Integrated molecular approaches for fermented food microbiome research

AM Walsh, J Leech, C Huttenhower… - FEMS Microbiology …, 2023 - academic.oup.com
Molecular technologies, including high-throughput sequencing, have expanded our
perception of the microbial world. Unprecedented insights into the composition and function …

Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women

CJ Worby, HL Schreiber IV, TJ Straub, LR van Dijk… - Nature …, 2022 - nature.com
Recurrent urinary tract infections (rUTIs) are a major health burden worldwide, with history of
infection being a significant risk factor. While the gut is a known reservoir for uropathogenic …

[HTML][HTML] Metagenomics approaches for improving food safety: a review

C Billington, JM Kingsbury, L Rivas - Journal of food Protection, 2022 - Elsevier
Advancements in next-generation sequencing technology have dramatically reduced the
cost and increased the ease of microbial whole genome sequencing. This approach is …

Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement

MH Woodworth, RE Conrad, M Haldopoulos… - Science translational …, 2023 - science.org
Multidrug-resistant organism (MDRO) colonization is a fundamental challenge in
antimicrobial resistance. Limited studies have shown that fecal microbiota transplantation …

Genetic strategies for sex-biased persistence of gut microbes across human life

C Tarracchini, G Alessandri, F Fontana… - Nature …, 2023 - nature.com
Although compositional variation in the gut microbiome during human development has
been extensively investigated, strain-resolved dynamic changes remain to be fully …

Strong pathogen competition in neonatal gut colonisation

T Mäklin, HA Thorpe, AK Pöntinen… - Nature …, 2022 - nature.com
Opportunistic bacterial pathogen species and their strains that colonise the human gut are
generally understood to compete against both each other and the commensal species …

Gut microbiome perturbation, antibiotic resistance, and Escherichia coli strain dynamics associated with international travel: a metagenomic analysis

CJ Worby, S Sridhar, SE Turbett, MV Becker… - The Lancet …, 2023 - thelancet.com
Background Culture-based studies have shown that acquisition of extended-spectrum β-
lactamase-producing Enterobacterales is common during international travel; however, little …

High-resolution strain-level microbiome composition analysis from short reads

H Liao, Y Ji, Y Sun - Microbiome, 2023 - Springer
Background Bacterial strains under the same species can exhibit different biological
properties, making strain-level composition analysis an important step in understanding the …

Detection of Klebsiella pneumoniae human gut carriage: a comparison of culture, qPCR, and whole metagenomic sequencing methods

K Lindstedt, D Buczek, T Pedersen, E Hjerde… - Gut …, 2022 - Taylor & Francis
Klebsiella pneumoniae is an important opportunistic healthcare-associated pathogen and
major contributor to the global spread of antimicrobial resistance. Gastrointestinal …

Development of early life gut resistome and mobilome across gestational ages and microbiota-modifying treatments

A Bargheet, C Klingenberg, E Esaiassen, E Hjerde… - …, 2023 - thelancet.com
Background Gestational age (GA) and associated level of gastrointestinal tract maturation
are major factors driving the initial gut microbiota composition in preterm infants. Besides …