From Galactic archeology to soil metagenomics – surfing on massive data streams

Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)

“…This highlights the wealth of relevant scientific information that lies buried in the last few decades' worth of scientific publications -formally available, yet only available to those who know where to look, and reachable only to those with access to that literature. Fortunately, we live in a digital age where the infrastructure for recovering and sharing such information is falling into place (Martin and Martin 2010). Furthermore, there is a growing awareness of the need to annotate newly generated sequences beyond the barest minimum when these are first deposited into public sequence databases (Hyde et al 2013;Schoch et al 2014).…”

Recent progress and new challenges in metagenomics for biotechnology

“…Such efforts are already under way for the analysis of human microbiomes (Qin et al 2010;Turnbaugh et al 2007) and soil metagenomes (Vogel et al 2009), but they need to be expanded to other environments. Major initiatives and integrated solutions are also needed for data sharing that is essential for mining the ever-growing databases (Martin and Martin 2010). When this is achieved, synthetic metagenomics will near a state of the art allowing for not only high-resolution gene mining but for assembling entire metabolic pathways in silico, akin to pathway construction from the well studied enzyme systems (Atsumi et al 2009;Dueber et al 2009).…”

From Dust Bowl to Dust Bowl: Soils are Still Very Much a Frontier of Science

“…For a time, it seemed that metagenomics could dramatically change this picture, and provide a wealth of information about soil biota, while bypassing the need to cultivate the myriad of yet uncharacterized soil organisms. As some authors put it, "the blind survey of the streams of microbial sequences will undoubtedly facilitate the understanding of the mechanisms ruling the subterranean communities and bring exciting, unexpected discoveries" (Martin and Martin, 2010). Yet, the results to date are falling short of expectations.…”

“…This is clearly illustrated in a study by Ascher et al (2009), who applied a novel DNA extraction protocol to two forest soils and observed that sequential extraction leads to increased DNA recovery, that extracellular DNA can represent a very sizeable (34.6%) portion of the sum of extracellular and intracellular DNA, and that a very different perception of microbial diversity emerges if one considers the total extracted DNA or just the extracted intracellular DNA. Even if one could somehow resolve these DNA extraction problems, as well as the enormous computational "metagenome analysis gridlock" that has apparently taken microbiologists by surprise (Martin and Martin, 2010), it is still unclear whether metagenomics, without a suite of other "omics", like metabolomics or proteomics, can really shed light on soil biodiversity (Baveye, 2009;Singh et al, 2009). Indeed, some of the experts in the field recently admitted that it will be necessary in the near future to "develop and apply new approaches to cultivate the previously uncultivated and rare members of the soil community to assign functions to the vast number of unknown or hypothetical genes that will undoubtedly be found."…”