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

Recklessness in context: Individual and situational correlates to aggressive driving

Traffic-related injury and fatality are major health risks in the United States and worldwide. One contributor to road accidents is unsafe and aggressive driving practices. We examined individual and situational aspects of aggressive driving by having 152 undergraduate students complete self-report measures. Aggressive driving was related to personality variables, such as hostility, sensation seeking, and competitiveness, as well as to social variables such as driving without passengers and characteristics of the target vehicle (e.g., passengers, age, and status of driver), environmental variables (e.g., type of road, traffic, and weather), and temporal variables (e.g., time pressure and time of day)

A reliability analysis of the Revised Competitiveness Index

This study examined the reliability of the Revised Competitiveness Index by investigating the test-retest reliability, interitem reliability, and factor structure of the measure based on a sample of 280 undergraduates (200 women, 80 men) ranging in age from 18 to 28 years (M=20.1, SD=2.1). The findings indicate that the Revised Competitiveness Index has high test-retest reliability, high interitem reliability, and a stable factor structure. The results support the assertion that the Revised Competitiveness Index assesses competitiveness as a stable trait rather than a dynamic state

Socioeconomic stereotypes among undergraduate college students

Classism, i.e., socioeconomic stereotypes, prejudice, and discrimination that college students direct toward their peers, was examined. A sample of 53 undergraduate students (36 women and 17 men), ages 18 to 22 years (M = 19.0, SD = 1.2), were recruited from psychology courses. Utilizing a computer-administered questionnaire, participants were randomly assigned to rate a fictitious student whose family income was specified as among the lowest or highest at the college. Upper Income targets were rated as more sociable, judgmental, attractive, more likely to use alcohol and drugs, and more likely to belong to a fraternity or sorority. Lower Income targets were rated as more likable, agreeable, conscientious, intelligent, creative, and better able to maintain close friendships. Research directed toward the middle class could help fill a gap in the classism literature. Research on classism in higher education could clarify this potentially divisive issue among undergraduates

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

Peer reviewedPublisher PD

Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes

Acknowledgements The Rowett Institute of Nutrition and Health (University of Aberdeen) receives financial support from the Scottish Government Rural and Environmental Sciences and Analytical Services (RESAS). POS is a PhD student supported by the Scottish Government (RESAS) and the Science Foundation Ireland, through a centre award to the APC Microbiome Institute, Cork, Ireland. Data Summary The high-quality draft genomes generated in this work were deposited at the European Nucleotide Archive under the following accession numbers: 1. Eubacterium rectale T1-815; CVRQ01000001–CVRQ0100 0090: http://www.ebi.ac.uk/ena/data/view/PRJEB9320 2. Roseburia faecis M72/1; CVRR01000001–CVRR010001 01: http://www.ebi.ac.uk/ena/data/view/PRJEB9321 3. Roseburia inulinivorans L1-83; CVRS01000001–CVRS0 100 0151: http://www.ebi.ac.uk/ena/data/view/PRJEB9322Peer reviewedPublisher PD

Phylogenomics and comparative genomics of Lactobacillus salivarius, a mammalian gut commensal

The genus Lactobacillus is a diverse group with a combined species count of over 200. They are the largest group within the lactic acid bacteria and one of the most important bacterial groups involved in food microbiology and human nutrition because of their fermentative and probiotic properties. Lactobacillus salivarius, a species commonly isolated from the gastrointestinal tract of humans and animals, has been described as having potential probiotic properties and results of previous studies have revealed considerable functional diversity existing on both the chromosomes and plasmids. Our study consists of comparative genomic analyses of the functional and phylogenomic diversity of 42 genomes of strains of L . salivarius using bioinformatic techniques. The main aim of the study was to describe intra-species diversity and to determine how this diversity is spread across the replicons. We found that multiple phylogenomic and non-phylogenomic methods used for reconstructing trees all converge on similar tree topologies, showing that different metrics largely agree on the evolutionary history of the species. The greatest genomic variation lies on the small plasmids, followed by the repA-type circular megaplasmid, with the chromosome varying least of all. Additionally, the presence of extra linear and circular megaplasmids is noted in several strains, while small plasmids are not always present. Glycosyl hydrolases, bacteriocins and proteases vary considerably on all replicons while two exopolysaccharide clusters and several clustered regularly interspaced short palindromic repeats-associated systems show a lot of variation on the chromosome. Overall, despite its reputation as a mammalian gastrointestinal tract specialist, the intra-specific variation of L. salivarius reveals potential strain-dependant effects on human health

Non Markovian persistence in the diluted Ising model at criticality

We investigate global persistence properties for the non-equilibrium critical dynamics of the randomly diluted Ising model. The disorder averaged persistence probability $\bar{{P}_c}(t)$ of the global magnetization is found to decay algebraically with an exponent $\theta_c$ that we compute analytically in a dimensional expansion in $d=4-\epsilon$. Corrections to Markov process are found to occur already at one loop order and $\theta_c$ is thus a novel exponent characterizing this disordered critical point. Our result is thoroughly compared with Monte Carlo simulations in $d=3$, which also include a measurement of the initial slip exponent. Taking carefully into account corrections to scaling, $\theta_c$ is found to be a universal exponent, independent of the dilution factor $p$ along the critical line at $T_c(p)$, and in good agreement with our one loop calculation.Comment: 7 pages, 4 figure

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

Adapting to time: Duration channels do not mediate human time perception

Accurately encoding the duration and temporal order of events is essential for survival and important to everyday activities, from holding conversations to driving in fastflowing traffic. Although there is a growing body of evidence that the timing of brief events (< 1 s) is encoded by modality-specific mechanisms, it is not clear how such mechanisms register event duration. One approach gaining traction is a channel-based model; this envisages narrowly-tuned, overlapping timing mechanisms that respond preferentially to different durations. The channelbased model predicts that adapting to a given event duration will result in overestimating and underestimating the duration of longer and shorter events, respectively. We tested the model by having observers judge the duration of a brief (600 ms) visual test stimulus following adaptation to longer (860 ms) and shorter (340 ms) stimulus durations. The channel-based model predicts perceived duration compression of the test stimulus in the former condition and perceived duration expansion in the latter condition. Duration compression occurred in both conditions, suggesting that the channel-based model does not adequately account for perceived duration of visual events