Controlled Complexity: Optimized Systems to Study the Role of the Gut Microbiome in Host Physiology

Abstract

The profound impact of the gut microbiome on host health has led to a revolution in biomedical research, motivating researchers from disparate fields to define the specific molecular mechanisms that mediate host-beneficial effects. The advent of genomic technologies allied to the use of model microbiomes in gnotobiotic mouse models has transformed our understanding of intestinal microbial ecology and the impact of the microbiome on the host. However, despite incredible advances, our understanding of the host-microbiome dialogue that shapes host physiology is still in its infancy. Progress has been limited by challenges associated with developing model systems that are both tractable enough to provide key mechanistic insights while also reflecting the enormous complexity of the gut ecosystem. Simplified model microbiomes have facilitated detailed interrogation of transcriptional and metabolic functions of the microbiome but do not recapitulate the interactions seen in complex communities. Conversely, intact complex communities from mice or humans provide a more physiologically relevant community type, but can limit our ability to uncover high-resolution insights into microbiome function. Moreover, complex microbiomes from lab-derived mice or humans often do not readily imprint human-like phenotypes. Therefore, improved model microbiomes that are highly defined and tractable, but that more accurately recapitulate human microbiome-induced phenotypic variation are required to improve understanding of fundamental processes governing host-microbiome mutualism. This improved understanding will enhance the translational relevance of studies that address how the microbiome promotes host health and influences disease states. Microbial exposures in wild mice, both symbiotic and infectious in nature, have recently been established to more readily recapitulate human-like phenotypes. The development of synthetic model communities from such “wild mice” therefore represents an attractive strategy to overcome the limitations of current approaches. Advances in microbial culturing approaches that allow for the generation of large and diverse libraries of isolates, coupled to ever more affordable large-scale genomic sequencing, mean that we are now ideally positioned to develop such systems. Furthermore, the development of sophisticated in vitro systems is allowing for detailed insights into host-microbiome interactions to be obtained. Here we discuss the need to leverage such approaches and highlight key challenges that remain to be addressed.

Probiotics in Women and Pediatrics Health; A Narrative Review

“…Probiotics are crucial in maintaining a healthy GM, which is essential for overall female wellness. Earlier studies have shown that probiotics can improve digestion, enhance immunity, and reduce inflammatory responses [1][2][3]. Moreover, probiotics help treat a range of ailments, including diarrhea and urinary tract infections.…”

“…GM metabolizes undigested meal remnants, from which more energy is derived. A balanced relationship between bacterial strains and our bodies enables homeostasis [3]. The diversity of natural flora varies with age, health, living situations, and the use of antibacterial, disinfectants, and certain cosmetics.…”

Denoising sparse microbial signals from single-cell sequencing of mammalian host tissues

“…The microbiome plays an integral role in healthy development, aging, and multiple disease contexts 1 . However, integrated analyses of host-microbiome ecosystems in vivo have been difficult to achieve in part due to the lack of relevant model systems 2 and substantial differences across patients 3,4 . Recently, it has been shown that microbial nucleic acids are captured in polyA-selected RNA sequencing of clinical samples from humans 5–7 .…”

“…The microbiome plays an integral role in healthy development, aging, and multiple diseases, however the nature of its influence in many contexts remains poorly understood 1 . This is because integrated analyses of host-microbiome ecosystems in vivo have been difficult to achieve in part due to the lack of relevant model systems 2 , technological barriers to directly profiling host-microbial interactions at high resolution in human tissues, and substantial heterogeneity across patients 3,4 .…”