Abstract:
:Antibiotics in animal husbandry are used to maintain welfare, but lead to the generation of resistant strains. We analyzed commensal multidrug-resistant Escherichia coli from pigs at the beginning and end of the production cycle in a farm with a farrow-to-finish system in order to investigate whether clonal spread or horizontal gene transfer constitutes the main factor responsible for the prevalence of resistance in this environment. Among 380 isolates, 56 multidrug-resistant E. coli with a similar resistant phenotype were selected for more detailed investigations including a genomic similarity analysis and the detection of mobile elements. Isolates carried blaTEM-1, aadA1, strA/B, tetA, tetB, tetC, dfrA1, dfrA5, dfrA7, dfrA12, sul1, sul2, sul3, and qnrS resistance genes, with the common co-occurrence of genes encoding the same resistance phenotype. A pulse-field gel electrophoresis analysis of the genomic similarity of multidrug-resistant E. coli showed ≤65% similarity of most of the tested strains and did not reveal a dominant clone responsible for the prevalence of resistance. Class 1 and 2 integrons and transposons 7 and 21 were detected among mobile elements; however, some were truncated. Plasmids were represented by 11 different incompatibility groups (K, FIB, I1, FIIA, FIC, FIA, Y, P, HI1, B/O, and T). Genetic resistance traits were unevenly spread in the clonal groups and suggested the major rearrangement of genetic material by horizontal gene transfer. The present results revealed that in commensal E. coli from pigs in a homogeneous farm environment, there was no dominant clone responsible for the spread of resistance and persistence in the population.
journal_name
Microbes Environjournal_title
Microbes and environmentsauthors
Mazurek J,Bok E,Baldy-Chudzik Kdoi
10.1264/jsme2.ME17041subject
Has Abstractpub_date
2018-09-29 00:00:00pages
242-248issue
3eissn
1342-6311issn
1347-4405journal_volume
33pub_type
杂志文章abstract::Growth inhibition due to continuous cropping of asparagus is a major problem; the yield of asparagus in replanted fields is low compared to that in new fields, and missing plants occur among young seedlings. Although soil-borne disease and allelochemicals are considered to be involved in this effect, this is still con...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.me11222
更新日期:2012-01-01 00:00:00
abstract::HcRNAV is a small icosahedral virus that infects the shellfish-killing marine dinoflagellate Heterocapsa circularisquama, which harbors a dicistronic linear single-stranded RNA (ssRNA) genome ca. 4.4 kb in length. Its major capsid protein (MCP) gene sequence is not expressed by various strains of Escherichia coli, pos...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.me12046
更新日期:2012-01-01 00:00:00
abstract::The simultaneous extraction of plant organelle (mitochondria and plastid) genes during the DNA extraction step is a major limitation in investigating the community structures of bacteria associated with plants because organelle SSU rRNA genes are easily amplified by PCR using primer sets that are specific to bacteria....
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.me14061
更新日期:2014-09-17 00:00:00
abstract::We investigated biofilm formation on biodegradable plastics in freshwater samples. Poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBH) was covered by a biofilm after an incubation in freshwater samples. A next generation sequencing analysis of the bacterial communities of biofilms that formed on PHBH films revealed t...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.ME18033
更新日期:2018-09-29 00:00:00
abstract::Chemosynthetic microbial communities develop and form dense cell aggregates in slightly alkaline sulfidic hot springs in the temperature range of 70-86°C at Nakabusa, Japan. Nitrogenase activity has recently been detected in the microbial communities collected. To identify possible members capable of nitrogen fixation...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.ME18030
更新日期:2018-12-28 00:00:00
abstract::The addition of ferrihydrite to methanogenic microbial communities obtained from a thermophilic anaerobic digester suppressed methanogenesis in a dose-dependent manner. The amount of reducing equivalents consumed by the reduction of iron was significantly smaller than that expected from the decrease in the production ...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.me14026
更新日期:2014-01-01 00:00:00
abstract::We established artificial consortia of bacteria inoculated from soil and a green alga, Chlorella vulgaris NIES-227. The bacteria and the alga were mixed in a tube or partitioned in a dialysing culture vessel, and the bacterial composition was examined after cultivation. The community of bacteria formed in the consorti...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.me09177
更新日期:2010-01-01 00:00:00
abstract::We examined the colonization rate and communities of arbuscular mycorrhizal fungi (AMF) in the roots of Pyrus pyrifolia var. culta (Japanese pear) in orchards to investigate the effect of phosphorus (P) fertilization on AMF. Soil cores containing the roots of Japanese pear were collected from 13 orchards in Tottori Pr...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.me12118
更新日期:2013-01-01 00:00:00
abstract::A dissimilatory nitrate reduction to ammonium (DNRA) microbial community was developed under a high organic carbon to nitrate (C/NO3-) ratio in an anoxic semi-continuous sequencing batch reactor (SBR) fed with glucose as the source of carbon and NO3- as the electron acceptor. Activated sludge collected from a municipa...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.ME17193
更新日期:2018-09-29 00:00:00
abstract::Fusarium oxysporum is an ascomycetous fungus that is well-known as a soilborne plant pathogen. In addition, a large population of nonpathogenic F. oxysporum (NPF) inhabits various environmental niches, including the phytosphere. To obtain an insight into the origin of plant pathogenic F. oxysporum, we focused on the t...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.me13184
更新日期:2014-01-01 00:00:00
abstract::The biological flux and lifetime of methanol in anoxic marine sediments are largely unknown. We herein reported, for the first time, quantitative methanol removal rates in subsurface sediments. Anaerobic incubation experiments with radiotracers showed high rates of microbial methanol consumption. Notably, methanol oxi...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.ME15204
更新日期:2016-06-25 00:00:00
abstract::The emergence of drug-resistant bacteria is a severe problem in aquaculture. The ability of drug resistance genes to transfer from a bacterial cell to another is thought to be responsible for the wide dissemination of these genes in the aquaculture environment; however, little is known about the gene transfer mechanis...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.me11338
更新日期:2012-01-01 00:00:00
abstract::N-Acylhomoserine lactones (AHLs) are used as quorum-sensing signaling molecules by many Gram-negative bacteria. Here, 413 bacterial strains were obtained from the roots of potato plants and screened for AHL-degrading bacteria using Chromobacterium violaceum reporter strains. Sixty one isolates degraded N-hexanoyl-L-ho...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.me10207
更新日期:2011-01-01 00:00:00
abstract::To clarify altitudinal changes in the bacterial community on Gulkana Glacier in Alaska, we analyzed bacterial 16S rRNA gene by low-cycle PCR amplification, denaturing gradient gel electrophoresis (DGGE), and culturing in a snowmelt medium at 4°C. Low-cycle PCR-based cloning revealed the presence of 100 bacterial OTUs;...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.me10119
更新日期:2010-01-01 00:00:00
abstract::Microbes interact with each other in multicellular communities and this interaction enables certain microorganisms to survive in various environments. Pseudomonas aeruginosa is a highly adaptable bacterium that ubiquitously inhabits diverse environments including soil, marine habitats, plants and animals. Behind this ...
journal_title:Microbes and environments
pub_type: 杂志文章,评审
doi:10.1264/jsme2.me12167
更新日期:2013-01-01 00:00:00
abstract::A cellular approach combining Direct Viable Counting and Fluorescent In Situ Hybridization using a one-step multiple-probe technique and Solid Phase Cytometry (DVC-FISH-SPC) was developed to monitor total viable vibrios and cover the detection of a large diversity of vibrios. FISH combined three probes in the same ass...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.ME17028
更新日期:2017-09-27 00:00:00
abstract::Diarrhea is often associated with marked alterations in the intestinal microbiota, termed dysbiosis; however, limited information is currently available on the intestinal microbiota in captive golden snub-nosed monkeys (Rhinopithecus roxellana) with diarrhea. We herein characterized the fecal microbiota in diarrhea an...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.ME17163
更新日期:2018-09-29 00:00:00
abstract::The aim of the study was to survey cultivable heterotrophic bacteria from sea ice samples collected from Peter the Great Bay of the Sea of Japan, and to test the isolates for antagonistic activity. A total of 195 strains were isolated and investigated by a phenotypic approach. The 16S rRNA gene sequence analysis of th...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.23.209
更新日期:2008-01-01 00:00:00
abstract::Termites depend nutritionally on their gut microbes, and protistan, bacterial, and archaeal gut communities have been extensively studied. However, limited information is available on viruses in the termite gut. We herein report the complete genome sequence (99,517 bp) of a phage obtained during a genome analysis of "...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.ME16175
更新日期:2017-06-24 00:00:00
abstract::Terrestrial hydrocarbon seeps are an important source of naturally emitted methane over geological time. The exact community compositions responsible for carbon cycling beneath these surface features remain obscure. As sulfate reduction represents an essential process for anoxic organic mineralization, this study coll...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.ME14086
更新日期:2014-01-01 00:00:00
abstract::The mining industry generates huge amounts of wastewater, containing toxic heavy metals. Treatment to remove heavy metals is necessary and recent work has been focused on finding more environmentally friendly materials for removing heavy metals from wastewater. Biosorption can be an effective process for heavy metal r...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.me11331
更新日期:2012-01-01 00:00:00
abstract::This study aimed to characterize soil fungal communities in upland rice fields managed with tillage/non-tillage and winter cover-cropping (hairy vetch and cereal rye) practices, using PCR-based molecular methods. The study plots were maintained as upland fields for 5 years and the soils sampled in the second and fifth...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.me10108
更新日期:2010-01-01 00:00:00
abstract::Four hundred and fifty nine isolates of fluorescent pseudomonads were obtained from the leaves and roots of potato plants. Of these, 20 leaf isolates and 28 root isolates induced violacein production in two N-acylhomoserine lactone (AHL)-reporter strains-Chromobacterium violaceum CV026 and VIR24. VIR24 is a new report...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.me09155
更新日期:2009-01-01 00:00:00
abstract::Diazotrophs had not previously been identified among bacterial species in the phylum Bacteroidetes until the rapid expansion of bacterial genome sequences, which revealed the presence of nitrogen fixation (nif) genes in this phylum. We herein determined the draft genome sequences of Bacteroides graminisolvens JCM 1509...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.ME14142
更新日期:2015-01-01 00:00:00
abstract::Trichophyton ajelloi is a geophilic dermatophyte that specializes in the decomposition of native keratin. It exists in soil with a permanent influx of keratin matter. In the present study, two PCR-based methods were used for the identification and intra-species differentiation of T. ajelloi strains isolated from 3 typ...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.me13160
更新日期:2014-01-01 00:00:00
abstract::Marine fungus-like eukaryotic unicellular protists (thraustochytrids) are considered to play an important role in the marine microbial food web. However, their abundance, distribution, and relative biomass in coastal waters have not yet been examined in detail. By using a flow cytometry method (FCM) for the rapid enum...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.ME17162
更新日期:2018-07-04 00:00:00
abstract::Ultra-small microorganisms are ubiquitous in Earth's environments. Ultramicrobacteria, which are defined as having a cell volume of <0.1 μm3, are often numerically dominant in aqueous environments. Cultivated representatives among these bacteria, such as members of the marine SAR11 clade (e.g., "Candidatus Pelagibacte...
journal_title:Microbes and environments
pub_type: 杂志文章,评审
doi:10.1264/jsme2.ME20025
更新日期:2020-01-01 00:00:00
abstract::Giant viruses of 'Megaviridae' have the ability to widely disperse around the globe. We herein examined 'Megaviridae' communities in four distinct aquatic environments (coastal and offshore seawater, brackish water, and hot spring freshwater), which are distantly located from each other (between 74 and 1,765 km), usin...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.ME19037
更新日期:2019-09-25 00:00:00
abstract::Oligosaline lakes in arid regions provide indispensable water resources for humans; however, information on the bacterial community composition (BCC) of this ecosystem is limited. In the present study, we explored seasonal and vertical variations in BCC in Lake Bosten, a unique oligosaline lake (1.2‰ salinity) in arid...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.ME14177
更新日期:2015-01-01 00:00:00
abstract::Due to their obligate symbiotic nature and lack of long-term storage methods, the strain collection of arbuscular mycorrhizal (AM) fungi requires periodic proliferation using a pot culture with host plants. Therefore, a method to evaluate the purity of proliferated AM fungal cultures is critical for the quality contro...
journal_title:Microbes and environments
pub_type: 杂志文章
doi:10.1264/jsme2.ME19074
更新日期:2019-12-27 00:00:00