Ecology drives a global network of gene exchange connecting the human microbiome

By Chris S. Smillie, Mark B. Smith, Jonathan Friedman, O. Cordero, Lawrence A. David, Eric J. Alm. Nature, 2011

900 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/6a301f20c9249944c82b73e0c2569e951dacdf28

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Citations in the corpus

Diverse and abundant antibiotic resistance genes in Chinese swine farms (2013, background): “The coenrichment of ARGs and transposases further exacerbates the risks of transfer of ARGs from livestock animals to human-associated bacteria, and then spread among human populations (4, 6).”
Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes (2015, background): “Strikingly, recent studies revealed that the exchange of ARGs between bacteria from farm animals/soils and clinical pathogens occurred via horizontal gene transfer (Smillie et al., 2011; Forsberg et al., 2012).”
Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data (2014, background): “The fast microbial turnover and enormous selective pressures in the colonic environment promote large-scale HGT (32).”
Ecology in an anthropogenic biosphere (2015, background): “…is the recent discovery and rapid scientific advances in understanding the novel global ecology of the human microbiome, in which humans serve as both host environments and biological recipients of microbial benefits and detriments (Smillie et al. 2011, Kembel et al. 2012, O’Doherty et al. 2014).”
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes (2016, background): “This information can be utilized for in depth studies of selected environments or comparisons between different habitats such as (27).”
Environmental factors influencing the development and spread of antibiotic resistance (2017, neutral): “Furthermore, horizontal gene transfer is much more likely to occur between phylogenetically closely related bacteria (Philip-pot et al. 2010; Smillie et al. 2011).”
Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics (2015, neutral): “Yet based on data from the CDC and HealthMap.org (http:// www.healthmap.org/en/), which uses machine-learning algorithms to track all reported infections, there has not been a single reported case of Y. pestis in New York City since our collections began.”
The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota (2017, background): “In this scenario, horizontal gene transfer events, often driven by phages, may represent one of the main forces responsible for microbial diversification, especially for those microbes that share the same ecological niche (20).”
A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics (2014, result): “Taken together, these results are consistent with the possibility that thiopeptide gene clusters are mobile and that they undergo horizontal transfer among the microbiota within a body site (Smillie et al., 2011).”
Species concepts and speciation factors in cyanobacteria, with connection to the problems of diversity and classification (2015, background): “The most extensively studied HGT events are concerned with the human microbiome (e.g. Smillie et al. 2011) and marine picoplankton, mostly of the genera Synechococcus and Prochlorococcus (e.g. Marston et al. 2012).”
Computational meta'omics for microbial community studies (2013, background): “…and lateral gene transfer/recombination have recently been shown to arise in vivo (Croucher et al , 2011; Lieberman et al , 2011), with evidence suggesting the latter is particularly frequent among microbes that stably inhabit shared communities (McDaniel et al , 2010; Smillie et al , 2011).”