Journal articles: 'Microbiology, n.e.c'

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Renaud, François N. R., Marianne Dutaur, Salah Daoud, Dominique Aubel, Philippe Riegel, Daniel Monget, and Jean Freney. "Differentiation of Corynebacterium amycolatum, C. minutissimum, and C. striatum by Carbon Substrate Assimilation Tests." Journal of Clinical Microbiology 36, no. 12 (1998): 3698–702. http://dx.doi.org/10.1128/jcm.36.12.3698-3702.1998.

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We tested the carbon substrate assimilation patterns of 40Corynebacterium amycolatum strains, 19 C. minutissimum strains, 50 C. striatum strains, and 1C. xerosis strain with the Biotype 100 system (bioMérieux, Marcy-l’Étoile, France). Twelve carbon substrates of 99 allowed discrimination among the species tested. Additionally, assimilation of 3 of these 12 carbon substrates (maltose, N -acetyl-d-glucosamine, and phenylacetate) was tested with the API 20 NE identification system (bioMérieux). Since concordant results were observed with the two systems for these three carbon substrates, either identification system can be used as a supplementary tool to achieve phenotypic differential identification ofC. amycolatum, C. minutissimum, and C. striatum in the clinical microbiology laboratory.

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Bastos, Margarida, Regina Adão, Kamran Nazmi, and JanG M. Bolscher. "C- and N-truncated antimicrobial peptides from LFampin 265 - 284: Biophysical versus microbiology results." Journal of Pharmacy and Bioallied Sciences 3, no. 1 (2011): 60. http://dx.doi.org/10.4103/0975-7406.76467.

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Drury, C. F., R. P. Voroney, and E. G. Beauchamp. "Availability of NH4+-N to microorganisms and the soil internal N cycle." Soil Biology and Biochemistry 23, no. 2 (January 1991): 165–69. http://dx.doi.org/10.1016/0038-0717(91)90130-c.

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Taylor-Robinson, D., J. S. Jensen, G. Fehler, F. Radebe, and R. C. Ballard. "Observations on the microbiology of urethritis in black South African men." International Journal of STD & AIDS 13, no. 5 (May 1, 2002): 323–25. http://dx.doi.org/10.1258/0956462021925144.

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The occurrence of Neisseria gonorrhoeae, Chlamydia trachomatis and Mycoplasma genitalium was determined by molecular techniques in urine specimens from 182 black South African men who had symptoms and/or overt signs of urethritis. Eighty-six (47.3%) of these men were infected with N. gonorrhoeae. There were 185 men without overt evidence of urethritis, 16 (8.6%) of whom were also infected with N. gonorrhoeae. Of the 96 men who had non-gonococcal urethritis, 14 (14.6%) were infected with C. trachomatis, 16 (16.7%) with M. genitalium and only one with both microorganisms. In comparison, 15 (8.9%) of 169 men without overt urethritis and without N. gonorrhoeae were infected with C. trachomatis and 15 (8.9%) with M. genitalium, proportions that were about half the size of those in the group with overt urethritis.

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BRUUN, S., B. STENBERG, T. BRELAND, J. GUDMUNDSSON, T. HENRIKSEN, L. JENSEN, A. KORSATH, J. LUXHOI, F. PALMASON, and A. PEDERSEN. "Empirical predictions of plant material C and N mineralization patterns from near infrared spectroscopy, stepwise chemical digestion and C/N ratios." Soil Biology and Biochemistry 37, no. 12 (December 2005): 2283–96. http://dx.doi.org/10.1016/j.soilbio.2005.04.006.

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Hopkins, D. W., L. Anderson, and S. E. Scott. "N and C mineralization in soil amended with the N immobilization inhibitor, methionine sulphoximine." Soil Biology and Biochemistry 27, no. 3 (March 1995): 377–79. http://dx.doi.org/10.1016/0038-0717(94)00180-9.

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Raubuch, Markus, and Rainer Georg Joergensen. "C and net N mineralisation in a coniferous forest soil: the contribution of the temporal variability of microbial biomass C and N." Soil Biology and Biochemistry 34, no. 6 (June 2002): 841–49. http://dx.doi.org/10.1016/s0038-0717(02)00016-0.

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Wojcik, Robin, Johanna Donhauser, Beat Frey, Stine Holm, Alexandra Holland, Alexandre M. Anesio, David A. Pearce, Lucie Malard, Dirk Wagner, and Liane G. Benning. "Linkages between geochemistry and microbiology in a proglacial terrain in the High Arctic." Annals of Glaciology 59, no. 77 (December 2018): 95–110. http://dx.doi.org/10.1017/aog.2019.1.

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ABSTRACTProglacial environments are ideal for studying the development of soils through the changes of rocks exposed by glacier retreat to weathering and microbial processes. Carbon (C) and nitrogen (N) contents as well as soil pH and soil elemental compositions are thought to be dominant factors structuring the bacterial, archaeal and fungal communities in the early stages of soil ecosystem formation. However, the functional linkages between C and N contents, soil composition and microbial community structures remain poorly understood. Here, we describe a multivariate analysis of geochemical properties and associated microbial community structures between a moraine and a glaciofluvial outwash in the proglacial area of a High Arctic glacier (Longyearbreen, Svalbard). Our results reveal distinct differences in developmental stages and heterogeneity between the moraine and the glaciofluvial outwash. We observed significant relationships between C and N contents,δ13Corgandδ15N isotopic ratios, weathering and microbial abundance and community structures. We suggest that the observed differences in microbial and geochemical parameters between the moraine and the glaciofluvial outwash are primarily a result of geomorphological variations of the proglacial terrain.

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Peltroche-Llacsahuanga, Heidrun, Norbert Schnitzler, Rudolf Lütticken, and Gerhard Haase. "Rapid Identification of Candida glabrataby Using a Dipstick To Detect Trehalase-Generated Glucose." Journal of Clinical Microbiology 37, no. 1 (1999): 202–5. http://dx.doi.org/10.1128/jcm.37.1.202-205.1999.

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Candida glabrata is a yeast frequently isolated from human specimens. Based upon its well-known ability to rapidly hydrolyze trehalose, we have developed a novel and cost-effective test incubating one yeast colony emulsified in 50 μl of citrate buffer (0.1 M [pH 5.0]) containing 4% (wt/vol) trehalose for 3 h at 37°C. Trehalase-generated glucose is detected with a commercially available dipstick (range, 1.0 to 50 g/liter). For evaluation, consecutive clinical isolates and several reference strains of C. glabrata (n = 160), C. albicans(n = 120), and other yeast species with potential ability for utilization of trehalose (C. dubliniensis,n = 11; C. famata, n = 15; C. guilliermondii, n = 5; C. lusitaniae, n = 16; C. parapsilosis,n = 20; C. tropicalis, n= 34; C. viswanathii, n = 5; Pichia angusta, n = 2; C. zeylanoides,n = 2; Saccharomyces cerevisiae,n = 16; C. neoformans, n= 7) were tested. Identification of C. glabrata is achieved within 3 h, with a specificity of 99.1% and a sensitivity of 98.8% when grown on Sabouraud dextrose agar supplemented with 4% glucose.

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Dhalluin, Anne, Ingrid Bourgeois, Martine Pestel-Caron, Emilie Camiade, Gregory Raux, Pascal Courtin, Marie-Pierre Chapot-Chartier, and Jean-Louis Pons. "Acd, a peptidoglycan hydrolase of Clostridium difficile with N-acetylglucosaminidase activity." Microbiology 151, no. 7 (July 1, 2005): 2343–51. http://dx.doi.org/10.1099/mic.0.27878-0.

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A gene encoding a putative peptidoglycan hydrolase was identified by sequence similarity searching in the Clostridium difficile 630 genome sequence, and the corresponding protein, named Acd (autolysin of C. difficile) was expressed in Escherichia coli. The deduced amino acid sequence of Acd shows a modular structure with two main domains: an N-terminal domain exhibiting repeated sequences and a C-terminal catalytic domain. The C-terminal domain exhibits sequence similarity with the glucosaminidase domains of Staphylococcus aureus Atl and Bacillus subtilis LytD autolysins. Purified recombinant Acd produced in E. coli was confirmed to be a cell-wall hydrolase with lytic activity on the peptidoglycan of several Gram-positive bacteria, including C. difficile. The hydrolytic specificity of Acd was studied by RP-HPLC analysis and MALDI-TOF MS using B. subtilis cell-wall extracts. Muropeptides generated by Acd hydrolysis demonstrated that Acd hydrolyses peptidoglycan bonds between N-acetylglucosamine and N-acetylmuramic acid, confirming that Acd is an N-acetylglucosaminidase. The transcription of the acd gene increased during vegetative cellular growth of C. difficile 630. The sequence of the acd gene appears highly conserved in C. difficile strains. Regarding deduced amino acid sequences, the C-terminal domain with enzymic function appears to be the most conserved of the two main domains. Acd is the first known autolysin involved in peptidoglycan hydrolysis of C. difficile.

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Personeni, E., A. Lüscher, and P. Loiseau. "Rhizosphere activity, grass species and N availability effects on the soil C and N cycles." Soil Biology and Biochemistry 37, no. 5 (May 2005): 819–27. http://dx.doi.org/10.1016/j.soilbio.2004.08.012.

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Villamagna, Angela H., P. Maureen Cassidy, Rebecca Pierce, Dat Tran, Chad Nix, and Christopher Pfeiffer. "2340. Diagnostic Stewardship: Survey of Urine Culturing and C. difficile Testing Practices Amongst Oregon Microbiology Labs." Open Forum Infectious Diseases 6, Supplement_2 (October 2019): S804—S805. http://dx.doi.org/10.1093/ofid/ofz360.2018.

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Abstract Background Testing for urinary tract infection (UTI) and Clostridiodes difficile infection (CDI) poses diagnostic and antimicrobial stewardship challenges. Both diagnoses hinge on local microbiology laboratory algorithms. For UTI testing, the definition of “abnormal” urinalysis and the use of reflex urine cultures, both of which alter the frequency of bacteriuria detection, likely differs between laboratories. For CDI, pretest probability, choice and sequence of diagnostic tests are likely variable and impact the chances of accurate diagnosis. Methods To understand laboratory practices and determine variations in local testing algorithms, we deployed a self-administered survey to microbiology laboratories serving Oregon healthcare facilities via SurveyMonkey in September 2018. Responses were collected through April 2019. We analyzed a subset of questions focused on UTI and CDI diagnosis. Results Of 51 surveyed laboratories, response rate was 86% (n = 44). 91% of respondents (n = 40) process bacterial cultures. 47.5% (n = 19) primarily perform urine culture when ordered, whereas the remainder primarily perform cultures in a reflex algorithm when ordered (n = 12; 30%) or a reflex algorithm automatically (n = 9; 22.5%) (Figure 1). The definition of an abnormal urinalysis varied widely (Figure 2). 15% (n = 6) of laboratories reported considering changes to their workflow; two cited a goal of reducing unnecessary testing. Of the 32 laboratories that perform in-house C. difficile testing, the assays and sequence in which they were implemented in testing algorithms varied substantially (Figure 3) and most commonly included NAAT testing. Seven (21.8%) laboratories reported recently changed practices; these changes did not favor any particular algorithm. 84.2% (n = 32) reported stool rejection criteria to limit unnecessary testing, but these criteria varied (Figure 4). Conclusion Wide variation exists in laboratory workflows for UTI and CDI diagnoses in Oregon, suggesting lack of consensus on optimal practices. Encouragingly, multiple labs described recently implemented or planned interventions to reduce unnecessary testing for both infections. This snapshot will inform statewide education and interventions to optimize testing and help prevent patient and population harm. Disclosures All authors: No reported disclosures.

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Ghosh, Sudipta Kumar, Asit K. Mukhopadhyay, and Dipankar Saha. "Inorganic and organic N-transformations in limed and unlimed soil as influenced by cropping and N-saturation." Soil Biology and Biochemistry 22, no. 3 (January 1990): 327–30. http://dx.doi.org/10.1016/0038-0717(90)90108-c.

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Suhaimi, M., J. Liessens, and W. Verstraete. "NH+/4-N assimilation byRhodobacter capsulatusATCC 23782 grown axenically and non-axenically in N and C rich media." Journal of Applied Bacteriology 62, no. 1 (January 1987): 53–64. http://dx.doi.org/10.1111/j.1365-2672.1987.tb02380.x.

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Lebbad, Marianne, Jadwiga Winiecka-Krusnell, Christen Rune Stensvold, and Jessica Beser. "High Diversity of Cryptosporidium Species and Subtypes Identified in Cryptosporidiosis Acquired in Sweden and Abroad." Pathogens 10, no. 5 (April 26, 2021): 523. http://dx.doi.org/10.3390/pathogens10050523.

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The intestinal protozoan parasite Cryptosporidium is an important cause of diarrheal disease worldwide. The aim of this study was to expand the knowledge on the molecular epidemiology of human cryptosporidiosis in Sweden to better understand transmission patterns and potential zoonotic sources. Cryptosporidium-positive fecal samples were collected between January 2013 and December 2014 from 12 regional clinical microbiology laboratories in Sweden. Species and subtype determination was achieved using small subunit ribosomal RNA and 60 kDa glycoprotein gene analysis. Samples were available for 398 patients, of whom 250 (63%) and 138 (35%) had acquired the infection in Sweden and abroad, respectively. Species identification was successful for 95% (379/398) of the samples, revealing 12 species/genotypes: Cryptosporidium parvum (n = 299), C. hominis (n = 49), C. meleagridis (n = 8), C. cuniculus (n = 5), Cryptosporidium chipmunk genotype I (n = 5), C. felis (n = 4), C. erinacei (n = 2), C. ubiquitum (n = 2), and one each of C. suis, C. viatorum, C. ditrichi, and Cryptosporidium horse genotype. One patient was co-infected with C. parvum and C. hominis. Subtyping was successful for all species/genotypes, except for C. ditrichi, and revealed large diversity, with 29 subtype families (including 4 novel ones: C. parvum IIr, IIs, IIt, and Cryptosporidium horse genotype VIc) and 81 different subtypes. The most common subtype families were IIa (n = 164) and IId (n = 118) for C. parvum and Ib (n = 26) and Ia (n = 12) for C. hominis. Infections caused by the zoonotic C. parvum subtype families IIa and IId dominated both in patients infected in Sweden and abroad, while most C. hominis cases were travel-related. Infections caused by non-hominis and non-parvum species were quite common (8%) and equally represented in cases infected in Sweden and abroad.

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Pfaller, M. A., S. A. Messer, A. Houston, K. Mills, A. Bolmstrom, and R. N. Jones. "Evaluation of the Etest Method for Determining Voriconazole Susceptibilities of 312 Clinical Isolates ofCandida Species by Using Three Different Agar Media." Journal of Clinical Microbiology 38, no. 10 (2000): 3715–17. http://dx.doi.org/10.1128/jcm.38.10.3715-3717.2000.

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Performance of the Etest for voriconazole susceptibility testing of 312 isolates of Candida spp. was assessed against that of the National Committee for Clinical Laboratory Standards (NCCLS) microdilution broth method. The NCCLS method employed RPMI 1640 broth medium, and MICs were read after incubation for 48 h at 35°C. Etest MICs were determined with RPMI agar containing 2% glucose (RPG), Casitone agar (CAS), and antibiotic medium 3 (AM3) agar and were read after incubation for 48 h at 35°C. The Candida spp. isolates included C. albicans (n = 174),C. glabrata (n = 55), C. tropicalis (n = 31), C. parapsilosis(n = 39), C. krusei (n = 5), C. lusitaniae (n = 2), and C. guilliermondii (n = 6). The Etest results obtained using RPG correlated well with the reference MICs. Overall agreement ranged from 91% for C. glabrata to 100% forC. tropicalis, C. parapsilosis, C. guilliermondii, C. krusei, and C. lusitaniae. When CAS was used, agreement ranged from 80% forC. krusei to 100% for C. parapsilosis,C. guilliermondii, and C. lusitaniae. With AM3, agreement ranged from 58% for C. glabrata to 100% forC. lusitaniae and C. guilliermondii. The Etest method using RPG appears to be a useful method for determining voriconazole susceptibilities of Candida species.

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Mu, Zhijian, Aiying Huang, Sonoko D. Kimura, Tao Jin, Shiqiang Wei, and Ryusuke Hatano. "Linking N2O emission to soil mineral N as estimated by CO2 emission and soil C/N ratio." Soil Biology and Biochemistry 41, no. 12 (December 2009): 2593–97. http://dx.doi.org/10.1016/j.soilbio.2009.09.013.

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Burrell, Paul C., JÃ¯Â¿Â½rg Keller, and Linda L. Blackall. "Microbiology of a Nitrite-Oxidizing Bioreactor." Applied and Environmental Microbiology 64, no. 5 (May 1, 1998): 1878–83. http://dx.doi.org/10.1128/aem.64.5.1878-1883.1998.

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ABSTRACT The microbiology of the biomass from a nitrite-oxidizing sequencing batch reactor (NOSBR) fed with an inorganic salts solution and nitrite as the sole energy source that had been operating for 6 months was investigated by microscopy, by culture-dependent methods, and by molecular biological methods, and the seed sludge that was used to inoculate the NOSBR was investigated by molecular biological methods. The NOSBR sludge comprised a complex and diverse microbial community containing gram-negative and gram-positive rods, cocci, and filaments. By culture-dependent methods (i.e., micromanipulation and sample dilution and spread plate inoculation), 16 heterotrophs (6 gram positive and 10 gram negative) were identified in the NOSBR sludge (RC), but no autotrophs were isolated. 16S ribosomal DNA clone libraries of the two microbial communities revealed that the seed sludge (GC) comprised a complex microbial community dominated byProteobacteria (29% beta subclass; 18% gamma subclass) and high G+C gram-positive bacteria (10%). Three clones (4%) were closely related to the autotrophic nitrite-oxidizer Nitrospira moscoviensis. The NOSBR sludge was overwhelmingly dominated by bacteria closely related to N. moscoviensis (89%). Two clone sequences were similar to those of the genusNitrobacter. Near-complete insert sequences of eight RC and one GC N. moscoviensis clone were determined and phylogenetically analyzed. This is the first report of the presence of bacteria from the Nitrospira phylum in wastewater treatment systems, and it is hypothesized that these bacteria are the unknown nitrite oxidizers in these processes.

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Ježková, Jana, Zlata Limpouchová, Jitka Prediger, Nikola Holubová, Bohumil Sak, Roman Konečný, Dana Květoňová, et al. "Cryptosporidium myocastoris n. sp. (Apicomplexa: Cryptosporidiidae), the Species Adapted to the Nutria (Myocastor coypus)." Microorganisms 9, no. 4 (April 12, 2021): 813. http://dx.doi.org/10.3390/microorganisms9040813.

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Cryptosporidium spp., common parasites of vertebrates, remain poorly studied in wildlife. This study describes the novel Cryptosporidium species adapted to nutrias (Myocastor coypus). A total of 150 faecal samples of feral nutria were collected from locations in the Czech Republic and Slovakia and examined for Cryptosporidium spp. oocysts and specific DNA at the SSU, actin, HSP70, and gp60 loci. Molecular analyses revealed the presence of C. parvum (n = 1), C. ubiquitum subtype family XIId (n = 5) and Cryptosporidium myocastoris n. sp. XXIIa (n = 2), and XXIIb (n = 3). Only nutrias positive for C. myocastoris shed microscopically detectable oocysts, which measured 4.8–5.2 × 4.7–5.0 µm, and oocysts were infectious for experimentally infected nutrias with a prepatent period of 5–6 days, although not for mice, gerbils, or chickens. The infection was localised in jejunum and ileum without observable macroscopic changes. The microvilli adjacent to attached stages responded by elongating. Clinical signs were not observed in naturally or experimentally infected nutrias. Phylogenetic analyses at SSU, actin, and HSP70 loci demonstrated that C. myocastoris n. sp. is distinct from other valid Cryptosporidium species.

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Pfaller, M. A., S. A. Messer, Å. Karlsson, and A. Bolmström. "Evaluation of the Etest Method for Determining Fluconazole Susceptibilities of 402 Clinical Yeast Isolates by Using Three Different Agar Media." Journal of Clinical Microbiology 36, no. 9 (1998): 2586–89. http://dx.doi.org/10.1128/jcm.36.9.2586-2589.1998.

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The performance of the Etest for fluconazole susceptibility testing of 402 yeast isolates was assessed against the National Committee for Clinical Laboratory Standards (NCCLS) microdilution broth method. The NCCLS method employed RPMI 1640 broth medium, and MICs were read after incubation for 48 h at 35°C. Etest MICs were determined with RPMI agar containing 2% glucose (RPG), Casitone agar (CAS), and Mueller-Hinton agar (MHA) and were read after incubation for 48 h at 35°C. The yeast isolates included Candida albicans(n = 161), Candida glabrata(n = 41), Candida tropicalis(n = 35), Candida parapsilosis(n = 29), Candida krusei(n = 32), Candida lusitaniae(n = 31), Candida species (n = 19), Cryptococcus neoformans(n = 40), and miscellaneous yeast species (n = 14). The Etest results correlated well with reference MICs. Overall agreement was 94% with RPG, 97% with CAS, and 53% with MHA. When RPG was used, agreement ranged from 89% forCandida spp. to 100% for C. krusei. When CAS was utilized, agreement ranged from 93% for Cryptococcus neoformans to 100% for C. tropicalis, C. parapsilosis, C. lusitaniae, Candidaspp., and miscellaneous yeast species. With MHA, agreement ranged from 17% for C. parapsilosis to 90% for C. krusei. Both RPG and CAS supported growth of all yeast species, whereas growth on MHA was comparatively weaker. Etest results were somewhat easier to read on CAS. The Etest method using either RPG or CAS, but not MHA, appears to be a viable alternative to the NCCLS reference method for determining fluconazole susceptibilities of yeasts.

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Xu, Wujie, Guoliang Wen, Haochang Su, Yu Xu, Xiaojuan Hu, and Yucheng Cao. "Effect of Input C/N Ratio on Bacterial Community of Water Biofloc and Shrimp Gut in a Commercial Zero-Exchange System with Intensive Production of Penaeus vannamei." Microorganisms 10, no. 5 (May 20, 2022): 1060. http://dx.doi.org/10.3390/microorganisms10051060.

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Although increasing attention has been attracted to the study and application of biofloc technology (BFT) in aquaculture, few details have been reported about the bacterial community of biofloc and its manipulation strategy for commercial shrimp production. An 8-week trial was conducted to investigate the effects of three input C/N ratios (8:1, 12:1 and 16:1) on the bacterial community of water biofloc and shrimp gut in a commercial BFT tank system with intensive aquaculture of P. vannamei. Each C/N ratio group had three randomly assigned replicate tanks (culture water volume of 30 m3), and each tank was stocked with juvenile shrimp at a density of 300 shrimp m−3. The tank systems were operated with zero-water exchange, pH maintenance and biofloc control. During the trial, the microbial biomass and bacterial density of water biofloc showed similar variation trends, with no significant difference under respective biofloc control measures for the three C/N ratio groups. Significant changes were found in the alpha diversity, composition and relative abundance of bacterial communities across the stages of the trial, and they showed differences in water biofloc and shrimp gut among the three C/N ratio groups. Meanwhile, high similarity could be found in the composition of the bacterial community between water biofloc and shrimp gut. Additionally, nitrogen dynamics in culture water showed some differences while shrimp performance showed no significant difference among the three C/N ratio groups. Together, these results confirm that the manipulation of input C/N ratio could affect the bacterial community of both water biofloc and shrimp gut in the environment of a commercial BFT system with intensive production of P. vannamei. Moreover, there should be different operations for the nitrogen dynamics and biofloc management during shrimp production process under different C/N ratios.

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Mao, Ling, Lili Tang, Shaoming Ye, and Shengqiang Wang. "Soil organic C and total N as well as microbial biomass C and N affect aggregate stability in a chronosequence of Chinese fir plantations." European Journal of Soil Biology 106 (September 2021): 103347. http://dx.doi.org/10.1016/j.ejsobi.2021.103347.

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Prieto-Fernández, A., M. J. Acea, and T. Carballas. "Soil microbial and extractable C and N after wildfire." Biology and Fertility of Soils 27, no. 2 (June 19, 1998): 132–42. http://dx.doi.org/10.1007/s003740050411.

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Rapp, Peter, and Lotte H. E. Gabriel-Jürgens. "Degradation of alkanes and highly chlorinated benzenes, and production of biosurfactants, by a psychrophilic Rhodococcus sp. and genetic characterization of its chlorobenzene dioxygenase." Microbiology 149, no. 10 (October 1, 2003): 2879–90. http://dx.doi.org/10.1099/mic.0.26188-0.

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Rhodococcus sp. strain MS11 was isolated from a mixed culture. It displays a diverse range of metabolic capabilities. During growth on 1,2,4-trichlorobenzene, 1,2,4,5-tetrachlorobenzene (1,2,4,5-TeCB) and 3-chlorobenzoate stoichiometric amounts of chloride were released. It also utilized all three isomeric dichlorobenzenes and 1,2,3-trichlorobenzene as the sole carbon and energy source. Furthermore, the bacterium grew well on a great number of n-alkanes ranging from n-heptane to n-triacontane and on the branched alkane 2,6,10,14-tetramethylpentadecane (pristane) and slowly on n-hexane and n-pentatriacontane. It was able to grow at temperatures from 5 to 30 °C, with optimal growth at 20 °C, and could tolerate 6 % NaCl in mineral salts medium. Genes encoding the initial chlorobenzene dioxygenase were detected by using a primer pair that was designed against the α-subunit (TecA1) of the chlorobenzene dioxygenase of Ralstonia (formerly Burkholderia) sp. strain PS12. The amino acid sequence of the amplified part of the α-subunit of the chlorobenzene dioxygenase of Rhodococcus sp. strain MS11 showed >99 % identity to the α-subunit of the chlorobenzene dioxygenase from Ralstonia sp. strain PS12 and the parts of both α-subunits responsible for substrate specificity were identical. The subsequent enzymes dihydrodiol dehydrogenase and chlorocatechol 1,2-dioxygenase were induced in cells grown on 1,2,4,5-TeCB. During cultivation on medium-chain-length n-alkanes ranging from n-decane to n-heptadecane, including 1-hexadecene, and on the branched alkane pristane, strain MS11 produced biosurfactants lowering the surface tension of the cultures from 72 to ⩽29 mN m−1. Glycolipids were extracted from the supernatant of a culture grown on n-hexadecane and characterized by 1H- and 13C-NMR-spectroscopy and mass spectrometry. The two major components consisted of α,α-trehalose esterified at C-2 or C-4 with a succinic acid and at C-2′ with a decanoic acid. They differed from one another in that one 2,3,4,2′-trehalosetetraester, found in higher concentration, was esterified at C-2, C-3 or C-4 with one octanoic and one decanoic acid and the other one, of lower concentration, with two octanoic acids. The results demonstrate that Rhodococcus sp. strain MS11 may be well suited for bioremediation of soils and sediments contaminated for a long time with di-, tri- and tetrachlorobenzenes as well as alkanes.

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Chaves, Bruno, Marciel Redin, Sandro José Giacomini, Raquel Schmatz, Joël Léonard, Fabien Ferchaud, and Sylvie Recous. "The combination of residue quality, residue placement and soil mineral N content drives C and N dynamics by modifying N availability to microbial decomposers." Soil Biology and Biochemistry 163 (December 2021): 108434. http://dx.doi.org/10.1016/j.soilbio.2021.108434.

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Jervis, Adrian J., Rebecca Langdon, Paul Hitchen, Andrew J. Lawson, Alison Wood, Joanne L. Fothergill, Howard R. Morris, Anne Dell, Brendan Wren, and Dennis Linton. "Characterization of N-Linked Protein Glycosylation in Helicobacter pullorum." Journal of Bacteriology 192, no. 19 (June 25, 2010): 5228–36. http://dx.doi.org/10.1128/jb.00211-10.

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ABSTRACT The first bacterial N-linked glycosylation system was discovered in Campylobacter jejuni, and the key enzyme involved in the coupling of glycan to asparagine residues within the acceptor sequon of the glycoprotein is the oligosaccharyltransferase PglB. Emerging genome sequence data have revealed that pglB orthologues are present in a subset of species from the Deltaproteobacteria and Epsilonproteobacteria, including three Helicobacter species: H. pullorum, H. canadensis, and H. winghamensis. In contrast to C. jejuni, in which a single pglB gene is located within a larger gene cluster encoding the enzymes required for the biosynthesis of the N-linked glycan, these Helicobacter species contain two unrelated pglB genes (pglB1 and pglB2), neither of which is located within a larger locus involved in protein glycosylation. In complementation experiments, the H. pullorum PglB1 protein, but not PglB2, was able to transfer C. jejuni N-linked glycan onto an acceptor protein in Escherichia coli. Analysis of the characterized C. jejuni N-glycosylation system with an in vitro oligosaccharyltransferase assay followed by matrix-assisted laser desorption ionization (MALDI) mass spectrometry demonstrated the utility of this approach, and when applied to H. pullorum, PglB1-dependent N glycosylation with a linear pentasaccharide was observed. This reaction required an acidic residue at the −2 position of the N-glycosylation sequon, as for C. jejuni. Attempted insertional knockout mutagenesis of the H. pullorum pglB2 gene was unsuccessful, suggesting that it is essential. These first data on N-linked glycosylation in a second bacterial species demonstrate the similarities to, and fundamental differences from, the well-studied C. jejuni system.

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Robertson, Kerstin, Johan Schnorer, Marianne Clarholm, Torben A. Bonde, and Thomas Rosswall. "Microbial biomass in relation to C and N mineralization during laboratory incubations." Soil Biology and Biochemistry 20, no. 3 (January 1988): 281–86. http://dx.doi.org/10.1016/0038-0717(88)90004-1.

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Smolander, A., and E. Mälkönen. "Microbial biomass C and N in limed soil of norway spruce stands." Soil Biology and Biochemistry 26, no. 4 (April 1994): 503–9. http://dx.doi.org/10.1016/0038-0717(94)90183-x.

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Pata, Yavuz Selim, Candan Öztürk, Yücel Akbaş, Murat Ünal, Kemal Görür, and Cengiz Özcan. "Microbiology of cerumen in patients with recurrent otitis externa and cases with open mastoidectomy cavities." Journal of Laryngology & Otology 118, no. 4 (April 2004): 260–62. http://dx.doi.org/10.1258/002221504323011978.

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This study investigated the common flora of human cerumen in patients with recurrent otitis externa, and subjects who had been operated on and had an open mastoidectomy cavity from chronic otitis media.Cerumen samples were collected from three groups; group A (n = 20) consisted of patients with recurrent otitis externa, group B (n = 20) consisted of patients with an open cavity and group C (n = 30) consisted of healthy subjects.The mean of the microbial count was 3.4 × 104 in group A, 3.08 × 104 in group B and 2.48 × 104 in group C. The most commonly isolated microorganism from the three groups was Staphylococcus epidermidis. No growth was observed in five cases (25 per cent) in group A and in three cases (10 per cent) in group C. In groupB antimicrobial growth was observed in all samples. In 46 (65 per cent) of the cerumen samples,the isolates were monomicrobial and 24 (35 per cent) of the cerumen samples were polymicrobial. The isolates were polymicrobial in 65 per cent of group A, 20 per cent in group B and 23.3 per cent in group C.In the process of investigating the microbial flora of cerumen in all the three groups, microbial growth was observed from all the samples from patients with an open cavity, unlike the other groups, and it was determined that the group with recurrent external otitis had the most abundant microbial flora.

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Jiang, Lei, Xiuyan Ma, Yanyu Song, Siqi Gao, Jiusheng Ren, Hao Zhang, and Xianwei Wang. "Warming-Induced Labile Carbon Change Soil Organic Carbon Mineralization and Microbial Abundance in a Northern Peatland." Microorganisms 10, no. 7 (June 30, 2022): 1329. http://dx.doi.org/10.3390/microorganisms10071329.

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Climate warming affects the carbon cycle of northern peatlands through temperature rises and a changing carbon availability. To clarify the effects of elevated temperature and labile carbon addition on SOC mineralization, as well as their microbial driving mechanisms, topsoil (0–10 cm) and subsoil (10–20 cm) were collected from a peatland in the Great Hing’an Mountains and incubated with or without 13C-glucose at 10 °C and 15 °C for 42 days. The results showed that 5 °C warming significantly stimulated SOC mineralization along with NH4+-N and NO3−-N content increases, as well as a decrease in invertase and urease activities. Glucose addition triggered a positive priming effect (PE) in the early stage of the incubation but changed to a negative PE in the late stage of the incubation. Glucose likely regulates carbon dynamics by altering fungi: bacteria, soil invertase, and β-glucodase activities, and MBC, DOC, NH4+-N contents. Glucose addition increased fungal abundance in 0–10 cm at 10 °C and 15 °C, and 10–20 cm at 10 °C, respectively, but significantly decreased fungal abundance in 10–20 cm at 15 °C. Glucose addition decreased bacterial abundance in 0–10 cm at 10 °C but increased bacterial abundance in 10–20 cm soil at 10 °C, and in 0–10 and 10–20 cm soils at 15 °C, respectively. Glucose addition significantly decreased the fungi: bacteria ratio in 0–20 cm soils at 15 °C. In addition, Q10 was significantly positively correlated with the changes in soil DOC, NH4+-N contents, invertase, and β-glucosidase activities, while negatively correlated with fungi: bacteria and urease activities after 5 °C of warming, and glucose addition significantly increased the Q10. Labile carbon may decrease carbon losses in northern peatlands that inhibit warming-induced carbon emission increase, thus partially buffering soil carbon content against change.

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Peles, Ferenc, Martin Wagner, Péter Keresztúri, Béla Béri, and András Szabó. "Comparative analysis of Staphylococcus aureus strains by molecular microbiology methods." Acta Agraria Debreceniensis, no. 26 (July 16, 2007): 34–39. http://dx.doi.org/10.34101/actaagrar/26/3051.

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Staphylococcus aureus is a very important pathogen for dairy farms and milk processing plants. Subclinical mastitis is often caused by this species, and it can contaminate bulk tank milk when milking cows are suffering from mastitis. Additionally, thermostable enterotoxins (SE) produced by some types of this bacterium can cause food poisoning.The aim of our research was to examine the number of S. aureus in bulk tank milk in two dairy farms and the enterotoxin-producing ability, genetic relation (pulsotype) and antibiotic resistance of S. aureus strains from different sources (bulk tank milk, udder quarter milk and environment).The results show that the mean number of S. aureus of bulk tank milk of two farms significantly differed (P<0.05). Fourteen isolates were selected for further molecular genetic studies (five isolates were from bulk tank milk and nine isolates were from udder quarter milk). S. aureus was not recovered from the environmental samples. Three of the fourteen isolates (21.4%) tested by multiplex PCR were positive for SE genes. Two isolates carried one gene (seb) and one isolate carried two genes (seg and sei). The fourteen strains were classified into three pulsotypes and two subtypes at 86% similarity level. Isolates from bulk tank milk (n=5), were divided into 2 pulsotypes (A, C) and one subtype (C1). The isolates from udder quarter milk (n=9) belonged to three different pulsotypes (A, B, C) and two subtypes (A1, C1). The distribution of pulsotypes in the present study revealed genetic relationship between S. aureus isolated from udder quarter milk and bulk tank milk. This could be explained by the fact that in farms with a high number of infected cows, these cows could represent the main source of contamination. The results of the antibiotic resistance investigations show, that all strains were susceptible to methicillin, cefoxitin, lincomycin, tetracycline, erythromycin and sulfamethoxazole/trimethoprim. Thirteen out of fourteen strains were resistant to penicillin (A and C pulsotypes, A1 and C1 subtypes) and just one isolate was susceptible (B pulsotype) to all antibiotics tested.

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de Menezes, Alexandre B., Miranda T. Prendergast-Miller, Pabhon Poonpatana, Mark Farrell, Andrew Bissett, Lynne M. Macdonald, Peter Toscas, Alan E. Richardson, and Peter H. Thrall. "C/N Ratio Drives Soil Actinobacterial Cellobiohydrolase Gene Diversity." Applied and Environmental Microbiology 81, no. 9 (February 20, 2015): 3016–28. http://dx.doi.org/10.1128/aem.00067-15.

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ABSTRACTCellulose accounts for approximately half of photosynthesis-fixed carbon; however, the ecology of its degradation in soil is still relatively poorly understood. The role of actinobacteria in cellulose degradation has not been extensively investigated despite their abundance in soil and known cellulose degradation capability. Here, the diversity and abundance of the actinobacterial glycoside hydrolase family 48 (cellobiohydrolase) gene in soils from three paired pasture-woodland sites were determined by using terminal restriction fragment length polymorphism (T-RFLP) analysis and clone libraries with gene-specific primers. For comparison, the diversity and abundance of general bacteria and fungi were also assessed. Phylogenetic analysis of the nucleotide sequences of 80 clones revealed significant new diversity of actinobacterial GH48 genes, and analysis of translated protein sequences showed that these enzymes are likely to represent functional cellobiohydrolases. The soil C/N ratio was the primary environmental driver of GH48 community compositions across sites and land uses, demonstrating the importance of substrate quality in their ecology. Furthermore, mid-infrared (MIR) spectrometry-predicted humic organic carbon was distinctly more important to GH48 diversity than to total bacterial and fungal diversity. This suggests a link between the actinobacterial GH48 community and soil organic carbon dynamics and highlights the potential importance of actinobacteria in the terrestrial carbon cycle.

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Ramatla, Tsepo, Kealeboga Mileng, Rendani Ndou, Mpho Tawana, Lehlohonolo Mofokeng, Michelo Syakalima, Kgaugelo E. Lekota, and Oriel Thekisoe. "Campylobacter jejuni from Slaughter Age Broiler Chickens: Genetic Characterization, Virulence, and Antimicrobial Resistance Genes." International Journal of Microbiology 2022 (May 19, 2022): 1–13. http://dx.doi.org/10.1155/2022/1713213.

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Campylobacter jejuni is a major cause of food-borne human gastroenteritis worldwide and is designated as a high priority antimicrobial-resistant pathogen by the World Health Organization (WHO). In this study, a total of 26 C. jejuni isolates from broiler chickens were screened for the presence of virulence and antimicrobial resistance genes by PCR. As a result, the study detected 11/26 (42.3%), 9/26 (34.6%), 8/26 (30.8%), 7/26 (26.9%), 6/26 (23.1%), and 6/26 (23.1%) of cdtC, pldA, cdtB, cdtA, cadF, and ciaB virulence genes, respectively, with seven of the isolates carrying more than two virulence genes. The majority of the isolates n = 25 (96.1%) were resistant to nalidixic acid, followed by n = 21 (80.7%), n = 22 (84.6%), and n = 5 (19.2%) for tetracycline, erythromycin, and ciprofloxacin, respectively. Most isolates were harboring catI (n = 16; 84.2%), catII (n = 15; 78.9%), catIII (n = 10; 52.6%), catIV (n = 2; 10.5%), floR (n = 10; 52.6%), ermB (n = 14; 73.7%), tetO (n = 13; 68.4%), tetA (n = 9; 47.4%), mcr-4 (n = 8; 42.1%), and ampC (n = 2; 10.5%). Meanwhile, mcr-1, mcr-2, mcr-3, mcr-5, tet(X), tet(P), and tet(W) genes were not detected in all isolates. Class I and Class II integrons were detected in 92.3% (n = 24) and 65.4% (n = 17) isolates, respectively. About 31% (8 of the 26 isolates) isolates were carrying more than two resistance genes. According to our knowledge, this is the first study to detect class II integrons in Campylobacter spp. (C. jejuni). The high prevalence of cdtA, cdtB, cdtC, cadF, pldA, and ciaB genes and antibiotic resistance genes in C. jejuni in this study indicates the pathogenic potential of these isolates. Majority of the isolates demonstrated resistance to nalidixic acid, tetracycline (tet), and erythromycin (ermB), which are the drugs of choice for treating Campylobacter infections. Therefore, these findings highlight the importance of implementing an efficient strategy to control Campylobacter in chickens and to reduce antimicrobial use in the poultry industry, which will help to prevent the spread of infections to humans.

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Shin, Bo-Moon, Eun Young Kuak, Hyeon Mi Yoo, Eui Chong Kim, Kyungwon Lee, Jung-Oak Kang, Dong Hee Whang, and Jeong-Hwan Shin. "Multicentre study of the prevalence of toxigenic Clostridium difficile in Korea: results of a retrospective study 2000–2005." Journal of Medical Microbiology 57, no. 6 (June 1, 2008): 697–701. http://dx.doi.org/10.1099/jmm.0.47771-0.

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The prevalence of toxigenic Clostridium difficile in Korea has been reported to be approximately 60–80 %. Although the prevalence of the tcdA−tcdB+ C. difficile strain was less then 5 % prior to the year 2000, it has become an emerging nosocomial pathogen in Korea. Therefore, we have attempted to determine the multicentre nationwide prevalence of tcdA+tcdB+ and tcdA−tcdB+ C. difficile for epidemiological purposes. C. difficile strains (n=724, 30 from 2000, 80 from 2001, 74 from 2002, 76 from 2003, 179 from 2004, 285 from 2005) were obtained retrospectively from January 2000 to December 2005 from in-patients at 6 hospitals, all of whom were suspected of having C. difficile-associated disease (CDAD), colitis or pseudomembranous colitis. The numbers of participating hospitals varied yearly (1 in 2000, 2 in 2001–2003, 3 in 2004, 5 in 2005). The hospitals were located in Seoul (n=4), Kyunggi Province (n=1) and Busan (n=1), Korea. PCR assays for tcdA and tcdB genes were conducted using 724 unduplicated C. difficile isolates. The mean prevalence of tcdA+tcdB+ and tcdA−tcdB+ C. difficile strains over the 6 years was 51.8 % (38.4–59.3 %) and 25.8 %(10–56.0 %), respectively. The mean prevalence of tcdA−tcdB+ C. difficile strains was less than 7 % until 2002, but began to increase in 2003 (13.2 %) and achieved a peak in 2004 (50.3 %). In 2005, the mean prevalence of tcdA+tcdB+ and tcdA−tcdB+ C. difficile strains was 47.7 % (30.9–60.3 %) and 27.0 % (17.6–54.8 %), respectively. This nationwide epidemiological study showed that tcdA−tcdB+ C. difficile strains have already spread extensively throughout Korea, and our results provide basic data regarding the controversies currently surrounding the toxigenicity of tcdA−tcdB+ C. difficile. The use of enzyme immunoassays capable of detecting both TcdA and TcdB is strongly recommended for the diagnosis of CDAD in microbiology laboratories, in order to control the spread of the tcdA−tcdB+ strains of C. difficile.

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Oppegård, Camilla, Per Rogne, Per Eugen Kristiansen, and Jon Nissen-Meyer. "Structure analysis of the two-peptide bacteriocin lactococcin G by introducing d-amino acid residues." Microbiology 156, no. 6 (June 1, 2010): 1883–89. http://dx.doi.org/10.1099/mic.0.038430-0.

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The importance of 3D structuring in the N- and C-terminal ends of the two peptides (39-mer LcnG-α and 35-mer LcnG-β) that constitute the two-peptide bacteriocin lactococcin G was analysed by replacing residues in the end regions with the corresponding d-isomeric residues. When assayed for antibacterial activity in combination with the complementary wild-type peptide, LcnG-α with four d-residues in its C-terminal region and LcnG-β with four d-residues in either its N- or its C-terminal region were relatively active (two- to 20-fold reduction in activity). 3D structuring of the C-terminal region in LcnG-α and the C- and N-terminal regions in LcnG-β is thus not particularly critical for retaining antibacterial activity, indicating that the 3D structure of these regions is not vital for interpeptide interactions or for interactions between the peptides and cellular components. The 3D structure of the N-terminal region in LcnG-α may be more important, as LcnG-α with four N-terminal d-residues was the least active of these four peptides (10- to 100-fold reduction in activity). The results are consistent with a proposed structural model of lactococcin G in which LcnG-α and -β form a transmembrane parallel helix–helix structure involving approximately 20 residues in each peptide, starting near the N terminus of LcnG-α and at about residue 13 in LcnG-β. Upon expressing the lactococcin G immunity protein, sensitive target cells became resistant to all of these d-residue-containing peptides. The end regions of the two lactococcin G peptides are consequently not involved in essential structure-dependent interactions with the immunity protein. The relatively high activity of most of the d-residue-containing peptides suggests that bacteriocins with increased resistance to exopeptidases may be generated by replacing their N- and C-terminal residues with d-residues.

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Paolini, Chantal, Raffaele De Francesco, and Paola Gallinari. "Enzymatic properties of hepatitis C virus NS3-associated helicase." Microbiology 81, no. 5 (May 1, 2000): 1335–45. http://dx.doi.org/10.1099/0022-1317-81-5-1335.

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The hepatitis C virus non-structural protein 3 (NS3) possesses a serine protease activity in the N-terminal one-third, whereas RNA-stimulated NTPase and helicase activities reside in the C-terminal portion. In this study, an N-terminal hexahistidine-tagged full-length NS3 polypeptide was expressed in Escherichia coli and purified to homogeneity by conventional chromatography. Detailed characterization of the helicase activity of NS3 is presented with regard to its binding and strand release activities on different RNA substrates. On RNA double-hybrid substrates, the enzyme was shown to perform unwinding activity starting from an internal ssRNA region of at least 3 nt and moving along the duplex in a 3′ to 5′ direction. In addition, data are presented suggesting that binding to ATP reduces the affinity of NS3 for ssRNA and increases its affinity for duplex RNA. Furthermore, we have ascertained the capacity of NS3 to specifically interact with and resolve the stem–loop RNA structure (SL I) within the 3′-terminal 46 bases of the viral genome. Finally, our analysis of NS3 processive unwinding under single cycle conditions by addition of heparin in both helicase and RNA-stimulated ATPase assays led to two conclusions: (i) NS3-associated helicase acts processively; (ii) most of the NS3 RNA-stimulated ATPase activity may not be directly coupled to translocation of the enzyme along the substrate RNA molecule.

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Hu, Lan, Richard B. Raybourne, and Dennis J. Kopecko. "Ca2+ release from host intracellular stores and related signal transduction during Campylobacter jejuni 81-176 internalization into human intestinal cells." Microbiology 151, no. 9 (September 1, 2005): 3097–105. http://dx.doi.org/10.1099/mic.0.27866-0.

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Campylobacter jejuni is the leading bacterial cause of human diarrhoeal disease in many parts of the world, including the USA. The ability of C. jejuni to invade the host intestinal epithelium is an important determinant of virulence. A common theme among pathogenic invasive micro-organisms is their ability to usurp the eukaryotic cell-signalling systems both to allow for invasion and to trigger disease pathogenesis. Ca2+ is very important in a great variety of eukaryotic cell-signalling processes (e.g. calmodulin-activated enzymes, nuclear transcriptional upregulation, and cytoskeletal rearrangements). This study analyses the effects of Ca2+ availability on invasion of human INT407 intestinal epithelial cells by C. jejuni strain 81-176. The ability of C. jejuni to invade INT407 cells was not blocked by chelation of any remaining extracellular Ca2+ from host cells incubated in Ca2+-free, serum-free media. In contrast, C. jejuni invasion was markedly reduced either by chelating host intracellular Ca2+ with 1,2-bis-(2-)ethane-N,N,N′,N′-tetraacetic acid acetoxymethyl ester (BAPTA, AM) or by blocking the release of Ca2+ from intracellular stores with dantrolene or U73122. Moreover, Bay K8644, a plasma-membrane Ca2+-channel agonist, was observed to stimulate C. jejuni invasion, presumably by increasing host intracellular free Ca2+ levels. Measurement of host-cell cytosolic Ca2+ via spectrofluorimetry and fluorescence microscopy revealed an increase in Ca2+ from 10 min post-infection. Monolayer pretreatment with either a calmodulin antagonist or a specific inhibitor of protein kinase C was found to cause a marked reduction in C. jejuni invasion, suggesting roles for these Ca2+-activated modulators in signal-transduction events involved in C. jejuni invasion. These results demonstrate that C. jejuni induces the mobilization of Ca2+ from host intracellular stores, which is an essential step in the invasion of intestinal cells by this pathogen.

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Huang, Xuejiao, Wenzhou Tie, Deti Xie, and Zhenlun Li. "Low C/N Ratios Promote Dissimilatory Nitrite Reduction to Ammonium in Pseudomonas putida Y-9 under Aerobic Conditions." Microorganisms 9, no. 7 (July 17, 2021): 1524. http://dx.doi.org/10.3390/microorganisms9071524.

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The biogeochemical consequences of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) have a significant influence on nitrogen (N) cycling in the ecosystem. Many researchers have explored these two pathways in soil and sediment ecosystems under anaerobic conditions. However, limited information is available regarding the influence of external environmental conditions on these two pathways in a well-defined experimental system under aerobic conditions. In this study, the impacts of the external environmental factors (carbon source, C/N ratio, pH, and dissolved oxygen) on nitrite reduction through the denitrification and DNRA routes in Pseudomonas putida Y-9 were studied. Results found that sodium citrate and sodium acetate favored denitrification and DNRA, respectively. Furthermore, neutral pH and aerobic conditions both facilitated DNRA and denitrification. Especially, low C/N ratios motivated the DNRA while high C/N ratios stimulated the denitrification, which was opposite to the observed phenomena under anaerobic conditions.

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Mayali, Xavier, Peter K. Weber, and Jennifer Pett-Ridge. "Taxon-specific C/N relative use efficiency for amino acids in an estuarine community." FEMS Microbiology Ecology 83, no. 2 (September 20, 2012): 402–12. http://dx.doi.org/10.1111/j.1574-6941.12000.x.

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Rousk, Johannes, and Erland BÃ¥Ã¥th. "Fungal and bacterial growth in soil with plant materials of different C/N ratios." FEMS Microbiology Ecology 62, no. 3 (December 2007): 258–67. http://dx.doi.org/10.1111/j.1574-6941.2007.00398.x.

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Bonanomi, Giuliano, Guido Incerti, Francesco Giannino, Antonio Mingo, Virginia Lanzotti, and Stefano Mazzoleni. "Litter quality assessed by solid state 13C NMR spectroscopy predicts decay rate better than C/N and Lignin/N ratios." Soil Biology and Biochemistry 56 (January 2013): 40–48. http://dx.doi.org/10.1016/j.soilbio.2012.03.003.

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Llosa, Matxalen, John Zupan, Christian Baron, and Patricia Zambryski. "The N- and C-Terminal Portions of theAgrobacterium VirB1 Protein Independently Enhance Tumorigenesis." Journal of Bacteriology 182, no. 12 (June 15, 2000): 3437–45. http://dx.doi.org/10.1128/jb.182.12.3437-3445.2000.

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ABSTRACT Genetic transformation of plants by Agrobacterium tumefaciens is mediated by a virulence (vir)-specific type IV secretion apparatus assembled from 11 VirB proteins and VirD4. VirB1, targeted to the periplasm by an N-terminal signal peptide, is processed to yield VirB1*, comprising the C-terminal 73 amino acids. The N-terminal segment, which shares homology with chicken egg white lysozyme as well as lytic transglycosylases, may provide local lysis of the peptidoglycan cell wall to create channels for transporter assembly. Synthesis of VirB1* followed by its secretion to the exterior of the cell suggests that VirB1* may also have a role in virulence. In the present study, we provide evidence for the dual roles of VirB1 in tumorigenesis as well as the requirements for processing and secretion of VirB1*. Complementation of a virB1 deletion strain with constructs expressing either the N-terminal lysozyme-homologous region or VirB1* results in tumors intermediate in size between those induced by a wild-type strain and a virB1 deletion strain, suggesting that each domain has a unique role in tumorigenesis. The secretion of VirB1* translationally fused to the signal peptide indicates that processing and secretion are not coupled. When expressed independently of all other vir genes, VirB1 was processed and VirB1* was secreted. When restricted to the cytoplasm by deletion of the signal peptide, VirB1 was neither processed nor secreted and did not restore virulence to the virB1 deletion strain. Thus, factors that mediate processing of VirB1 and secretion of VirB1* are localized in the periplasm or outer membrane and are not subject tovir regulation.

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Uusitalo, M., V. Kitunen, and A. Smolander. "Response of C and N transformations in birch soil to coniferous resin volatiles." Soil Biology and Biochemistry 40, no. 10 (October 2008): 2643–49. http://dx.doi.org/10.1016/j.soilbio.2008.07.009.

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Kazakov, Teymur, Gaston H. Vondenhoff, Kirill A. Datsenko, Maria Novikova, Anastasia Metlitskaya, Barry L. Wanner, and Konstantin Severinov. "Escherichia coli Peptidase A, B, or N Can Process Translation Inhibitor Microcin C." Journal of Bacteriology 190, no. 7 (January 25, 2008): 2607–10. http://dx.doi.org/10.1128/jb.01956-07.

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ABSTRACT The heptapeptide-nucleotide microcin C (McC) targets aspartyl-tRNA synthetase. Upon its entry into a susceptible cell, McC is processed to release a nonhydrolyzable aspartyl-adenylate that inhibits aspartyl-tRNA synthetase, leading to the cessation of translation and cell growth. Here, we surveyed Escherichia coli cells with singly, doubly, and triply disrupted broad-specificity peptidase genes to show that any of three nonspecific oligopeptidases (PepA, PepB, or PepN) can effectively process McC. We also show that the rate-limiting step of McC processing in vitro is deformylation of the first methionine residue of McC.

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Hudson, Lauren K., William E. Andershock, Runan Yan, Mugdha Golwalkar, Nkuchia M. M’ikanatha, Irving Nachamkin, Linda S. Thomas, et al. "Phylogenetic Analysis Reveals Source Attribution Patterns for Campylobacter spp. in Tennessee and Pennsylvania." Microorganisms 9, no. 11 (November 5, 2021): 2300. http://dx.doi.org/10.3390/microorganisms9112300.

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Campylobacteriosis is the most common bacterial foodborne illness in the United States and is frequently associated with foods of animal origin. The goals of this study were to compare clinical and non-clinical Campylobacter populations from Tennessee (TN) and Pennsylvania (PA), use phylogenetic relatedness to assess source attribution patterns, and identify potential outbreak clusters. Campylobacter isolates studied (n = 3080) included TN clinical isolates collected and sequenced for routine surveillance, PA clinical isolates collected from patients at the University of Pennsylvania Health System facilities, and non-clinical isolates from both states for which sequencing reads were available on NCBI. Phylogenetic analyses were conducted to categorize isolates into species groups and determine the population structure of each species. Most isolates were C. jejuni (n = 2132, 69.2%) and C. coli (n = 921, 29.9%), while the remaining were C. lari (0.4%), C. upsaliensis (0.3%), and C. fetus (0.1%). The C. jejuni group consisted of three clades; most non-clinical isolates were of poultry (62.7%) or cattle (35.8%) origin, and 59.7 and 16.5% of clinical isolates were in subclades associated with poultry or cattle, respectively. The C. coli isolates grouped into two clades; most non-clinical isolates were from poultry (61.2%) or swine (29.0%) sources, and 74.5, 9.2, and 6.1% of clinical isolates were in subclades associated with poultry, cattle, or swine, respectively. Based on genomic similarity, we identified 42 C. jejuni and one C. coli potential outbreak clusters. The C. jejuni clusters contained 188 clinical isolates, 19.6% of the total C. jejuni clinical isolates, suggesting that a larger proportion of campylobacteriosis may be associated with outbreaks than previously determined.

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CHEN, CHEE-SHAN, WAN-YU LIAU, and GUO-JANE TSAI. "Antibacterial Effects of N-Sulfonated and N-Sulfobenzoyl Chitosan and Application to Oyster Preservation." Journal of Food Protection 61, no. 9 (September 1, 1998): 1124–28. http://dx.doi.org/10.4315/0362-028x-61.9.1124.

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The antibacterial effects of sulfonated and sulfobenzoyl chitosans were evaluated and compared with that of 69% deacetylated chitosan (DD69 chitosan). Minimal inhibitory concentrations of sulfonated chitosan (SC1, 0.63% sulfur content) against Shigella dysenteriae, Aeromonas hydrophila, Salmonella typhimurium, and Bacillus cereus were found to be lower than those of DD69 chitosan. A high sulfur content in sulfonated chitosan adversely influenced its antibacterial effect. Sulfobenzoyl chitosan (SBC) has excellent water solubility and an antibacterial effect comparable to that of SC1. SBC at 1,000 and 2,000 ppm extended the shelf life of oysters at 5°C by 4 days at the former or by 7 days at least at the latter concentration. The growth of coliforms and Pseudomonas, Aeromonas, and Vibrio species on oysters was retarded by the addition of DD69 chitosan or SBC.

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OSCAR, THOMAS P. "Development and Validation of a Predictive Microbiology Model for Survival and Growth of Salmonella on Chicken Stored at 4 to 12°C†." Journal of Food Protection 74, no. 2 (February 1, 2011): 279–84. http://dx.doi.org/10.4315/0362-028x.jfp-10-314.

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Salmonella spp. are a leading cause of foodborne illness. Mathematical models that predict Salmonella survival and growth on food from a low initial dose, in response to storage and handling conditions, are valuable tools for helping assess and manage this public health risk. The objective of this study was to develop and to validate the first predictive microbiology model for survival and growth of a low initial dose of Salmonella on chicken during refrigerated storage. Chicken skin was inoculated with a low initial dose (0.9 log) of a multiple antibiotic-resistant strain of Salmonella Typhimurium DT104 (ATCC 700408) and then stored at 4 to 12°C for 0 to 10 days. A general regression neural network (GRNN) model that predicted log change of Salmonella Typhimurium DT104 as a function of time and temperature was developed. Percentage of residuals in an acceptable prediction zone, from −1 (fail-safe) to 0.5 (fail-dangerous) log, was used to validate the GRNN model by using a criterion of 70% acceptable predictions. Survival but not growth of Salmonella Typhimurium DT104 was observed at 4 to 8°C. Maximum growth of Salmonella Typhimurium DT104 during 10 days of storage was 0.7 log at 9°C, 1.1 log at 10°C, 1.8 log at 11°C, and 2.9 log at 12°C. Performance of the GRNN model for predicting dependent data (n = 163) was 85% acceptable predictions, for predicting independent data for interpolation (n = 77) was 84% acceptable predictions, and for predicting independent data for extrapolation (n = 70) to Salmonella Kentucky was 87% acceptable predictions. Thus, the GRNN model provided valid predictions for survival and growth of Salmonella on chicken during refrigerated storage, and therefore the model can be used with confidence to help assess and manage this public health risk.

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48

Mashock, Michael J., Matthew L. Faron, Blake W. Buchan, and Nathan A. Ledeboer. "Evaluation of Copan FecalSwab as Specimen Type for Use in Xpert C. difficile Assay." Journal of Clinical Microbiology 55, no. 10 (August 9, 2017): 3123–29. http://dx.doi.org/10.1128/jcm.00369-17.

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ABSTRACT Liquid-based microbiology (LBM) devices incorporating flocked swabs and preservation medium ease transport of specimens and improve specimen yield compared to traditional fiber wound swabs; however, the performance of LBM collection devices has not been evaluated in many molecular assays. It is unclear how the differences in matrix and specimen loading with an LBM device will affect test performance compared to traditional collection devices. The purpose of this study was to evaluate the performance of specimens collected in FecalSwab transport medium (Copan Diagnostics, Murrieta, CA) compared to unpreserved stool using the Cepheid Xpert C. difficile assay (Cepheid, Sunnyvale, CA). Results equivalent to unpreserved stool samples were obtained when 400 μl of FecalSwab-preserved stool was employed in the Xpert assay. The positive and negative percent agreement of specimens inoculated with FecalSwab medium ( n = 281) was 97.0% (95% confidence interval [CI], 90.9 to 96.4%) and 99.4% (95% CI, 96.4 to 99.9%), respectively, compared to reference results obtained using unpreserved stool. Throughout this study, only four discrepant results occurred when comparing preserved specimens to unpreserved stool specimens in the Xpert C. difficile PCR assay. Post discrepant analysis, using the BD MAX Cdiff assay, the specificity and sensitivity both increased to 100%. The high positive and negative percent agreements observed in this study suggest that stool preserved in FecalSwab media yields equivalent results to using unpreserved stool when tested on the Xpert C. difficile assay, allowing laboratories to adopt this liquid-based microbiology collection device.

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HELKE, DAVID M., and AMY C. L. WONG. "Survival and Growth Characteristics of Listeria monocytogenes and Salmonella typhimurium on Stainless Steel and Buna-N Rubber." Journal of Food Protection 57, no. 11 (November 1, 1994): 963–68. http://dx.doi.org/10.4315/0362-028x-57.11.963.

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Microorganisms harbored on food-contact surfaces are part of a complex ecosystem. The interactions of temperature, relative humidity (RH), soil and surface on the survival of Listeria monocytogenes and Salmonella typhimurium were studied. Survival and growth were monitored at 25°C and 6°C and 32.5% RH and 75.5% RH. Survival in phosphate-buffered saline and dilute pasteurized whole milk on both stainless steel and buna-n was highest at 6°C and 75.5% RH. Both organisms were recoverable on the two surfaces after 10 days storage at 6°C and 75.5% RH. Survival of L. monocytogenes and S. typhimurium at 25°C and 75.5% RH was increased in dilute pasteurized whole milk on stainless steel, but not on buna-n. Organisms grew in pasteurized whole milk on stainless steel at 25°C and 75.5% RH, but failed to grow on buna-n. At 25°C and 75.5% RH, S. typhimurium was not recoverable on buna-n after 10 days in whole milk; however, L. monocytogenes remained close to initial levels. The survival and growth of both organisms in raw milk soil was similar to that in pasteurized whole milk soil. Buna-n was not bacteriostatic towards all organisms, as the total viable count in raw milk increased by more than a factor of 10 after 1 day storage at 25°C and 75.5% RH. Unlike other soils tested, survival of S. typhimurium at in conditions and L. monocytogenes at 25°C and both RHs in whey was higher on buna-n than on stainless steel. At 6°C and both RHs, L. monocytogenes levels remained constant on both surfaces in whey. The bacteriostatic effect of buna-n was not affected significantly by exposure to 20 cycles of a simulated clean-in-place (CIP) process.

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Hedges, R. W. "R factors from Providence." Microbiology 81, no. 1 (January 1, 2000): 171–81. http://dx.doi.org/10.1099/00221287-81-1-171.

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Of more than 100 R factors transferred from naturally occurring Providence strains, approximately 60 % belonged to the A-C compatibility complex. Plasmids of groups F1, J, N, P and X, and the prototype of a new group G were also transferred. The Providence R factor set differs from those of Proteus rettgeri and P. morganii most strikingly in the abundance of plasmids of the A-C group and the infrequency of N group plasmids.

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Journal articles on the topic 'Microbiology, n.e.c'

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