Meta-Apo supports cheaper, quicker microbiome functional assessment

January 22, 2021

A new algorithm may reduce the need for expensive, time-consuming whole-genome sequencing computations to understand how a microbiome functions. A team led by JING Gongchao of the Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT) of the Chinese Academy of Sciences (CAS) and SU Xiaoquan of Qingdao University, published their approach, called Meta-Apo, on Jan. 6 in BMC Genomics.

Researchers routinely sequence samples of microbial communities found on human skin, in human guts, and in the environment to understand what genes they contain with the ultimate goal of understanding how they function.

According to JING, the first author of the study, two main approaches exist: shotgun whole-genome sequencing and 16S rRNA gene amplicons. Whole-genome sequencing requires significant sequencing cost as well as computing power to determine all of the genes and their functions in a single sample, while 16S rRNA gene amplicons can quickly tease 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," said JING. "Our approach, Meta-Apo, greatly reduces or even eliminates such deviation, deducing more consistent diversity patterns between the two approaches."

Meta-Apo matches pairs of data from whole-genome sequencing and 16S amplicons - each pair is sequenced via both methods - to teach new 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," JING added. "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% percent using the 16S-derived functional profiles, produced by training the whole-genome sequencing pairs.

"With the low cost of 16S-amplicon sequencing, Meta-Apo can produce a reliable, high-resolution view of microbiome function equivalent to that offered by shotgun whole-genome sequencing," SU, senior author of the study, explained.
Other contributors include LIU Lu and XU Jian, Single-Cell Center, CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT); CUI Wenzhi, College of Control Science and Engineering, China University of Petroleum; and ZHANG Yufeng, College of Computer Science and Technology, Qingdao University.

The Natural Science Foundation of China, the Shandong Provincial Natural Science Foundation and China Postdoctoral Science Foundation supported this work.

Chinese Academy of Sciences Headquarters

Related Training Articles from Brightsurf:

Online training helps preemies
An international team of researchers has now found that computerised training can support preterm children's academic success.

Assessing training in health disparities
This survey study described and compared the curriculum on health disparities from the perspective of program directors and perceptions of training among internal medicine residents.

Music training may not make children smarter after all
Music training does not have a positive impact on children's cognitive skills, such as memory, and academic achievement, such as maths, reading or writing, according to a study published in Memory & Cognition.

Traditional strength training vs jump training for physically inactive young adults
The aim of this study was to compare the effects of 4-weeks of Traditional Resistance Training versus Plyometric Jump Training programs on the muscular fitness of sedentary and physically inactive participants.

Strength training benefits patients with cirrhosis
Three hours of weekly strength training combined with protein supplements leads to both bigger and stronger muscles in patients with cirrhosis.

Mindfulness training shows promise for people with MS
New research suggests mindfulness training may help multiple sclerosis patients in two very different ways: regulating negative emotions and improving processing speed.

The retention effect of training
Company training increases the loyalty of its employees. Loyalty also increases if the training improves the employees' chances on the labour market.

Training the mind in resilience
Two new studies from University of Miami researchers found that offering mindfulness training in high-demand settings bolsters attention and resilience.

Memory training builds upon strategy use
Researchers from Åbo Akademi University, Finland, and Umeå University, Sweden, have for the first time obtained clear evidence of the important role strategies have in memory training.

One or the other: Why strength training might come at the expense of endurance muscles
The neurotransmitter brain-derived neurotrophic factor (BDNF) acts in the muscle, so that during strength training endurance muscle fiber number is decreased.

Read More: Training News and Training Current Events is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to