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Introduction Bovine respiratory disease (BRD) is a multifactorial disease that affects cattle worldwide, with severe animal health, well-being, and economic ramifications (Rice et al. 2007). BRD can result from combinations [...], Common bacterial causes of bovine respiratory disease (BRD) include Histophilus somni, Mannheimia haemolytica, and Pasteurella multocida.Within M. haemolytica, two major genotypes are commonly found in cattle (1 and 2); however, genotype 2 strains are isolated from diseased lungs much more frequently than genotype 1 strains. Outer membrane proteins (OMPs) of H. somni, P. multocida, and genotype 2 M. haemolytica may be important factors for acquired host immunity. The predicted OMP differences between genotypes 1 and 2 M. haemolytica have been previously identified. In this study, we expanded the focus to include bovine-isolated strain genomes representing all three species and the two M. haemolytica genotypes. Reported here are the core genomes unique to each of them, core genomes shared between some or all combinations of the three species and two M. haemolytica genotypes, and predicted OMPs within these core genomes. The OMPs identified in this study are potential candidates for further studies and the development of interventions against BRD. Key words: Histophilus somni, Mannheimia haemolytica, Pasteurella multocida, outer membrane proteins, bovine respiratory disease. Les bacteries le plus souvent en cause dans les maladies respiratoires des bovins (MRB) incluent Histophilus somni, Mannheimia haemolytica et Pasturella multocida. Au sein du M. haemolytica, deux genotypes majeurs sont communement rencontres chez les bovins (genotypes 1 et 2), mais les souches du genotype 2 sont isolees de poumons atteints beaucoup plus souvent que les souches du genotype 1. Les proteines de la membrane externe (PME) de H. somni, P. multocida et du genotype 2 de M. haemolytica pourraient constituer des facteurs importants pour l'immunite acquise chez l'hote. Des differences predites au niveau des PME entre les genotypes 1 et 2 de M. haemolytica ont ete identifiees precedemment. Dans ce travail, les auteurs elargissent la portee de ces recherches en etudiant les genomes de souches isolees de bovins pour les trois especes et les deux genotypes de M. haemolytica. Les auteurs rapportent ici les genomes partages qui sont uniques a chacune d'elles, les portions de ces genomes qui sont communes a toutes ou a certaines combinaisons de ces trois especes et deux genotypes de M. haemolytica, ainsi que les PME predites au sein de ces genomes partages. Les PME identifies dans ce travail constituent des candidats potentiels pour des etudes plus approfondies et pour la mise au point de methodes d'intervention pour contrer les MRB. [Traduit par la Redaction] Mots-cles: Histophilus somni, Mannheimia haemolytica, Pasturella multocida, proteines de la membrane externe, maladies respiratoires des bovins.

Author(s): Erica C. Pehrsson [1]; Pablo Tsukayama [1]; Sanket Patel [1, 2]; Melissa Meja-Bautista [1, 3]; Giordano Sosa-Soto [1, 3]; Karla M. Navarrete [3]; Maritza Calderon [4]; Lilia Cabrera [5]; [...], Antibiotic-resistant infections annually claim hundreds of thousands of lives worldwide. This problem is exacerbated by exchange of resistance genes between pathogens and benign microbes from diverse habitats. Mapping resistance gene dissemination between humans and their environment is a public health priority. Here we characterized the bacterial community structure and resistance exchange networks of hundreds of interconnected human faecal and environmental samples from two low-income Latin American communities. We found that resistomes across habitats are generally structured by bacterial phylogeny along ecological gradients, but identified key resistance genes that cross habitat boundaries and determined their association with mobile genetic elements. We also assessed the effectiveness of widely used excreta management strategies in reducing faecal bacteria and resistance genes in these settings representative of low- and middle-income countries. Our results lay the foundation for quantitative risk assessment and surveillance of resistance gene dissemination across interconnected habitats in settings representing over two-thirds of the worlds population.

Author(s): Christian Jobin (corresponding author) [1] From birth, the surfaces and cavities of the human body are populated by microbes that, in tight partnership with the host, maintain a complex [...]

This study was conducted to analyze the effects various pretreatments on the ability of Trichoderma reesei, Pycnoporus cinnabarinus, Fusarium solani, an unknown bacterial isolate, and an unknown fungal isolate in the degradation of lignocellulosic biomass of Southern pine sawdust under aerobic and anaerobic conditions. Samples of Southern pine sawdust were either autoclaved or treated with 25% [H.sub.2]S[O.sub.4]. Liquid medium was prepared and added to each of 48 Erlenmeyer flasks. Various microorganisms were inoculated into each flask and left to incubate for 0, 6, 9, 13, 16, and 22 days under aerobic and anaerobic conditions. At specific time intervals samples were analyzed to determine the concentration of glucose present using the Dinitrosalicylic Acid (DNS) method. Our results revealed that Fusarium solani produced more reducing sugar followed by Trichoderma reesei, across all days as compared to other isolates. Additionally, we found that more reducing sugar was produced under aerobic conditions as compared to anaerobic conditions. We concluded that pretreatment methods may play significant roles in the degradation of lignocellulosic biomass of Southern pine sawdust and that the rate of degradation may depend on aerobic and anaerobic conditions., INTRODUCTION Increased concern for the negative impact of fossil fuels on the environment, particularly greenhouse gas emissions into the atmosphere, and rising prices of crude oil due to increasing fuel [...]

Chinese hickory (Carya cathayensis Sarg.) is a woody nut and oil tree from China. Intensive management including heavy application of chemical fertiliser and long-term application of herbicides has resulted in serious soil loss and degradation. This study aimed to test the hypothesis that intercropping in the soil under Chinese hickory stands may improve soil fertility and microbial community functional diversity. A field experiment consisting of four treatments (clean tillage; intercropping rape (Brassica rapa L.), ryegrass (Lolium perenne L.) or Chinese milk vetch (Astragalus sinicus L.) was conducted to study the effects of intercropping on soil organic carbon (SOC) structure and microbial community functional diversity under C. cathayensis stand, by means of 13C-nuclear magnetic resonance (NMR), and EcoPlates incubated at 25°C. After 4 years of treatment, intercropping increased available nitrogen (N), phosphorus and potassium in the soil by 25.1-54.2, 4.2-6.0 and 0-22.5 mg kg-1, respectively, relative to the clean tillage treatment; intercropping rape, ryegrass and Chinese milk vetch increased SOC, microbial biomass C (MBC), and water-soluble organic C (WOC) by 23.1-24.7, 138.6-159.7 and 56.2-69.5% (P Additional keywords: cover crop, interplanting, microbial functional diversity, [sup.13]C-nuclear magnetic resonance., Introduction Chinese hickory (Carya cathayensis Sarg.) is a unique, woody nut and oil tree species. It is mainly distributed in Zhejiang and Anhui provinces of eastern China (Chen et al. [...]

Soil organic matter (SOM) quality and carbon (C) availability may be major features influencing the effect of earthworms on the aerobic processes in clayey tropical soils. In this study, we assessed the effect of an anecic (Polypheretima elongata), an endogeic (Pontoscolex corethrurus) and an epigeic (Eudrilus eugeniae) earthworm on the aerobic microbial activity of two tropical soils, a calcic Vertisol and an acid Ferralsol, with clay content >70% and very different organic C content and SOM stability. The soil-earthworm interaction was studied in a 6-month mesocosm experiment in a greenhouse using soils with and without (control soil) earthworm addition. Potential C mineralisation, actual net nitrogen (N) mineralisation and dehydrogenase activity (DHA), as indicators of the aerobic activity of the soils, and phosphorus (P) availability were determined during the trial. DHA was used as an indicator of the global aerobic activity. Earthworms had little effect on potential C mineralisation but significantly increased actual net N mineralisation. The increase in N mineralisation in the Vertisol was twice as great as, and longer (6 v. 3 months) than for the Ferralsol. Differences between soils for N mineralisation were associated with a less recalcitrant SOM in the Vertisol. Available P increased 10% in the earthworm treatments. Earthworm activity improved N and P availability. DHA was 15 times higher for the Vertisol than for the Ferralsol, but the positive effect of earthworms on DHA was greater for the Ferralsol. This effect was greater for E. eugeniae, probably because of surface burrows generated by this epigeic earthworm, which favoured oxygen entry into the soil. Differences between the two soils were greater for DHA than for C and N mineralisation, and this was observed for the control soils as well as for the earthworm treatments. This indicates that earthworm activity modified the rate of the aerobic processes but it did not affect the intrinsic biological properties of these tropical soils, which were controlled mainly by SOM quality and C availability. Additional keywords: Eudrilus eugeniae, Ferralsol, Polypheretima elongata, Pontoscolex corethrurus, SOM mineralisation, Vertisol., Introduction Earthworms contribute to many ecosystem services, including water regulation, nutrient cycling, carbon (C) sequestration and primary production (Blouin et al. 2013). Earthworm species and populations vary widely with the [...]

Adaptation of soil microbes to salinity requires substantial amounts of energy. We hypothesised that addition of glucose would increase microbial activity and growth and alleviate the negative effect of salinity on microbes. An incubation experiment was conducted with four salinity levels by using one non-saline and three saline soils of similar texture (sandy clay loam), with electrical conductivities ([EC.sub.1:5]) of 0.1, 1.1, 3.1 and 5.2 dS [m.sup.-1]. Glucose was added to achieve five organic carbon concentrations (0, 0.5, 1,2.5, 5 g C [kg.sup.-1]). Soluble nitrogen (N) and phosphorus (P) were added to achieve a carbon (C): N ratio of 20 and a C: P ratio of 200 to ensure that these nutrients did not limit microbial growth. A water content of 50% of the water-holding capacity (optimal for microbial activity in soils of this texture) was maintained throughout the incubation. Soil respiration was measured continuously over 21 days; microbial biomass C and available N and P were determined on days 2, 5, 14 and 21. Cumulative respiration was increased by addition of glucose and was reduced by salinity. The percentage decrease in cumulative respiration in saline soils compared with non-saline soil was greatest in the unamended soil and lowest with addition of 5 g C [kg.sup.-1]. At this rate of C addition, the percentage decrease in cumulative respiration increased with increasing salinity level. Microbial biomass C (MBC) concentration on days 2 and 5 was strongly increased by ≥ 1 g C [kg.sup.-1] but decreased over time with the strongest decrease at the highest C addition rate. The MBC concentration was negatively correlated with EC at all C rates at each sampling date. Addition of C resulted in N and P immobilisation in the first 5 days. Biomass turnover as a result of depletion of readily available C released previously immobilised N and P after day 5, particularly in the soils with low salinity. This study showed that over a period of 3 weeks, addition of glucose increased microbial activity and growth in saline soils and alleviated the negative impact of salinity on microbes. Additional keywords: available N, available P, glucose, microbial biomass, respiration, salinity., Introduction Soil salinity is a major threat to agricultural production and ecosystem sustainability in arid and semi-arid regions, reducing plant growth and yield. Globally, the area of primary salt-affected soils [...]

ABSTRACT The efficiency of depuration of the Indian backwater oyster Crassostrea madrasensis (Preston, 1916) using the fill-draw method (static method) with high-loading density was evaluated in this study. Depuration experiments [...]

The global market for probiotics is projected to be worth almost $USD 100 billion by 2020, (1) reflecting growing acceptance that our intestinal microbiota can influence physiologic systems, including but [...]

Background: Preoperative biliary bacterial colonization (bacterobilia) is considered a risk factor for infectious complications after pancreaticoduodenectomy (PD). The aim of this study was to investigate the role of the microbiome [...]

There is growing concern that recent lifestyle innovations, most notably the high-fat/high-sugar 'Western' diet, have altered the genetic composition and metabolic activity of our resident microorganisms (the human gut microbiome) [...], Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut (1-5), but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bactteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals (2), reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease (6). In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.

Incidences of bacterial foodborne illness caused by ingestion of fresh produce are rising. Instead of this being due to incidental contamination, the animal pathogen Salmonella enterica utilizes specific molecular mechanisms to attach to and colonize plants. This work characterizes two S. enterica genes of unknown function: a putative periplasmic protein, STM0278, and a putative protein with a hydrolase in the C-terminus, STM0650. STM0278 and STM0650 are important for seedling colonization but appear to have different roles during the process of colonization. Mutants of either STM0278 or STM0650 showed reduced colonization of alfalfa seedlings at 24 h, and the STM0278 mutant also showed reduced colonization at 48 h. Both genes were expressed in planta at 4 h following inoculation of 3-day-old seedlings and at 72 h after seed inoculation. This suggests that the role of STM0650 in seedling colonization is less important later in the process or is duplicated by other mechanisms. Mutants of STM0278 and STM0650 were defective in swarming. The STM0278 mutant failed to swarm in 24 h, while swarming of the STM0650 mutant was delayed. Addition of surfactant restored swarming of the STM0278 mutant, suggesting that STM0278 is involved in surfactant or osmotic agent production or deployment. Alfalfa seed exudates as the sole nutrient source were capable of perpetuating S. enterica swarming. Sequence analysis revealed sequences homologous to STM0278 and STM0650 in plant-associated bacteria, but none in Escherichia coli Phylogenetic analysis of STM0650 showed similar sequences from diverse classes of plant-associated bacteria. Bacteria that preferentially colonize roots, including S. enterica, may use a similar hydrolase for swarming or biofilm production on plants. Multicellular behaviours by S. enterica appear central to plant colonization. S. enterica genes involved in plant colonization and survival outside of a host are most likely among the 'function unknown' genes of this bacterium. DOI 10.1099/mic.0.032029-0

Bacteria communicate and cooperate to perform a wide range of social behaviors including production of extracellular products (public goods) that are crucial for growth and virulence. Their expression may be switched on by the detection of threshold densities of diffusible signals [Quorum-Sensing (QS)]. Studies using the opportunistic pathogen Pseudomonas aeruginosa suggest that QS 'cheats'--individuals that don't respond to the QS signal, but are still able to use public goods produced by others--have a selective advantage in the presence of QS cooperators. It is, however, unclear whether this type of social exploitation is relevant in clinical contexts. Here, we report the evolutionary dynamics and virulence of P. aeruginosa populations during lung colonization of mechanically ventilated patients in the absence of antimicrobial treatments. We observed a large diversity of QS phenotypes among initial colonizing isolates. This diversity decreased over a matter of days, concomitant with a gradual increase in the proportion of QS cheating mutants (lasR mutants), which were found in 80% of the patients after 9 days of colonization. These mutants often evolved from initial wild-type genotypes. The fitness advantage of the lasR mutants is almost certainly due to social exploitation, because this advantage was only apparent in the presence of QS wild-type cells. Crucially, ventilator-associated pneumonia occurred significantly earlier in patients predominantly colonized by QS wild-type populations, highlighting the importance of QS in this clinical situation. These results demonstrate that social interactions can shape the short-term evolution and virulence of bacterial pathogens in humans, providing novel opportunities for therapy. infection | quorum sensing | social interactions

Ruminant fat is rich in SFA, partly due to the biohydrogenation of dietary PUFA to SFA in the rumen. This process can be inhibited by the dietary inclusion of fish oil. The only bacteria isolated from the rumen capable of converting PUFA to SFA are closely related to Clostridium proteoclasticum. The aim of this study was to investigate if a correlation could be found in vivo between dietary fish oil inclusions and the composition of the ruminal bacterial community and specifically of C. proteoclasticum. Six Hereford x Friesian steers, prepared with ruminal and duodenal cannulae, received grass silage plus 1 of 3 concentrates resulting in total dietary fish oil contents of 0, 1, or 3% of dry matter. A dual flow marker technique was employed to estimate the relative flow of fatty acids. Steers fed the 3% fish oil diet had 100% increases in trans 18:1 flow, whereas 18:0 flow declined to 39% of steers fed the control diet. 16S ribosomal RNA-based denaturing gradient gel electrophoresis profiles obtained from ruminal digesta showed major changes in the bacterial community within steers fed the 3% fish oil diet. Quantitative PCR indicated only a weak relation between numbers of C. proteoclasticum and 18:0 flow between treatments and in individual steers (P < 0.05, but the percentage variance accounted for only 22.8) and did not provide unambiguous evidence that numbers of C. proteoclasticum in the rumen dictate the ratios of SFA:PUFA available for absorption by the animal. Understanding which microbes biohydrogenate PU FA in the rumen is key to developing novel strategies to improve the quality of ruminant products.

Author(s): J Most [1]; J Penders [2]; M Lucchesi [2]; G H Goossens [1]; E E Blaak [1] Introduction The human intestinal microbiota consists of 10[sup.12] -10[sup.14] bacteria and may [...], Background/Objectives: The intestinal microbiota may have a profound impact on host metabolism. As evidence suggests that polyphenols affect substrate utilization, the present study aimed to investigate the effects of polyphenol supplementation on intestinal microbiota composition in humans. Furthermore, we examined whether (changes in) gut microbiota composition may determine the metabolic response to polyphenol supplementation. Subjects/Methods: In this randomized, double-blind, placebo (PLA)-controlled trial, 37 overweight and obese men and women (18 males/19 females, 37.8[+ or -]1.6 years, body mass index: 29.6[+ or -]0.5 kg/m[sup.2]) received either epigallocatechin-3-gallate and resveratrol (EGCG+RES, 282 and 80 mg/day, respectively) or PLA for 12 weeks. Before and after intervention, feces samples were collected to determine microbiota composition. Fat oxidation was assessed by indirect calorimetry during a high-fat mixed meal test (2.6 MJ, 61 energy% fat) and skeletal muscle mitochondrial oxidative capacity by means of ex vivo respirometry on isolated skeletal muscle fibers. Body composition was measured by dual-energy X-ray absorptiometry. Results: Fecal abundance of Bacteroidetes was higher in men as compared with women, whereas other assessed bacterial taxa were comparable. EGCG+RES supplementation significantly decreased Bacteroidetes and tended to reduce Faecalibacterium prausnitzii in men (P=0.05 and P=0.10, respectively) but not in women (P=0.15 and P=0.77, respectively). Strikingly, baseline Bacteroidetes abundance was predictive for the EGCG+RES-induced increase in fat oxidation in men but not in women. Other bacterial genera and species were not affected by EGCG+RES supplementation. Conclusions: We demonstrated that 12-week EGCG+RES supplementation affected the gut microbiota composition in men but not in women. Baseline microbiota composition determined the increase in fat oxidation after EGCG+RES supplementation in men. European Journal of Clinical Nutrition (2017) 71, 1040-1045; doi: 10.1038/ejcn.2017.89; published online 7 June 2017

Author(s): Sara Reardon Genetically modified viruses that cause bacteria to kill themselves could be the next step in https://www.nature.com/articles/509S9a . Several companies have engineered such viruses, called bacteriophages, to use [...]

The intestinal epithelium of the adult gut supports a complex, dynamic microbial ecosystem and expresses highly fucosylated glycans on its surface. Uncolonized gut contains little fucosylated glycan. The transition toward adult colonization, such as during recovery from germ-free status or from antibiotic treatment, increased expression of fucosylated epitopes in the colonic epithelium. This increase in fucosylation is accompanied by induction of fut2 mRNA expression and [alpha]l,2/3-fucosyltransferase activity. Colonization stimulates ERK and JNK signal transduction pathways, resulting in activation of transcription factors ATF2 and c-Jun, respectively. This increases transcription of fut2 mRNA and expression of [alpha]1,2/3-fucosyltransferase activity, resulting in a highly fucosylated intestinal mucosa characteristic of the adult mammalian gut. Blocking the ERK and JNK signaling cascade inhibits the ability of colonization to induce elevated fut2 mRNA and fucosyltransferase activity in the mature colon. Thus pioneer-mutualist symbiotic bacteria may utilize the ERK and JNK signaling cascade to induce the high degree of fucosylation characteristic of adult mammalian colon, and we speculate that this fucosylation facilitates colonization by adult microbiota. bacterial colonization; fucosylation

The two primary human inflammatory bowel diseases, Crohn's disease (CD) and ulcerative colitis (UC), are idiopathic relapsing disorders characterized by chronic inflammation of the intestinal tract. Although several lines of reasoning suggest that gastrointestinal (GI) microbes influence inflammatory bowel disease (IBD) pathogenesis, the types of microbes involved have not been adequately described. Here we report the results of a culture-independent rRNA sequence analysis of GI tissue samples obtained from CD and UC patients, as well as non-IBD controls. Specimens were obtained through surgery from a variety of intestinal sites and included both pathologically normal and abnormal states. Our results provide comprehensive molecular-based analysis of the microbiota of the human small intestine. Comparison of clone libraries reveals statistically significant differences between the microbiotas of CD and UC patients and those of non-IBD controls. Significantly, our results indicate that a subset of CD and UC samples contained abnormal GI microbiotas, characterized by depletion of commensal bacteria, notably members of the phyla Firmicutes and Bacteroidetes. Patient stratification by GI microbiota provides further evidence that CD represents a spectrum of disease states and suggests that treatment of some forms of IBD may be facilitated by redress of the detected microbiological imbalances. Crohn's disease | culture-independent microbiology | ulcerative colitis | rRNA

Author(s): R E Steinert [1]; M Sadaghian Sadabad [2]; H J M Harmsen [2]; P Weber [1] Introduction Emerging evidence suggests that the gut microbiota has a critical role in [...], Emerging evidence suggests that the gut microbiota has a critical role in both the maintenance of human health and the pathogenesis of many diseases. Modifying the colonic microbiota using functional foods has attracted significant research effort and product development. The pioneering concept of prebiotics, as introduced by Gibson and Roberfroid in the 1990s, emphasized the importance of diet in the modulation of the gut microbiota and its relationships to human health. Increasing knowledge of the intestinal microbiota now suggests a more comprehensive definition. This paper briefly reviews the basics of the prebiotic concept with a discussion of recent attempts to refine the concept to open the door for novel prebiotic food ingredients, such as polyphenols, minerals and vitamins. European Journal of Clinical Nutrition (2016) 70, 1348-1353; doi: 10.1038/ejcn.2016.119; published online 6 July 2016

Author(s): David A. Relman (corresponding author) [1] High blood pressure is a leading cause of cardiovascular disease and hence preventable death in the United States [1], and is an increasingly [...]

Author(s): Hea-Jin Jung [1, 2]; Eric G. Pamer (corresponding author) [2] The mammalian intestine is a natural habitat for trillions of bacteria, including harmless species called commensals and potentially pathogenic [...]