Researchers develop more accurate, cheaper approach to microbiome data mining

03-Feb-2021 - Last updated on 04-Feb-2021 at 13:50 GMT

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Although microbiome research has been around for many years, the ways in which it is studied has evolved over the years. Research that was once hindered due to its costly price tag is now coming down, opening the doors for more studies. Major advances in sequencing technologies have also helped make microbiome research more accessible.

Currently, the two main technical approaches for profiling microbial communities are shotgun whole-genome sequencing and 16S rRNA gene amplicons.

However, researchers in China said they are able to predict gut health in a more economical and accurate way with a new algorithm. According to Jing Gongchao and his team, the Metagenomic Apochromat (Meta-Apo) will reduce the need for costly, time-consuming whole-genome sequencing computations that are traditionally used.

The researchers, who hail from the Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT) of the Chinese Academy of Sciences (CAS) and Su Xiaoquan of Qingdao University made their case for Meta-Apo in the journal BMC Genomics.

Technical approaches

Whole-genome sequencing demands significant sequencing, is very expensive and requires serious computing power to determine all of the genes and their functions in a single sample. While not as accurate, 16S rRNA is more practical, with gene amplicons that can quickly filter out a sample's specific gene for taxonomy information and thus predict how they function.

"However, due to the potential biases in how the amplicons are prepared and gene profile variation among genomes, functional profiles predicted from 16S amplicons may deviate from whole-genome sequencing ones, resulting in misleading results," explained Gongchao, the first author on the study. "Our approach, Meta-Apo, greatly reduces or even eliminates such deviation, deducing more consistent diversity patterns between the two approaches."

How it works

Using the best from both worlds, Meta-Apo matches pairs of data from whole-genome sequencing and 16S amplicons, with each pair sequenced via both methods. The process teaches 16S amplicon samples to better recognize gene function. The results are much more consistent with the whole-genome sequencing results.

"Tests of Meta-Apo on more than 5,000 16S amplicon human microbiome samples from four body sites showed the deviation between the two strategies is significantly reduced by using only 15 training sample pairs," explained Gongchao. "Moreover, Meta-Apo enables cross-platform functional comparison between whole-genome sequencing and amplicon samples, greatly improving 16S-based microbiome diagnoses."

To test this experimentally, the researchers were able to improve the accuracy of a gingivitis diagnosis from 65% to 95% using the 16S-derived functional profiles, produced by training the whole-genome sequencing pairs.

The future of personalized nutrition

Gongchao told NutraIngredients-USA that for less than a quarter of the price, Meta-Apo can produce a reliable, high-resolution snapshot of microbiome function equivalent to that offered by shotgun whole-genome sequencing.

“From my perspective, Meta-Apo services are a strong impetus to the future of personalized nutrition. Meta-Apo can search for the functional information of individual gut microbiomes at a lower price as well as in a more accurate way, which is one of the sore points of precision medicine and personalized nutrition at present,” said Gongchao.

Source: BMG Genomics

22, 9 (2021) doi.org/10.1186/s12864-020-07307-1

“Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function”

Authors: J. Gongchao et al.