• Journal of Microbiology and Biotechnology
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• v.20 no.5
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• pp.853-861
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• 2010

High substrate costs decrease the profitability of polyhydroxyalkanoates (PHAs) production, and thus low-cost carbon substrates coming from agricultural and industrial residuals are tested for the production of these biopolymers. Among them, crude glycerol, formed as a by-product during biodiesel production, seems to be the most promising source of carbon. The object of this study was to characterize the mixed population responsible for the conversion of crude glycerol into PHAs by cultivation-dependent and -independent methods. Enrichment of the microbial community was monitored by applying the Ribosomal Intergenic Spacer Analysis (RISA), and the identification of community members was based on 16S rRNA gene sequencing of cultivable species. Molecular analysis revealed that mixed populations consisted of microorganisms affiliated with four bacterial lineages: ${\alpha}$, ${\gamma}$-Proteobacteria, Actinobacteria, and Bacteroides. Among these, three Pseudomonas strains and Rhodobacter sp. possessed genes coding for polyhydroxyalkanoates synthase. Comparative analysis revealed that most of the microorganisms detected by direct molecular analysis were obtained by the traditional culturing method.

• Journal of Microbiology and Biotechnology
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• v.29 no.1
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• pp.91-104
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• 2019

The taxonomic and functional characteristics of bacterial communities in the pre-chlorinated rapid filters and ozonated biological activated carbon (BAC) filters were compared using Illumina MiSeq sequencing of the 16S rRNA gene and community-level physiological profiling (CLPP) based on sole-carbon-source utilization patterns. Both the rapid filters and BAC filters were dominated by Rhizobiales within ${\alpha}-proteobacteria$, but other abundant orders and genera were significantly different in both types of filter. Firmicutes were abundant only in the intermediate chlorinated rapid filter, while Acidobacteria were abundant only in the BAC filters. Bacterial communities in the rapid filter showed high utilization of carbohydrates, while those in the BAC filters showed high utilization of polymers and carboxylic acids. These different characteristics of the bacterial communities could be related to the different substrates in the influents, filling materials, and residual disinfectants. Chlorination and ozonation inactivated the existing bacteria in the influent and formed different bacterial communities, which could be resistant to the oxidants and effectively utilize different substrates produced by the oxidant, including Phreatobacter in the rapid filters and Hyphomicrobium in the BAC filters. Bradyrhizobium and Leptothrix, which could utilize compounds adsorbed on the GAC, were abundant in the BAC filters. Ozonation increased taxonomic diversity but decreased functional diversity of the bacterial communities in the BAC filters. This study provides some new insights into the effects of oxidation processes and filling materials on the bacterial community structure in the biological filters of drinking water treatment plants.

• Journal of Life Science
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• v.34 no.7
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• pp.453-464
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• 2024

The fermentation of ganjang is known to be greatly influenced by the microbial communities derived from its primary ingredients, meju and sea salt. This study investigated the effects of changes in meju size on the distribution and correlation of microbial communities in ganjang fermentation, to enhance its fermentation process. Ganjang was prepared using whole meju and meju divided into thirds, and samples were collected at 7-day intervals over a period of 28 days for microbial community analysis based on 16S rRNA gene sequencing. At the genus level, during fermentation, ganjang made with whole meju exhibited a dominance of Chromohalobacter (day 7), Pediococcus (day 14), Bacillus (day 21), and Pediococcus (day 28), whereas ganjang made with meju divided into thirds consistently showed a Pediococcus predominance over the 28 days. Beta-diversity analysis of microbial communities in ganjang with different meju sizes revealed significant separation of microbial communities at fermentation days 7 and 14 but not at days 21 and 28 across all experimental groups. The linear discriminant analysis effect size (LEfSe) was determined to identify biomarkers contributing to microbial community differences at days 7 and 14, showing that on day 7, potentially halophilic microbes such as Gammaproteobacteria, Firmicutes, Oceanospirillales, Halomonadaceae, Bacilli, and Chromohalobacter were prominent, whereas on day 14, lactic acid bacteria such as Pediococcus acidilactici, Lactobacillaceae, Pediococcus, Bacilli, Leuconostocaceae, and Weissella were predominant. Furthermore, correlation analysis of microbial communities at the genus and species levels revealed differences in correlation patterns between meju sizes, suggesting that meju size may influence microbial interactions within ganjang.

• Journal of Korean Society on Water Environment
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• v.36 no.6
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• pp.581-591
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• 2020

In this study, two types of reactors were operated to examine the properties of methanol uptake under the high-rate denitrification process. In a sequencing batch reactor, the denitrifying activity was enriched up to 0.80 g-N/g-VSS-day for 72 days. Then, the enriched denitrifying sludge was transferred to a completely stirred tank reactor (CSTR). At the final phase on Day 46-50, the nitrogen removal efficiency was around 100% and the total nitrogen removal rate reached 0.097±0.003 kg-N/㎥-day. During the continuous process, the sludge settling index (SVI30) was stabilized as 118.3 mL/g with the biomass concentration of 1,607 mg/L. The continuous denitrifying process was accelerated by using a sequencing batch reactor (SBR) with a total nitrogen removal rate of 0.403±0.029 kg-N/㎥-day with a high biomass concentration of 8,433 mg-VSS/L. Because the reactor was open to ambient air with the dissolved oxygen range of 0.2-0.5 mg-O2/L, an increased organic carbon requirement of 5.58±0.70 COD/NO3--N was shown for the SBR in comparison to the value of 4.13±0.94 for the test of the same biomass in a completely anaerobic batch reactor. The molecular analysis based on the 16S rRNA gene showed that Methyloversatilis discipulorum and Hyphomicrobium zavarzinii were the responsible denitrifiers with the sole organic carbon source of methanol.

• Korean Journal of Microbiology
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• v.50 no.4
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• pp.308-312
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• 2014

In this study, we conducted a next generation sequencing based microbial community analysis to investigate gut microbiota of the two commercially most available swine breeds, Yorkshire and Landrace. Bacterial 16S rRNA gene was amplified from fecal DNA using universal primer sets designed for V4 regions. Our comparison analysis of the gut microbiota of the two breeds suggested that their gut microbiota changed depending on the growth stages, while the difference between the two breeds was insignificant. However, there was a limited number of genera, the abundance of which was found to be different between the breeds. Those included the genus Xylanibacter in the Yorkshire samples, which was previously reported as a fiber digesting bacteria, likely increasing energy harvesting capacity of swine. In addition, others included opportunistic pathogens mostly found in the Yorkshire samples while the Landrace samples had significantly more prevalent Clostridium_IV species that were known to play a key role in systemic immunity of hosts. While microbial community shifts was found to be associated with growth stages, the difference between the two breeds seemed to be insignificant. However, there were several bacterial genera showing differential abundance, which may affect growth of hosts.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.8
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• pp.1233-1241
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• 2020

Objective: The present investigation was aimed to explore the potential of lactobacilli for conjugated linoleic acid (CLA) production, isolated from rumen fluid samples of lactating goats. Methods: A total of 64 isolates of lactobacilli were obtained using deMan-Rogosa-Sharpe (MRS) agar from rumen fluid of goats and further subjected to morphological and biochemical characterizations. Isolates found as gram-positive, catalase negative rods were presumptively identified as Lactobacillus species and further confirmed by genus specific polymerase chain reaction (PCR). The phylogenetic tree was constructed from the nucleotide sequences using MEGA6. Results: Out of the 64 isolates, 23 isolates were observed positive for CLA production by linoleate isomerase gene-based amplification and quantitatively by UV-spectrophotometric assay for the conversion of linoleic acid to CLA as well as gas chromatography-based assay. In all Lactobacillus species cis9, trans11 isomer was observed as the most predominant CLA isomer. These positive isolates were identified by 16S rRNA gene-based PCR sequencing and identified to be different species of L. ingluviei (2), L.salivarius (2), L. curvatus (15), and L. sakei (4). Conclusion: The findings of the present study concluded that lactic acid bacteria isolated from ruminal fluid samples of goat have the potential to produce bioactive CLA and may be applied as a direct fed microbial to enhance the nutraceutical value of animal food products.

• Microbiology and Biotechnology Letters
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• v.43 no.2
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• pp.134-141
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• 2015

An agarolytic marine bacterium (H9) was isolated from the coastal seawater of the West Sea, South Korea. The isolate, H9, was gram-negative and rod-shaped with a smooth surface and polar flagellum. Cells grew at 20-30℃, between pH 5.0 and 9.0, and in ASW-YP (Artificial Sea Water-Yeast extract, Peptone) media containing 1-5% (w/v) NaCl. The G+C content was 41.56 mol%. The predominant isoprenoid quinone in strain H9 was ubiquinone-8. The major fatty acids (>10%) were C_16:1ω7c (34.3%), C_16:0 (23.72%), and C_18:1ω7c (13.64%). Based on 16S rRNA gene sequencing, and biochemical and chemotaxonomic characterization, the strain was designated as Pseudoalteromonas sp. H9 (=KCTC23887). In liquid culture supplemented with 0.2% agar, the cell density and agarase activity reached a maximum level of OD = 4.32 (48 h) and OD = 3.87 (24 h), respectively. The optimum pH and temperature for the extracellular crude agarases of H9 were 7.0 and 40℃, respectively. Thin-layer chromatography analysis of the agarase hydrolysis products revealed that the crude agarases hydrolyze agarose into neoagarotetraose and neoagarohexaose. Therefore, the new agar-degrading strain, H9, can be applicable for the production of valuable neoagarooligosaccharides and for the complete degradation of agar in bio-industries.

• Korean Journal of Microbiology
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• v.52 no.3
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• pp.352-364
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• 2016

In this study, we examined in vitro the potential probiotic properties of lactic acid bacteria (LAB) obtained from the fish intestine and their ability to degrade histamine through the production of diamine oxidase (DAO) enzymes and bacteriocin. Among 97 LAB strains isolated from the intestine of croaker, flatfish, pollack, and rockfish, CIL08, CIL16, FIL20, FIL31, PIL45, PIL49, PIL52, and RIL60 isolates exhibited excellent survival rates under simulated gastrointestinal tract conditions, high adhesion ability to HT-29 epithelial cells, and resistance to the antibiotics such as amoxicillin, ampicillin, erythromycin, penicillin G, streptomycin, tetracycline, or vancomycin. In addition, these strains did not produce histamine in decarboxylating broth containing histidine. In particular, 4 strains (CIL08, FIL20, PIL52, and RIL60) that may produce DAO were significantly able to degrade histamine. The bacteriocins produced by FIL20, FIL31, and PIL52 LAB inhibited the growth and histamine production of Enterococcus aerogenes CIH05, Serratia marcescens CIH09, Enterococcus faecalis FIH11, Pediococcus halophilus FIH15, Lactobacillus sakei PIH16, Enterococcus faecium PIH19, Leuconostoc mesenteroides RIH25, or Aeromonas hydrophilia RIH28. Histamine-producing strains isolated from fish intestine were found to reduce histamine accumulation during co-culture with CIL08, FIL20, PIL52, and RIL60 LAB showing histamine degradation or bacteriocin production ability. The probiotic strains preventing histamine formation were identified as Pediococcus pentosaceus CIL08, Lactobacillus plantarum FIL20, Lactobacillus paracasei FIL31, Lactobacillus sakei PIL52, and Leuconostoc mesenteroides RIL60 with high similarity based on 16S rRNA gene sequencing.

• Journal of Microbiology and Biotechnology
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• v.27 no.5
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• pp.995-1004
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• 2017

Culture-dependent methods, such as heterotrophic plate counting (HPC), are usually applied to evaluate the bacteriological quality of hemodialysis water. However, these methods cannot detect the uncultured or viable but non-culturable (VBNC) bacteria, both of which may be quantitatively predominant throughout the hemodialysis water treatment system. Therefore, propidium monoazide (PMA)-qPCR associated with HPC was used together to profile the distribution of the total viable bacteria in such a system. Moreover, high-throughput sequencing of 16S rRNA gene amplicons was utilized to analyze the microbial community structure and diversity. The HPC results indicated that the total bacterial counts conformed to the standards, yet the bacteria amounts were abruptly enhanced after carbon filter treatment. Nevertheless, the bacterial counts detected by PMA-qPCR, with the highest levels of $2.14{\times}10^7copies/100ml$ in softener water, were much higher than the corresponding HPC results, which demonstrated the occurrence of numerous uncultured or VBNC bacteria among the entire system before reverse osmosis (RO). In addition, the microbial community structure was very different and the diversity was enhanced after the carbon filter. Although the diversity was minimized after RO treatment, pathogens such as Escherichia could still be detected in the RO effluent. In general, both the amounts of bacteria and the complexity of microbial community in the hemodialysis water treatment system revealed by molecular approaches were much higher than by traditional method. These results suggested the higher health risk potential for hemodialysis patients from the up-to-standard water. The treatment process could also be optimized, based on the results of this study.

• Restorative Dentistry and Endodontics
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• v.36 no.6
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• pp.498-505
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• 2011

Objectives: The purpose of this in vivo study was to investigate the microbial diversity in symptomatic and asymptomatic canals with primary endodontic infections by using GS FLX Titanium pyrosequencing. Materials and Methods: Sequencing was performed on 6 teeth (symptomatic, n = 3; asymptomatic, n = 3) with primary endodontic infections. Amplicons from hypervariable region of the small-subunit ribosomal RNA gene were generated by polymerized chain reaction (PCR), and sequenced by means of the GS FLX Titanium pyrosequencing. Results: On average, 10,639 and 45,455 16S rRNA sequences for asymptomatic and symptomatic teeth were obtained, respectively. Based on Ribosomal Database Project Classifier analysis, pyrosequencing identified the 141 bacterial genera in 13 phyla. The vast majority of sequences belonged to one of the seven phyla: Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria, Spirochetes, and Synergistetes. In genus level, Pyramidobacter, Streptococcus, and Leptotrichia constituted about 50% of microbial profile in asymptomatic teeth, whereas Neisseria, Propionibacterium, and Tessaracoccus were frequently found in symptomatic teeth (69%). Grouping the sequences in operational taxonomic units (3%) yielded 450 and 1,997 species level phylotypes in asymptomatic and symptomatic teeth, respectively. The total bacteria counts were significantly higher in symptomatic teeth than that of asymptomatic teeth (p < 0.05). Conclusions: GS FLX Titanium pyrosequencing could reveal a previously unidentified high bacterial diversity in primary endodontic infections.