Defined gut microbial communities: promising tools to understand and combat disease

Modeling Dynamics of Human Gut Microbiota Derived from Gluten Metabolism: Obtention, Maintenance and Characterization of Complex Microbial Communities

Western diets are rich in gluten-containing products, which are frequently poorly digested. The human large intestine harbors microorganisms able to metabolize undigested gluten fragments that have escaped digestion by human enzymatic activities. The aim of this work was obtaining and culturing complex human gut microbial communities derived from gluten metabolism to model the dynamics of healthy human large intestine microbiota associated with different gluten forms. For this purpose, stool samples from six healthy volunteers were inoculated in media containing predigested gluten or predigested gluten plus non-digested gluten. Passages were carried out every 24 h for 15 days in the same medium and community composition along time was studied via V3-V4 16S rDNA sequencing. Diverse microbial communities were successfully obtained. Moreover, communities were shown to be maintained in culture with stable composition for 14 days. Under non-digested gluten presence, communities were enriched in members of Bacillota, such as Lachnospiraceae, Clostridiaceae, Streptococcaceae, Peptoniphilaceae, Selenomonadaceae or Erysipelotrichaceae, and members of Actinomycetota, such as Bifidobacteriaceae and Eggerthellaceae. Contrarily, communities exposed to digested gluten were enriched in Pseudomonadota. Hence, this study shows a method for culture and stable maintenance of gut communities derived from gluten metabolism. This method enables the analysis of microbial metabolism of gluten in the gut from a community perspective.

The Effect of Akkermansia muciniphila and Its Outer Membrane Vesicles on MicroRNAs Expression of Inflammatory and Anti-inflammatory Pathways in Human Dendritic Cells

Probiotics play a crucial role in immunomodulation by regulating dendritic cell (DC) maturation and inducing tolerogenic DCs. Akkermansia muciniphila affects inflammatory response by elevating inhibitory cytokines. We aimed to evaluate whether Akkermansia muciniphila and its outer membrane vesicles (OMVs) affect microRNA-155, microRNA-146a, microRNA-34a, and let-7i expression of inflammatory and anti-inflammatory pathways. Peripheral blood mononuclear cells (PBMCs) were isolated from the healthy volunteers. To produce DCs, monocytes were cultivated with granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin-4 (IL-4). DCs were allocated into six subgroups: DC + Lipopolysaccharide (LPS), DC + dexamethasone, DC + A. muciniphila (MOI 100, 50), DC + OMVs (50 µg/ml), and DC + PBS. The surface expression of human leukocyte antigen-antigen D related (HLA-DR), CD86, CD80, CD83, CD11c, and CD14 was examined using flow cytometry, and the expression of microRNAs was assessed using qRT-PCR, and the levels of IL-12 and IL-10 were measured using ELISA. A. muciniphila (MOIs 50, 100) could significantly decrease IL-12 levels relative to the LPS group. The IL-10 levels were decreased in the DC + LPS group than the DC + dexamethasone group. Treatment with A. muciniphila (MOI 100) and OMVs could elevate the concentrations of IL-10. DC treatment with LPS led to a significant increment in the expression of microRNA-155, microRNA-34a, and microRNA-146a. The expression of these microRNAs was reversed by A. muciniphilia and its OMVs treatment. Let-7i increased in treatment groups compared to the DC + LPS group. A. muciniphilia (MOI 50) had a substantial effect on the expression of HLA-DR, CD80, and CD83 on DCs. Therefore, DCs treatment with A. muciniphila led to induce tolerogenic DCs and the production of anti-inflammatory IL-10.

Effects of exercise and physical activity on gut microbiota composition and function in older adults: a systematic review

BACKGROUND

The characterization and research around the gut microbiome in older people emphasize microbial populations change considerably by losing the diversity of species. Then, this review aims to determine if there is any effect on the gut microbiota of adults older than 65 that starts an exercise intervention or improves physical activity level. Also, this review describes the changes in composition, diversity, and function of the gut microbiota of older subjects that had improved their physical activity level.

METHODS

The type of studies included in this review were studies describing human gut microbiota responses to any exercise stimulus; cross-sectional studies focused on comparing gut microbiota in older adults with different physical activity levels-from athletes to inactive individuals; studies containing older people (women and men), and studies written in English. This review's primary outcomes of interest were gut microbiota abundance and diversity.

RESULTS

Twelve cross-sectional studies and three randomized controlled trials were examined. Independently of the type of study, diversity metrics from Alpha and Beta diversity remained without changes in almost all the studies. Likewise, cross-sectional studies do not reflect significant changes in gut microbiota diversity; no significant differences were detected among diverse groups in the relative abundances of the major phyla or alpha diversity measures. Otherwise, relative abundance analysis showed a significant change in older adults who conducted an exercise program for five weeks or more at the genus level.

CONCLUSIONS

Here, we did not identify significant shifts in diversity metrics; only one study reported a significant difference in Alpha diversity from overweight people with higher physical activity levels. The abundance of some bacteria is higher in aged people, after an exercise program, or in comparison with control groups, especially at the genus and species levels. There needs to be more information related to function and metabolic pathways that can be crucial to understand the effect of exercise and physical activity in older adults.

TRIAL REGISTRATION

PROSPERO ID: CRD42022331551.

Assembling symbiotic bacterial species into live therapeutic consortia that reconstitute microbiome functions

Increasing experimental evidence suggests that administering live commensal bacterial species can optimize microbiome composition and lead to reduced disease severity and enhanced health. Our understanding of the intestinal microbiome and its functions has increased over the past two decades largely due to deep sequence analyses of fecal nucleic acids, metabolomic and proteomic assays to measure nutrient use and metabolite production, and extensive studies on the metabolism and ecological interactions of a wide range of commensal bacterial species inhabiting the intestine. Herein, we review new and important findings that have emerged from this work and provide thoughts and considerations on approaches to re-establish and optimize microbiome functions by assembling and administering commensal bacterial consortia.

The Robogut: A Bioreactor Model of the Human Colon for Evaluation of Gut Microbial Community Ecology and Function

The human colon is inhabited by a complex community of microbes. These microbes are integral to host health and physiology. Understanding how and when the microbiome causally influences host health will require microbiome models that can be tightly controlled and manipulated. While in vivo models are unrivalled in their ability to study host-microbial interplay, in vitro models are gaining in popularity as methods to study the ecology and function of the gut microbiota, and benefit from tight controllability and reproducibility, as well as reduced ethical constraints. In this set of protocols, we describe the Robogut, a single-stage bioreactor system designed to replicate the conditions of the distal human colon, to culture whole microbial communities derived from stool and/or colonic biopsy samples, with consideration of methods to create culture medium formulations and to build, run, and sample the bioreactor apparatus. Cleaning and maintenance of the bioreactor system are also described. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Growth medium preparation Support Protocol 1: Preparing medium supplements Basic Protocol 2: Preparing the bioreactor vessels Support Protocol 2: Making acid and base bottles Support Protocol 3: Preparing the effluent bottles Support Protocol 4: Making acid solution Support Protocol 5: Making base solution Basic Protocol 3: Preparing inoculum and inoculating bioreactors Alternate Protocol 1: Preparing inoculum less than 0.5% (w/v) of vessel volume Alternate Protocol 2: Preparing synthetic community aliquots and inoculation via the septum Alternate Protocol 3: Preparing inoculum from a tissue sample Basic Protocol 4: Sampling the bioreactor vessel Basic Protocol 5: Harvesting bioreactor vessel contents at end of experiment Support Protocol 6: Cleaning and sterilizing sampling needles Basic Protocol 6: Cleaning the bioreactor vessel Support Protocol 7: Cleaning bioreactor support bottles.

A network perspective on the ecology of gut microbiota and progression of type 2 diabetes: Linkages to keystone taxa in a Mexican cohort

Introduction

The human gut microbiota (GM) is a dynamic system which ecological interactions among the community members affect the host metabolism. Understanding the principles that rule the bidirectional communication between GM and its host, is one of the most valuable enterprise for uncovering how bacterial ecology influences the clinical variables in the host.

Methods

Here, we used SparCC to infer association networks in 16S rRNA gene amplicon data from the GM of a cohort of Mexican patients with type 2 diabetes (T2D) in different stages: NG (normoglycemic), IFG (impaired fasting glucose), IGT (impaired glucose tolerance), IFG + IGT (impaired fasting glucose plus impaired glucose tolerance), T2D and T2D treated (T2D with a 5-year ongoing treatment).

Results

By exploring the network topology from the different stages of T2D, we observed that, as the disease progress, the networks lose the association between bacteria. It suggests that the microbial community becomes highly sensitive to perturbations in individuals with T2D. With the purpose to identify those genera that guide this transition, we computationally found keystone taxa (driver nodes) and core genera for a Mexican T2D cohort. Altogether, we suggest a set of genera driving the progress of the T2D in a Mexican cohort, among them Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-010, Ruminococcaceae UCG-002, Ruminococcaceae UCG-005, Alistipes, Anaerostipes, and Terrisporobacter.

Discussion

Based on a network approach, this study suggests a set of genera that can serve as a potential biomarker to distinguish the distinct degree of advances in T2D for a Mexican cohort of patients. Beyond limiting our conclusion to one population, we present a computational pipeline to link ecological networks and clinical stages in T2D, and desirable aim to advance in the field of precision medicine.

The intestinal microbiota: from health to disease, and back

Our understanding of the composition and the function of the intestinal microbiota has significantly increased over the past few years. In a series of reviews focusing on the role of the intestinal microbiota in health and disease, we explore recent conceptual and technological advances in this rapidly evolving research arena.