CURRENT CONTROVERSIES IN MICROBIOLOGY
How many 16S-based studies should be included in a metagenomic conference? It may be a matter of etymology Alfonso Esposito1 & Matthias Kirschberg2 Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy; and 2Westf€ alische Hochschule, Recklinghausen, Germany
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Correspondence: Alfonso Esposito, Faculty of Science and Technology, Free University of Bozen-Bolzano, piazza universita 1, 39100 Bolzano, Italy. Tel.: +39 0471 017009; fax: +39 0471 017009; e-mail:
[email protected] Received 18 December 2013; revised 3 January 2014; accepted 4 January 2014. Final version published online 30 January 2014.
Abstract The word ‘metagenomic’ is one of the most used words in environmental microbiology especially in recent years, yet sometimes it is a little overused. Can studies targeting a single gene be considered ‘metagenomic’? It is more controversial than once thought, maybe a possible solution may come from an etymological analysis of the word.
DOI: 10.1111/1574-6968.12375 Editor: Jeff Cole
MICROBIOLOGY LETTERS
Keywords metagenomics; metagenetics; nomenclature.
How many 16S based studies should be included in a metagenomic conference or symposium? This question raised by Timothy Vogel during the final open discussion session of the Th€ unen symposium on soil metagenomics in December 2013 triggered an interesting debate. The question arose from the fact that most metagenomic studies presented in that symposium were based on 16S analysis. Implicitly, the question was whether a 16S study, which is useful in enumerating the bacterial species existing in a sample, could be regarded as a ‘pure metagenomic’ study or rather just one of the many applications employed in metagenomic research. During the following 40 min, the whole audience (which included some of the top scientists in this field) debated the legitimacy of calling a 16S study ‘metagenomic’. There were many interesting (sometimes provocative) implications arising from that debate that merit further thought and debate. The number of metagenomic studies using the shotgun approach is increasing but still the majority focus on 16S. Not only is it just a single gene, but very often only a portion of it is sequenced. The advent of high-throughput sequencing methods has catalyzed this process because more of the ‘rare biosphere’ can be detected, so it has brought a new stimulus to environmental microbiology.
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The cost of sequencing has dropped significantly, the amount of 16S sequences in the databases has increased dramatically, and the resolution of the methods has also improved. Undoubtedly, a metagenomic study should include the knowledge of the organisms living there, and as microorganisms are not easily detectable other than by molecular methods, 16S does remain a good starting point. One remark during the discussion was that the DNA extracted from an environmental sample was a metagenome by definition, as it is a mixture not only of the DNA of all organisms that are living there but also the nondegraded fraction of those that lived there in the recent past. However, when metagenomic DNA is used as a template for PCR and the product is the actual object of the study, it should then no longer be considered ‘pure metagenomic’. This also holds true for all studies targeting other genes, including functional genes, from metagenomic DNA. How can this issue in environmental microbiology be resolved? One possibility mentioned during the discussion was that people differ in their perspective of what constitutes a metagenomic analysis. Another view is that it simply comes down to semantics. Names always carry the ª 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved
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footprint of their origin. The term metagenomics is a composite word. The first part (‘meta-’ from the Greek word for ‘above’, ‘beyond’) means that we are looking at the emerging properties of the system, regardless of what specific part of the system is connected to this property. The second part ‘genomics’ is also a composite word that means the study of the properties of a genome. Genome itself is a derivative word, the collective noun defining all of the genes belonging to an organism. It could be possible to find the answer to this issue by drawing parallels with the ‘nonmeta’ sciences. The study of genes is the field called genetics; the study of the genomes is the field called genomics. Many genetic studies are based on the amplification of a single gene from the genomic DNA, therefore, the ‘meta-’ version of this procedure should be called ‘metagenetic’. A google search with the keyword ‘metagenetics’ revealed that the term exists and perfectly describes these kinds of studies, but it is seldom used in our field with only 965 hits for the keywords ‘16S metagenetics’ against more than 16 000 hits for ‘16S metagenomics’ (scholar.google on December 15, 2013). The aim of this search was to show that the keyword 16S is more often associated to ‘metagenomic’ than to ‘metagenetic’ (which probably would make more sense). Indeed, this term is already used in studies that
ª 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved
A. Esposito & M. Kirschberg
do exactly the same things, but with the eukaryotes (e.g. Bik et al., 2011; Machida & Knowlton, 2012). Using the word ‘metagenetics’ (as it is applied in the studies among microbial eukaryotes) instead of metagenomic would accommodate several studies involving PCR methods that target just one gene on the metagenomic DNA, helping to solve this small controversy.
Acknowledgement The authors acknowledge the help of Prof. Jeff Cole in editing the manuscript.
References Bik HM, Sung W, De Ley P, Baldwin JG, Sharma J, Rocha-Olivares A & Thomas K (2011) Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments. Mol Ecol 21: 1048–1059. Machida RJ & Knowlton N (2012) PCR Primers for metazoan nuclear 18S and 28S ribosomal DNA sequences. PLoS One 7: e46180.
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