Metrics matter in community detection

We present a critical evaluation of normalized mutual information (NMI) as an evaluation metric for community detection. NMI exaggerates the leximin method's performance on weak communities: Does leximin, in finding the trivial singletons clustering, truly outperform eight other community detection methods? Three NMI improvements from the literature are AMI, rrNMI, and cNMI. We show equivalences under relevant random models, and for evaluating community detection, we advise one-sided AMI under the $\mathbb{M}_{\mathrm{all}}$ model (all partitions of $n$ nodes). This work seeks (1) to start a conversation on robust measurements, and (2) to advocate evaluations which do not give "free lunch"

Effect of simulated microgravity on the virulence properties of the opportunistic bacterial pathogen Staphylococcus aureus

Extended manned space flight will result in a diminution of immune status and cause profound changes in the human bacterial microbiota, leading to increased risk of infection. Experiments conducted during short-term flight suggest that growth in microgravity leads to increases in bacterial antibiotic resistance and to cell wall changes. Growth under low-shear modelled microgravity (LSMMG) indicated that a reduced gravitational field acts as an environmental signal for expression of enhanced bacterial virulence in Gram-negative pathogens. We examined the effect of simulated microgravity on parameters of virulence in clinical isolates of Staphylococcus aureus. Three strains were grown under LSMMG in a High Aspect Ratio Vessel and compared with cells grown under normal gravity (NG) in the same vessel. There were no significant differences in the antibiotic susceptibility, growth rate or morphology of staphylococci grown under LSMMG compared to NG. LSMMG-induced reductions in synthesis of the pigment staphyloxanthin were noted. Strains secreted less protein under LSMMG and reductions in haemolysin secretion were found. Reduced expression of the major virulence determinant "-toxin in the microgravity environment was found by gene amplification. Thus, in contrast to published data on Gram-negative pathogens, simulated microgravity reduces the expression of key virulence determinants of S. aureus

The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts

© 2015 International Society for Microbial Ecology All rights reserved. Despite being one of the simplest metazoans, corals harbor some of the most highly diverse and abundant microbial communities. Differentiating core, symbiotic bacteria from this diverse hostassociated consortium is essential for characterizing the functional contributions of bacteria but has not been possible yet. Here we characterize the coral core microbiome and demonstrate clear phylogenetic and functional divisions between the micro-scale, niche habitats within the coral host. In doing so, we discover seven distinct bacterial phylotypes that are universal to the core microbiome of coral species, separated by thousands of kilometres of oceans. The two most abundant phylotypes are co-localized specifically with the corals' endosymbiotic algae and symbiont-containing host cells. These bacterial symbioses likely facilitate the success of the dinoflagellate endosymbiosis with corals in diverse environmental regimes