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The effects of prescription diets on canine intestinal microbiota are unknown. In this study, we used next generation sequencing to investigate the impact of four commercially available prescription diet regimens on the fecal microbiome in six healthy dogs. The diet regimens used were as follows: weight-loss diet, low-fat diet, renal diet, and anallergenic diet. We found a significantly decreased proportion of phylum Actinobacteria with the weight-loss diet compared to the anallergenic diet. There were no significant differences in the proportion of phylum Bacteroidetes between the four diets. The proportion of phylum Firmicutes was significantly decreased with the weight-loss diet compared to the anallergenic diet. The proportion of phylum Fusobacteria was significantly increased with the weight-loss diet compared to the anallergenic diet. There were no significant differences in the proportion of phylum Proteobacteria after consumption of the four diets. We therefore demonstrated that commercial prescription diet influences the fecal microbiome in healthy dogs. These results might be useful when choosing a prescription diet for targeting a disease.

Background Studies of the microbiomes on surfaces in built environment have largely focused on indoor spaces, while outdoor spaces have received far less attention. Piers are engineered infrastructures commonly found in coastal areas, and due to their unique locations at the interface between terrestrial and aquatic ecosystems, pier surfaces are likely to harbor interesting microbiology. In this study, the microbiomes on the metal and concrete surfaces at nine piers located along the coastline of Hong Kong were investigated by metagenomic sequencing. The roles played by different physical attributes and environmental factors in shaping the taxonomic composition and functional traits of the pier surface microbiomes were determined. Metagenome-assembled genomes were reconstructed and their putative biosynthetic gene clusters were characterized in detail. Results Surface material was found to be the strongest factor in structuring the taxonomic and functional compositions of the pier surface microbiomes. Corrosion-related bacteria were significantly enriched on metal surfaces, consistent with the pitting corrosion observed. The differential enrichment of taxa mediating biodegradation suggests differences between the metal and concrete surfaces in terms of specific xenobiotics being potentially degraded. Genome-centric analysis detected the presence of many novel species, with the majority of them belonging to the phylum Proteobacteria. Genomic characterization showed that the potential metabolic functions and secondary biosynthetic capacity were largely correlated with taxonomy, rather than surface attributes and geography. Conclusions Pier surfaces are a rich reservoir of abundant novel bacterial species. Members of the surface microbial communities use different mechanisms to counter the stresses under oligotrophic conditions. A better understanding of the outdoor surface microbiomes located in different environments should enhance the ability to maintain outdoor surfaces of infrastructures.

Unique bacterial associations were formed in the polluted soils from territory of the industrial factories Open Joint Stock Company “The Middle Volga Chemical Plant,” Chapaevsk, Russia and Open Joint Stock Company “Lubricant Producing Plant,” Perm, Russia. This study evaluates the influence of the biphenyl/polychlorinated biphenyls (PCB) on the formation of aerobic bacterial associations and their biodegradative potential. Enrichment cultivation of the soil samples from the territories of these industrial factories with PCB (commercial mixture Sovol) was lead for forming aerobic bacterial enrichment cultures showing a unique composition. The dominating in these bacterial cultures was the phylum Proteobacteria (Beta- and Gammaproteobacteria). Using biphenyl as a carbon source led to decrease of biodiversity in the final stable bacterial associations. Periodic cultivation experiments demonstrated that the association PN2-B has a high degradative potential among the six studied bacterial associations. PN2-B degraded 100% mono-chlorobiphenyls (94.5 mg/L), 86.2% di-chlorobiphenyls (22.3 mg/L), 50.9% Sovol, and 38.4% Delor 103 (13.8 mg/L). Qualitative analysis of metabolites showed that association performed transformation of chlorobenzoic acids (PCB degradation intermediates) into metabolites of citrate cycle. Twelve individual strain-destructors were isolated. The strains were found to degrade 17.7–100% PCB1, 36.2–100% PCB2, 18.8–100% PCB3 (94.5 mg/L), and 15.7–78.2% PCB8 (22.3 mg/L). The strains were shown to metabolize chlorobenzoic acids formed during degradation of chlorobiphenyls. A unique ability of strains Micrococcus sp. PNS1 and Stenotrophomonas sp. PNS6 to degrade ortho-, meta-, and para-monosubstituted chlorobenzoic acids was revealed. Our results suggest that PN2-B and individual bacterial strains will be perspective for cleaning of the environment from polychlorinated biphenyls.

Despite the risks that hydrocarbon contamination from pipeline leaks or train derailments impose on the health of peatlands in hydrocarbon production areas and transportation corridors, assessing the effect of such contaminations on the health and sustainability of peatlands has received little attention. This study investigates the impacts of hydrocarbons on peat microbial communities. Column experiments were conducted on non-aqueous phase liquid (NAPL) contaminated undisturbed peat core (0–35 cm) under static and fluctuating water table conditions. Water table fluctuations reduced residual NAPL saturation from 8.1-11.3% to 7.7–9.5%. Biodegradation of n-C8 and n-C12 along with oxidation of CH4 together produced high CO2 concentrations in the headspace. Clear patterns in dynamics in the microbial community structure were observed, with a more pronounced population growth. However, a significant loss of microbial richness was observed in contaminated columns. The result indicates that the phylum Proteobacteria benefited most from NAPL; however, their families differed between static and fluctuating water table conditions. This study established strong evidence that peat microbes and water table fluctuation can be an excellent tool for hydrocarbon removal and its control in peatlands.

Rainbow trout that were resistant or susceptible to Flavobacterium psychrophilum infection were compared with respect to their microbial composition by using 16S rRNA V3-V4 sequencing. The differences occurred in gills, where resistant fish displayed a greater abundance of the phylum Proteobacteria and a smaller proportion of Firmicutes relative to those of susceptible fish.

Taxonomic status: Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadaceae; Genus Xanthomonas; Species Xanthomonas citri ssp. citri (Xcc). Host range: Compatible hosts vary in their susceptibility to citrus canker (CC), with grapefruit, lime and lemon being the most susceptible, sweet orange being moderately susceptible, and kumquat and calamondin being amongst the least susceptible. Microbiological properties: Xcc is a rod‐shaped (1.5–2.0 × 0.5–0.75 µm), Gram‐negative, aerobic bacterium with a single polar flagellum. The bacterium forms yellow colonies on culture media as a result of the production of xanthomonadin. Distribution: Present in South America, the British Virgin Islands, Africa, the Middle East, India, Asia and the South Pacific islands. Localized incidence in the USA, Argentina, Brazil, Bolivia, Uruguay, Senegal, Mali, Burkina Faso, Tanzania, Iran, Saudi Arabia, Yemen and Bangladesh. Widespread throughout Paraguay, Comoros, China, Japan, Malaysia and Vietnam. Eradicated from South Africa, Australia and New Zealand. Absent from Europe.

Aquatic bacteria were isolated from the hands of working staffs by an adapted culture protocol. When the sample solution obtained by the" glove juice method" was incubated for 3 days at room temperature, viable cell counts increased up to 105-fold, and the majority of the isolated colonies were shown to be Gram-negative aquatic bacteria, which carry the risk of contaminating water. Using R2A medium, coagulase-negative staphylococci were the dominant microbes immediately after recovery from the hands. Here it was revealed that bacteria of the phylum Proteobacteria isolated from the hand can be the causative bacteria of aqueous contamination. This modification in the GJ method may be useful as an effective training protocol to demonstrate the importance of hand hygiene and clean operation for aseptic manufacturing.

International audience; Urbanization influences food quality and availability for many wild species, but our knowledge of the consequences urbanization has on the nutritional physiology of these animals is currently limited. To fill this gap, we captured House Sparrows (Passer domesticus) from rural and urban environments and hypothesized that increased access to human refuse in urban areas may significantly alter the gut microbiome and nutritional physiology of Sparrows. While there were no significant differences in circulating triglycerides or free glycerol concentrations between populations, urban birds had significantly greater blood glucose concentrations, which suggests greater circulating glucagon concentrations, accessibility to carbohydrates, and/or higher rates of gluconeogenesis in an urban setting. Rural birds had significantly more plasma uric acid, suggesting that they may metabolize more proteins or experience lower inflammation than urban birds. Rural birds also had significantly higher liver free glycerol concentrations, indicating that they metabolize more fat than urban birds. There were no significant differences in the relative abundance of gut microbial taxa at the phyla level between the two populations, but linear discriminant analysis effect size (LEfSe) showed that urban House Sparrows were more enriched with class- and order-level microbes from the phylum Proteobacteria, which are implicated in several mammalian intestinal and extra-intestinal diseases. These findings demonstrate that urbanization significantly alters the nutritional physiology and the composition of the gut microbiome of House Sparrows.

A female Risso’s dolphin (Grampus griseus) carcass was found stranded in fresh condition at Jeju Island of the Republic of Korea on February 18, 2018. Body surface lacerations, gross pathology and histology of the lung indicated the cause of death as drowning by fishing gear entanglement. The dolphin was a five-year-old mature female having ovaries with follicles and a corpus albican. This is the lowest recorded age thus far of a Risso’s dolphin with active ovaries. The stomach was filled with Japanese flying squid and based on their distribution, it is believed that the dolphin was foraging in the South Sea, which had not been known as their habitat before. Intestinal microbiome analysis revealed that the bacterial community predominantly comprised phylum Proteobacteria (92.8 per cent). To our knowledge, this is the first microbiome analysis and the first official necropsy report of stranding in Jeju Island of the Risso’s dolphin.

Presented here is the draft genome sequence of Enterobacter cloacae 3D9. This candidate seed endophyte was isolated from Zea nicaraguensis., Presented here is the draft genome sequence of Enterobacter cloacae 3D9. This candidate seed endophyte was isolated from Zea nicaraguensis. The genome contains 4,653,375 bp in 28 contigs.

Presented here is the draft genome sequence of Enterobacter cloacae 3F11. This seed endophyte solubilizes rock phosphate and was isolated from Zea nicaraguensis., Presented here is the draft genome sequence of Enterobacter cloacae 3F11. This seed endophyte solubilizes rock phosphate and was isolated from Zea nicaraguensis. The genome contains 4,579,108 bp in 264 contigs.

Colonic diverticula are protrusions of the mucosa through weak areas of the colonic musculature. The etiology of diverticulosis is poorly understood, but could be related to gut bacteria. Using mucosal biopsies from the sigmoid colon of 226 subjects with and 309 subjects without diverticula during first-time screening colonoscopy, we assessed whether individuals with incidental colonic diverticulosis have alternations in the adherent bacterial communities in the sigmoid colon. We found little evidence of substantial associations between the microbial community and diverticulosis among cases and controls. Comparisons of bacterial abundances across all taxonomic levels showed differences for phylum Proteobacteria (p = 0.038) and family Comamonadaceae (p = 0.035). The r-squared values measuring the strength of these associations were very weak, however, with values ~2%. There was a similarly small association between the abundance of each taxa and total diverticula counts. Cases with proximal only diverticula and distal only diverticula likewise showed little difference in overall microbiota profiles. This large study suggests little association between diverticula and the mucosal microbiota overall, or by diverticula number and location. We conclude that the mucosal adherent microbiota community composition is unlikely to play a substantial role in development of diverticulosis.

Culture independent techniques have allowed a better understanding of association between tobacco-smoke exposed COPD (TS-COPD) & lung microbiome, but there is limited knowledge about lung microbiome in non-smoker COPD (NS-COPD) subjects. We aimed to study lung microbiome in smoker & non-smoker COPD subjects and its association with lung function in rural Indian subjects. Induced sputum samples were obtained from 11 healthy-nonsmokers (H-Nonsmokers), 10 healthy-smokers (H-Smokers), 18 biomass-smoke exposed healthy (H-Biomass), 15 TS-COPD & 20 NS-COPD subjects. Samples were sequenced using V3 & V4 hypervariable region (Illumina MiSeq Platform) and taxanomic diversity information was obtained with QIIME pipeline, & R script package. Bacterial abundance was significantly higher in NS-COPD subjects compared to H-Nonsmokers, H-Biomass, & TS-COPD subjects (Fig.1A). Exposure to tobacco-smoke caused decrease in bacterial diversity (Fig.1B). Firmicutes, Bacteriodetes, Proteobacteria, Actinobcater & Fusobacter were the most prevalent phyla in our samples. Phylum Proteobacteria, which includes many pathogens showed higher abundance in COPD subjects (Fig.1C) & were negatively associated with lung function (Fig.1D). The impaired lung function observed in COPD is associated with in increased abundance of pathogenic microbiome & a decline in its diversity, which may have implications in COPD pathophysiology.

The total ammonia nitrogen (TAN) removal efficiency and bacterial community composition of bioflocs with 50-μm particle size and un-sieved bioflocs were investigated in the current study. The initial ratio of dissolved organic carbon to TAN (DOC/TAN) in the three groups were about 14:1. No significant difference was found in the removal rate of TAN, average concentrations of TAN and nitrite nitrogen among the three groups (P > 0.05). The C/N (w/w) ratio of the > 50-μm bioflocs was significantly higher than those of the other groups. No significant differences were found in the crude protein content in the bioflocs among the three groups. The development of the bacterial community compositions of the bioflocs was analyzed by Illumina MiSeq sequencing analyses. Most OTUs were shared among the three groups at all the sampled time points. With the increase in the relative abundance of phylum Firmicutes, that of phylum Proteobacteria, Chorolexi, and Bacteroidetes decreased in all the three groups. The phylum Firmicutes and genus Bacillus were predominant in all the sampled time points. At the end of the experiment, genus Bacillus accounted for 81% in the 50-μm group, and 75% in the un-sieved group.

The most serious biotic constraint to finger millet worldwide is blast caused by the fungus Pyricularia grisea. Its management has been very challenging. However not a formidable control solution has been offered and therefore a need for other approachs. Actinomycetes belong to the phylum proteobacteria, they are gram +ve, terrestrial or aquatic with high guanine and cytosine content. Soil actinomycetes have antagonistic activity against a wide range of plant pathogens.This study isolated and characterizes some soil actinomycetes in Maseno area (Western Kenya) and studied their antifungal effect on P. grisea pathogenic on finger millet. Soil sample collected was dissolved in distilled water, homogenized and spread over modified Kuster's agar. Colonies of actiomycetes were isolated as from the fourth day of incubation. . Finger millet heads and leaves displaying symptoms of blast were collected and Pyricularia grisea isolated on autoclaved powered finger-millet debris and maintained on PDA. A single steak of actinomycetes culture was made on a fresh Kuster's agar and incubated for 3-4 days at 26 0 C -28°C, and P. grisea, 20 mm, at right angles to the original streak of actinomycetes. The results indicate that isolates AT2 and AT4 are pathogenic to Pyricularia grisea and can be a basis for bio-control of blast in finger millet.

Here, we present the draft genome sequences of Pseudoalteromonas porphyrae UCD-SED9 and UCD-SED14 (phylum Proteobacteria ). These strains were isolated from sediment surrounding the roots of the seagrass, Zostera marina , collected near the UC, Davis Bodega Marine Laboratory (Bodega Bay, California). The assemblies contain 4,847,456 bp and 4,817,752 bp, respectively.

Here, we present the draft genome sequences of Vibrio splendidus UCD-SED7 and UCD-SED10 (phylum Proteobacteria ). These strains were isolated from sediment surrounding Zostera marina roots near the UC Davis Bodega Marine Laboratory (Bodega, Bay, California). These assemblies contain 5,334,236 bp and 5,904,824 bp, respectively.

Here, we present the draft genome of Enterobacter sp. strain UCD-UG_FMILLET. This strain is an endophyte isolated from the roots of finger millet, an Afro-Indian cereal crop. The genome contains 4,801,411 bp in 53 scaffolds.

Here, we present the draft genome of Burkholderia gladioli strain UCD-UG_CHAPALOTE. This strain is an endophyte isolated from surface sterilized seeds of an ancient Mexican landrace of corn, Chapalote. The genome contains 8,527,129 bp in 109 scaffolds.

Here, we present the draft genome of the endosymbiont “ Candidatus Ruthia magnifica” UCD-CM, a member of the phylum Proteobacteria , found from the gills of a deep-sea giant clam, Calyptogena magnifica . The assembly consists of 1,160,249 bp contained in 18 contigs.

Here we present the draft genome of Tatumella sp. strain UCD-D_suzukii, the first member of this genus to be sequenced. The genome contains 3,602,931 bp in 72 scaffolds. This strain was isolated from Drosophila suzukii larvae as part of a larger project to study the microbiota of D. suzukii .