Research graph
References from Nasopharyngeal microbiome and resistome profiles in dairy calves fed milk replacer with low-level β-lactams. Local targets link to admitted publications; unresolved targets remain external evidence.
Intranasal bacterial therapeutics reduce colonization by the respiratory pathogen Mannheimia haemolytica in dairy calves
10.1128/msystems.00629-19 · 2020 · External reference
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Risk for the development of antimicrobial resistance (AMR) due to feeding of calves with milk containing residues of antibiotics
2017 · External reference
Trimmomatic: A flexible trimmer for Illumina sequence data
10.1093/bioinformatics/btu170 · 2014 · External reference
Identification of bovine respiratory disease through the nasal microbiome
10.1186/s42523-022-00167-y · 2022 · External reference
Dynamics of the nasopharyngeal microbiome of apparently healthy calves and those with clinical symptoms of bovine respiratory disease from disease diagnosis to recovery
10.3389/fvets.2023.1297158 · 2023 · External reference
Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data
10.1186/s40168-018-0605-2 · 2018 · External reference
MEGARes 2.0: A database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data
10.1093/nar/gkz1010 · 2020 · External reference
MultiQC: Summarize analysis results for multiple tools and samples in a single report
10.1093/bioinformatics/btw354 · 2016 · External reference
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A cross-sectional study of dairy cattle metagenomes reveals increased antimicrobial resistance in animals farmed in a heavy metal contaminated environment
10.3389/fmicb.2020.590325 · 2020 · External reference
Economic analysis of feeding pasteurized nonsaleable milk versus conventional milk replacer to dairy calves
10.2460/javma.2005.226.1547 · 2005 · External reference
Selection of resistant bacteria at very low antibiotic concentrations
10.1371/journal.ppat.1002158 · 2011 · External reference
The nasopharyngeal microbiota of beef cattle before and after transport to a feedlot
10.1186/s12866-017-0978-6 · 2017 · External reference
Spread of tetracycline resistance genes at a conventional dairy farm
10.3389/fmicb.2015.00536 · 2015 · External reference
Antibiotic resistance in gut bacteria from dairy calves: A dose response to the level of antibiotics fed in milk
10.3168/jds.s0022-0302(03)74006-5 · 2003 · External reference
Common contaminants in next-generation sequencing that hinder discovery of low-abundance microbes
10.1371/journal.pone.0097876 · 2014 · External reference
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Fast and accurate short read alignment with Burrows-Wheeler transform
10.1093/bioinformatics/btp324 · 2009 · External reference
The Sequence Alignment/Map format and SAMtools
10.1093/bioinformatics/btp352 · 2009 · External reference
The upper respiratory tract microbiome and its potential role in bovine respiratory disease and otitis media
10.1038/srep29050 · 2016 · External reference
The gastrointestinal microbiome in dairy cattle is constrained by the deterministic driver of the region and the modified effect of diet
10.1186/s40168-022-01453-2 · 2023 · External reference
The fecal resistome of dairy cattle is associated with diet during nursing
10.1038/s41467-019-12111-x · 2019 · External reference
Bracken: Estimating species abundance in metagenomics data
2017 · External reference
Metagenome analysis using the Kraken software suite
10.1038/s41596-022-00738-y · 2022 · External reference
A single intranasal dose of essential oil spray confers modulation of the nasopharyngeal microbiota and short-term inhibition of Mannheimia in feedlot cattle: A pilot study
10.1038/s41598-023-50704-1 · 2024 · External reference
10.1177/1040638717737589
10.1177/1040638717737589 · 2018 · External reference
Feeding pasteurized waste milk to preweaned dairy calves changes fecal and upper respiratory tract microbiota
10.3389/fvets.2019.00159 · 2019 · External reference
Timely diagnosis of dairy calf respiratory disease using a standardized scoring system
10.1017/s1466252314000267 · 2014 · External reference
Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data
10.1371/journal.pone.0061217 · 2013 · External reference
Multiresidue screening of milk withheld for sale at dairy farms in central New York State
10.3168/jds.2013-7421 · 2014 · External reference
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The nasopharyngeal microbiota of preweaned dairy calves with and without ultrasonographic lung lesions
10.3168/jds.2020-19096 · 2021 · External reference
The archaeal and bacterial community structure in composted cow manures is defined by the original populations: A shotgun metagenomic approach
10.3389/fmicb.2024.1425548 · 2024 · External reference
Calves as main reservoir of antibiotic resistance genes in dairy farms
10.3389/fpubh.2022.918658 · 2022 · External reference
Changes in fecal microbiota of dairy cows with and without endometritis
10.1186/s12917-025-04580-8 · 2025 · External reference
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Multidrug residues and antimicrobial resistance patterns in waste milk from dairy farms in Central California
10.3168/jds.2018-14398 · 2018 · External reference
Excretion of antibiotic resistance genes by dairy calves fed milk replacers with varying doses of antibiotics
10.3389/fmicb.2012.00139 · 2012 · External reference
Prevalence and antimicrobial susceptibility of Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni isolated from the lower respiratory tract of healthy feedlot cattle and those diagnosed with bovine respiratory disease
10.1016/j.vetmic.2017.07.013 · 2017 · External reference
Analysis of pathogenic bacteria and antimicrobial residues in bovine waste milk on dairy farms in southern Chile
10.3389/fvets.2025.1613185 · 2025 · External reference
Preweaned heifer management on US dairy operations: Part I. Descriptive characteristics of preweaned heifer raising practices
10.3168/jds.2017-14010 · 2018 · External reference
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Neisseria models of infection and persistence in the upper respiratory tract
10.1093/femspd/ftx031 · 2017 · External reference
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Improved metagenomic analysis with Kraken 2
10.1186/s13059-019-1891-0 · 2019 · External reference
The impact of rumen and hindgut microbiomes on the persistent productivity of long-lived dairy cows
10.1186/s40168-025-02309-1 · 2026 · External reference
