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Ecological relationships between bacteria mediate the services that gut microbiomes provide to their hosts. Knowing the overall direction and strength of these relationships within hosts, and their generalizability across hosts, is essential to learn how microbial ecology scales up to affect microbiome assembly, dynamics, and host health. Here we gain insight into these patterns by inferring thousands of correlations in bacterial abundance between pairs of gut microbiome taxa from extensive time series data, consisting of 5,534 microbiome profiles from 56 wild baboon hosts over a 13-year period. We model these time series using a statistically robust, multinomial logistic-normal modeling framework and test the degree to which bacterial abundance correlations are consistent across hosts (i.e., "univeral") or individualized to each host. We also compare these patterns to two publicly available human data sets. We find that baboon gut microbial relationships are largely universal: correlation patterns within each baboon host reflect a mixture of idiosyncratic and shared patterns, but the shared pattern dominates by almost 2-fold. Surprisingly, the strongest and most consistently correlated bacterial pairs across hosts were overwhelmingly positively correlated and typically belonged to the same family - a 3-fold enrichment compared to pairs drawn from the data set as amore »whole. The bias towards universal, positive bacterial correlations was also apparent in monthly samples from human infants, and bacterial families that had universal relationships in baboons also tended to be universal in human infants. Together, our results advance our understanding of the relationships that shape gut microbial ecosystems, with implications for microbiome personalization, community assembly and stability, and the feasibility of microbiome interventions to improve host health.« less

https://jmlr.org/papers/ v22/18-780

Time-delay cosmography of lensed quasars has achieved 2.4% precision on the measurement of the Hubble constant, H 0 . As part of an ongoing effort to uncover and control systematic uncertainties, we investigate three potential sources: 1- stellar kinematics, 2- line-of-sight effects, and 3- the deflector mass model. To meet this goal in a quantitative way, we reproduced the H0LiCOW/SHARP/STRIDES (hereafter TDCOSMO) procedures on a set of real and simulated data, and we find the following. First, stellar kinematics cannot be a dominant source of error or bias since we find that a systematic change of 10% of measured velocity dispersion leads to only a 0.7% shift on H 0 from the seven lenses analyzed by TDCOSMO. Second, we find no bias to arise from incorrect estimation of the line-of-sight effects. Third, we show that elliptical composite (stars + dark matter halo), power-law, and cored power-law mass profiles have the flexibility to yield a broad range in H 0 values. However, the TDCOSMO procedures that model the data with both composite and power-law mass profiles are informative. If the models agree, as we observe in real systems owing to the “bulge-halo” conspiracy, H 0 is recovered precisely and accurately bymore »both models. If the two models disagree, as in the case of some pathological models illustrated here, the TDCOSMO procedure either discriminates between them through the goodness of fit, or it accounts for the discrepancy in the final error bars provided by the analysis. This conclusion is consistent with a reanalysis of six of the TDCOSMO (real) lenses: the composite model yields H 0 = 74.0 −1.8 +1.7 km s −1 Mpc −1 , while the power-law model yields 74.2 −1.6 +1.6 km s −1 Mpc −1 . In conclusion, we find no evidence of bias or errors larger than the current statistical uncertainties reported by TDCOSMO.« less