 11.

By: T. Gin n, E. Petzold*, D. Uthappa*, C. Neighbors*, A. Borough*, C. Gin n, E. Lashnits*, G. Sempowski* ...

author keywords: COVID-19; Coronavirus; SARS-CoV-2; Dogs; Cats; Antibody; Serology
TL;DR: Raw ELISA results scrutinized relative to known negative samples suggested that cut-off for IgG seropositivity may require adjustment relative to previously proposed values, while proposed cut-offs for IgM require more extensive validation. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: November 27, 2023

2023 journal article

Gallbladder microbiota in healthy dogs and dogs with mucocele formation

PLOS ONE, 18(2).

By: J. Gookin n, A. Hartley n, K. Aicher n, K. Mathews n, R. Cullen n, J. Cullen n, B. Callahan n, D. Stowe n ...

MeSH headings : Dogs; Animals; Gallbladder / pathology; Mucocele / veterinary; RNA, Ribosomal, 16S / genetics; Bile / microbiology; Gallbladder Diseases / veterinary; Microbiota / genetics; Bile Duct Diseases; Dog Diseases / diagnosis
TL;DR: Results of this study do not support existence of a core microbiome in the bile of healthy dogs or gallbladder mucus from dogs with mucocele formation, and document how contaminating sequences can significantly contribute to the results of sequencing analysis when performed on samples with low bacterial biomass. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: April 24, 2023

2023 article

GardnerellaDiversity and Ecology in Pregnancy and Preterm Birth

Berman, H. L., Goltsman, D. S. A., Anderson, M., Relman, D. A., & Callahan, B. J. (2023, February 4).

By: H. Berman n, D. Goltsman*, M. Anderson n, D. Relman* & B. Callahan n

TL;DR: The diversity of Gardnerella both across populations and within individual vaginal microbiomes has long been unappreciated, as has been the intra-species diversity of many other members of the vaginal microbiome. (via Semantic Scholar)
Source: ORCID
Added: February 5, 2023

2023 journal article

Longitudinal Analysis of Canine Oral Microbiome Using Whole Genome Sequencing in Aging Companion Dogs

ANIMALS, 13(24).

By: G. Templeton n, G. Fefer n, B. Case n, J. Roach*, M. Azcarate-Peril*, M. Gruen n, B. Callahan n, N. Olby n

author keywords: oral; microbiome; canine cognitive dysfunction syndrome; Alzheimer's disease
TL;DR: The importance of defining the oral microbiota in aged dogs with a view to understanding potential therapeutic targets is shown, with an increased fungal and bacterial alpha diversity in aging dogs over time and nearly universal oral dysbiosis. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: January 16, 2024

2023 journal article

Meta-analysis reveals the vaginal microbiome is a better predictor of earlier than later preterm birth

BMC Biology.

By: C. Huang n, C. Gin n, J. Fettweis*, B. Foxman*, B. Gelaye*, D. MacIntyre*, A. Subramaniam*, W. Fraser, N. Tabatabaei, B. Callahan n

TL;DR: An integrated analysis of previously published datasets from 12 cohorts of pregnant women whose vaginal microbiomes were measured by 16S rRNA gene sequencing revealed a highly significant negative association between L. crispatus and PTB that was consistent across almost all studies. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Source: ORCID
Added: February 1, 2024

2023 article

Microbiome analysis of bile from apparently healthy cats and cats with suspected hepatobiliary disease

Slead, T. S., Callahan, B. J., Schreeg, M. E., Seiler, G. S., Stowe, D. M., Azcarate-Peril, M. A., … Gookin, J. L. (2023, September 13). JOURNAL OF VETERINARY INTERNAL MEDICINE, Vol. 9.

By: T. Slead n, B. Callahan n, M. Schreeg n, G. Seiler n, D. Stowe n, M. Azcarate-Peril*, M. Jacob n, J. Gookin n

author keywords: cholangitis; feline; gallbladder; microbiota
TL;DR: Cat bile does not harbor a core microbiota composed of bacterial taxa common to many individuals and Uncultured bacteria may contribute to pathogenesis of hepatobiliary disease in cats with bile E. coli infection. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: September 14, 2023

2023 article

Rookery through rehabilitation: Microbial community assembly in newborn harbour seals after maternal separation

Switzer, A. D., Callahan, B. J., Costello, E. K., Bik, E. M., Fontaine, C., Gulland, F. M. D., & Relman, D. A. (2023, June 16). ENVIRONMENTAL MICROBIOLOGY, Vol. 6.

By: A. Switzer*, B. Callahan n, E. Costello*, E. Bik, C. Fontaine*, F. Gulland*, D. Relman*

TL;DR: While early life maternal contact may provide seeding for microbial assembly, co-housing of conspecifics during rehabilitation may help neonatal mammals achieve a healthy host-specific microbiota with features of resilience. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: July 10, 2023

2023 article

Serovar-level Identification of Bacterial Foodborne Pathogens From Full-length 16S rRNA Gene Sequencing

Grinevich, D., Harden, L., Thakur, S., & Callahan, B. J. (2023, June 28).

By: D. Grinevich, L. Harden, S. Thakur & B. Callahan n

TL;DR: A novel algorithm for serotype prediction, implemented as an R package (Seroplacer), which takes as input full-length 16S rRNA gene sequences and outputs serovar predictions after phylogenetic placement into a reference phylogeny is developed, achieving over 89% accuracy in predicting Salmonella serotypes on in silico test data. (via Semantic Scholar)
Source: ORCID
Added: February 1, 2024

2022 journal article

Identification of microbial taxa present in Ctenocephalides felis (cat flea) reveals widespread co-infection and associations with vector phylogeny

PARASITES & VECTORS, 15(1).

By: C. Manvell, H. Berman n, B. Callahan n, E. Breitschwerdt n, W. Swain n, K. Ferris n, R. Maggi n, E. Lashnits*

author keywords: Flea microbiome; Bartonella; Wolbachia; Rickettsia; Flea phylogenetics; Flea diversity; DNA barcoding; 16S NGS
MeSH headings : Animals; Cats; Bartonella / genetics; Cat Diseases / parasitology; Coinfection; Ctenocephalides / microbiology; Flea Infestations / epidemiology; Flea Infestations / veterinary; Phylogeny; Rickettsia / genetics
TL;DR: The findings confirm the widespread coinfection of fleas with multiple bacterial genera and strains, proposing three additional microbiome members and have important implications for flea-borne pathogen transmission and control. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: November 14, 2022

2022 article

Implications of taxonomic bias for microbial differential-abundance analysis

McLaren, M. R., Nearing, J. T., Willis, A. D., Lloyd, K. G., & Callahan, B. J. (2022, August 19).

By: M. McLaren*, J. Nearing*, A. Willis*, K. Lloyd* & B. Callahan n

TL;DR: It is found that, for analyses based on species proportions, taxonomic bias can cause significant errors in DA results if the average measurement efficiency of the community is associated with the condition of interest, and these errors can be avoided by using more robust DA methods. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: ORCID
Added: August 24, 2022

2022 article

Meta-Analysis Reveals the Vaginal Microbiome is a Better Predictor of Earlier Than Later Preterm Birth

Huang, C., Gin, C., Fettweis, J., Foxman, B., Gelaye, B., MacIntyre, D. A., … Callahan, B. (2022, September 27).

By: C. Huang n, C. Gin n, J. Fettweis*, B. Foxman*, B. Gelaye*, D. MacIntyre*, A. Subramaniam*, W. Fraser*, N. Tabatabaei*, B. Callahan n

UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Source: ORCID
Added: October 20, 2022

2022 journal article

Phylogeny-guided microbiome OTU-specific association test (POST)

MICROBIOME, 10(1).

By: C. Huang n, B. Callahan n, M. Wu*, S. Holloway n, H. Brochu n, W. Lu n, X. Peng n, J. Tzeng n

author keywords: Association test; Phylogenetic tree; Kernel machine regression
MeSH headings : Computational Biology / methods; Computer Simulation; Female; Humans; Infant, Newborn; Microbiota / genetics; Phylogeny; Premature Birth
TL;DR: This work proposes a local collapsing test called phylogeny-guided microbiome OTU-specific association test (POST), and develops a user friendly R package POSTm, which can enhance the selection performance of associated microbiome features by improving the overall true-positive and false-positive detection. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: June 20, 2022

2021 journal article

Effects of danofloxacin dosing regimen on gastrointestinal pharmacokinetics and fecal microbiome in steers

SCIENTIFIC REPORTS, 11(1).

By: J. Halleran n, B. Callahan n, M. Jacob n, H. Sylvester n, T. Prange n, M. Papich n, D. Foster n

MeSH headings : Animals; Anti-Bacterial Agents / pharmacology; Cattle; Enterococcus / drug effects; Escherichia coli / drug effects; Fluoroquinolones / pharmacology; Gastrointestinal Microbiome / drug effects; Gastrointestinal Tract / drug effects; Gastrointestinal Tract / microbiology; Male
TL;DR: Danofloxacin treatment consistently resulted in the Euryarchaeota phyla decreasing over time, specifically due to a decrease in Methanobrevibacter, and although microbiome differences were minor between dosing groups, the low dose group had a higher number of isolates with MIC values high enough to cause clinically relevant resistance. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: July 26, 2021

2021 journal article

Ultra-accurate microbial amplicon sequencing with synthetic long reads

MICROBIOME, 9(1).

By: B. Callahan n, D. Grinevich n, S. Thakur n, M. Balamotis & T. Ben Yehezkel

author keywords: Synthetic long reads; Amplicon sequencing; Metagenomics; Long-read sequencing
MeSH headings : High-Throughput Nucleotide Sequencing; Metagenome; Microbiota / genetics; RNA, Ribosomal, 16S / genetics; Sequence Analysis, DNA
TL;DR: L loopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens. (via Semantic Scholar)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: June 6, 2021

2020 journal article

Clostridioides difficile carriage in animals and the associated changes in the host fecal microbiota

ANAEROBE, 66.

By: R. Thanissery n, M. McLaren n, A. Rivera n, A. Reed n, N. Betrapally n, T. Burdette n, J. Winston n, M. Jacob n, B. Callahan n, C. Theriot n

author keywords: C. difficile; C. hiranonis; Microbiome; Ribotype; Antibiotic resistance; Animal; Canine; Equine; Feline
MeSH headings : Animals; Anti-Bacterial Agents / pharmacology; Bacterial Toxins / genetics; Bacterial Toxins / metabolism; Bacterial Typing Techniques; Cats; Chlorocebus aethiops; Clostridioides difficile / classification; Clostridioides difficile / drug effects; Clostridioides difficile / physiology; Clostridium Infections / epidemiology; Clostridium Infections / microbiology; Clostridium Infections / veterinary; Coculture Techniques; Dogs; Feces / microbiology; Female; Gastrointestinal Microbiome; Horses; Hospitals, Animal; Host-Pathogen Interactions; Male; Microbial Interactions; Microbial Sensitivity Tests; North Carolina; Polymerase Chain Reaction; Prevalence; RNA, Ribosomal, 16S; Ribotyping; Risk Factors; Tertiary Healthcare; Vero Cells
TL;DR: Experimental results showed a clear antagonistic relationship between the two strains in vitro, suggesting that commensal Clostridia might play a role in colonization resistance against C. difficile in different hosts. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: January 11, 2021

2020 journal article

Pathogen resistance may be the principal evolutionary advantage provided by the microbiome

Philosophical Transactions of the Royal Society B: Biological Sciences, 375(1808), 20190592.

By: M. McLaren n & B. Callahan n

author keywords: colonization resistance; commensal bacteria; defensive symbionts; evolution of immunity; host-microbiome interactions; microbiome
MeSH headings : Animals; Biological Evolution; Disease Resistance; Host Microbial Interactions; Invertebrates / microbiology; Plant Diseases; Plants / microbiology; Symbiosis; Vertebrates / microbiology
TL;DR: It is argued that pathogen resistance vies with other commensal-provided benefits for being the principal evolutionary advantage provided by the microbiome to host lineages across the tree of life. (via Semantic Scholar)
Source: ORCID
Added: August 12, 2020

2020 journal article

The role of the microbiome in host evolution

Philosophical Transactions of the Royal Society B: Biological Sciences, 375(1808), 20190588.

By: O. Kolodny*, B. Callahan n & A. Douglas*

author keywords: beneficial microbes; coevolution; commensals; eco-evolutionary dynamics
MeSH headings : Animals; Biological Evolution; Communicable Disease Control; Crops, Agricultural / microbiology; Host Microbial Interactions; Humans; Microbiota; Nutritive Value; Pest Control
TL;DR: The role of the microbiome in host evolution and the relationship between microbiome composition and host phenotype is studied in order to develop novel strategies for improved human and animal health, enhanced crop yield and nutritional quality, and the control of various pests and disease agents. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (OpenAlex)
Source: ORCID
Added: August 12, 2020

2020 article

Ultra-accurate Microbial Amplicon Sequencing Directly from Complex Samples with Synthetic Long Reads

Callahan, B. J., Grinevich, D., Thakur, S., Balamotis, M. A., & Yehezkel, T. B. (2020, July 7). (Vol. 7). Vol. 7.

By: B. Callahan n, D. Grinevich n, S. Thakur n, M. Balamotis & T. Yehezkel

TL;DR: Analysis of rinsate from retail meat samples demonstrated that LoopSeq full-length 16S rRNA synthetic long-reads could accurately classify organisms down to the species level, and could differentiate between different strains within species identified by the CDC as potential foodborne pathogens. (via Semantic Scholar)
Source: ORCID
Added: July 9, 2020

2020 journal article

Understanding and interpreting community sequencing measurements of the vaginal microbiome

BJOG: An International Journal of Obstetrics & Gynaecology, 127(2), 139–146.

By: H. Berman n, . McLaren n & B. Callahan n

author keywords: 16S rRNA gene; amplicon sequencing; metagenomics; metatranscriptomics; vaginal microbiome
MeSH headings : Female; Humans; Microbiota / genetics; RNA, Ribosomal, 16S; Reproducibility of Results; Sequence Analysis, DNA; Vagina / microbiology
TL;DR: Suggestions for critically interpreting research results and potential clinical applications based on community sequencing of the vaginal microbiome, and the advantages and limitations of community sequencing generally, are developed. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: ORCID
Added: November 2, 2019

2019 journal article

Ceftiofur formulation differentially affects the intestinal drug concentration, resistance of fecal Escherichia coli, and the microbiome of steers

PLOS ONE, 14(10).

MeSH headings : Animals; Anti-Bacterial Agents / administration & dosage; Anti-Bacterial Agents / chemistry; Anti-Bacterial Agents / pharmacokinetics; Cattle; Cattle Diseases / drug therapy; Cattle Diseases / microbiology; Cephalosporins / administration & dosage; Cephalosporins / chemistry; Cephalosporins / pharmacokinetics; Drug Resistance, Bacterial; Escherichia coli / classification; Escherichia coli / drug effects; Escherichia coli / genetics; Feces / microbiology; Microbial Sensitivity Tests; Microbiota; RNA, Ribosomal, 16S / genetics
TL;DR: CCFA leads to prolonged, low intestinal drug concentrations, and is associated with decreased E. coli concentration, an increased MIC of ceftiofur in E. Escherichia coli at specific time points, and shifts in the fecal microbiota. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: June 1, 2020

2019 article

Consistent and correctable bias in metagenomic sequencing experiments

McLaren, M. R., Willis, A. D., & Callahan, B. J. (2019, February 25). BioRxiv, Vol. 2, p. 559831.

By: M. McLaren n, A. Willis* & B. Callahan n

Source: ORCID
Added: February 26, 2019

2019 journal article

Consistent and correctable bias in metagenomic sequencing experiments

ELife.

By: M. McLaren n, A. Willis* & B. Callahan n

MeSH headings : Bacteria / classification; Bacteria / genetics; Bias; Biota; Cluster Analysis; DNA, Ribosomal / chemistry; DNA, Ribosomal / genetics; Metagenomics / methods; Models, Theoretical; Phylogeny; RNA, Ribosomal, 16S / genetics; Sequence Analysis, DNA / methods
TL;DR: This work proposes a mathematical model for how bias distorts community measurements based on the properties of real experiments and validate this model with 16S rRNA gene and shotgun metagenomics data from defined bacterial communities. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: ORCID
Added: September 10, 2019

2019 journal article

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution

Nucleic Acids Research, 7.

By: B. Callahan n, J. Wong*, C. Heiner*, S. Oh*, C. Theriot n, A. Gulati*, S. McGill*, M. Dougherty*

MeSH headings : Escherichia coli K12 / classification; Escherichia coli K12 / genetics; Escherichia coli O157 / classification; Escherichia coli O157 / genetics; Feces / microbiology; High-Throughput Nucleotide Sequencing; Humans; Microbiota / genetics; Phylogeny; Polymerase Chain Reaction / methods; Polymorphism, Single Nucleotide / genetics; RNA, Ribosomal, 16S / genetics; Sequence Analysis, DNA
TL;DR: A high-throughput amplicon sequencing methodology based on PacBio circular consensus sequencing and the DADA2 sample inference method that measures the full-length 16S rRNA gene with single-nucleotide resolution and a near-zero error rate is presented. (via Semantic Scholar)
Source: ORCID
Added: August 21, 2019

2019 journal article

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy

BIOINFORMATICS, 35(1), 95–103.

By: M. Ghaemi*, D. DiGiulio*, K. Contrepois*, B. Callahan n, T. Ngo*, B. Lee-McMullen*, B. Lehallier*, A. Robaczewska* ...

Ed(s): J. Wren

MeSH headings : Computational Biology; Female; Humans; Metabolome; Microbiota; Pregnancy; Proteome; Transcriptome
TL;DR: This model not only significantly increased predictive power by combining all datasets, but also revealed novel interactions between different biological modalities, which provides the frameworks for future studies examining deviations implicated in pregnancy‐related pathologies including preterm birth and preeclampsia. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
5. Gender Equality (Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: March 11, 2019

2018 article

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution

Callahan, B. J., Wong, J., Heiner, C., Oh, S., Theriot, C. M., Gulati, A. S., … Dougherty, M. K. (2018, August 15). (Vol. 8). Vol. 8.

By: B. Callahan n, J. Wong*, C. Heiner*, S. Oh*, C. Theriot n, A. Gulati*, S. McGill*, M. Dougherty*

Source: ORCID
Added: August 21, 2019

2018 article

In Nature, There Is Only Diversity

MBIO, Vol. 9.

By: M. McLaren n & B. Callahan n

author keywords: metagenomics; microbial ecology; microbiome
MeSH headings : Metagenomics; RNA, Ribosomal, 16S
TL;DR: The need for investigators to choose the right molecular methods for their biological problem, as nature does not respect the limitations and conventions associated with the authors' methods is specifically noted. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018

2018 journal article

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

MICROBIOME, 6(1).

By: N. Davis*, D. Proctor*, S. Holmes*, D. Relman* & B. Callahan n

author keywords: Microbiome; Metagenomics; Marker-gene; 16S rRNA gene; DNA contamination
MeSH headings : Bacteria / classification; Bacteria / genetics; DNA Contamination; DNA, Bacterial / genetics; DNA, Ribosomal / genetics; Databases, Genetic; Genetic Markers; Humans; Internet; Metagenomics / methods; Models, Statistical; Mouth / microbiology; RNA, Ribosomal, 16S / genetics; Sequence Analysis, DNA / methods; Software
TL;DR: The application of decontam to two recently published datasets corroborated and extended their conclusions that little evidence existed for an indigenous placenta microbiome and that some low-frequency taxa seemingly associated with preterm birth were contaminants. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: January 7, 2019

2017 journal article

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

The ISME Journal, 11(12), 2639–2643.

By: B. Callahan n, P. McMurdie & S. Holmes*

MeSH headings : Bacteria / classification; Bacteria / genetics; Bacteria / isolation & purification; Classification / methods; Databases, Nucleic Acid; Genetic Variation; Sequence Analysis, DNA
TL;DR: It is argued that the improvements in reusability, reproducibility and comprehensiveness are sufficiently great that ASVs should replace OTUs as the standard unit of marker-gene analysis and reporting. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: July 21, 2019

2017 journal article

Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(37), 9966–9971.

By: B. Callahan n, D. DiGiulio*, D. Goltsman*, C. Sun*, E. Costello*, P. Jeganathan*, J. Biggio*, R. Wong* ...

author keywords: pregnancy; prematurity; vaginal microbiota; Lactobacillus; Gardnerella
MeSH headings : Adult; Black or African American; Case-Control Studies; Cohort Studies; DNA Replication; Female; Gardnerella vaginalis / classification; Humans; Lactobacillus / classification; Microbiota / genetics; Microbiota / immunology; Pregnancy; Premature Birth / etiology; Premature Birth / microbiology; RNA, Ribosomal, 16S / genetics; United States / epidemiology; Vagina / microbiology; White People
TL;DR: It is argued that the vaginal microbiota is better represented by the quantitative frequencies of these key taxa than by classifying communities into five community state types, and that previous conflicting results may reflect the different risk profile of women of black race. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2017 journal article

Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women

Proceedings of the National Academy of Sciences, 201705899.

By: B. Callahan, D. DiGiulio, D. Goltsman, C. Sun, E. Costello, P. Jeganathan, J. Biggio, R. Wong ...

Source: ORCID
Added: August 21, 2019

2017 article

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A., & Callahan, B. J. (2017, November 17). (Vol. 11). Vol. 11.

By: N. Davis*, D. Proctor*, S. Holmes*, D. Relman* & B. Callahan n

Source: ORCID
Added: August 21, 2019

2016 journal article

1,2-Dichloroethane Exposure Alters the Population Structure, Metabolism, and Kinetics of a Trichloroethene-Dechlorinating Dehalococcoides mccartyi Consortium

Environmental Science & Technology, 50(22), 12187–12196.

By: K. Mayer-Blackwell*, M. Fincker*, O. Molenda*, B. Callahan*, H. Sewell*, S. Holmes*, E. Edwards*, A. Spormann*

MeSH headings : Biodegradation, Environmental; Chloroflexi / metabolism; Halogenation; Kinetics; Trichloroethylene / metabolism; Vinyl Chloride / metabolism
TL;DR: The structure of Dehalococcoides populations in a continuously fed reactor system under changing chloroethene/ethane influent conditions was investigated and it was observed that increasing the influent ratio of 1,2-dichloroethane to trichloraethene was associated with ecological selection of a tceA-containing Dehalitis mccartyi population relative to a vcrA- containing De Halococcoide population. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Crossref, ORCID
Added: July 21, 2019

2016 journal article

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses

F1000Research, 5, 1492.

By: B. Callahan*, K. Sankaran*, J. Fukuyama*, P. McMurdie & S. Holmes*

TL;DR: By providing a complete workflow in R, this paper enables the user to do sophisticated downstream statistical analyses, whether parametric or nonparametric, and provides examples of using the R packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: July 21, 2019

2016 journal article

DADA2: High-resolution sample inference from Illumina amplicon data

Nature Methods, 13(7), 581–583.

By: B. Callahan*, P. McMurdie*, M. Rosen*, A. Han*, A. Johnson* & S. Holmes*

MeSH headings : Animals; Cohort Studies; Computational Biology / methods; DNA, Bacterial / genetics; False Positive Reactions; Feces / microbiology; Female; High-Throughput Nucleotide Sequencing / methods; Humans; Lactobacillus / classification; Lactobacillus / genetics; Lactobacillus / isolation & purification; Mice; Microbiota / genetics; Pregnancy; RNA, Ribosomal, 16S / genetics; Reproducibility of Results; Sequence Analysis, DNA / methods; Software; Vagina / microbiology
TL;DR: The open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors is presented, revealing a diversity of previously undetected Lactobacillus crispatus variants. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: July 21, 2019

2016 journal article

Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea

Nature Communications, 7(1), 10516.

MeSH headings : Animals; Bacteroidetes / genetics; Bottle-Nosed Dolphin / microbiology; Gastrointestinal Microbiome / genetics; Microbiota / genetics; Mouth / microbiology; Phylogeny; RNA, Ribosomal, 16S / genetics; Respiratory System / microbiology; Sea Lions / microbiology; Seawater / microbiology; Sequence Analysis, RNA; Tenericutes / genetics; Water Microbiology
TL;DR: The bacterial communities associated with various body sites in dolphins and sea lions, as well as the microbiota of their dietary fish and adjacent seawater are described, helping elucidate the factors structuring marine mammal microbiotas and may enhance monitoring of marine mammal health. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: Crossref, ORCID
Added: July 21, 2019

2016 journal article

Reproducible research workflow in R for the analysis of personalized human microbiome data

Pacific Symposium on Biocomputing, 21, 183–194.

By: B. Callahan, D. Proctor, D. Relman, J. Fukuyama & S. Holmes

Source: NC State University Libraries
Added: July 11, 2019

2016 conference paper

Reproducible research workflow in R for the analysis of personalized human microbiome data

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 21, 183.

By: B. Callahan, D. Proctor, D. Relman, J. Fukuyama & S. Holmes

Event: NIH Public Access

Source: ORCID
Added: August 21, 2019

2015 journal article

Temporal and spatial variation of the human microbiota during pregnancy

Proceedings of the National Academy of Sciences, 112(35), 11060–11065.

By: D. DiGiulio*, B. Callahan*, P. McMurdie*, E. Costello*, D. Lyell*, A. Robaczewska*, C. Sun*, D. Goltsman* ...

author keywords: 16S rRNA gene; pregnancy; preterm birth; microbiome; premature labor
MeSH headings : Female; Humans; Intestines / microbiology; Microbiota; Periodontium / microbiology; Pregnancy; Saliva / microbiology; Vagina / microbiology
TL;DR: It is suggested that pregnancy outcomes might be predicted by features of the microbiota early in gestation, as well as the potential impact of a persistent, altered postpartum microbiota on maternal health, including outcomes of pregnancies following short interpregnancy intervals. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Source: Crossref
Added: July 21, 2019

2015 journal article

Temporal and spatial variation of the human microbiota during pregnancy

Proceedings of the National Academy of Sciences, 112(35), 11060–11065.

By: D. DiGiulio, B. Callahan, P. McMurdie, E. Costello, D. Lyell, A. Robaczewska, C. Sun, D. Goltsman ...

Source: ORCID
Added: August 21, 2019

2014 journal article

Rapid evolution of adaptive niche construction in experimental microbial populations

Evolution, 68(11), 3307–3316.

By: B. Callahan*, T. Fukami* & D. Fisher*

author keywords: Adaptation; mutations; population biology; selection-experimental
MeSH headings : Adaptation, Biological; Directed Molecular Evolution; Environment; Genetic Fitness; Pseudomonas fluorescens / genetics; Pseudomonas fluorescens / physiology
TL;DR: It is found that adaptive niche construction emerged rapidly, within approximately 100 generations, and became ubiquitous after approximately 400 generations, suggesting that it may play a more important role in evolution than generally thought. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Crossref, ORCID
Added: July 21, 2019

2013 journal article

Evolutionary dynamics and information hierarchies in biological systems

Annals of the New York Academy of Sciences, 1305(1), 1–17.

author keywords: evolution; information hierarchy; chromatin; epigenetics; viruses; networks
MeSH headings : Animals; Biological Evolution; Chromatin / metabolism; Computational Biology / methods; Epigenomics; Evolution, Molecular; Humans
TL;DR: This work argues that the model of evolution as a passive filter selecting for random changes at the nucleotide level is being replaced with a paradigm in which evolution is a dynamic process both constrained and driven by the informational architecture of organisms across scales. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: July 21, 2019

2012 journal article

Denoising PCR-amplified metagenome data

BMC Bioinformatics, 13(1), 283.

By: M. Rosen, B. Callahan, D. Fisher & S. Holmes

Sources: NC State University Libraries, ORCID
Added: July 28, 2019

2012 journal article

The length scale of selection in protein evolution

Fly, 6(1), 16–20.

By: B. Callahan*

author keywords: molecular evolution; epistasis; fitness landscape; protein; correlation function; length scale; Drosophila; positive selection; molecular clock; overdispersion
MeSH headings : Animals; Drosophila; Drosophila Proteins / chemistry; Drosophila Proteins / genetics; Drosophila melanogaster; Evolution, Molecular; Selection, Genetic
TL;DR: The evidence presented in the study supporting a substantial role for epistasis in the process of molecular evolution is focused on, and the implications of this widespread epistasis on the overdispersion of the molecular clock and the efficacy of common tests for positive selection are discussed. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: July 21, 2019

2011 journal article

Correlated Evolution of Nearby Residues in Drosophilid Proteins

PLoS Genetics, 7(2), e1001315.

Ed(s): G. McVean

MeSH headings : Amino Acid Substitution; Animals; Drosophila Proteins / genetics; Drosophila melanogaster / genetics; Evolution, Molecular; Multigene Family; Mutation; Phylogeny; Selection, Genetic
TL;DR: It is found that amino acid substitutions are “clustered” along the protein sequence, that is, the frequency of additional substitutions is strongly enhanced within ≈10 residues of a first such substitution, but no such clustering is observed for synonymous substitutions, supporting a “correlation length” associated with selection on proteins as the causative mechanism. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: July 28, 2019

2011 journal article

Heterozygote advantage as a natural consequence of adaptation in diploids

Proceedings of the National Academy of Sciences, 108(51), 20666–20671.

By: D. Sellis, B. Callahan*, D. Petrov & P. Messer

MeSH headings : Adaptation, Physiological / genetics; Alleles; Animal Migration; Animals; Diploidy; Emigration and Immigration; Gene Expression; Genetic Variation; Haploidy; Heterozygote; Humans; Models, Genetic; Mutation; Phenotype; Polymorphism, Genetic; Selection, Genetic
TL;DR: It is found that in diploids, adaptation should often proceed through a succession of short-lived balanced states that maintain substantially higher levels of phenotypic and fitness variation in the population compared with classic adaptive walks. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: July 21, 2019

2009 journal article

Emergent gene order in a model of modular polyketide synthases

Proceedings of the National Academy of Sciences, 106(46), 19410–19415.

By: B. Callahan*, M. Thattai* & B. Shraiman*

author keywords: polyketides; horizontal transfer; evolution; collinearity; evolvability
MeSH headings : Animals; Bacteria / enzymology; Bacteria / genetics; Computer Simulation; Evolution, Molecular; Gene Order; Macrolides / metabolism; Models, Genetic; Plants / enzymology; Plants / genetics; Polyketide Synthases / biosynthesis; Polyketide Synthases / genetics; Protein Biosynthesis / genetics; Selection, Genetic
TL;DR: This work proposes an evolutionary origin for collinearity and demonstrates the mechanism by using a computational model of PKS evolution in a population, and provides a mathematical framework describing the secondary selection mechanism, which generalizes beyond the context of the present model. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: July 28, 2019

2009 thesis

Evolution on an interacting fitness landscape: The effects of the interplay of epistasis and recombination on genetic structure

University of California, Santa Barbara.

By: B. Callahan

Source: ORCID
Added: August 21, 2019

2003 journal article

Exploring the Interplay between Topology and Secondary Structural Formation in the Protein Folding Problem

The Journal of Physical Chemistry B, 107(40), 11193–11200.

By: M. Cheung*, J. Finke*, B. Callahan* & J. Onuchic*

Sources: Crossref, ORCID
Added: July 28, 2019

Employment

Updated: November 17th, 2017 13:45

2017 - present

NC State University, College of Veterinary Medicine Raleigh, NC, US
Assistant Professor Population Health & Pathobiology

Education

Updated: November 17th, 2017 13:44

2003 - 2009

University of California, Santa Barbara Santa Barbara, CA, US
Ph.D. Physics

1998 - 2002

Iowa State University Ames, IA, US
Bachelors of Science Physics, Math

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