Who are the microbes on your fruits and veggies?

Nice paper from Jonathan Leff and Noah Fierer in PLOS One: Bacterial Communities Associated with the Surfaces of Fresh Fruits and Vegetables

Abstract: Fresh fruits and vegetables can harbor large and diverse populations of bacteria. However, most of the work on produce-associated bacteria has focused on a relatively small number of pathogenic bacteria and, as a result, we know far less about the overall diversity and composition of those bacterial communities found on produce and how the structure of these communities varies across produce types. Moreover, we lack a comprehensive view of the potential effects of differing farming practices on the bacterial communities to which consumers are exposed. We addressed these knowledge gaps by assessing bacterial community structure on conventional and organic analogs of eleven store-bought produce types using a culture-independent approach, 16 S rRNA gene pyrosequencing. Our results demonstrated that the fruits and vegetables harbored diverse bacterial communities, and the communities on each produce type were significantly distinct from one another. However, certain produce types (i.e., sprouts, spinach, lettuce, tomatoes, peppers, and strawberries) tended to share more similar communities as they all had high relative abundances of taxa belonging to the family Enterobacteriaceae when compared to the other produce types (i.e., apples, peaches, grapes, and mushrooms) which were dominated by taxa belonging to the Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria phyla. Although potentially driven by factors other than farming practice, we also observed significant differences in community composition between conventional and organic analogs within produce types. These differences were often attributable to distinctions in the relative abundances of Enterobacteriaceae taxa, which were generally less abundant in organically-grown produce. Taken together, our results suggest that humans are exposed to substantially different bacteria depending on the types of fresh produce they consume with differences between conventionally and organically farmed varieties contributing to this variation.

Getting press attention.  Examples include:

Definitely worth a look.

Great ideas in this #PLoSOne paper; except we published same idea 12 fu$*# years ago

Figure 1 from Pollock et al. 2000

Wow. I mean, imitation is a form of flattery. But this paper … Grrrrrrr PLOS ONE: Conveniently Pre-Tagged and Pre-Packaged: Extended Molecular Identification and Metagenomics Using Complete Metazoan Mitochondrial Genomes In the paper the authors basically argue that for many purposes, including phylogenetic studies in particular, one could obtain many mitochondrial genomes at once by just pooling together samples from different organisms, shotgun sequencing the samples, and assembling the separate mitochondrial genomes out.  All one would need to do is to make sure the organisms pooled were distantly related enough such that their mitochondrial sequences would not cross assemble with each other.  They say things like:

We propose a novel approach for the isolation and sequencing of a universal, useful and popular marker across distant, non-model metazoans: the complete mitochondrial genome. It relies on the properties of metazoan mitogenomes for enrichment, on careful choice of the organisms to multiplex, as well as on the wide collection of accumulated mitochondrial reference datasets for post-sequencing sorting and identification instead of individual tagging. Multiple divergent organisms can be sequenced simultaneously, and their complete mitogenome obtained at a very low cost. We provide in silico testing of dataset assembly for a selected set of example datasets.


We describe here the approach, the type of sequence data it generates, the procedure to recover mitochondrial genomes without external tagging, and some potential uses. We perform an in-silico validation test based on the analysis of a simulated dataset with read lengths of two different sizes to represent average read length of three 2nd generation desktop sequencing platforms, Illumina Mi-Seq, 454 GS junior and Ion Torrent PGM. Thus we can contrast their relative efficiencies for the experimental protocol proposed here.

Sounds great. Except I wrote a paper with David Pollock, Norman Doggett, and Michael Cummings published in 2000 proposing the same thing. Our paper:  Pollock DD, Eisen JA, Doggett NA, Cummings MP. Mol Biol Evol. 2000 Dec;17(12):1776-88. A case for evolutionary genomics and the comprehensive examination of sequence biodiversity.

 Our abstract:

Comparative analysis is one of the most powerful methods available for understanding the diverse and complex systems found in biology, but it is often limited by a lack of comprehensive taxonomic sampling. Despite the recent development of powerful genome technologies capable of producing sequence data in large quantities (witness the recently completed first draft of the human genome), there has been relatively little change in how evolutionary studies are conducted. The application of genomic methods to evolutionary biology is a challenge, in part because gene segments from different organisms are manipulated separately, requiring individual purification, cloning, and sequencing. We suggest that a feasible approach to collecting genome-scale data sets for evolutionary biology (i.e., evolutionary genomics) may consist of combination of DNA samples prior to cloning and sequencing, followed by computational reconstruction of the original sequences. This approach will allow the full benefit of automated protocols developed by genome projects to be realized; taxon sampling levels can easily increase to thousands for targeted genomes and genomic regions. Sequence diversity at this level will dramatically improve the quality and accuracy of phylogenetic inference, as well as the accuracy and resolution of comparative evolutionary studies. In particular, it will be possible to make accurate estimates of normal evolution in the context of constant structural and functional constraints (i.e., site-specific substitution probabilities), along with accurate estimates of changes in evolutionary patterns, including pairwise coevolution between sites, adaptive bursts, and changes in selective constraints. These estimates can then be used to understand and predict the effects of protein structure and function on sequence evolution and to predict unknown details of protein structure, function, and functional divergence. In order to demonstrate the practicality of these ideas and the potential benefit for functional genomic analysis, we describe a pilot project we are conducting to simultaneously sequence large numbers of vertebrate mitochondrial genomes.

And not any mention of our paper in this new one.  I could do a detailed side by side comparison but I am too angry right now.  It’s either stealing on purpose or just shoddy work.  I think stealing is unlikely so I will conclude just poor work.  Shoddy job by the authors (Dettai A, Gallut C, Brouillet S, Pothier J, Lecointre G et al).  Shoddy job by the editor Dirk Steinke from Guelph.  Annoying as all heck.

UPDATE 11 AM 12/22: I got carried away with anger when I wrote the last few sentences crossed out above.  Upon further, more rational consideration, I do not think the authors or editors did anything really wrong here.  Yes, they missed some prior literature on the topic and our prior paper is indeed quite similar to theirs.  But our prior paper is pretty hard to find by literature searches (see comments/discussion) and they clearly came up with their ideas independently.  I truly regret the aggressive, obnoxious tone of my post and sincerely apologize to the authors of the new paper.

PS.  I wish to thank @DrShmoo on Twitter for knocking some sense into me