Non-Specificity of Staphylococcus Generic Primers
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The Oral and Conjunctival Microbiotas in Cats with and Without Feline
The oral and conjunctival microbiotas in cats with and without feline immunodeficiency virus infection Scott J Weese, Jamieson Nichols, Mohammad Jalali, Annette Litster To cite this version: Scott J Weese, Jamieson Nichols, Mohammad Jalali, Annette Litster. The oral and conjunctival microbiotas in cats with and without feline immunodeficiency virus infection. Veterinary Research, BioMed Central, 2015, 46 (1), pp.21. 10.1186/s13567-014-0140-5. hal-01290670 HAL Id: hal-01290670 https://hal.archives-ouvertes.fr/hal-01290670 Submitted on 18 Mar 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Weese et al. Veterinary Research (2015) 46:21 DOI 10.1186/s13567-014-0140-5 VETERINARY RESEARCH RESEARCH Open Access The oral and conjunctival microbiotas in cats with and without feline immunodeficiency virus infection Scott J Weese1*, Jamieson Nichols2, Mohammad Jalali1 and Annette Litster2 Abstract The oral and conjunctival microbiotas likely play important roles in protection from opportunistic infections, while also being the source of potential pathogens. Yet, there has been limited investigation in cats, and the impact of comorbidities such as feline immunodeficiency virus (FIV) infection has not been reported. Oral and conjunctival swabs were collected from cats with FIV infection and FIV-uninfected controls, and subjected to 16S rRNA gene (V4) PCR and next generation sequencing. -
Biodegradability of Woody Film Produced by Solvent Volatilisation Of
www.nature.com/scientificreports OPEN Biodegradability of woody flm produced by solvent volatilisation of Japanese Beech solution Yuri Nishiwaki-Akine1*, Sui Kanazawa2, Norihisa Matsuura3 & Ryoko Yamamoto-Ikemoto3 To address the problem of marine pollution from discarded plastics, we developed a highly biodegradable woody flm, with almost the same components as wood, from the formic acid solution of ball-milled wood. We found that the woody flm was not easily degraded by cultured solution of hand bacteria (phylum Proteobacteria was dominant). However, the flm was easily biodegraded when in cultured solution of soil (Firmicutes, especially class Bacilli, was dominant) for 4 weeks at 37 °C, or when buried in the soil itself, both under aerobic conditions (Acidobacteria and Proteobacteria were dominant) for 40 days at room temperature and under anaerobic conditions (Firmicutes, especially family Ruminococcaceae, was dominant) for 5 weeks at 37 °C. Moreover, when flm was buried in the soil, more carbon dioxide was generated than from soil alone. Therefore, the flm was not only brittle but formed of decomposable organic matter. We showed that the flm does not decompose at the time of use when touched by the hand, but it decomposes easily when buried in the soil after use. We suggest that this biodegradable woody flm can be used as a sustainable raw material in the future. In recent years, plastics dumped as garbage afer use have ofen been released into the sea, leading to frequent ingestion of microplastics by marine organisms. Terefore, the low biodegradability of plastics has become a major social problem. Development of materials with high biodegradability is an important approach to help solve this problem. -
Demonstrating the Potential of Abiotic Stress-Tolerant Jeotgalicoccus Huakuii NBRI 13E for Plant Growth Promotion and Salt Stress Amelioration
Annals of Microbiology (2019) 69:419–434 https://doi.org/10.1007/s13213-018-1428-x ORIGINAL ARTICLE Demonstrating the potential of abiotic stress-tolerant Jeotgalicoccus huakuii NBRI 13E for plant growth promotion and salt stress amelioration Sankalp Misra1,2 & Vijay Kant Dixit 1 & Shashank Kumar Mishra1,2 & Puneet Singh Chauhan1,2 Received: 10 September 2018 /Accepted: 20 December 2018 /Published online: 2 January 2019 # Università degli studi di Milano 2019 Abstract The present study aimed to demonstrate the potential of abiotic stress-tolerant Jeotgalicoccus huakuii NBRI 13E for plant growth promotion and salt stress amelioration. NBRI 13E was characterized for abiotic stress tolerance and plant growth-promoting (PGP) attributes under normal and salt stress conditions. Phylogenetic comparison of NBRI 13E was carried out with known species of the same genera based on 16S rRNA gene. Plant growth promotion and rhizosphere colonization studies were determined under greenhouse conditions using maize, tomato, and okra. Field experiment was also performed to assess the ability of NBRI 13E inoculation for improving growth and yield of maize crop in alkaline soil. NBRI 13E demonstrated abiotic stress tolerance and different PGP attributes under in vitro conditions. Phylogenetic and differential physiological analysis revealed considerable differences in NBRI 13E as compared with the reported species for Jeotgalicoccus genus. NBRI 13E colonizes in the rhizosphere of the tested crops, enhances plant growth, and ameliorates salt stress in a greenhouse experiment. Modulation in defense enzymes, chlorophyll, proline, and soluble sugar content in NBRI 13E-inoculated plants leads to mitigate the deleterious effect of salt stress. Furthermore, field evaluation of NBRI 13E inoculation using maize was carried out with recommended 50 and 100% chemical fertilizer controls, which resulted in significant enhancement of all vegetative parameters and total yield as compared to respective controls. -
The Relationship Between KRAS Gene Mutation and Intestinal Flora in Tumor Tissues of Colorectal Cancer Patients
1085 Original Article Page 1 of 9 The relationship between KRAS gene mutation and intestinal flora in tumor tissues of colorectal cancer patients Xinke Sui1#, Yan Chen1#, Baojun Liu2, Lianyong Li1, Xin Huang1, Min Wang1, Guodong Wang1, Xiaopei Gao1, Lu Zhang1, Xinwei Bao1, Dengfeng Yang3, Xiaoying Wang1, Changqing Zhong1 1Department of Gastroenterology, PLA Strategic Support Force Characteristic Medical Center, Beijing, China; 2Department of Medical Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, China; 3Laboratory department, Mian County Hospital, Mian, China Contributions: (I) Conception and design: X Sui, Y Chen, C Zhong, X Wang; (II) Administrative support: L Li; (III) Provision of study materials or patients: B Liu, D Yang; (IV) Collection and assembly of data: X Gao, L Zhang, X Bao; (V) Data analysis and interpretation: X Sui, Y Chen, C Zhong, X Wang, X Huang, M Wang, G Wang; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors. #These authors contributed equally to this work. Correspondence to: Changqing Zhong; Xiaoying Wang. Department of Gastroenterology, PLA Strategic Support Force Characteristic Medical Center, Beijing, China. Email: [email protected]; [email protected]. Background: Colorectal cancer is among the most prominent malignant tumors endangering human health, with affected populations exhibiting an increasingly younger trend. The Kirsten ras (KRAS) gene acts as a crucial regulator in this disease and influences multiple signaling pathways. In the present study, the KRAS gene mutation-induced alteration of intestinal flora in colorectal cancer patients was explored, and the intestinal microbes that may be affected by the KRAS gene were examined to provide new insights into the diagnosis and treatment of colorectal cancer. -
Characterization of Bacterial Communities Associated
www.nature.com/scientificreports OPEN Characterization of bacterial communities associated with blood‑fed and starved tropical bed bugs, Cimex hemipterus (F.) (Hemiptera): a high throughput metabarcoding analysis Li Lim & Abdul Hafz Ab Majid* With the development of new metagenomic techniques, the microbial community structure of common bed bugs, Cimex lectularius, is well‑studied, while information regarding the constituents of the bacterial communities associated with tropical bed bugs, Cimex hemipterus, is lacking. In this study, the bacteria communities in the blood‑fed and starved tropical bed bugs were analysed and characterized by amplifying the v3‑v4 hypervariable region of the 16S rRNA gene region, followed by MiSeq Illumina sequencing. Across all samples, Proteobacteria made up more than 99% of the microbial community. An alpha‑proteobacterium Wolbachia and gamma‑proteobacterium, including Dickeya chrysanthemi and Pseudomonas, were the dominant OTUs at the genus level. Although the dominant OTUs of bacterial communities of blood‑fed and starved bed bugs were the same, bacterial genera present in lower numbers were varied. The bacteria load in starved bed bugs was also higher than blood‑fed bed bugs. Cimex hemipterus Fabricus (Hemiptera), also known as tropical bed bugs, is an obligate blood-feeding insect throughout their entire developmental cycle, has made a recent resurgence probably due to increased worldwide travel, climate change, and resistance to insecticides1–3. Distribution of tropical bed bugs is inclined to tropical regions, and infestation usually occurs in human dwellings such as dormitories and hotels 1,2. Bed bugs are a nuisance pest to humans as people that are bitten by this insect may experience allergic reactions, iron defciency, and secondary bacterial infection from bite sores4,5. -
Guide to Turning an RDP File Into a Data Set
Guide to Turning an RDP File into a Data Set Berkley Shands, Patricio S. La Rosa, Elena Deych, William Shannon July 5, 2017 Below we will define the basic steps required to generate a data set from an RDP file 1. Take an RDP file such as this example: ;Root:1.0;Bacteria:1.0;Firmicutes:1.0;Bacilli:1.0;Bacillales:1.0;Staphylococcaceae:1.0; ;Root:1.0;Bacteria:1.0;Firmicutes:1.0;Bacilli:1.0;Lactobacillales:1.0;Carnobacteriaceae:0.8; ;Root:1.0;Bacteria:1.0;Bacteroidetes:1.0;Bacteroidia:1.0;Bacteroidales:1.0;Prevotellaceae:1.0; ;Root:1.0;Bacteria:1.0;Bacteroidetes:1.0;Bacteroidia:1.0;Bacteroidales:1.0;Prevotellaceae:1.0; ;Root:1.0;Bacteria:1.0;Bacteroidetes:1.0;Bacteroidia:1.0;Unclassified:0.5;Unclassified:0.5; 2. Take the first entry and seperate each level into its own row, while seper- ating levels by a period: Root, 1 Root.Bacteria, 1 Root.Bacteria.Firmicutes, 1 Root.Bacteria.Firmicutes.Bacilli, 1 Root.Bacteria.Firmicutes.Bacilli.Bacillales, 1 Root.Bacteria.Firmicutes.Bacilli.Bacillales.Staphylococcaceae, 1 3. Do the same with each following row, adding to the number at the end if it is the same: Root, 5 Root.Bacteria, 5 Root.Bacteria.Firmicutes, 2 Root.Bacteria.Firmicutes.Bacilli, 2 Root.Bacteria.Firmicutes.Bacilli.Bacillales, 1 Root.Bacteria.Firmicutes.Bacilli.Bacillales.Staphylococcaceae, 1 Root.Bacteria.Firmicutes.Bacilli.Lactobacillales, 1 Root.Bacteria.Firmicutes.Bacilli.Lactobacillales.Carnobacteriaceae, .8 Root.Bacteria.Bacteroidetes, 3 Root.Bacteria.Bacteroidetes.Bacteroidia, 3 Root.Bacteria.Bacteroidetes.Bacteroidia.Bacteroidales, 2 Root.Bacteria.Bacteroidetes.Bacteroidia.Bacteroidales.Prevotellaceae, 2 Root.Bacteria.Bacteroidetes.Bacteroidia.Unclassified, .5 Root.Bacteria.Bacteroidetes.Bacteroidia.Unclassified.Unclassified, .5 4. -
Inter Subfamily Comparison of Gut Microbial Diversity in Twelve Wild
Inter subfamily comparison of gut microbial diversity in twelve wild spider species of family Araneidae Kaomud Tyagi1, Inderjeet Tyagi1, Priya Prasad2, Kailash Chandra1, and Vikas Kumar1 1Zoological Survey of India 2Affiliation not available August 12, 2020 Abstract Spiders are among the most diverse groups of arthropods remarkably known for extra oral digestion. The largest effort based on targeted 16S amplicon next generation sequencing was carried out to decipher the inter subfamily comparison of gut bacterial diversity in spiders and their functional relationship. Twelve spider species belonging to three subfamilies, Araneinae (8), Argiopinae (2) and Gasteracanthinae (2) of family Araneidae have been studied. Analysis revealed the presence of 22 phyla, 145 families, and 364 genera of microbes in the gut microbiome, with Proteobacteria as the highest abundant Phylum. Moreover, the phyla Firmicutes, Actinobacteria and Deinococcus Thermus were also detected. The bacterial phyla Bacteriodetes and Chlamydiae dominated in Cyclosa mulmeinensis and Neoscona bengalensis respectively. At genera level, Acinetobacter, Pseudomonas, Cutibacterium, Staphylococcus, and Bacillus were the most dominant genera in their gut. In addition to this, the genus Prevotella was observed only in one species, Cyclosa mulmeinensis, and endosymbiont genus Wolbachia generally responsible for reproductive alterations was observed in one spider species Eriovixia laglaizei. Our study revealed that the gut bacterial diversity of the spiders collected from wild are quite different from the diet driven spider gut bacterial diversity as published earlier. A functional analysis revealed the involvement of gut microbiota in carbohydrate, lipid, amino acids, fatty acids and energy metabolism. Introduction Spiders (order Araneae) are arthropods that usually act as natural predators on insect pests in agricultural ecosystem (Michalko et al., 2018; Yang et al., 2017) bio-control agent for various diseases (Ndava et al., 2018), and indicator species for environment monitoring (Ossamy et al, 2016). -
Data of Read Analyses for All 20 Fecal Samples of the Egyptian Mongoose
Supplementary Table S1 – Data of read analyses for all 20 fecal samples of the Egyptian mongoose Number of Good's No-target Chimeric reads ID at ID Total reads Low-quality amplicons Min length Average length Max length Valid reads coverage of amplicons amplicons the species library (%) level 383 2083 33 0 281 1302 1407.0 1442 1769 1722 99.72 466 2373 50 1 212 1310 1409.2 1478 2110 1882 99.53 467 1856 53 3 187 1308 1404.2 1453 1613 1555 99.19 516 2397 36 0 147 1316 1412.2 1476 2214 2161 99.10 460 2657 297 0 246 1302 1416.4 1485 2114 1169 98.77 463 2023 34 0 189 1339 1411.4 1561 1800 1677 99.44 471 2290 41 0 359 1325 1430.1 1490 1890 1833 97.57 502 2565 31 0 227 1315 1411.4 1481 2307 2240 99.31 509 2664 62 0 325 1316 1414.5 1463 2277 2073 99.56 674 2130 34 0 197 1311 1436.3 1463 1899 1095 99.21 396 2246 38 0 106 1332 1407.0 1462 2102 1953 99.05 399 2317 45 1 47 1323 1420.0 1465 2224 2120 98.65 462 2349 47 0 394 1312 1417.5 1478 1908 1794 99.27 501 2246 22 0 253 1328 1442.9 1491 1971 1949 99.04 519 2062 51 0 297 1323 1414.5 1534 1714 1632 99.71 636 2402 35 0 100 1313 1409.7 1478 2267 2206 99.07 388 2454 78 1 78 1326 1406.6 1464 2297 1929 99.26 504 2312 29 0 284 1335 1409.3 1446 1999 1945 99.60 505 2702 45 0 48 1331 1415.2 1475 2609 2497 99.46 508 2380 30 1 210 1329 1436.5 1478 2139 2133 99.02 1 Supplementary Table S2 – PERMANOVA test results of the microbial community of Egyptian mongoose comparison between female and male and between non-adult and adult. -
The Genera Staphylococcus and Macrococcus
Prokaryotes (2006) 4:5–75 DOI: 10.1007/0-387-30744-3_1 CHAPTER 1.2.1 ehT areneG succocolyhpatS dna succocorcMa The Genera Staphylococcus and Macrococcus FRIEDRICH GÖTZ, TAMMY BANNERMAN AND KARL-HEINZ SCHLEIFER Introduction zolidone (Baker, 1984). Comparative immu- nochemical studies of catalases (Schleifer, 1986), The name Staphylococcus (staphyle, bunch of DNA-DNA hybridization studies, DNA-rRNA grapes) was introduced by Ogston (1883) for the hybridization studies (Schleifer et al., 1979; Kilp- group micrococci causing inflammation and per et al., 1980), and comparative oligonucle- suppuration. He was the first to differentiate otide cataloguing of 16S rRNA (Ludwig et al., two kinds of pyogenic cocci: one arranged in 1981) clearly demonstrated the epigenetic and groups or masses was called “Staphylococcus” genetic difference of staphylococci and micro- and another arranged in chains was named cocci. Members of the genus Staphylococcus “Billroth’s Streptococcus.” A formal description form a coherent and well-defined group of of the genus Staphylococcus was provided by related species that is widely divergent from Rosenbach (1884). He divided the genus into the those of the genus Micrococcus. Until the early two species Staphylococcus aureus and S. albus. 1970s, the genus Staphylococcus consisted of Zopf (1885) placed the mass-forming staphylo- three species: the coagulase-positive species S. cocci and tetrad-forming micrococci in the genus aureus and the coagulase-negative species S. epi- Micrococcus. In 1886, the genus Staphylococcus dermidis and S. saprophyticus, but a deeper look was separated from Micrococcus by Flügge into the chemotaxonomic and genotypic proper- (1886). He differentiated the two genera mainly ties of staphylococci led to the description of on the basis of their action on gelatin and on many new staphylococcal species. -
Bacterial Flora on the Mammary Gland Skin of Sows and in Their Colostrum
Brief communication Peer reviewed Bacterial flora on the mammary gland skin of sows and in their colostrum Nicole Kemper, Prof, Dr med vet; Regine Preissler, DVM Summary Resumen - La flora bacteriana en la piel de Résumé - Flore bactérienne cutanée de la Mammary-gland skin swabs and milk la glándula mamaria de las hembras y en su glande mammaire de truies et de leur lait calostro samples were analysed bacteriologically. All Des écouvillons de la peau de la glande skin samples were positive, with 5.2 isolates Se analizaron bacteriológicamente hisopos de mammaire ainsi que des échantillons de lait on average, Staphylococcaceae being the la piel de la glándula mamaria y muestras de ont été soumis à une analyse bactériologique. dominant organisms. In 20.8% of milk leche. Todas las muestras de piel resultaron Tous les échantillons provenant de la peau samples, no bacteria were detected. Two iso- positivas, con 5.2 aislados en promedio, étaient positifs, avec en moyenne 5.2 isolats lates on average, mainly Staphylococcaceae siendo los Staphylococcaceae los organismos bactériens, les Staphylococcaceae étant de loin and Streptococcaceae, were isolated from the dominantes. En 20.8% de las muestras de les micro-organismes dominants. Aucune positive milk samples. leche, no se detectaron bacterias. De las bactérie ne fut détectée dans 20.8% des Keywords: swine, bacteria, colostrum, muestras de leche positivas, se aislaron échantillons de lait. En moyenne, on trouvait mammary gland, skin dos aislados en promedio, principalmente deux isolats bactériens par échantillon de lait Staphylococcaceae y los Streptococcaceae. positif, et ceux-ci étaient principalement des Received: April 7, 2010 Staphylococcaceae et des Streptococcaceae. -
Supplement of Biogeographical Distribution of Microbial Communities Along the Rajang River–South China Sea Continuum
Supplement of Biogeosciences, 16, 4243–4260, 2019 https://doi.org/10.5194/bg-16-4243-2019-supplement © Author(s) 2019. This work is distributed under the Creative Commons Attribution 4.0 License. Supplement of Biogeographical distribution of microbial communities along the Rajang River–South China Sea continuum Edwin Sien Aun Sia et al. Correspondence to: Moritz Müller ([email protected]) The copyright of individual parts of the supplement might differ from the CC BY 4.0 License. Supp. Fig. S1: Monthly Mean Precipitation (mm) from Jan 2016 to Sep 2017. Relevant months are highlighted red (Aug 2016), blue (Mar 2017) and dark blue (Sep 2017). Monthly precipitation for the period in between the cruises (August 2016 to September 2017) were obtained from the Tropical Rainfall Measuring Mission website (NASA 2019) in order to gauge the seasonality (wet or dry). As the rainfall data do not correlate with the monsoonal periods, the seasons in which the sampling cruises coincide with were classified based on the mean rainfall that occurred for each month. The August 2016 cruise (colored red) is classified as the dry season based on the lower mean rainfall value as compared to the other two (March 2017 and September 2017), in which the both are classified as the wet season. Supp. Fig. S2: Non-metric Multi-dimensional Scaling (NMDS) diagram of seasonal (August 2016, March 2017 and September 2017) and particle association (particle-attached or free-living) Seasonality was observed within the three cruises irrespective of the particle association (Supp. Fig. 3). The August 2016 cruise was found to cluster with the September 2017 whereas the March 2017 cruise clustered separately from the other two cruises. -
Antibiotic Resistance and Biofilm Production in Catalase-Positive Gram-Positive Cocci Isolated from Brazilian Pasteurized Milk M.A.A
Journal of Food Quality and Hazards Control 7 (2020) 67-74 Antibiotic Resistance and Biofilm Production in Catalase-Positive Gram-Positive Cocci Isolated from Brazilian Pasteurized Milk M.A.A. Machado 1, W.A. Ribeiro 1, V.S. Toledo 1, G.L.P.A. Ramos 2, H.C. Vigoder 1, J.S. Nascimento 1* 1. Laboratório de Microbiologia, Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro (IFRJ), Rio de Janeiro, RJ, Brazil 2. Laboratório de Higiene e Microbiologia de Alimentos, Faculdade de Farmácia, Universidade Federal Fluminense (UFF), Niterói, RJ, Brazil HIGHLIGHTS Kocuria varians, Macrococcus caseolyticus, and Staphylococcus epidermidis were detected in pasteurized milk samples. Four isolates of K. varians exhibited multidrug resistant phenotype. Five isolates of K. varians and one isolate of S. epidermidis were biofilm producers. Antibiotic-resistance of the isolates highlights the possible role of milk as a reservoir of resistance genes. Article type ABSTRACT Original article Background: Milk is a reservoir for several groups of microorganisms, which may pose Keywords health risks. The aim of this work was to assess the antibiotic resistance and biofilm pro- Gram-Positive Cocci duction in catalase-positive Gram-positive cocci isolated from Brazilian pasteurized milk. Drug Resistance, Microbial Biofilms Methods: The bacteria were isolated using Baird-Parker agar and identified by Matrix- Milk Assisted Laser Desorption/Ionization-Time-Of-Flight (MALDI-TOF) mass spectrometer. Brazil Disk diffusion technique was used to evaluate antimicrobial susceptibility. For qualitative evaluation of biofilm production, the growth technique was used on Congo Red Agar. Article history Received: 16 Apr 2020 Results: Totally, 33 out of 64 isolates were identified, including Staphylococcus Revised: 18 May 2020 epidermidis (n=3; 4.7%), Macrococcus caseolyticus (n=14; 21.9%), and Kocuria varians Accepted: 22 May 2020 (n=16; 25%).