Still M.A.G.s

Been thinking a lot about metagenome assembled genomes (MAGs) and the potential for discovering novel microbial lineages. These offer a lot of insights into the metabolic function across diverse microbes with the potential for connecting previously undiscovered taxa to key biogeochemical processes. I figured I would condense my thoughts into this blog post in case it was of interest for any other microbial ecologists or microbiome scientists out there. Just my two cents on the topic...

Brief Background on MAGs

Most bacteria evade culturing efforts and most of the reference genomes in databases provide a limited, and highly biased, perspective of microbial diversity. With the advancements of sequencing technology and computational resources, it was becoming increasingly more apparent that creative and novel approaches could be used to assess microbial community composition. One of the earliest (if not the first?) approach using this "culture-independent" method was from Tyson et al. (2004) that looked at a relatively simple microbial community in biofilms [1]. Basically, we can sequence the entire genetic composition of the community, use genomic signatures of the abundant members, and cluster the contigs into similar "bins". 

These MAGs provided unprecedented insights into the genomic potential of these previously unknown microbial lineages. For example, the recovered MAGs in the biofilm community revealed a self-sustaining community in terms fo carbon and nitrogen exchange. Other revelations also included the ability to identify evolutionary processes structuring the extant MAGs (Figure 1). And probably, the most important aspect of this paper was the statement: "However, even in more complex environments, it should be possible to extend the random shotgun sequencing approach to recover the genomes of uncultivated strains and species". This approach would revolutionize modern approaches to microbiomes.

Figure 1. Recovered MAG demonstrating the diversity of mosaic genome types within the Ferroplasma type II population from three closely related ancestral genome [1].

Modern Approaches and Applications

I can spend all year covering the recent papers using MAGs, but I will focus on a few of my favorites that are relatively recent. In general, most of the following papers are derived from more or less the same dataset [2]. Using dozens of metagenomes, the authors were able to reconstruct nearly 800 MAGs from a really complex and diverse soil community. By correlating environmental metadata with metabolic potential, the authors discovered differential metabolic pathways across MAGs that were directly associated with environmental gradients. In addition, this approach enabled insights into what the heck Acidobacteria might be doing. For those unfamiliar, this phyla of bacteria are incredibly difficult to culture, but are one of the most abundant phyla in soil systems. However, we barely know anything about them! The Acidobacteria MAGs encode a lot of CAZy enzymes, which are responsible for the breakdown of carbohydrates. Another earlier study also highlighted this phyla as a possible source for the discovery of new small molecules or specialized metabolites [3]. Furthermore, the distribution of the biosynthetic gene clusters (BGCs) encoding the production of these specialized metabolites varied across bacterial lineages and were correlated to environmental parameters, including soil depth and plant vegetation [4]. In any case, what I really like about these papers are the thorough work in characterizing these MAGs, especially the open source data and clear methodologies to complete such analyses. Just read the methods section in [2] and see what I mean - anyone can follow along and replicate the work done!

Papers:

1. GW Tyson, J Chapman, P Hugenholtz, EE Allen, RJ Ram, PM Richardson, VV Solovyev, EM Rubin, DS Rokhsar, JF Banfield. (2004). Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature
DOI: 10.1038/nature02340

2. S Diamond, PF Andeer, Z Li, A Crits-Christoph, D Burstein, K Anantharaman, KR Lane, BC Thomas, Chongle Pan, TR Northen, JF Banfield. (2019). Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms. Nature Microbiology
DOI: 10.1038/s41564-019-0449-y

​3. A Crits-Christoph, S Diamond, CN Butterfield, BC Thomas, JF Banfield. (2018). Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis. Nature
DOI: 10.1038/s41586-018-0207-y

4. AM Sharrar, A Crits-Christoph, R Méheust, S Diamond, EP Starr, JF Banfield. (2020). Bacterial secondary metabolite biosynthetic potential in soil varies with phylum, depth, and vegetation type. mBio
DOI: 10.1128/mBio.00416-20