Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties

Microbe-microbe interactions in the human gut are influenced by host-derived glycans and diet. The high complexity of the gut microbiome poses a major challenge for unraveling the metabolic interactions and trophic roles of key microbes. Synthetic minimal microbiomes provide a pragmatic approach to investigate their ecology including metabolic interactions. Here, we rationally designed a synthetic microbiome termed Mucin and Diet based Minimal Microbiome (MDb-MM) by taking into account known physiological features of 16 key bacteria. We combined 16S rRNA gene-based composition analysis, metabolite measurements and metatranscriptomics to investigate community dynamics, stability, inter-species metabolic interactions and their trophic roles. The 16 species co-existed in the in vitro gut ecosystems containing a mixture of complex substrates representing dietary fibers and mucin. The triplicate MDb-MM's followed the Taylor's power law and exhibited strikingly similar ecological and metabolic patterns. The MDb-MM exhibited resistance and resilience to temporal perturbations as evidenced by the abundance and metabolic end products. Microbe-specific temporal dynamics in transcriptional niche overlap and trophic interaction network explained the observed co-existence in a competitive minimal microbiome. Overall, the present study provides crucial insights into the co-existence, metabolic niches and trophic roles of key intestinal microbes in a highly dynamic and competitive in vitro ecosystem.Peer reviewe

A new spin-anisotropic harmonic honeycomb iridate

The physics of Mott insulators underlies diverse phenomena ranging from high temperature superconductivity to exotic magnetism. Although both the electron spin and the structure of the local orbitals play a key role in this physics, in most systems these are connected only indirectly --- via the Pauli exclusion principle and the Coulomb interaction. Iridium-based oxides (iridates) open a further dimension to this problem by introducing strong spin-orbit interactions, such that the Mott physics has a strong orbital character. In the layered honeycomb iridates this is thought to generate highly spin-anisotropic interactions, coupling the spin orientation to a given spatial direction of exchange and leading to strongly frustrated magnetism. The potential for new physics emerging from such interactions has driven much scientific excitement, most recently in the search for a new quantum spin liquid, first discussed by Kitaev \cite{kitaev_anyons_2006}. Here we report a new iridate structure that has the same local connectivity as the layered honeycomb, but in a three-dimensional framework. The temperature dependence of the magnetic susceptibility exhibits a striking reordering of the magnetic anisotropy, giving evidence for highly spin-anisotropic exchange interactions. Furthermore, the basic structural units of this material suggest the possibility of a new family of structures, the `harmonic honeycomb' iridates. This compound thus provides a unique and exciting glimpse into the physics of a new class of strongly spin-orbit coupled Mott insulators.Comment: 12 pages including bibliography, 5 figure

HerMES: A Statistical Measurement of the Redshift Distribution of Herschel-SPIRE Sources Using the Cross-correlation Technique

The wide-area imaging surveys with the Herschel Space Observatory at submillimeter (sub-mm) wavelengths have now resulted in catalogs of the order of one-hundred-thousand dusty, starburst galaxies. These galaxies capture an important phase of galaxy formation and evolution, but, unfortunately, the redshift distribution of these galaxies, N(z), is still mostly uncertain due to limitations associated with counterpart identification at optical wavelengths and spectroscopic follow-up. We make a statistical estimate of N(z) using a clustering analysis of sub-mm galaxies detected at each of 250, 350 and 500 μm from the Herschel Multi-tiered Extragalactic Survey centered on the Boötes field. We cross-correlate Herschel galaxies against galaxy samples at optical and near-IR wavelengths from the Sloan Digital Sky Survey, the NOAO Deep Wide Field Survey, and the Spitzer Deep Wide Field Survey. We create optical and near-IR galaxy samples based on their photometric or spectroscopic redshift distributions and test the accuracy of those redshift distributions with similar galaxy samples defined with catalogs from the Cosmological Evolution Survey (COSMOS), which has superior spectroscopic coverage. We model the clustering auto- and cross-correlations of Herschel and optical/IR galaxy samples to estimate N(z) and clustering bias factors. The S_(350) > 20 mJy galaxies have a bias factor varying with redshift as b(z) = 1.0^(+1.0)_(–0.5)(1 + z)^1.2^(+0.3)_(–0.7). This bias and the redshift dependence is broadly in agreement with galaxies that occupy dark matter halos of mass in the range of 1012 to 10^(13) M_☉. We find that galaxy selections in all three Spectral and Photometric Imaging Receiver (SPIRE) bands share a similar average redshift, with = 1.8 ± 0.2 for 250 μm selected samples, and = 1.9 ± 0.2 for both 350 and 500 μm samples, while their distributions behave differently. For 250 μm selected galaxies we find the a larger number of sources with z ≤ 1 when compared with the subsequent two SPIRE bands, with 350 and 500 μm selected SPIRE samples having peaks in N(z) at progressively higher redshifts. We compare our clustering-based N(z) results to sub-mm galaxy model predictions in the literature, and with an estimate of N(z) using a stacking analysis of COSMOS 24 μm detections

Lean Breed Landrace Pigs Harbor Fecal Methanogens at Higher Diversity and Density than Obese Breed Erhualian Pigs

The diversity of fecal methanogens of Erhualian (obese type) and Landrace (lean type) pigs was examined using separate 16S rRNA gene libraries for each breed. A total of 763 clones were analyzed; 381 from the Erhualian library and 382 from the Landrace library were identified belonging to the genus Methanobrevibacter. Others were identified belonging to the genus Methanosphaera. The two libraries showed significant differences in diversity (P <0.05) and composition (P <0.0001). Only two operational taxonomic units (OTUs) were found in both libraries, whereas six OTUs were found only in the Erhualian library and 23 OTUs were found only in the Landrace library. Real-time PCR showed that the abundance of fecal methanogens in Landrace pigs was significantly higher than that in Erhualian pigs (P <0.05). Results showed that the Landrace pig (lean) harbored a greater diversity and higher numbers of methanogen mcrA gene copies than the Erhualian pig (obese). These differences may be related to the fatness or leanness in these two pig breeds. The results provide new leads for further investigations on the fat storage of pigs or even humans

Non-Gaussianities from the Standard Model Higgs

We have recently proposed that the Standard Model Higgs might be responsible for generating the cosmological perturbations of the universe by acting as an isocurvature mode during a de Sitter inflationary stage. In this paper we study the level of non-Gaussianity in the cosmological perturbations which are inevitably generated due to the non-linearities of the Standard Model Higgs potential. In particular, for the current central value of the top mass, we find that a future detection of non-Gaussianity would exclude the detection of tensor modes by the PLANCK satellite

Functional genomics of corrinoid starvation in the organohalide-respiring bacterium Dehalobacter restrictus strain PER-K23

De novo corrinoid biosynthesis represents one of the most complicated metabolic pathways in nature. Organohalide-respiring bacteria (OHRB) have developed different strategies to deal with their need of corrinoid, as it is an essential cofactor of reductive dehalogenases, the key enzymes in OHR metabolism. In contrast to Dehalococcoides mccartyi, the genome of Dehalobacter restrictus strain PER-K23 contains a complete set of corrinoid biosynthetic genes, of which cbiH appears to be truncated and therefore non-functional, possibly explaining the corrinoid auxotrophy of this obligate OHRB. Comparative genomics within Dehalobacter spp. revealed that one (operon-2) of the five distinct corrinoid biosynthesis associated operons present in the genome of D. restrictus appeared to be present only in that particular strain, which encodes multiple members of corrinoid transporters and salvaging enzymes. Operon-2 was highly up-regulated upon corrinoid starvation both at the transcriptional (346-fold) and proteomic level (46-fold on average), in line with the presence of an upstream cobalamin riboswitch. Together, these data highlight the importance of this operon in corrinoid homeostasis in D. restrictus and the augmented salvaging strategy this bacterium adopted to cope with the need for this essential cofacto

Quadra-Spectrum and Quint-Spectrum from Inflation and Curvaton Models

We calculate the quadra-spectrum and quint-spectrum, corresponding to five and six point correlation functions of the curvature perturbation. For single field inflation with standard kinetic term, the quadra-spectrum and quint-spectrum are small, which are suppressed by slow roll parameters. The calculation can be generalized to multiple fields. When there is no entropy perturbation, the quadra-spectrum and quint-spectrum are suppressed as well. With the presence of entropy perturbation, the quadra-spectrum and quint-spectrum can get boosted. We illustrate this boost in the multi-brid inflation model. For the curvaton scenario, the quadra-spectrum and quint-spectrum are also large in the small r limit. We also calculate representative terms of quadra-spectrum and quint-spectrum for inflation with generalized kinetic terms, and estimate their order of magnitude for quasi-single field inflation.Comment: 16 pages; v2: references added

Local stochastic non-Gaussianity and N-body simulations

Large-scale clustering of highly biased tracers of large-scale structure has emerged as one of the best observational probes of primordial non-Gaussianity of the local type (i.e. f_{NL}^{local}). This type of non-Gaussianity can be generated in multifield models of inflation such as the curvaton model. Recently, Tseliakhovich, Hirata, and Slosar showed that the clustering statistics depend qualitatively on the ratio of inflaton to curvaton power \xi after reheating, a free parameter of the model. If \xi is significantly different from zero, so that the inflaton makes a non-negligible contribution to the primordial adiabatic curvature, then the peak-background split ansatz predicts that the halo bias will be stochastic on large scales. In this paper, we test this prediction in N-body simulations. We find that large-scale stochasticity is generated, in qualitative agreement with the prediction, but that the level of stochasticity is overpredicted by ~30%. Other predictions, such as \xi independence of the halo bias, are confirmed by the simulations. Surprisingly, even in the Gaussian case we do not find that halo model predictions for stochasticity agree consistently with simulations, suggesting that semi-analytic modeling of stochasticity is generally more difficult than modeling halo bias.Comment: v3: minor changes matching published versio