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

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

Down Selection of Polymerized Bovine Hemoglobins for Use as Oxygen Releasing Therapeutics in a Guinea Pig Model

Editor's Highlight: The development of hemoglobin-based oxygen carriers (HBOCs) as a replacement for whole-blood transfusions has been impeded by their systemic toxicity. This paper presents data from a series of HBOCs, demonstrating one candidate that meets predetermined safety criteria. This approach may allow the development of an acceptable blood substitute for human us

Molecular Tracers of the Central 12 pc of the Galactic Center

We have used the BIMA array to image the Galactic Center with a 19-pointing mosaic in HCN(1-0), HCO+(1-0), and H 42-alpha emission with 5 km/s velocity resolution and 13'' x 4'' angular resolution. The 5' field includes the circumnuclear ring (CND) and parts of the 20 and 50 km/s clouds. HCN(1-0) and HCO+ trace the CND and nearby giant molecular clouds while the H 42-alpha emission traces the ionized gas in Sgr A West. We find that the CND has a definite outer edge in HCN and HCO+ emission at ~45'' radius and appears to be composed of two or three distinct streams of molecular gas rotating around the nucleus. Outside the CND, HCN and HCO+ trace dense clumps of high-velocity gas in addition to optically thick emission from the 20 and 50 km/s clouds. A molecular ridge of compressed gas and dust, traced in NH3 emission and self-absorbed HCN and HCO+, wraps around the eastern edge of Sgr A East. Just inside this ridge are several arcs of gas which have been accelerated by the impact of Sgr A East with the 50 km/s cloud. HCN and HCO+ emission trace the extension of the northern arm of Sgr A West which appears to be an independent stream of neutral and ionized gas and dust originating outside the CND. Broad line widths and OH maser emission mark the intersection of the northern arm and the CND. Comparison to previous NH3 and 1.2mm dust observations shows that HCN and HCO+ preferentially trace the CND and are weaker tracers of the GMCs than NH3 and dust. We discuss possible scenarios for the emission mechanisms and environment at the Galactic center which could explain the differences in these images.Comment: 24 pages, including 17 figures; to appear in The Astrophysical Journa

WormBook: the online review of Caenorhabditis elegans biology

WormBook () is an open-access, online collection of original, peer-reviewed chapters on the biology of Caenorhabditis elegans and related nematodes. Since WormBook was launched in June 2005 with 12 chapters, it has grown to over 100 chapters, covering nearly every aspect of C.elegans research, from Cell Biology and Neurobiology to Evolution and Ecology. WormBook also serves as the text companion to WormBase, the C.elegans model organism database. Objects such as genes, proteins and cells are linked to the relevant pages in WormBase, providing easily accessible background information. Additionally, WormBook chapters contain links to other relevant topics in WormBook, and the in-text citations are linked to their abstracts in PubMed and full-text references, if available. Since WormBook is online, its chapters are able to contain movies and complex images that would not be possible in a print version. WormBook is designed to keep up with the rapid pace of discovery in the field of C.elegans research and continues to grow. WormBook represents a generic publishing infrastructure that is easily adaptable to other research communities to facilitate the dissemination of knowledge in the field

Tectonic interleaving along the Main Central Thrust, Sikkim Himalaya

Geochemical and geochronological analyses provide quantitative evidence about the origin, development and motion along ductile faults, where kinematic structures have been overprinted. The Main Central Thrust is a key structure in the Himalaya that accommodated substantial amounts of the India–Asia convergence. This structure juxtaposes two isotopically distinct rock packages across a zone of ductile deformation. Structural analysis, whole-rock Nd isotopes, and U–Pb zircon geochronology reveal that the hanging wall is characterized by detrital zircon peaks at c. 800–1000 Ma, 1500–1700 Ma and 2300–2500 Ma and an εNd(0) signature of –18.3 to –12.1, and is intruded by c. 800 Ma and c. 500–600 Ma granites. In contrast, the footwall has a prominent detrital zircon peak at c. 1800–1900 Ma, with older populations spanning 1900–3600 Ma, and an εNd(0) signature of –27.7 to –23.4, intruded by c. 1830 Ma granites. The data reveal a c. 5 km thick zone of tectonic imbrication, where isotopically out-of-sequence packages are interleaved. The rocks became imbricated as the once proximal and distal rocks of the Indian margin were juxtaposed by Cenozoic movement along the Main Central Thrust. Geochronological and isotopic characterization allows for correlation along the Himalayan orogen and could be applied to other cryptic ductile shear zones

Core fecal microbiota of domesticated herbivorous ruminant, hindgut fermenters, and monogastric animals

peer-reviewedIn this pilot study, we determined the core fecal microbiota composition and overall microbiota diversity of domesticated herbivorous animals of three digestion types: hindgut fermenters, ruminants, and monogastrics. The 42 animals representing 10 animal species were housed on a single farm in Ireland and all the large herbivores consumed similar feed, harmonizing two of the environmental factors that influence the microbiota. Similar to other mammals, the fecal microbiota of all these animals was dominated by the Firmicutes and Bacteroidetes phyla. The fecal microbiota spanning all digestion types comprised 42% of the genera identified. Host phylogeny and, to a lesser extent, digestion type determined the microbiota diversity in these domesticated herbivores. This pilot study forms a platform for future studies into the microbiota of nonbovine and nonequine domesticated herbivorous animals.Science Foundation Irelan

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