Co-occurrence of Campylobacter Species in Children From Eastern Ethiopia, and Their Association With Environmental Enteric Dysfunction, Diarrhea, and Host …

Y Terefe, L Deblais, M Ghanem, YA Helmy… - Frontiers in public …, 2020 - frontiersin.org
High Campylobacter prevalence during early childhood has been associated with stunting
and environmental enteric dysfunction (EED), especially in low resource settings. This study …

Cobamide sharing is predicted in the human skin microbiome

MH Swaney, S Sandstrom, LR Kalan - Msystems, 2022 - journals.asm.org
The skin microbiome is a key player in human health, with diverse functions ranging from
defense against pathogens to education of the immune system. While recent studies have …

Upper respiratory microbial communities of healthy populations are shaped by niche and age

S Zelasko, MH Swaney, S Sandstrom, TC Davenport… - Microbiome, 2024 - Springer
Background Alterations in upper respiratory microbiomes have been implicated in sha**
host health trajectories, including by limiting mucosal pathogen colonization. However …

[HTML][HTML] Investigating the cow skin and teat canal microbiomes of the bovine udder using different sampling and sequencing approaches

CJ Dean, IB Slizovskiy, KK Crone, AX Pfennig… - Journal of Dairy …, 2021 - Elsevier
There is a need for standardized, efficient, and practical sampling methods to support large
population-based studies of the internal and external epithelial microbiomes of the bovine …

Qmatey: an automated pipeline for fast exact matching-based alignment and strain-level taxonomic binning and profiling of metagenomes

AK Adams, BD Kristy, M Gorman… - Briefings in …, 2023 - academic.oup.com
Metagenomics is a powerful tool for understanding organismal interactions; however,
classification, profiling and detection of interactions at the strain level remain challenging …

Metagenomic tracking of antibiotic resistance genes through a pre‐harvest vegetable production system: an integrated lab‐, microcosm‐and greenhouse‐scale …

I Keenum, L Wind, P Ray, G Guron… - Environmental …, 2022 - Wiley Online Library
Prior research demonstrated the potential for agricultural production systems to contribute to
the environmental spread of antibiotic resistance genes (ARGs). However, there is a need …

Microbiome-informed food safety and quality: longitudinal consistency and cross-sectional distinctiveness of retail chicken breast microbiomes

S Li, DA Mann, S Zhang, Y Qi, RJ Meinersmann… - Msystems, 2020 - journals.asm.org
Microorganisms and their communities on foods are important determinants and indicators
of food safety and quality. Despite growing interests in studying food and food-related …

[HTML][HTML] Whole-genome sequencing analysis to identify infection with multiple species of nontuberculous mycobacteria

V Khieu, P Ananta, O Kaewprasert, M Laohaviroj… - Pathogens, 2021 - mdpi.com
Mixed infection with multiple species of nontuberculous mycobacteria (NTM) is difficult to
identify and to treat. Current conventional molecular-based methods for identifying mixed …

Clinical metagenomics is increasingly accurate and affordable to detect enteric bacterial pathogens in stool

CL Peterson, D Alexander, JCY Chen, H Adam… - Microorganisms, 2022 - mdpi.com
Stool culture is the gold standard method to diagnose enteric bacterial infections; however,
many clinical laboratories are transitioning to syndromic multiplex PCR panels. PCR is …

[HTML][HTML] Efficient and quality-optimized metagenomic pipeline designed for taxonomic classification in routine microbiological clinical tests

S Buffet-Bataillon, G Rizk, V Cattoir, M Sassi, V Thibault… - Microorganisms, 2022 - mdpi.com
Efficient and Quality-Optimized Metagenomic Pipeline Designed for Taxonomic Classification
in Routine Microbiological Clinical Tests Next Article in Journal First Record of Hepatozoon …