From sequencing to strategy: converting big data into on-farm value

In Brief:

• DNA research has advanced rapidly since the completion of the Human Genome Project in 2003, driven by improved sequencing technologies, deeper genetic understanding, and powerful computational tools such as supercomputers.
• Interpreting the vast quantity of microbiome data requires combining sequencing results with field observations.
• Linking microbiome data with health indicators can unlock valuable insights about flock performance. 

A brief history of DNA sequencing

DNA research started in 1869 when Friedrich Miescher first isolated DNA in the form of chromatin. It was nearly a century later when Francis Crick, James Watson and Rosalind Franklin discovered the double helix structure of DNA.

The first complete gene sequence was determined by Walter Fiers in 1972, while the  first semi-automated DNA sequencing machines were developed in the late 1980s by the company ABI. Since then, rapid improvements in technologies and increasing capabilities have driven an explosion in DNA sequencing progress. The hardware required to carry out sequencing is now pocket-sized, and DNA sequencing is even happening on the Moon. 

Rapid technological advances have driven an explosion in sequencing progress

The microbiome analysis workflow

To analyze the gut microbiome, dsm-firmenich follows a specific standardized workflow. The first step is to collect samples which are then analyzed using the latest generation sequencing tools.

Table 1 shows the difference in the microbiome workflow between 2020 and 2025. The number of sequencing platforms used has doubled from one to two, while sample processing has shifted from a manual process to an automated process with the use of robotics. The time needed for one operator to complete 100 samples has fallen dramatically from 52 hours to only 16 hours. These improvements have increased the number of samples that can be sequenced in a week from 144 in 2020 to 800 in 2025. In addition to the increased throughput, sequencing costs have fallen to only 46% of what they were in 2020. Continuous investment and optimization of the microbiome workflow have enabled faster turnaround times and the ability to serve more customers. 

This standardized workflow, from sampling and next-generation sequencing through automated processing and data interpretation, is embedded in dsm-firmenich’s SciTell™ Microbiome Analytics services, which translate complex microbiome data into structured, decision-ready outputs for customers.

Continuous investment and improvements in the microbiome service have enabled serving more customers and more quickly.

Big data – turning sequencing into insight

Once the microbiome sequencing is complete, the sequencing data is uploaded to the cloud where the same bioinformatics pipelines and settings are applied. This process is necessary to ensure consistency and accuracy, and is using our own built metagenome database for identifying more microbial species than typical public genome databases.

The next step is to compare the standardized data to other known samples using our internal chicken gut microbiome database. dsm-firmenich has created its own reference database from the nearly 9000 samples it has collected and analyzed to date.

By anchoring customer results against this extensive internal reference database, SciTell™ Microbiome Analytics enables contextual interpretation — helping customers understand whether observed microbial patterns are typical, exceptional, or indicative of a specific performance risk or opportunity.

The final step is to explore the data together with input and feedback from people ‘on the ground’ with the birds, including scientists, vets, and members of the commercial team. It is only through this collaborative exploration and discussion that the real value of the data is found.

Answering practical questions

A large amount of data can be overwhelming and, without interpretation, it only has limited value to producers. The real challenge is to connect the dots to answer important practical questions such as:

• Which microbial species are present?
• What do those species do?
• Are these species resistant to antibiotics?
• What sugars do they like? Or which metabolic pathways do they express? Some questions are easier to answer than others. Identifying microbial species by body site is possible (Figure 1a) but will vary according to the age of the birds (Figure 1b).

Understanding the role of each species is also possible by looking at the microbial genes that they carry and associated to specific functional pathways (e.g. sugar and protein metabolism, nitrogen degradation, vitamin biosynthesis,…)(Figure 1).

Customer case study

Gut microbiome analysis was conducted for a specific customer. Samples were taken from 7 birds on each of five farms at five different stages of the production cycle (Table 2). 

The study looked at the lactic acid bacteria (LAB) in the samples, and the abundances were compared with the internal reference database. The results (Figure 4) showed that the LAB species were more abundant in this study compared to the baseline.

Blood analysis of the same birds is shown in Figure 5. 

Surprisingly, higher LAB was associated with lower pH for that specific field study. LAB ferment undigested starch and fiber into lactate. If too much lactate builds up, it can cross the intestinal epithelium and enter the bloodstream. Too much lactate in the blood can cause systemic acidosis. There are two stereoisomers of lactate: L-lactate which is metabolized by the host and D-lactate which is less efficiently cleared.

As a result of the microbiome and blood analysis and interpretation, dsm-firmenich suggested the following strategies:

- Reduce D-lactate production by:

• Enhancing starch recovery
• Using exogenous amylase so that less undigested starch reaches the ceca
• Improving gizzard function through feed particle size examination
• Enhancing pellet quality to slow the passage rate of the feed and stimulate gizzard activity and development
• Checking corn quality and avoiding the use of highly resistant starch which escapes digestion

- Enhance D-lactate conversion to pyruvate by:

• Increasing vitamin B2 and manganese inclusion in the premix to support the conversion of D-lactate to pyruvate

- Consider involvement of L-lactate by:

• Monitoring lighting, ambient CO₂ and activity levels of the birds
• Boosting B3 and Zn inclusion in the premix

What have we learned so far?

1. To make data more valuable, it is important to have all the necessary pieces of information.
2. Data interpretation requires discussion and validation
3. Sources of variation need to be considered – the age and breed of the birds have an influence on the microbiome as does diet and environment.
4. The microbiome is dynamic and site-specific, changing as you travel through the digestive tract.
5. Data is the future, but data quality is the key to unlocking its true value.

Through services such as SciTell™ Microbiome Analytics, microbiome data can move beyond descriptive science to become a reliable decision-support tool, enabling consistent interpretation, informed dialogue, and targeted on-farm actions.

Advances in DNA sequencing have transformed gut microbiome analysis. Combining high-quality sequencing with collaborative interpretation from reference databases and field expertise means that information about microbiomes can be translated from an invisible ecosystem into actionable insight.