Study describes new method for probing the bewildering diversity of the microbiome

In recent years, researchers have begun to explore the vast amount of microbes on and within the human body. Protists, archaea, fungi, viruses, and vast numbers ofbacteria are included.

The human microbiome is a collection of tiny entities that influence a wide range of activities, from metabolism to behavior and play a central role in health and disease. 39 trillion non-human microbes flourish on and within us, in a ceaseless, interdependent bustle. They make up over half of the human body and may have 500 times the number of genes found in human cells. Researchers have been challenged to identify and make sense of the mélange.

A new method for probing the microbiome is described in a new study. The technique gives greater simplicity and ease of use. The researchers show an improved ability to identify biologically relevant characteristics using the new technique.

The promise of the innovative research is that it will lead to the advancement of investigations into the mysteries of the microbiome. Researchers hope to better understand how these microbes act to safeguard human health and how their malfunction can lead to a wide range of diseases. Drug and therapy may be tailored to a patient's microbiomic profile in the future.

Professor Zhu is a researcher at the Biodesign Center for Fundamental and Applied Microbiology and the School of Life Sciences. The University of California, San Diego has collaborated with the research team.

The results of the research are in the current issue of the journal.

There are tools for the trade.

Two powerful technologies have been used to help researchers understand the diversity and complexity of the microbiome. These are known as 16S and metagenomics. The technique described in the current study draws on the strengths of both methods to create a new way of processing data.

We borrow some of the wisdom that was developed from 16SRNAsequencing and apply it to metagenomics. Metagenomics allows researchers to sequence all the information present in a sample. The new study shows that the metagenomic approach has room for improvement.

The new technique, known as Operational Genomic Units (OGU), does away with the practice of assigning species and genera to a sample. The method uses individual genomes as the basic units for statistical analysis and attempts to align the sequence of the sample to the sequence in the existing databases.

Researchers can get much more fine-grained resolution by doing this. This is true because most of the classifications are based on sequence similarity. The OGU approach can help researchers tell the difference between the two sequences.

The method overcomes errors in the taxonomy that persist from the pre-sequencing era, when different species were defined by their morphology.

Researchers can use OGU to analyze data using what are known as phylogenetic trees. These are structures that can describe the degree of relatedness between organisms based on their sequence similarity. Two distantly related species like worms and antelope will show up on more distant branches of a tree.

There are innovations in the field of sequencing.

A simple idea is the basis of the most widely used technique for probing the microbiome. The 16S gene is essential to the machinery that thebacteria need to initiateProtein synthesis. The 16S gene has 1500 base pairs in length. Some of the regions change very little between differentbacteria, while others are very variable.

The conserved and variable regions of the 16S gene allow it to act as a clock, keeping track ofbacteria that are more closely related to each other. The 8 conserved and 9 variable regions of 16S can be used to identifybacteria.

The sample is collected first. This could be a fecal sample, or a sample from the skin or the mouth. Each body site has different types ofbacteria.

The 16S gene is amplified with the help of the technology. A broad swath ofbacteria can be identified, while variable regions help narrow the identity of particularbacteria.

16S is an inexpensive and well-developed method, but it has limitations. The technique only gives a general idea of the types ofbacteria present. 16S is only accurate to the level of identification.

Enter metagenomics. This technique is used to sequence the full genomes of all the microbes present in a sample. Researchers can sequence thousands of organisms in parallel with the help of metagenomics. The costs come from the greater resolution. Metagenomic data is more difficult to analyze than 16S data and it is more expensive to process.

There is a new path for metagenomics.

The OGU technique provides even greater resolution. The approach doesn't require an assignment for the classification of microbes in a sample. Researchers can evaluate the degree of species diversity in a sample with the approach.

The new approach is superior in ferreting out biologically relevant information. The study shows better correlation between body site and host sex with the help of the classic Human Microbiome Project dataset.

A random sample of the Finns were analyzed using both 16S and metagenomics. The samples are from a large group of Finns. The goal was to predict the age of the people. The OGU method provided more accurate predictions.

The resolution of the new technique will be further enhanced by a new research drawing on larger datasets.

More information: Qiyun Zhu et al, Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy, mSystems (2022). DOI: 10.1128/msystems.00167-22 Citation: Study describes new method for probing the bewildering diversity of the microbiome (2022, April 4) retrieved 5 April 2022 from https://phys.org/news/2022-04-method-probing-bewildering-diversity-microbiome.html This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no part may be reproduced without the written permission. The content is provided for information purposes only.