Bioinformatic Genome Comparisons for Taxonomic and Phylogenetic Assignments Using Aeromonas as a Test Case

SM Colston, MS Fullmer, L Beka, B Lamy, JP Gogarten… - MBio, 2014 - Am Soc Microbiol
Prokaryotic taxonomy is the underpinning of microbiology, as it provides a framework for the
proper identification and naming of organisms. The “gold standard” of bacterial species …

[HTML][HTML] Fluorescence in situ hybridization (FISH) and cell sorting of living bacteria

G Batani, K Bayer, J Böge, U Hentschel, T Thomas - Scientific reports, 2019 - nature.com
Despite the development of several cultivation methods, the rate of discovery of
microorganisms that are yet-to-be cultivated outpaces the rate of isolating and cultivating …

[HTML][HTML] Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment

L Wurch, RJ Giannone, BS Belisle, C Swift… - Nature …, 2016 - nature.com
Biological features can be inferred, based on genomic data, for many microbial lineages that
remain uncultured. However, cultivation is important for characterizing an organism's …

Gut metabotypes govern health effects of dietary polyphenols

S Bolca, T Van de Wiele, S Possemiers - Current opinion in biotechnology, 2013 - Elsevier
Polyphenols are thought to be responsible for some of the health effects conferred by a diet
rich in fruit and vegetables. Both the formation of bioactive polyphenol-derived metabolites …

Increasing phytoremediation efficiency and reliability using novel omics approaches

TH Bell, S Joly, FE Pitre, E Yergeau - Trends in biotechnology, 2014 - cell.com
Phytoremediation is a cost-effective green alternative to traditional soil remediation
technologies, but has experienced varied success in practice. The recent omics revolution …

Oral biofilms: molecular analysis, challenges, and future prospects in dental diagnostics

T Do, D Devine, PD Marsh - Clinical, cosmetic and investigational …, 2013 - Taylor & Francis
Oral biofilms are functionally and structurally organized polymicrobial communities that are
embedded in an extracellular matrix of exopolymers on mucosal and dental surfaces. These …

How do species interactions affect evolutionary dynamics across whole communities?

TG Barraclough - Annual Review of Ecology, Evolution, and …, 2015 - annualreviews.org
Theories of how species evolve in changing environments mostly consider single species in
isolation or pairs of interacting species. Yet all organisms live in diverse communities …

A new perspective on microbial landscapes within food production

NA Bokulich, ZT Lewis, K Boundy-Mills… - Current opinion in …, 2016 - Elsevier
Highlights•Microbes affect the quality and safety of food.•New DNA sequencing tools hold
great promise for studying microbial impacts on food.•Microbes in man-made environments …

In vivo fermentation of a Pleurotus eryngii polysaccharide and its effects on fecal microbiota composition and immune response

G Ma, BM Kimatu, L Zhao, W Yang, F Pei, Q Hu - Food & function, 2017 - pubs.rsc.org
A novel, homogeneous Pleurotus eryngii polysaccharide (PEP)(molecular weight 426 kDa,
purity 91.25±3.14%) which mainly consisted of glucose with β-type glycosidic linkages was …

Deprivation of dietary fiber in specific-pathogen-free mice promotes susceptibility to the intestinal mucosal pathogen Citrobacter rodentium

M Neumann, A Steimle, ET Grant, M Wolter… - Gut …, 2021 - Taylor & Francis
The change of dietary habits in Western societies, including reduced consumption of fiber, is
linked to alterations in gut microbial ecology. Nevertheless, mechanistic connections …