Knowledge about the human microbiome is requiring scientists to re-define the relationship between microbes and disease. Based on our Gut Microbiota-Based Diagnostics Platform, Creative Biolabs provides high-quality gut microbiome model development and validation services. Our microbiome services experts are pleased to help customize test panels to suit your specific needs.

Background

Human gut microbiome analysis has primarily focussed on the analysis of high-throughput multi-omics systems (such as 16S rRNA amplicon sequencing, shotgun sequencing metagenomics, metatranscriptomics, metaproteomics and metabolomics). Mathematical modeling has become valuable in understanding gut microbial community dynamics and emergent behaviors. By describing the system with mathematical concepts and languages, it has been possible to quantify and predict the behavior of the system under different conditions, such as different diets, diseases, or treatment conditions.

Fig.1 The gene/genome-centric approach for the gut microbiome. (Ji, 2015)

Modeling Techniques

Multivariate statistical modeling techniques, such as generalized linear modeling, factor analysis, variations on ordination, correspondence analysis, partial least-squares analysis, or nonparametric analysis of variance, are applied in data analysis. For example, linear modeling is typically adapted to associate multiple population variables (such as health outcomes, demographics, biometrics) with microbial variables, taking into account the mathematical properties of typical microbial measurements (sparse, zero-inflated, count-based, or proportional data). Nonparametric tests originally developed for quantitative ecology are appropriate for determining whether overall variance in microbial community structure, as opposed to individual microbial features, is explained by covariates. Predictive models, such as random forests or support vector machines, can also be used to link microbial features to health outcomes or covariates.

Our Services

• Model Development

Bioinformaticians at Creative Biolabs are proficient at analyzing large data sets and developing multiple models for clinical and research purposes. To clarify the robustness of microbiome-disease associations and the potential diseases' mechanisms by which the microbiome, multiple models are constructed including k-nearest neighbors, support vector machine, decision tree, random forest, adaptive boosting, naive Bayes, gradient boosted regression trees, logistic regression, and least absolute shrinkage and selection operator. The performance of the predictive model is then evaluated with a fivefold cross-validation approach and measured by the area under the curve (AUC) as the performance indicator.

• Model Validation

In addition, various tools and technologies have emerged for experimental hypotheses validation which encompasses both in vitro and in vivo approaches. We can provide four main mouse models including specific pathogen-free (SPF) mice, antibiotic-treated (ABX) mice, germ-free (GF) mice and gnotobiotic mice. We also provide three in vitro models in gut microbiome studies: immortalized cell lines, organoids and organ-on-a-chip. A powerful platform will meet your multiple demands.

Our workflow in microbiome research is as below, which integrates advances in computational, statistical, and experimental methods.

Creative Biolabs has a team of experienced experts in the microbiome and a powerful platform to enable novel biomarker discovery and validation. Our gut microbiome model development and validation service ensures the reliability of the potential biomarker and enables the detection of disease based on the gut microbiome. We provide our customers with the best possible solutions and state-of-the-art analysis. For more information, please feel free to contact us.

Reference

1. Ji, B.; Nielsen, J. From next-generation sequencing to systematic modeling of the gut microbiome. Frontiers in genetics. 2015, 6: 219.

For Research Use Only | Not For Clinical Use