Toward hypothesis-driven, personalized microbiome screening

Sedrani, Catherine; Wilmes, Paul

doi:10.1016/j.crmeth.2021.100139

Cited by 4 publications

(5 citation statements)

References 15 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It will particularly be beneficial in understanding the disease‐triggering microbial strains helping to discover tailored‐treatment approaches. The genomic screening will help to account for the significant degree of interpersonal variations and will become increasingly relevant to precisely study the genotype and phenotype of an individual 44 . Taken together, they will enhance the quality of oral microbiome studies to identify the diagnostic and treatment markers.…”

Section: Discussionmentioning

confidence: 99%

Multistability and hysteresis in states of oral microbiota: Is it impacting the dental clinical cohort studies?

Mangal

Noh

Lee

et al. 2023

J of Periodontal Research

View full text Add to dashboard Cite

Introduction Microbiome from a “healthy cohort” is used as a reference for comparison to cases and intervention. However, the studies with cohort‐based clinical research have not sufficiently accounted for the multistability in oral microbial community. The screening is limited to phenotypic features with marked variations in microbial genomic markers. Herein, we aimed to assess the stability of the oral microbiome across time from an intervention‐free “healthy” cohort. Methods We obtained 33 supragingival samples of 11 healthy participants from the biobank. For each participant, we processed one sample as baseline (T0) and two samples spaced at 1‐month (T1) and 3‐month (T2) intervals for 16S ribosomal RNA gene sequencing analysis. Results We observed that taxonomic profiling had a similar pattern of dominant genera, namely, Rothia, Prevotella, and Hemophilus, at all time points. Shannon diversity revealed a significant increase from T0 (p < .05). Bray Curtis dissimilarity was significant (R = −.02, p < .01) within the cohort at each time point. Community stability had negative correlation to synchrony (r = −.739; p = .009) and variance (r = −.605; p = .048) of the species. Clustering revealed marked differences in the grouping patterns between the three time points. For all time points, the clusters presented a substantially dissimilar set of differentially abundant taxonomic and functional biomarkers. Conclusion Our observations indicate towards the presence of multistable states within the oral microbiome in an intervention‐free healthy cohort. For a conclusive and meaningful long‐term reference, dental clinical research should account for multistability in the personalized therapy approach to improve the identification and classification of reliable markers.

show abstract

Section: Discussionmentioning

confidence: 99%

Multistability and hysteresis in states of oral microbiota: Is it impacting the dental clinical cohort studies?

Mangal

Noh

Lee

et al. 2023

J of Periodontal Research

View full text Add to dashboard Cite

show abstract

“…Going forward, it would be important to not only have iPSC-derived ENs, but also iPSC-derived epithelial cells inside the device, to transition the device into a personalized model. Importantly, this personalized model could be used to test pre-, pro-, and synbiotics 10 , 11 and potentially develop personalized screening and therapeutic approaches 17 . Personalized neuroHuMiX could eventually shed light on the 'dark matter' of the human gut microbiome and its interactions with the nervous system along the gut microbiome-nervous system axis, paving the way for therapeutic assessment and interventions.…”

Section: Discussionmentioning

confidence: 99%

A Gut-on-a-Chip Model to Study the Gut Microbiome-Nervous System Axis

Sedrani

Gomez-Giro

Grandmougin

et al. 2023

JoVE

View full text Add to dashboard Cite

The human body is colonized by at least the same number of microbial cells as it is composed of human cells, and most of these microorganisms are located in the gut.Though the interplay between the gut microbiome and the host has been extensively studied, how the gut microbiome interacts with the enteric nervous system remains largely unknown. To date, a physiologically representative in vitro model to study gut microbiome-nervous system interactions does not exist.To fill this gap, we further developed the human-microbial crosstalk (HuMiX) guton-chip model by introducing induced pluripotent stem cell-derived enteric neurons into the device. The resulting model, 'neuroHuMiX', allows for the co-culture of bacterial, epithelial, and neuronal cells across microfluidic channels, separated by semi-permeable membranes. Despite separation of the different cell types, the cells can communicate with each other through soluble factors, simultaneously providing an opportunity to study each cell type separately. This setup allows for first insights into how the gut microbiome affects the enteric neuronal cells. This is a critical first step in studying and understanding the human gut microbiome-nervous system axis.

show abstract

“…A limitation of these metagenomic approaches compared to culture-based method is the potential loss of information on low-abundance strains as well as low strain-resolution accuracy, problems that can be addressed by combining metagenome-assembled regions with newly discovered single-cell metagenomic methods. However, these methods remain prohibitive in terms of costs and analysis challenges ( 310 , 311 ). New microfluidic methods based on droplets containing microbial cells from fecal samples are also under evaluation to produce complete and precise microbial characterization that would enable an improved definition of overall microbial function ( 311 , 312 ).…”

Section: Personal Genomicsmentioning

confidence: 99%

“…However, these methods remain prohibitive in terms of costs and analysis challenges ( 310 , 311 ). New microfluidic methods based on droplets containing microbial cells from fecal samples are also under evaluation to produce complete and precise microbial characterization that would enable an improved definition of overall microbial function ( 311 , 312 ).…”

Section: Personal Genomicsmentioning

confidence: 99%

Exploring the gut microbiota: lifestyle choices, disease associations, and personal genomics

Pedroza Matute,

Iyavoo

2023

Front. Nutr.

View full text Add to dashboard Cite

The gut microbiota is a rich and dynamic ecosystem that actively interacts with the human body, playing a significant role in the state of health and disease of the host. Diet, exercise, mental health, and other factors have exhibited the ability to influence the gut bacterial composition, leading to changes that can prevent and improve, or favor and worsen, both intestinal and extra-intestinal conditions. Altered gut microbial states, or ‘dysbiosis’, associated with conditions and diseases are often characterized by shifts in bacterial abundance and diversity, including an impaired Firmicutes to Bacteroidetes ratio. By understanding the effect of lifestyle on the gut microbiota, personalized advice can be generated to suit each individual profile and foster the adoption of lifestyle changes that can both prevent and ameliorate dysbiosis. The delivery of effective and reliable advice, however, depends not only on the available research and current understanding of the topic, but also on the methods used to assess individuals and to discover the associations, which can introduce bias at multiple stages. The aim of this review is to summarize how human gut microbial variability is defined and what lifestyle choices and diseases have shown association with gut bacterial composition. Furthermore, popular methods to investigate the human gut microbiota are outlined, with a focus on the possible bias caused by the lack of use of standardized methods. Finally, an overview of the current state of personalized advice based on gut microbiota testing is presented, underlining its power and limitations.

show abstract

Toward hypothesis-driven, personalized microbiome screening

Cited by 4 publications

References 15 publications

Multistability and hysteresis in states of oral microbiota: Is it impacting the dental clinical cohort studies?

Multistability and hysteresis in states of oral microbiota: Is it impacting the dental clinical cohort studies?

A Gut-on-a-Chip Model to Study the Gut Microbiome-Nervous System Axis

Exploring the gut microbiota: lifestyle choices, disease associations, and personal genomics

Contact Info

Product

Resources

About