• Journal of Microbiology and Biotechnology
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• v.33 no.6
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• pp.715-723
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• 2023

Microbial biofilms are resilient, immune-evasive, often antibiotic-resistant health challenges, and increasingly the target for research into novel therapeutic strategies. We evaluated the effects of a nutraceutical enzyme and botanical blend (NEBB) on established biofilm. Five microbial strains with known implications in chronic human illnesses were tested: Candida albicans, Staphylococcus aureus, Staphylococcus simulans (coagulase-negative, penicillin-resistant), Borrelia burgdorferi, and Pseudomonas aeruginosa. The strains were allowed to form biofilm in vitro. Biofilm cultures were treated with NEBB containing enzymes targeted at lipids, proteins, and sugars, also containing the mucolytic compound N-acetyl cysteine, along with antimicrobial extracts from cranberry, berberine, rosemary, and peppermint. The post-treatment biofilm mass was evaluated by crystal-violet staining, and metabolic activity was measured using the MTT assay. Average biofilm mass and metabolic activity for NEBB-treated biofilms were compared to the average of untreated control cultures. Treatment of established biofilm with NEBB resulted in biofilm-disruption, involving significant reductions in biofilm mass and metabolic activity for Candida and both Staphylococcus species. For B. burgdorferi, we observed reduced biofilm mass, but the remaining residual biofilm showed a mild increase in metabolic activity, suggesting a shift from metabolically quiescent, treatment-resistant persister forms of B. burgdorferi to a more active form, potentially more recognizable by the host immune system. For P. aeruginosa, low doses of NEBB significantly reduced biofilm mass and metabolic activity while higher doses of NEBB increased biofilm mass and metabolic activity. The results suggest that targeted nutraceutical support may help disrupt biofilm communities, offering new facets for integrative combinational treatment strategies.

• Journal of Microbiology and Biotechnology
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• v.33 no.11
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• pp.1495-1505
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• 2023

The western honeybee Apis mellifera L., a vital crop pollinator and producer of honey and royal jelly, faces numerous threats including diseases, chemicals, and mite infestations, causing widespread concern. While extensive research has explored the link between gut microbiota and their hosts. However, the impact of Varroa destructor infestation remains understudied. In this study, we employed massive parallel amplicon sequencing assays to examine the diversity and structure of gut microbial communities in adult bee groups, comparing healthy (NG) and Varroa-infested (VG) samples. Additionally, we analyzed Varroa-infested hives to assess the whole body of larvae. Our results indicated a notable prevalence of the genus Bombella in larvae and the genera Gillamella, unidentified Lactobacillaceae, and Snodgrassella in adult bees. However, no statistically significant difference was observed between NG and VG. Furthermore, our PICRUSt analysis demonstrated distinct KEGG classification patterns between larval and adult bee groups, with larvae displaying a higher abundance of genes involved in cofactor and vitamin production. Notably, despite the complex nature of the honeybee bacterial community, methanogens were found to be present in low abundance in the honeybee microbiota.

• Journal of Microbiology and Biotechnology
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• v.34 no.6
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• pp.1260-1269
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• 2024

The gastrointestinal (GI) tract of shrimp, which is comprised of the stomach, hepatopancreas, and intestine, houses microbial communities that play crucial roles in immune defense, nutrient absorption, and overall health. While the intestine's microbiome has been well-studied, there has been limited research investigating the stomach and hepatopancreas. The present study addresses this gap by profiling the bacterial community in these interconnected GI segments of Pacific whiteleg shrimp. To this end, shrimp samples were collected from a local aquaculture farm in South Korea, and 16S rRNA gene amplicon sequencing was performed. The results revealed significant variations in bacterial diversity and composition among GI segments. The stomach and hepatopancreas exhibited higher Proteobacteria abundance, while the intestine showed a more diverse microbiome, including Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Chloroflexi, and Verrucomicrobia. Genera such as Oceaniovalibus, Streptococcus, Actibacter, Ilumatobacter, and Litorilinea dominated the intestine, while Salinarimonas, Sphingomonas, and Oceaniovalibus prevailed in the stomach and hepatopancreas. It is particularly notable that Salinarimonas, which is associated with nitrate reduction and pollutant degradation, was prominent in the hepatopancreas. Overall, this study provides insights into the microbial ecology of the Pacific whiteleg shrimp's GI tract, thus enhancing our understanding of shrimp health with the aim of supporting sustainable aquaculture practices.

• Korean Journal of Soil Science and Fertilizer
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• v.43 no.2
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• pp.180-187
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• 2010

The study was performed to investigate the property of rhizosphere microorganisms, and community structure during GMO, and Non-GMO rice cultivation. In the dilution plate technique, there were no significant differences in microbial populations of rhizosplane with genetically modified, and non-genetically modified rice cultivation, and rhizosphere were also the same results. Dominant bacterial genera were Afipia 12.5%, Spingomonas 10.0%, Ramlibacter 10.0%, Mycobacterium 7.5%, and Tetrasphaera 7.5% in rhizosphere soil of genetically modified rice plant, while Afipia 7.3%, Spingomonas 12.2%, Ramlibacter 7.3%, Mycobacterium 17.1%, Tetrasphaera 14.6% in non-genetically modified cultivated at Suwon test fields in 2006. Majorgenera isolated from root surface cultivated in Yesan fields were Arthrobacter 12.7% in rhizoplane of genetically modified plant, and Burkholderia 22.2% of non-genetically modified plant in 2007, Paucimonas 26.6% of genetically modified plant, Chryseobacterium 15.4% of non-genetically modified plant in 2008. Also the microbial communities in rhizosphere soils of genetically modified, and non-genetically modified plants were characterized using phospholipid fatty acid, and denaturing gradient gel electrophoresis. The phospholipid fatty acid profiles of soils in this condition showed different pattern, but did not show significant differences between soils cultivated with genetically or non-genetically modified rice plants.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.4
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• pp.543-549
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• 2007

Two experiments were conducted to investigate the effects of disodium fumarate on the in vitro rumen fermentation profiles of different substrates and microbial communities. In experiment 1, nine diets (high-forage diet (forage:concentrate, e.g. F:C = 7:3, DM basis), medium-forage diet (F:C = 5:5, DM basis), low-forage diet(F:C = 1:9, DM basis), cracked corn, cracked wheat, soluble starch, tall elata (Festuca elata), perennial ryegrass and rice straw) were fermented in vitro by rumen microorganisms from local goats. The results showed that during 24 h incubations, for all substrates, disodium fumarate increased (p<0.05) the gas production, and tended to increase (p<0.10) the acetate, propionate and total VFA concentration and decrease the ratio of acetate to propionate, whereas no treatment effect was observed for the lactate concentration. The apparent DM loss for tall elata, perennial ryegrass and rice straw increased (p<0.05) with the addition of disodium fumarate. With the exception of tall elata, perennial ryegrass and rice straw, disodium fumarate addition increased the final pH (p<0.05) for all substrates. In experiment 2, three substrates (a high-forage diet, a medium-forage diet and a high concentrate diet) were fermented by mixed rumen microbes in vitro. A polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) technique was applied to compare microbial DNA fingerprints between substrates at the end of 24 h incubation. The results showed that when Festuca elata was used as substrate, the control and disodium fumarate treatments had similar DGGE profiles, with their similarities higher than 96%. As the ratio of concentrate increased, however, the similarities in DGGE profiles decreased between the control and disodium fumarate treatment. Overall, these results suggest that disodium fumarate is effective in increasing the pH and gas production for the diets differing in forage: concentrate ratio, grain cereals and soluble starch, and in increasing dry matter loss for the forages (tall elata, perennial ryegrass and rice straw) in vitro, whereas its effect on changes of ruminal microbial community may largely depend on the general nature of the substrate.

• Korean Journal of Environmental Agriculture
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• v.39 no.1
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• pp.65-74
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• 2020

BACKGROUND: Soil carbon sequestration has been investigated for a long time because of its potential to mitigate the greenhouse effect. No- or reduced tillage, crop rotations, or cover crops have been investigated and practiced to sequester carbon in soils but the roles of soil biota, particularly microorganisms, have been mostly ignored although they affect the amount and stability of soil organic matters. METHODS AND RESULTS: In this study we analyzed the organic matter and microbial community in organically cultivated corn field soils where no-tillage (NT) or conventional tillage (CT) had been practiced for about three years. The amounts of organic matter and recalcitrant carbon pool were 18.3 g/kg dry soil and 4.1 g C/kg dry soil, respectively in NT soils, while they were 12.4 and 2.5, respectively in CT soils. The amounts of RNA and DNA, and the copy numbers of bacterial 16S rRNA genes and fungal ITS sequences were higher in NT soils than in CT soils. No-tillage treatment increased the diversities of soil bacterial and fungal communities and clearly shifted the bacterial and fungal community structures. In NT soils the relative abundances of bacterial phyla known as copiotrophs, Betaproteobacteria and Bacteroidetes, increased while those known as oligotrophs, Acidobacteria and Verrucomicrobia, decreased compared to CT soils. The relative abundance of a fungal phylum, Glomeromycota, whose members are known as arbuscular mycorrhizal fungi, was about two time higher in NT soils than in CT soils, suggesting that the higher amount of organic matter in NT soils is related to its abundance. CONCLUSION: This study shows that no-tillage treatment greatly affects soil microbial abundance and community structure, which may affect the amount and stability of soil organic matter.

• Microbiology and Biotechnology Letters
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• v.38 no.4
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• pp.448-454
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• 2010

This study investigated the effect of PCE and TCE as electron acceptors on the bacterial composition of dechlorinating communities. The enrichment cultures reductively dechlorinating PCE and TCE were developed from three environment samples using acetate as electron donor. The cultures were prepared by sequential enrichment, which was seeded with sediment and dredged soil. Denatured gradient gel electrophresis (DGGE) of 16S rRNA gene fragment was used to compare the microbial communities of these three enrichment cultures. After incubation for 4 weeks, the removal efficiencies of PCE and TCE were highest from Yeocheon site (87.37% and 84.46%, respectively). PCE and TCE as electron acceptors affected the bacterial diversity and community profiles in the enrichment cultures. DGGE analysis showed that the dominant bacteria in PCE and TCE enrichment were belonged to Clostridium sp., Desulfotomaculum sp., and uncultured bacteria.

• Korean Journal of Ecology and Environment
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• v.51 no.4
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• pp.299-310
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• 2018

Odor compounds (geosmin, 2-MIB) have been causing problems in the Bukhan River system, but the causative organisms have not been clearly identified. To evaluate the relationship between dynamics of microbial community and odor compounds, two times monthly monitoring of water quality and microbial community from the three serial lakes (Lake Uiam, Lake Cheongpyeong and Lake Paldang) in the Bukhan River system were conducted from April to October 2017. The odor compounds were analyzed by HS-SPME analysis method using GC/MS. Bacteria communities were identified at the class level by NGS analysis. Actinobacteria and Betaproteobacteria were dominant taxon in bacteria community of three serial lakes. In the case of phytoplankton communities showed that seasonal changes by Bacillariophyceae and Cryptophyceae in spring, Cyanobacteria in summer, and Bacillariophyceae and Cryptophyceae in autumn. Dominant species was Dolichospermum (=Anabaena), Microcystis and Pseudanabaena in Bukhan River system in all study period. At the same time the odors geosmin and 2-MIB were also detected at high concentration. There is a significant positive correlation between proportion of Actinobaceria and 2-MIB concentration (r=0.491, p<0.01). In addition, proportion of cyanobacteria showed a significant correlation of geosmin (r=0.381, p<0.05) and 2-MIB (r=0.386, p<0.05) concentration. In this study, odor compounds in the Bukhan River system are considered to be a direct relationship between with Actinobacteria and cyanobacteria.

• Journal of Microbiology and Biotechnology
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• v.31 no.5
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• pp.686-695
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• 2021

Tricholoma matsutake is an ectomycorrhizal fungus that has a symbiotic relationship with the root of Pinus densiflora. Soil microbial communities greatly affect the growth of T. matsutake, however, few studies have examined the characteristics of these communities. In the present study, we analyzed soil fungal communities from Gyeongju and Yeongdeok using metagenomic pyrosequencing to investigate differences in fungal species diversity, richness, and taxonomic composition between the soil under T. matsutake fruiting bodies (Sample 2) and soil where the fairy ring of T. matsutake was no longer present (Sample 1). The same spot was investigated three times at intervals of four months to observe changes in the community. In the samples from Yeongdeok, the number of valid reads was lower than that at Gyeongju. The operational taxonomic units of most Sample 2 groups were less than those of Sample 1 groups, indicating that fungal diversity was low in the T. matsutake-dominant soil. The soil under the T. matsutake fruiting bodies was dominated by more than 51% T. matsutake. From fall to the following spring, the ratio of T. matsutake decreased. Basidiomycota was the dominant phylum in most samples. G-F1-2, G-F2-2, and Y-F1-2 had the genera Tricholoma, Umbelopsis, Oidiodendron, Sagenomella, Cladophialophora, and Phialocephala in common. G-F1-1, G-F2-1, and Y-F1-1 had 10 genera including Umbelopsis and Sagenomella in common. From fall to the following spring, the amount of phyla Basidiomycota and Mucoromycota gradually decreased but that of phylum Ascomycota increased. We suggest that the genus Umbelopsis is positively related to T. matsutake.

• Journal of Microbiology and Biotechnology
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• v.32 no.10
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• pp.1292-1298
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• 2022

Soil autotrophic bacterial communities play a significant role in the soil carbon (C) cycle in paddy fields, but little is known about how rhizosphere soil microorganisms respond to different long-term (35 years) fertilization practices under double rice cropping ecosystems in southern China. Here, we investigated the variation characteristics of rhizosphere soil RubisCO gene cbbL in the double rice ecosystems of in southern China where such fertilization practices are used. For this experiment we set up the following fertilizer regime: without any fertilizer input as a control (CK), inorganic fertilizer (MF), straw returning (RF), and organic and inorganic fertilizer (OM). We found that abundances of cbbL, 16S rRNA genes and RubisCO activity in rhizosphere soil with OM, RF and MF treatments were significantly higher than that of CK treatment. The abundances of cbbL and 16S rRNA genes in rhizosphere soil with OM treatment were 5.46 and 3.64 times higher than that of CK treatment, respectively. Rhizosphere soil RubisCO activity with OM and RF treatments increased by 50.56 and 45.22%, compared to CK treatment. Shannon and Chao1 indices for rhizosphere soil cbbL libraries with RF and OM treatments increased by 44.28, 28.56, 29.60, and 23.13% compared to CK treatment. Rhizosphere soil cbbL sequences with MF, RF and OM treatments mainly belonged to Variovorax paradoxus, uncultured proteobacterium, Ralstonia pickettii, Thermononospora curvata, and Azoarcus sp.KH33C. Meanwhile, cbbL-carrying bacterial composition was obviously influenced by soil bulk density, rhizosphere soil dissolved organic C, soil organic C, and microbial biomass C contents. Fertilizer practices were the principal factor influencing rhizosphere soil cbbL-carrying bacterial communities. These results showed that rhizosphere soil autotrophic bacterial communities were significantly changed under conditions of different long-term fertilization practices Therefore, increasing rhizosphere soil autotrophic bacteria community with crop residue and organic manure practices was found to be beneficial for management of double rice ecosystems in southern China.