Maternal & infant microbiome analysis

Early life microbiota is an important factor for long-term human health and development. The first bacteria populating the gut of naturally born infant come primarily from the maternal vaginal microbiota. Many factors such as birth by ceasarean section (C-section) and antibiotic use strongly influence the maternal-infant microbiota transfer and colonization process. BaseClear offers extensive maternal & infant microbiome research solutions that includes not only consultancy, study design, sampling solutions and sequencing, but also downstream bioinformatic, biostatistical analyses and data interpretation.

The New Infant Microbiome Pipeline: Advancing Your Research into Infant Nutrition and Health

BaseClear has recently developed a new platform specialised in analysing the infant gut microbiome. This targeted analysis pipeline uses shallow shotgun sequencing, a customised infant microbiome database, the powerful taxonomic classification tool Kraken 2, and the Bracken statistical method to create abundance profiles down to the strain level, and across microbial kingdoms.

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Our approach for maternal & infant microbiome analysis

Study design & expert advice

For the initial phase of research projects and clinical studies, we offer consultancy and support for project and study design. Our team includes a number of experienced PhD-level experts, who can advise you regarding the design of your research project and/or clinical trial, the optimal sampling methods, practical aspects regarding storage and logistics and the most appropriate technical approach.

Sampling, shipping and storage

BaseClear can advise you about the instructions on the sampling for standardized sampling. We can also supply all materials for storage and shipping with stabilizing buffers that allow for shipment at room temperature. Upon understanding the aim of the project, we can present our advice on study design & size and sample collection procedure.

Fully automated 16S rRNA and ITS gene-based profiling

We offer a complete microbial community analysis service, including fully automated DNA/RNA extraction from the samples. By using PCR and NGS technology we can determine the composition of bacteria, Archaea and fungi in your sample. Standard solutions for microbial profiling include 16S and/or ITS amplicon analysis for taxonomic classification and relative frequencies.

Quantification & tracking of strains within the microbiome

Using a quantitative PCR (qPCR) approach, we can measure changes in the abundance of specific strains within the maternal & infant microbiome. We offer this service including project design and performing the assays. Due to the quantitative method that is used, we can deliver the absolute abundance of the strains that are analysed.

Shotgun metagenomics for species level identification and functional analysis

With our state-of-the-art shotgun metagenomics pipeline, we offer a full analysis service, including quality control of the data, metagenome assembly and generation of tables that describe the abundance of different functional units and pathways across different samples. To this end, we use an in-house, improved analysis suite that includes metagenome assembly, gene prediction, gene catalogue creation and annotation, as well as abundance estimation of annotated genes and other functional units.

Data visualization & Interpretation

Interactive data visualization tool on BaseClear’s proprietary Genome Explorer browser including basic biostatical analysis options (e.g. PCA, RDA).

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Meet Eline Klaassens!

Human microbiome specialist Eline Klaassens joined BaseClear to use her expertise as Product Manager Human Health. “I’ve always had a strong interest in sustainability and human health. Many people have health problems related to gut dysbiosis. Through my studies, I’ve learnt a lot about the gut microbiome and I’d like to use my knowledge to improve people’s wellbeing through applications developed with microbial genomics,” she comments. Eline advises clients about genomics analyses for expert projects for clinical trials and the food industry. "As a human microbiome expert, customers value my contribution to interpretation of the analyses to support their projects. I make an important contribution to the success of their research due to my specialised academic background,” she notes.

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