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author = {Joseph Nesme and S{\'{e}}bastien C{\'{e}}cillon and Tom~O. Delmont and Jean-Michel Monier and Timothy~M. Vogel and Pascal Simonet},  title = {Large-Scale Metagenomic-Based Study of Antibiotic Resistance in the Environment},  journal = {Current Biology}  }" data-bib-key="Nesme_2014" contenteditable="false">Nesme 2014), in which soil metagenomes showed the most diverse pool of ARGs than human feces, ocean, cow and chicken gut and artic snow metagenomes. In the opposite, human gut, ocean and cow gut metagenomes, exhibit the lowest diversity values (19, 17 and 12 different type of b-lactamase genes respectively). The analysis of the supporting information accompanying the metagenome sequences, clearly indicate that different factor affect the b-lactamase diversity values here obtained. In this context is important indicate that despite that all the metagenomes share the same type of technology used in the sequencing process, differences in methodology can be expected. In the same context, despite that metagenomes can be grouped according different environments, some differences can affect the sequencing results; thus, in the ocean environment, metagenomes related to the Sydney harbour metagenome project (see Table S1) were obtained at 0,3 m in depth, in the estuary of Sydney, and metagenomes related to Amazon continuum metagenomes project were obtained at depths ranged from 3.63 to 4.47 meters, and the samples were obtained at different points, from seawater close to the cost line until seawater far from the cost line (open ocean). In the same way, agricultural metagenomes were exposed to different agricultural practices that can affect the microbiological content on soil and therefor, affect the genomic content on soil.
Finally, in the case of gut metagenomes, clearly the health situation and/or the drug supply can affect both the microbiological and genomic content. Our analysis take into account those variability, and steps oriented to reduce it were applied.

diversity vs richness

 
Supporting 

Despite the lower b-lactamase diversity in human gut metagenomes compared to other environments, the results show in average the human gut together with agricultural soils have the higher richness (0.01% of the total number of reads in the metagenome) between the analyzed metagenomes, indicating that in the case of human gut metagenomes, only few b-lactamase genes are present, but these genes are frequently found in human gut bacteria. In the case of agricultural soils, non-agricultural soils, and wastewater metagenomes, also high levels of b-lactamase richness (0.1, 0.0093 and 0.0092% of the total number of reads respectively) were observed (Table S2). Otherwise, fresh water and oceans metagenomes exhibit the lower richness values (0.0045 and 0.0022% respectively). 

 
Supporting  the differences in b-lactamase content and diversity, our indicator species analysis show habitat-specificity for some b-lactamase genes. Interestingly, four b-lactamase genes (blaEBR, CfxA, mecA HGI) showed a high faithfulness of occurrence in the human gut environment; those genes have been previously identified only in humans (both health and sick) ( ...
title = {Detection of antibiotic-resistant bacteria and their resistance genes in wastewater,  surface water, and drinking water biofilms},  journal = {{FEMS} Microbiology Ecology}  }" data-bib-key="Schwartz_2003" contenteditable="false">Schwartz 2003
), but there are no reports of their occurrence in natural environments.

Our gene network results show a high number of connections between nodes from the same type of environment, but only few connections between nodes of two different environments; suggesting that b-lactamase genes show a high intra-habitat mobility, but a limited inter-habitat transferability. Our findings are in concordance with metagenomic (Fondi et al. 2016 and    class="ltx_cite" data-bib-text="@article{Li_2015, doi = {10.1038/ismej.2015.59},  url = {http://dx.doi.org/10.1038/ismej.2015.59},  year = 2015,