Microbiota restoration therapies for recurrent Clostridioides difficile infection reach an important new milestone

The ladder of regulatory stringency and balance: an application to the US FDA's regulation of bacterial live therapeutics

The three main types of live bacterial therapies - probiotics, fecal/microbiome transplants, and engineered bacterial therapies - hold immense potential to revolutionize medicine. While offering targeted and personalized treatments for various diseases, these therapies also carry risks such as adverse immune reactions, antibiotic resistance, and the potential for unintended consequences. Therefore, developing and deploying these therapies necessitates a robust regulatory framework to protect public health while fostering innovation. In this paper, we propose a novel conceptual tool - the Ladder of Regulatory Stringency and Balance-which can assist in the design of robust regulatory regimes which encompass medicine practices based not only on definitive Randomized Controlled Trials (RCTs), but also on meta-analyses, observational studies, and clinicians experience. Regulatory stringency refers to the strictness of regulations, while regulatory balance concerns the degree of alignment between the regulatory framework governing a technology and the actual risks posed by specific products within that technology. Focusing on the US regulatory environment, we subsequently position the three types of live bacterial therapies on the Ladder. The insight gained from this exercise demonstrates that probiotics are generally positioned at the bottom of the Ladder, corresponding to low-stringency regulation, with a proportionate regulatory balance. However, probiotics intended for high-risk populations are currently subject to low-stringency regulations, resulting in under-regulation. Our analysis also supports the conclusion that fecal microbiota transplants (FMT) for recurrent Clostridium difficile infection should be positioned close to but below the threshold for under regulation by the U.S. Food and Drug Administration (FDA), and we recommend improved donor screening procedures, preservation and processing, storage, and distribution. Our framework can serve as a scale to assess regulatory gaps for live bacterial therapies and to identify potential solutions where such gaps exist.

Microbiota transplantation and administration of live biotherapeutic products for the treatment of dysbiosis-associated diseases

INTRODUCTION

The microbiota composition in humans varies according to the anatomical site and is crucial for maintaining homeostasis and an overall healthy state. Several gastrointestinal, vaginal, respiratory, and skin diseases are associated with dysbiosis. Alternative therapies such as microbiota transplantation can help restore microbiota normal composition and can be implemented to treat clinically relevant diseases.

AREAS COVERED

Current microbiota transplantation therapies conducted in clinical trials were included in this review (after searching on MEDLINE database from years 2017 to 2025) such as fecal microbiota transplantation (FMT) against recurrent Clostridioides difficile infection (rCDI) and vaginal microbiota transplantation (VMT) against bacterial vaginosis. Washed microbiota transplantation (WMT) and live biotherapeutic products (LBPs) were also reviewed.

EXPERT OPINION

In microbiota-based transplantation therapy, selecting optimal donors is a limitation. A stool or a vaginal microbiota bank should be implemented to overcome the time-consuming and expensive process of donor recruitment. Microbiota-based LBPs are also promising treatment alternatives for rCDI and other dysbiosis-associated diseases. Specific LBPs could be engineered out of donor fluids-derived strains to achieve the selection of specific beneficial microorganisms for the treatment of specific dysbiosis-associated diseases. Personalized microbiota-based treatments are promising solutions for dysbiosis-associated diseases, which remains an important necessity in clinical practice.

Enabling next-generation anaerobic cultivation through biotechnology to advance functional microbiome research

Microbiomes are complex communities of microorganisms that are essential for biochemical processes on Earth and for the health of humans, animals and plants. Many environmental and host-associated microbiomes are dominated by anaerobic microbes, some of which cannot tolerate oxygen. Anaerobic microbial communities have been extensively studied over the last 20 years using molecular techniques, especially next-generation sequencing. However, there is a renewed interest in microbial cultivation because isolates provide the basis for understanding the taxonomic and functional units of biodiversity, elucidating novel biochemical pathways and the mechanisms underlying microbe-microbe and microbe-host interactions and opening new avenues for biotechnological and clinical applications. In this Perspective, we present areas of research and applications that will benefit from advancement in anaerobic microbial cultivation. We highlight key technical and infrastructural hurdles associated with the development and deployment of sophisticated cultivation workflows. Improving the performance of cultivation techniques will set new trends in functional microbiome research in the coming years.

The global resistance problem and the clinical antibacterial pipeline

A comprehensive analysis of the clinical antibacterial pipeline demonstrates that there is a limited range of strategies that are primarily focused on modified versions of widely used chemical classes. These modifications aim to circumvent class-specific resistance mechanisms and reduce resistance rates in certain multidrug-resistant pathogens. Owing to the great variation in resistance rates and mechanisms, the clinical success of current approaches varies substantially across different countries, regions, and economic and environmental conditions, which affects the global societal value of these antibiotics that remain vulnerable to cross-resistance. Although there has been some progress in developing urgently needed antibiotics with novel targets and chemical structures, some of which have advanced to phase I/II trials, further breakthroughs are required. Additionally, adjunctive agents designed to enhance the outcome of conventional antibiotic therapies, along with bacteriophages that offer targeted and personalized treatments, are also under investigation. However, the potential of adjunctive therapeutics, such as antivirulence agents, and bacteriophages has yet to be realized in terms of feasibility and global societal impact.

Balancing act: counteracting adverse drug effects on the microbiome

The human gut microbiome, a community of microbes that plays a crucial role in our wellbeing, is highly adaptable but also vulnerable to drug treatments. This vulnerability can have serious consequences for the host, for example, increasing susceptibility to infections, immune, metabolic, and cognitive disorders. However, the microbiome's adaptability also provides opportunities to prevent, protect, or even reverse drug-induced damage. Recently, several innovative approaches have emerged aimed at minimizing the collateral damage of drugs on the microbiome. Here, we outline these approaches, discuss their applicability in different treatment scenarios, highlight current challenges, and suggest avenues that may lead to an effective protection of the microbiome.