RESUMO
Our understanding of human microbial communities, in particular in regard to diseases is advancing, yet the basic understanding of the microbiome in healthy subjects over time remains limited. The oropharynx is a key target for colonization by several important human pathogens. To understand how the oropharyngeal microbiome might limit infections, and how intercurrent infections might be associated with its composition, we characterized the oropharyngeal microbiome of 18 healthy adults, sampled weekly over a 40-weeks using culture-independent molecular techniques. We detected nine phyla, 202 genera and 1438 assignments on OTU level, dominated by Firmicutes, Bacteroidetes, and Proteobacteria on phylum level. Individual microbiomes of participants were characterized by levels of high alpha diversity (mean = 204.55 OTUs, sd = 35.64), evenness (19.83, sd = 9.74) and high temporal stability (mean Pearson's correlation between samples of 0.52, sd = 0.060), with greater differences in microbiome community composition between than within individuals. Significant changes in community composition were associated with disease states, suggesting that it is possible to detect specific changes in OTU abundance and community composition during illness. We defined the common core microbiota by varying occurrence and abundance thresholds showing that individual core microbiomes share a substantial number of OTUs across participants, chiefly Streptococci and Veillonella. Our results provide insights into the microbial communities that characterize the healthy human oropharynx, community structure and variability, and provide new approaches to define individual and shared cores. The wider implications of this result include the potential for modeling the general dynamics of oropharynx microbiota both in health and in response to antimicrobial treatments or probiotics.
RESUMO
Widespread and ever-increasing anthropogenic impacts in the marine environment are driving a need to develop more efficient survey methods for monitoring changes in marine biodiversity. There is a particular urgent need for survey methods that could more rapidly and effectively detect change in species richness, abundance and community composition. Here, test the suitability of the Mackinnon Lists Technique for use in the marine environment by testing its effectiveness for rapid assessment of fish communities. The MacKinnon Lists Technique is a time-efficient and cost-effective sampling method developed for studying avian tropical biodiversity, in which several list samples of species can be collected from a single survey. Using the well-established MaxN approach on data from deployments of a Baited Remote Underwater Video Systems for comparison, we tested the suitability of the MacKinnon Lists Technique for use in marine environments by analysing tropical reef fish communities. Using both methods for each data set, differences in community composition between depths and levels of protection were assessed. Both methods were comparable for diversity and evenness indices with similar ranks for species. Multivariate analysis showed that the MacKinnon Lists Technique and MaxN detected similar differences in community composition at different depths and protection status. However, the MacKinnon Lists Technique detected significant differences between factors when fewer videos (representing reduced survey effort) were used. We conclude that the MacKinnon Lists Technique is at least as effective as the widely used MaxN method for detecting differences between communities in the marine environment and suggest can do so with lower survey effort. The MacKinnon Lists Technique has the potential to be widely used as an effective new tool for rapid conservation monitoring in marine ecosystems.