Advancing functional and translational microbiome research using meta-omics approaches

X Zhang, L Li, J Butcher, A Stintzi, D Figeys - Microbiome, 2019 - Springer
The gut microbiome has emerged as an important factor affecting human health and
disease. The recent development of–omics approaches, including phylogenetic marker …

Sodium oligomannate therapeutically remodels gut microbiota and suppresses gut bacterial amino acids-shaped neuroinflammation to inhibit Alzheimer's disease …

X Wang, G Sun, T Feng, J Zhang, X Huang, T Wang… - Cell research, 2019 - nature.com
Recently, increasing evidence has suggested the association between gut dysbiosis and
Alzheimer's disease (AD) progression, yet the role of gut microbiota in AD pathogenesis …

Microbiota-directed biotherapeutics: Considerations for quality and functional assessment

EE Fekete, D Figeys, X Zhang - Gut Microbes, 2023 - Taylor & Francis
Mounting evidence points to causative or correlative roles of gut microbiome in the
development of a myriad of diseases ranging from gastrointestinal diseases, metabolic …

An in vitro model maintaining taxon-specific functional activities of the gut microbiome

L Li, E Abou-Samra, Z Ning, X Zhang, J Mayne… - Nature …, 2019 - nature.com
In vitro gut microbiome models could provide timely and cost-efficient solutions to study
microbiome responses to drugs. For this purpose, in vitro models that maintain the functional …

Effect of in vitro cultivation on human gut microbiota composition using 16S rDNA amplicon sequencing and metabolomics approach

P Średnicka, MŁ Roszko, D Popowski, M Kowalczyk… - Scientific Reports, 2023 - nature.com
Gut microbiota (GM) plays many key functions and helps maintain the host's health.
Consequently, the development of GM cultivation under in vitro stimulating physiological …

RapidAIM: a culture-and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs

L Li, Z Ning, X Zhang, J Mayne, K Cheng, A Stintzi… - Microbiome, 2020 - Springer
Background Human-targeted drugs may exert off-target effects or can be repurposed to
modulate the gut microbiota. However, our understanding of such effects is limited due to a …

Metaproteomics of the human gut microbiota: challenges and contributions to other OMICS

NI Isaac, D Philippe, A Nicholas, D Raoult… - Clinical Mass …, 2019 - Elsevier
Our digestive tract hosts more than a billion microorganisms comprising non-pathogenic
bacteria, viruses, fungi and parasites. Understanding and characterizing the human gut …

O-Mucin-degrading carbohydrate-active enzymes and their possible implication in inflammatory bowel diseases

A Labourel, JL Parrou, C Deraison… - Essays in …, 2023 - portlandpress.com
Inflammatory bowel diseases (IBD) are modern diseases, with incidence rising around the
world. They are associated with perturbation of the intestinal microbiota, and with alteration …

Designs and methodologies to recreate in vitro human gut microbiota models

F Biagini, C Daddi, M Calvigioni, C De Maria… - Bio-Design and …, 2023 - Springer
The human gut microbiota is widely considered to be a metabolic organ hidden within our
bodies, playing a crucial role in the host's physiology. Several factors affect its composition …

A flexible high-throughput cultivation protocol to assess the response of individuals' gut microbiota to diet-, drug-, and host-related factors

JN Zünd, S Plüss, D Mujezinovic, C Menzi… - ISME …, 2024 - academic.oup.com
The anaerobic cultivation of fecal microbiota is a promising approach to investigating how
gut microbial communities respond to specific intestinal conditions and perturbations. Here …