Biology subjects

Hernandez, A. M.

Publications and source records attributed to Hernandez, A. M..

2 recordsLinked to original sources

bioRxiv2019

Station and train surface microbiomes of Mexico City’s metro (subway/underground)

The metro is one of the more representative urban systems of Mexico City, and it transports approximately 4.5 million commuters every day. Large crowds promote the constant exchange of human and environmental microbes. In this study, we determined the bacterial diversity profile of the Mexico City subway by massive sequencing of the 16S rRNA gene. We identified a total of 50,197 operative taxonomic units (OTUs) and 1058 genera. The metro microbiome was dominated by the phylum Actinobacteria and by the genera Propionibacterium (15%) (P. acnes 13%), Corynebacterium (13%), Streptococcus (9%), and Staphylococcus (5%) (S. epidermidis; 4%), reflecting the microbe composition of normal human skin. The metro microbial sources were skin, dust, saliva, and vaginal, with no fecal contribution detected. A total of 420 bacterial genera were universal to the twelve metro lines tested, and they contributed to 99.10% of the abundance. The large OTUs number are probably reflecting the vast human influx, while selection from hosts and environments are constraining the genera diversity, shown by the OTUs to genus ratio. Finally, this study shows that the microbial composition of the Mexico City subway comes from a mixture of environmental and human sources and that commuters are exposed to normal human microbiota.

microbiology↗

bioRxiv2019

Six-state amino acid recoding is not an effective strategy to offset the effects of compositional heterogeneity and saturation in phylogenetic analyses

Six-state amino acid recoding strategies are commonly applied to combat the effects of compositional heterogeneity and substitution saturation in phylogenetic analyses. While these methods have been endorsed from a theoretical perspective, their performance has never been extensively tested. Here, we test the effectiveness of 6-state recoding approaches by comparing the performance of analyses on recoded and non-recoded datasets that have been simulated under gradients of compositional heterogeneity or saturation. In all of our simulation analyses, non-recoding approaches greatly outperformed 6-state recoding approaches. Our results suggest that 6-state recoding strategies are not effective in the face of high saturation. Further, while recoding strategies do buffer the effects of compositional heterogeneity, the loss of information that accompanies 6-state recoding outweighs its benefits, even in the most compositionally heterogeneous datasets. In addition, we evaluate recoding schemes with 9, 12, 15, and 18 states and show that these all outperform 6-state recoding. Our results have important implications for the more than 70 published papers that have incorporated 6-state recoding, many of which have significant bearing on relationships across the tree of life.

evolutionary biology↗