Lactobacillus ruminis strains cluster according to their mammalian gut source

peer-reviewedBackground Lactobacillus ruminis is a motile Lactobacillus that is autochthonous to the human gut, and which may also be isolated from other mammals. Detailed characterization of L. ruminis has previously been restricted to strains of human and bovine origin. We therefore sought to expand our bio-bank of strains to identify and characterise isolates of porcine and equine origin by comparative genomics. Results We isolated five strains from the faeces of horses and two strains from pigs, and compared their motility, biochemistry and genetic relatedness to six human isolates and three bovine isolates including the type strain 27780T. Multilocus sequence typing analysis based on concatenated sequence data for six individual loci separated the 16 L. ruminis strains into three clades concordant with human, bovine or porcine, and equine sources. Sequencing the genomes of four additional strains of human, bovine, equine and porcine origin revealed a high level of genome synteny, independent of the source animal. Analysis of carbohydrate utilization, stress survival and technological robustness in a combined panel of sixteen L. ruminis isolates identified strains with optimal survival characteristics suitable for future investigation as candidate probiotics. Under laboratory conditions, six human isolates of L. ruminis tested were aflagellate and non-motile, whereas all 10 strains of bovine, equine and porcine origin were motile. Interestingly the equine and porcine strains were hyper-flagellated compared to bovine isolates, and this hyper-flagellate phenotype correlated with the ability to swarm on solid medium containing up to 1.8% agar. Analysis by RNA sequencing and qRT-PCR identified genes for the biosynthesis of flagella, genes for carbohydrate metabolism and genes of unknown function that were differentially expressed in swarming cells of an equine isolate of L. ruminis. Conclusions We suggest that Lactobacillus ruminis isolates have potential to be used in the functional food industry. We have also identified a MLST scheme able to distinguish between strains of L. ruminis of different origin. Genes for non-digestible oligosaccharide metabolism were identified with a putative role in swarming behaviour.This work was supported by a Principal Investigator Award (07/IN.1/B1780) from Science Foundation Ireland to P.W. O’Toole

Suggestions for Biology or Nature Clubs

The very first requirement for a successful club of this nature is enthusiasm for and an interest in the. world of living things. The sparks for kindling enthusiasm must come from off the hearth of the sponsor. While the students must be guided they should be led to feel that it is their program that they are working out and not that of a teacher who grants credit for participation

Crystallographic orientations of magnesiochromite inclusions in diamonds: what do they tell us?

We have studied by X-ray diffractometry the crystallographic orientation relationships (CORs) between magnesiochromite (mchr) inclusions and their diamond hosts in gem-quality stones from the mines Udachnaya (Siberian Russia), Damtshaa (Botswana) and Panda (Canada); in total 36 inclusions in 23 diamonds. In nearly half of the cases (n = 17), [111]mchr is parallel within error to [111]diamond, but the angular misorientation for other crystallographic directions is generally significant. This relationship can be described as a case of rotational statistical COR, in which inclusion and host share a single axis (1 df). The remaining mchr\u2013diamond pairs (n = 19) have a random COR (2 df). The presence of a rotational statistical COR indicates that the inclusions have physically interacted with the diamond before their final incorporation. Of all possible physical processes that may have influenced mchr orientation, those driven by surface interactions are not considered likely because of the presence of fluid films around the inclusions. Mechanical interaction between euhedral crystals in a fluid-rich environment is therefore proposed as the most likely mechanism to produce the observed rotational COR. In this scenario, neither a rotational nor a random COR can provide information on the relative timing of growth of mchr and diamond. Some multiple, iso-oriented inclusions within single diamonds, however, indicate that mchr was partially dissolved during diamond growth, suggesting a protogenetic origin of these inclusions

Pro-inflammatory flagellin proteins of prevalent motile commensal bacteria are variably abundant in the intestinal microbiome of elderly humans

Peer reviewedPublisher PD

Draft genome sequence of Lactobacillus crispatus EM-LC1, an isolate with antimicrobial activity cultured from an elderly subject

Here we report the 1.86-Mb draft genome sequence of Lactobacillus crispatus EM-LC1, a fecal isolate with antimicrobial activity. This genome sequence is expected to provide insights into the antimicrobial activity of L. crispatus and improve our knowledge of its potential probiotic traits

Black carbon as an additional indicator of the adverse health effects of airborne particles compared with PM10 and PM2.5.

Current air quality standards for particulate matter (PM) use the PM mass concentration [PM with aerodynamic diameters ≤ 10 μm (PM(10)) or ≤ 2.5 μm (PM(2.5))] as a metric. It has been suggested that particles from combustion sources are more relevant to human health than are particles from other sources, but the impact of policies directed at reducing PM from combustion processes is usually relatively small when effects are estimated for a reduction in the total mass concentration

Inclusions in super-deep diamonds

Super-deep diamonds may originate from a depth of between 300 and 800 km, although their precise depth of origin remains uncertain. When growing, they trap other minerals from their surroundings, which remain unaltered in their diamond capsule on their journey up to the surface of our planet. Through the study of these inclusions it is thus possible to reveal the secrets of deep unseen environments. In this study we aim to determine the formation pressure of super- deep diamonds for the first time by characterising two types of inclusions: CaSiO3-walstromite and ferropericlase. To achieve this goal we investigated CaSiO3-walstromite inclusions by a combination of in situ single-crystal X-ray diffraction, \u201csingle-inclusion elastic barometry\u201d and in situ micro-Raman spectroscopy and we obtained an apparent entrapment pressure of 3c7.1 GPa, corresponding to 3c250 km, at a temperature of 1500 K. In addition, thermodynamic calculations suggested that single inclusions of CaSiO3-walstromite cannot derive from CaSiO3-perovskite. Preliminary X-ray micro-tomography and nuclear resonance scattering data were also collected on ferropericlase-bearing diamonds in order to detect micro-fractures around the inclusions and to determine whether the Fe3+/ 11Fe ratios are in agreement with lower mantle values or not

Spatially-explicit and spectral soil carbon modeling in Florida.

Profound shifts have occurred over the last three centuries in which human actions have become the main driver to global environmental change. In this new epoch, the Anthropocene, human-driven changes such as population growth, climate and land use change, are pushing the Earth system well outside its normal operating range causing severe and abrupt environmental change. In this context, we present research highlights from Florida (150,000 km2) showing how anthropogenic-induced changes have had major impacts on carbon dynamics in soils, including (i) modeling of carbon and nutrient dynamics and soil carbon sequestration impacted by climate and land use change; (ii) geospatial assessment of soil carbon stocks and pools, and (iii) spectral-based soil carbon modeling. Our research is embedded in the STEP-AWBH modeling concept which explicitly incorporates Human forcings and time-dependent evolution of Atmospheric, Water, and Biotic factors into the modeling process. Spatially-explicit soil carbon observations were fused with ancillary environmental data and various statistical and geostatistical methods were used to upscale soil carbon across the region. Our results suggest that soil hydrologic and taxonomic, biotic (vegetation and land use), and climatic properties show complex interactions explaining the variation of soil carbon within this heterogeneous subtropical landscape