Journal of Microbiology

Journal Article

Prevalence and characteristics of the mcr-1 gene in retail meat samples in Zhejiang Province, China: Biao Tang , Jiang Chang , Yi Luo , Han Jiang , Canying Liu , Xingning Xiao , Xiaofeng Ji , Hua Yang; J. Microbiol. 2022;60(6):610-619. Published online March 31, 2022; DOI: https://doi.org/10.1007/s12275-022-1597-y

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Abstract: Considering the serious threat to food safety and public health posed by pathogens with colistin resistance, colistin was banned as a growth promoter in 2017 in China. In recent years, the resistance rate of Escherichia coli isolated from animal intestines or feces to colistin has decreased. However, the prevalence and characteristics of the mcr-1 gene in retail meat have not been well explored. Herein, 106 mcr-1-negative and 16 mcr- 1-positive E. coli isolates were randomly recovered from 120 retail meat samples and screened using colistin. The 106 E. coli isolates showed maximum resistance to sulfafurazole (73.58%) and tetracycline (62.26%) but susceptibility to colistin (0.00%). All 16 mcr-1-positive E. coli isolates showed resistance to colistin, were extended spectrum beta-lactamase (ESBL)-positive and exhibited complex multidrug resistance (MDR). For these 16 isolates, 17 plasmid replicons and 42 antibiotic resistance genes were identified, and at least 7 antibiotic resistance genes were found in each isolate. Acquired disinfectant resistance genes were identified in 75.00% (12/16) of the isolates. Furthermore, comparative genomic and phylogenetic analysis
results
indicated that these 16 mcr-1-positive E. coli isolates and the most prevalent mcr-1-harboring IncI2 plasmid in this study were closely related to other previously reported mcr-1-positive E. coli isolates and the IncI2 plasmid, respectively, showing their wide distribution. Taken together, our findings showed that retail meat products were a crucial reservoir of mcr-1 during the colistin ban period and should be continuously monitored.

Research Support, Non-U.S. Gov'ts

Uncultured bacterial diversity in a seawater recirculating aquaculture system revealed by 16S rRNA gene amplicon sequencing: Da-Eun Lee , Jinhwan Lee , Young-Mog Kim , Jeong-In Myeong , Kyoung-Ho Kim; J. Microbiol. 2016;54(4):296-304. Published online April 1, 2016; DOI: https://doi.org/10.1007/s12275-016-5571-4

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Abstract: Bacterial diversity in a seawater recirculating aquaculture system (RAS) was investigated using 16S rRNA amplicon sequencing to understand the roles of bacterial communities in the system. The RAS was operated at nine different combinations of temperature (15°C, 20°C, and 25°C) and salinity (20‰, 25‰, and 32.5‰). Samples were collected from five or six RAS tanks (biofilters) for each condition. Fifty samples were analyzed. Proteobacteria and Bacteroidetes were most common (sum of both phyla: 67.2% to 99.4%) and were inversely proportional to each other. Bacteria that were present at an average of ≥ 1% included Actinobacteria (2.9%) Planctomycetes (2.0%), Nitrospirae (1.5%), and Acidobacteria (1.0%); they were preferentially present in packed bed biofilters, mesh biofilters, and maturation biofilters. The three biofilters showed higher diversity than other RAS tanks (aerated biofilters, floating bed biofilters, and fish tanks) from phylum to operational taxonomic unit (OTU) level. Samples were clustered into several groups based on the bacterial communities. Major taxonomic groups related to family Rhodobacteraceae and Flavobacteriaceae were distributed widely in the samples. Several taxonomic groups like [Saprospiraceae], Cytophagaceae, Octadecabacter, and Marivita showed a cluster-oriented distribution. Phaeobacter and Sediminicola-related reads were detected frequently and abundantly at low temperature. Nitrifying bacteria were detected frequently and abundantly in the three biofilters. Phylogenetic analysis of the nitrifying bacteria showed several similar OTUs were observed widely through the biofilters. The diverse bacterial communities and the minor taxonomic groups, except for Proteobacteria and Bacteroidetes, seemed to play important roles and seemed necessary for nitrifying activity in the RAS, especially in packed bed biofilters, mesh biofilters, and maturation biofilters.

Pyrosequencing reveals bacterial diversity in Korean traditional wheat-based nuruk: Jyotiranjan Bal , Suk-Hyun Yun , Myoung-Suk Choi , Soo-Hwan Yeo , Jung-Mi Kim , Dae-Hyuk Kim; J. Microbiol. 2015;53(12):812-819. Published online December 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5516-3

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16 Citations

Abstract: The emerging global importance of Korea’s alcoholic beverages emphasizes the need for quality enhancement of nuruk, a traditional Korean cereal starter that is used extensively in traditional brewing. Apart from fungi and yeasts, bacteria known to be ubiquitously present are also a part of the nuruk ecosystem and are known to influence fermentation activity by influencing fermentation favorable factors. In the current study, bacterial diversity and temporal variations in the traditional wheat-based nuruk, fermented at two representative temperature conditions for 30 days, along with two commercial wheat-based nuruk samples for comparison analysis were evaluated using libraries of PCR amplicons and 454 pyrosequencing targeting of the hypervariable regions V1 to V3 of the 16S rRNA gene. A total of 90,836 16S reads were analyzed and assigned to a total of 314, 321, and 141 Operational Taxonomic Units (OTUs) for nuruk A, B, and C, respectively. Diversity parameters clearly indicated nuruk B to be more diverse in terms of bacterial composition than nuruk A. Taxonomic assignments indicated that nuruk A was dominated by phylum Cyanobacteria, whereas nuruk B was dominated by phylum Actinobacteria. For both nuruk A and B, members of the phylum Firmicutes mostly converged into the family Bacillaceae; these microorganisms might be present in negligible numbers at the beginning but became significant as the fermentation progressed. The commercial samples were predominated by phylum Firmicutes, which is composed of Lactobacillaceae and Leoconostocaceae. The findings of this study provide new insights into understanding the changes in bacterial community structure during traditional nuruk starter production.

Characterization of bacterial diversity associated with deep sea ferromanganese nodules from the South China Sea: De-Chao Zhang , Yan-Xia Liu , Xin-Zheng Li; J. Microbiol. 2015;53(9):598-605. Published online August 27, 2015; DOI: https://doi.org/10.1007/s12275-015-5217-y

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Abstract: Deep sea ferromanganese (FeMn) nodules contain metallic mineral resources and have great economic potential. In this study, a combination of culture-dependent and culture-independent (16S rRNA genes clone library and pyrosequencing)
methods
was used to investigate the bacterial diversity in FeMn nodules from Jiaolong Seamount, the South China Sea. Eleven bacterial strains including some moderate thermophiles were isolated. The majority of strains belonged to the phylum Proteobacteria; one isolate belonged to the phylum Firmicutes. A total of 259 near full-length bacterial 16S rRNA gene sequences in a clone library and 67,079 valid reads obtained using pyrosequencing indicated that members of the Gammaproteobacteria dominated, with the most abundant bacterial genera being Pseudomonas and Alteromonas. Sequence analysis indicated the presence of many organisms whose closest relatives are known manganese oxidizers, iron reducers, hydrogen-oxidizing bacteria and methylotrophs. This is the first reported investigation of bacterial diversity associated with deep sea FeMn nodules from the South China Sea.

Effect of Long-Term Different Fertilization on Bacterial Community Structures and Diversity in Citrus Orchard Soil of Volcanic Ash: Jae Ho Joa , Hang Yeon Weon , Hae Nam Hyun , Young Chull Jeun , Sang Wook Koh; J. Microbiol. 2014;52(12):995-1001. Published online November 29, 2014; DOI: https://doi.org/10.1007/s12275-014-4129-6

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32 Citations

Abstract: This study was conducted to assess bacterial species richness, diversity and community distribution according to different fertilization regimes for 16 years in citrus orchard soil of volcanic ash. Soil samples were collected and analyzed from Compost (cattle manure, 2,000 kg/10a), 1/2 NPK+compost (14-20-14+2,000 kg/10a), NPK+compost (28-40-28+2,000 kg/10a), NPK (28-40-28 kg/10a), 3 NPK (84-120-84 kg/10a), and Control (no fertilization) plot which have been managed in the same manners with compost and different amount of chemical fertilization. The range of pyrosequencing reads and OTUs were 4,687–7,330 and 1,790–3,695, respectively. Species richness estimates such as Ace, Chao1, and Shannon index were higher in 1/2 NPK+compost than other treatments, which were 15,202, 9,112, 7.7, respectively. Dominant bacterial groups at level of phylum were Proteobacteria, Acidobacteria, and Actinobacteria. Those were occupied at 70.9% in 1/2 NPK+compost. Dominant bacterial groups at level of genus were Pseudolabrys, Bradyrhizobium, and Acidobacteria. Those were distributed at 14.4% of a total of bacteria in Compost. Soil pH displayed significantly closely related to bacterial species richness estimates such as Ace, Chao1 (p<0.05) and Shannon index (p<0.01). However, it showed the negative correlation with exchangeable aluminum contents (p<0.05). In conclusion, diversity of bacterial community in citrus orchard soil was affected by fertilization management, soil pH changes and characteristics of volcanic ash.

Analysis of Bacterial Diversity in Sponges Collected from Chuuk and Kosrae Islands in Micronesia: In-Hye Jeong , Kyoung-Ho Kim , Hyi-Seung Lee , Jin-Sook Park; J. Microbiol. 2014;52(1):20-26. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3619-x

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Abstract: The bacteria resident in sponges collected from Chuuk Lagoon and Kosrae Island of Micronesia were investigated using the 16S rRNA gene PCR-tagged pyrosequencing method. These sponges were clustered into 5 groups based on their bacterial composition. Diversity indexes and cumulative rank abundance curves showed the different compositions of bacterial communities in the various groups of sponges. Reads related to the phylum Chloroflexi were observed predominantly (9.7–68.2%) in 9 sponges of 3 groups and unobserved in the other 2 groups. The Chloroflexi-containing group had similar bacterial patterns at the phylum and lower taxonomic levels, for example, significant proportions of Acidobacteria, Gemmatimonadetes, SBR1093, and PAUC34f were observed in most members of this group. The three groups in the Chloroflexi- containing group, however, showed some minor differences in the composition and diversity. The other two groups contained high proportions of Proteobacteria (>87%) or Bacteroidetes (>61%) and different composition and diversity compared to the Chloroflexi-containing group and each other. Four pairs of specimens with the same species showed similar bacterial profiles, but, the bacteria in sponges were highly specific at the individual level.

Analysis of Bacterial Diversity in Sponges Collected off Chujado, an Island in Korea, Using Barcoded 454 Pyrosequencing: Analysis of a Distinctive Sponge Group Containing Chloroflexi: In-Hye Jeong , Kyoung-Ho Kim , Jin-Sook Park; J. Microbiol. 2013;51(5):570-577. Published online October 31, 2013; DOI: https://doi.org/10.1007/s12275-013-3426-9

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Abstract: The bacterial diversity of 14 sponges belonging to 5 different orders that were collected around Chuja Island, Korea was investigated using barcoded 454 pyrosequencing. The sponges contained many unidentified bacterial groups (e.g. more than half of the taxa at the family level) that were known only in environmental sequences and obtained from culture-independent methods. Five of the sponges were clustered into one notable group (CF group), which was distinguished from the other sponges in accordance with bacterial composition (the other sponges may be separated into more groups but clustering is not clear). The CF group contained high amounts of Chloroflexi (25.0–47.7%) and moderate amounts of Gemmatimonadetes (2.3–7.0%), AncK6 (0.6–2.2%), PAUC34f (0.8–6.0%), Acidobacteria (3.7–9.6%), and SBR1093 (1.8–5.6%) exclusively or almost exclusively to this group. Sponges in the CF group also showed higher diversity (e.g. Shannon index) than the other sponges and contained group-specific taxonomic lineages (e.g. class or family level) from group-specific phyla and even from the Proteobacteria and Actinobacteria, which were detected in all sponges at the phylum level. The CF group may be one of the most distinctive groups in sponges in terms of bacterial diversity.

Bacterial Diversity and Composition of an Alkaline Uranium Mine Tailings-Water Interface: Nurul H. Khan , Viorica F. Bondici , Prabhakara G. Medihala , John R. Lawrence , Gideon M. Wolfaardt , Jeff Warner , Darren R. Korber; J. Microbiol. 2013;51(5):558-569. Published online September 14, 2013; DOI: https://doi.org/10.1007/s12275-013-3075-z

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Abstract: The microbial diversity and biogeochemical potential associated with a northern Saskatchewan uranium mine watertailings interface was examined using culture-dependent and -independent techniques. Morphologically-distinct colonies from uranium mine water-tailings and a reference lake (MC) obtained using selective and non-selective media were selected for 16S rRNA gene sequencing and identification, revealing that culturable organisms from the uranium tailings interface were dominated by Firmicutes and Betaproteobacteria; whereas, MC organisms mainly consisted of Bacteroidetes and Gammaproteobacteria. Ion Torrent (IT) 16S rRNA metagenomic analysis carried out on extracted DNA from tailings and MC interfaces demonstrated the dominance of Firmicutes in both of the systems. Overall, the tailings-water interface environment harbored a distinct bacterial community relative to the MC, reflective of the ambient conditions (i.e., total dissolved solids, pH, salinity, conductivity, heavy metals) dominating the uranium tailings system. Significant correlations among the physicochemical data and the major bacterial groups present in the tailings and MC were also observed. Presence of sulfate reducing bacteria demonstrated by culture-dependent analyses and the dominance of Desulfosporosinus spp. indicated by Ion Torrent analyses within the tailings-water interface suggests the existence of anaerobic microenvironments along with the potential for reductive metabolic processes.

Cultured Bacterial Diversity and Human Impact on Alpine Glacier Cryoconite: Yung Mi Lee , So-Yeon Kim , Jia Jung , Eun Hye Kim , Kyeung Hee Cho , Franz Schinner , Rosa Margesin , Soon Gyu Hong , Hong Kum Lee; J. Microbiol. 2011;49(3):355-362. Published online June 30, 2011; DOI: https://doi.org/10.1007/s12275-011-0232-0

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27 Citations

Abstract: The anthropogenic effect on the microbial communities in alpine glacier cryoconites was investigated by cultivation and physiological characterization of bacteria from six cryoconite samples taken at sites with different amounts of human impact. Two hundred and forty seven bacterial isolates were included in Actinobacteria (9%, particularly Arthrobacter), Bacteroidetes (14%, particularly Olleya), Firmicutes (0.8%), Alphaproteobacteria (2%), Betaproteobacteria (16%, particularly Janthinobacterium), and Gammaproteobacteria (59%, particularly Pseudomonas). Among them, isolates of Arthrobacter were detected only in samples from sites with no human impact, while isolates affiliated with Enterobacteriaceae were detected only in samples from sites with strong human impact. Bacterial isolates included in Actinobacteria and Bacteroidetes were frequently isolated from pristine sites and showed low maximum growth temperature and enzyme secretion. Bacterial isolates included in Gammaproteobacteria were more frequently isolated from sites with stronger human impact and showed high maximum growth temperature and enzyme secretion. Ecotypic differences were not evident among isolates of Janthinobacterium lividum, Pseudomonas fluorescens, and Pseudomonas veronii, which were frequently isolated from sites with different degrees of anthropogenic effect.

Bacterial Diversity in the Sediment from Polymetallic Nodule Fields of the Clarion-Clipperton Fracture Zone: Chun-Sheng Wang , Li Liao , Hong-Xiang Xu , Xue-Wei Xu , Min Wu , Li-Zhong Zhu; J. Microbiol. 2010;48(5):573-585. Published online November 3, 2010; DOI: https://doi.org/10.1007/s12275-010-0151-5

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Abstract: The Clarion-Clipperton Fracture Zone (CCFZ) is located in the northeastern equatorial Pacific and contains abundant polymetallic nodules. To investigate its bacterial diversity, four libraries of 16S rRNA genes were constructed from sediments of four stations in different areas of the CCFZ. In total, 313 clones sequenced from the 4 libraries were assigned into 14 phylogenetic groups and 1 group of 28 unclassified bacteria. High bacterial diversity was predicted by the rarefaction analysis. The most dominant group overall was Proteobacteria, but there was variation in each library: Gammaproteobacteria was the most dominant group in two libraries, E2005-01 and ES0502, while Alphaproteobacteria and Deltaproteobacteria were the most dominant groups in libraries EP2005-03 and WS0505, respectively. Seven groups, including Alphaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Betaproteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes, were common to all four libraries. The remaining minor groups were distributed in libraries with different patterns. Most clones sequenced in this study were clustered with uncultured bacteria obtained from the environment, such as the ocean crust and marine sediment, but only distantly related to isolates. Bacteria involved in the cycling of metals, sulfur and nitrogen were detected, and their relationship with their habitat was discussed. This study sheds light on the bacterial communities associated with polymetallic nodules in the CCFZ and provides primary data on the bacterial diversity of this area.

Microbial Community Response to a Simulated Hydrocarbon Spill in Mangrove Sediments: Rodrigo Gouvêa Taketani , Natália Oliveira Franco , Alexandre Soares Rosado , Jan Dirk van Elsas; J. Microbiol. 2010;48(1):7-15. Published online March 11, 2010; DOI: https://doi.org/10.1007/s12275-009-0147-1

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Abstract: In this study, we examined the hypothesis that the microbial communities in mangrove sediments with different chemical and historical characteristics respond differently to the disturbance of a hydrocarbon spill. Two different mangrove sediments were sampled, one close to an oil refinery that had suffered a recent oil spill and another that had not been in contact with oil. Based on the sampled sediment, two sets of mesocosms were built, and oil was added to one of them. They were subjected to mimicked mangrove conditions and monitored for 75 days. Archaeal and bacterial communities were evaluated through PCRDGGE. Both communities showed the emergence of small numbers of novel bands in response to oil pollution. 16S rRNA gene clone libraries were constructed from both mesocosms before the addition of oil and at day 75 after oil addition. LIBSHUFF analysis showed that both mangrove-based mesocosms contained similar communities at the start of the experiment and that they were different from the initial one, as well as from each other, after 75 days. These results hint at a role of environmental history that is not obvious from community diversity indicators, but is apparent from the response to the applied stress.

Bacterial Diversity at Different Depths in Lead-Zinc Mine Tailings as Revealed by 16S rRNA Gene Libraries: Han-Bo Zhang , Wen Shi , Ming-Xia Yang , Tao Sha , Zhi-Wei Zhao; J. Microbiol. 2007;45(6):479-484.; DOI: https://doi.org/2648 [pii]

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Abstract: Bacterial communities at 10 cm, 100 cm, and 200 cm depths in a 100-year-old lead-zinc tailing heap were evaluated by constructing 16S rRNA gene libraries. In total, 98 operational taxonomic units (OTUs) were identified from 193 clones at a 3% sequence difference level. The OTU number and species richness decreased with the depth. Species composition was significantly different between the three libraries. Fifty-seven percent of the examined clones were Acidobacteria and 27% belonged to Proteobacteria. Other sequences included Chloroflexi, Firmicutes, Chlamydiae, Actinobacteria, Gemmatimonadetes, Nitrospira, and three unclassified OTUs. Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria were mainly distributed in the rhizosphere of naturally colonizing plants; however, Deltaproteobacteria, Acidobacteria, and Chloroflexi tended to inhabit the deeper tailings (below the 100 cm-depth).

Bacterial Diversity in the Human Saliva from Different Ages: Jung-Gyu Kang , Seong Hwan Kim , Tae-Young Ahn; J. Microbiol. 2006;44(5):572-576.; DOI: https://doi.org/2438 [pii]

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Abstract: To obtain primary idea on oral bacterium species that are generally present in periodotally healthy Koreans, the oral bacterial flora in the saliva of four periodontally healthy Koreans at different ages (5, 32, 35, 65) was investigated in this study. For this investigation, 16SrRNA gene clone libraries were generated from the saliva of the four healthy Koreans, and 50 clones were randomly selected from each saliva clone library and sequenced. Totally, 37 different kinds of bacterial 16S rRNA gene sequences were identified based on sequence homology search through GenBank database. The 37 kinds of saliva clone sequences were classified to 14 genera and 2 uncultured and 1 unidentified bacteria. Among the 14 identified genera, Streptococcus, Prevotella, and Veillonella were common genera, and Streptococcus was dominant genus that accounted for 7 different species. Among the seven Streptococcus species, S. salivarius appeared as the most common species. More numbers of species belonging to the genera Streptococcus and Prevotella was present in saliva from ages 32 and 35. While saliva from ages 5 and 65 showed more numbers of species belonging to the genera Rothia, including potential pathogenic species. Overall, saliva of a young child and a senior showed higher bacterial diversity than that of young adults.

The Diversity of Culturable Organotrophic Bacteria from Local Solar Salterns: Sun-Hee Yeon , Won-Jin Jeong , Jin-Sook Park; J. Microbiol. 2005;43(1):1-10.; DOI: https://doi.org/2146 [pii]

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Abstract: We isolated and cultured bacteria inhabiting solar saltern ponds in Taean-Gun, Chungnam Province, Korea. All of the isolated 64 strains were found to be moderately halophilic bacteria, growing in a salt range of 2-20 %, with an optimal concentration of 5% salt. Bacterial diversity among the isolated halophiles was evaluated via RFLP analyses of PCR-amplified 16S rDNAs, followed by phylogenetic analysis of the partial 16S rDNA sequences. The combination of restriction enzyme digestions with HaeIII, CfoI, MspI and RsaI generated 54 distinct patterns. A neighbor-joining tree of the partial 16S rDNA sequences resulted in the division of the 64 strains into 2 major groups, 45 strains of [gammar]-Proteobacteria (70.3%) and 19 strains of Firmicutes (29.7%). The [alpha]-Proteobacteria and Cytophaga-Flavobacterium-Bacterioides groups, which were repeatedly found to exist in thalassohaline environments, were not represented in our isolates. The [gammar]-Proteobacteria group consisted of several subgroups of the Vibrionaceae (37.5%), Pseudoalteromonadaceae (10.9%), Halomonadaceae (7.8%), Alteromonadaceae (7.8%), and Idiomarinaceae (6.3%). Members of Salinivibrio costicola (29.7%) were the most predominant species among all of the isolates, followed by Halobacillus treperi (12.5%). Additionally, three new species candidates were found, based on similarities of the 16S rDNA sequences to those of previously published species.

Genetic and Phenotypic Diversity of (R/S)-Mecoprop [2-(2-Methyl-4-Chlorophenoxy)Propionic Acid]-Degrading Bacteria Isolated fromSoils: Jong-Sung Lim , Mee-Kum Jung , Mi-Soon Kim , Jae-Hyung Ahn , Jong-Ok Ka; J. Microbiol. 2004;42(2):87-93.; DOI: https://doi.org/2040 [pii]

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Abstract: Twelve mecoprop-degrading bacteria were isolated from soil samples, and their genetic and phenotypic characteristics were investigated. Analysis of 16S rDNA sequences indicated that the isolates were related to members of the genus Sphingomonas. Ten different chromosomal DNA patterns were obtained by polymerase-chain-reaction (PCR) amplification of repetitive extragenic palindromic (REP) sequences from the 12 isolates. The isolates were found to be able to utilize the chiral herbicide mecoprop as a sole source of carbon and energy. While seven of the isolates were able to degrade both (R)- and (S)-mecoprop, four isolates exhibited enantioselective degradation of the (S)-type and one isolate could degrade only the (R)-enantiomer. All of the isolates were observed to possess plasmid DNAs. When certain plasmids were removed from isolates MP11, MP15, and MP23, those strains could no longer degrade mecoprop. This compelling result suggests that plasmid DNAs, in this case, conferred the ability to degrade the herbicide. The isolates MP13, MP15, and MP24 were identified as the same strain; however, they exhibited different plasmid profiles. This indicates that these isolates acquired different mecoprop-degradative plasmids in different soils through natural gene transfer.

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