• Animal Bioscience
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• 제36권9호
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• pp.1453-1464
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• 2023

Objective: This study investigated the changes in bacterial communities within decomposing swine microcosms, comparing soil with or without intact microbial communities, and under aerobic and anaerobic conditions. Methods: The experimental microcosms consisted of four conditions: UA, unsterilized soil-aerobic condition; SA, sterilized soil-aerobic condition; UAn, unsterilized soil-anaerobic condition; and San, sterilized soil-anaerobic condition. The microcosms were prepared by mixing 112.5 g of soil and 37.5 g of ground carcass, which were then placed in sterile containers. The carcass-soil mixture was sampled at day 0, 5, 10, 30, and 60 of decomposition, and the bacterial communities that formed during carcass decomposition were assessed using Illumina MiSeq sequencing of the 16S rRNA gene. Results: A total of 1,687 amplicon sequence variants representing 22 phyla and 805 genera were identified in the microcosms. The Chao1 and Shannon diversity indices varied in between microcosms at each period (p<0.05). Metagenomic analysis showed variation in the taxa composition across the burial microcosms during decomposition, with Firmicutes being the dominant phylum, followed by Proteobacteria. At the genus level, Bacillus and Clostridium were the main genera within Firmicutes. Functional prediction revealed that the most abundant Kyoto encyclopedia of genes and genomes metabolic functions were carbohydrate and amino acid metabolisms. Conclusion: This study demonstrated a higher bacteria diversity in UA and UAn microcosms than in SA and SAn microcosms. In addition, the taxonomic composition of the microbial community also exhibited changes, highlighting the impact of soil sterilization and oxygen on carcass decomposition. Furthermore, this study provided insights into the microbial communities associated with decomposing swine carcasses in microcosm.

• 한국미생물·생명공학회지
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• 제51권2호
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• pp.191-202
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• 2023

Elevated serum cholesterol is a main risk factor for heart disorders. Most probiotic products administered to lower cholesterol are dairy products which are not suitable for lactose-intolerant individuals. In this study, we assessed the cholesterol-lowering efficacy of LAB isolated from traditionally fermented drinks in diet-induced rats and determine their efficacy in the production of non-dairy, probiotic formulations using papaya juice. LAB were isolated from palm wine and corn beer on MRS agar using a pour-plate technique. Identification was carried out using 16S rRNA gene sequencing. A hypercholesterolemia model in which diet-induced Wistar albino rats were assigned into four groups was established. Oral gavage was carried out for 30 days. On the 31^st day, the rats were dissected and the serum lipid profile was analyzed using biochemical kits. A 10⁶ cfu/ml of a 24-h-old culture of selected lactobacilli was used to inoculate papaya juice and incubated at 37℃. Microbial and chemical changes were assessed during papaya fermentation and after four weeks of cold storage. Two selected isolates (Pw1 and Cb4) had in vitro cholesterol reduction of > 80%. These two isolates lowered lipid profile (triglyceride, total cholesterol, LDL-c) significantly, and increased HDL-c levels (p < 0.5) in the rat sera. Phylogenetic analysis showed that Pw1 was 98.86% similar to Limosilactobacillus fermentum, while Cb4 was 99.54% similar to Enteroccocus faecium. Both strains fermented papaya juice with cell viability reaching 8.92 × 10⁸ cfu/ml and 25.3 × 10⁸ cfu/ml respectively, and were still viable after 4 weeks of cold storage.

• The Plant Pathology Journal
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• 제39권6호
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• pp.600-613
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• 2023

Fusarium oxysporum is the main pathogen causing Fusarium basal rot in onion (Allium cepa L.), which incurs significant yield losses before and after harvest. Among management strategies, biological control is an environmentally safe and sustainable alternative to chemical control. In this study, we isolated and screened bacteria for antifungal activity against the basal rot pathogen F. oxysporum. Isolates 23-045, 23-046, 23-052, 23-055, and 23-056 significantly inhibited F. oxysporum mycelial growth and conidial germination. Isolates 23-045, 23-046, 23-052, and 23-056 suppressed the development of Fusarium basal rot in both onion seedlings and bulbs in pot and spray inoculation assays. Isolate 23-055 was effective in onion seedlings but exhibited weak inhibitory effect on onion bulbs. Based on analyses of the 16S rRNA and rpoB gene sequences together with morphological analysis, isolates 23-045, 23-046, 23-052, and 23-055 were identified as Bacillus thuringiensis, and isolate 23-056 as Bacillus toyonensis. All five bacterial isolates exhibited cellulolytic, proteolytic, and phosphate-solubilizing activity, which may contribute to their antagonistic activity against onion basal rot disease. Taken together B. thuringiensis 23-045, 23-046, 23-052, and 23-055 and B. toyonensis 23-056 have potential for the biological control of Fusarium basal rot in onion.

• 한국지하수토양환경학회지:지하수토양환경
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• 제28권5호
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• pp.12-24
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• 2023

The Songji lagoon is brackish environment with a mixture of saline and fresh water, and the interaction of groundwater-lagoon water creates a physicochemical gradient. Although some studies have been conducted on the hydrological and geochemical characteristics of the Songji lagoon, microbial ecological studies have not yet been conducted. In this study, we investigated the effect of groundwater and surface water interaction on water quality as well as microbial community changes in the Songji Lagoon using 16S rRNA gene sequencing. Hydrochemical analyses show that samples were classified as 5 hydrochemical facies (HF) and hydrochemical facies evolution (HFE) revealed the intrusion phase was more dominant (57.9%) than the freshening phase (42.1%). Higher microbial diversity was found in freshwater in comparison to saline water samples. The microbial community at the phylum level shows the most dominance of Proteobacteria with an average of 37.3%, followed by Bacteroidota, Actinobacteria, and Patescibacteria. Heat map analyses of the top 18 genera showed that samples were clustered into 5 groups based on type, and Pseudoalteromonas could be used potential indicator for seawater intrusion.

• Journal of Animal Science and Technology
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• 제65권4호
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• pp.856-864
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• 2023

There are a variety of microorganisms in the animal intestine, and it has been known that they play important roles in the host such as suppression of potentially pathogenic microorganisms, modulation of the gut immunity. In addition, the gut microbiota and the livestock growth performance have long been known to be related. Therefore, we evaluated the interrelation between the growth performance and the gut microbiome of the pigs from 3 different farms, with pigs of varied ages ready to be supplied to the market. When pigs reached average market weight of 118 kg, the average age of pigs in three different farms were < 180 days, about 190 days, and > 200 days, respectively. Fecal samples were collected from pigs of age of 70 days, 100 days, 130 days, and 160 days. The output data of the 16S rRNA gene sequencing by the Illumina Miseq platform was filtered and analyzed using Quantitative Insights into Microbial Ecology (QIIME)2, and the statistical analysis was performed using Statistical Analysis of Metagenomic Profiles (STAMP). The results of this study showed that the gut microbial communities shifted as pigs aged along with significant difference in the relative abundance of different phyla and genera in different age groups of pigs from each farm. Even though, there was no statistical differences among groups in terms of Chao1, the number of observed operational taxonomic units (OTUs), and the Shannon index, our results showed higher abundances of Bifidobacterium, Clostridium and Lactobacillus in the feces of pigs with rapid growth rate. These results will help us to elucidate important gut microbiota that can affect the growth performance of pigs.

• Animal Bioscience
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• 제37권2호
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• pp.240-252
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• 2024

Objective: The aim of this study was to investigate the impact of dietary nicotinic acid (NA) on apparent nutrient digestibility, rumen fermentation, and rumen microbiota in uncastrated Xiangzhong black cattle. Methods: Twenty-one uncastrated Xiangzhong black cattle (385.08±15.20 kg) aged 1.5 years were randomly assigned to the control group (CL, 0 mg/kg NA in concentrate diet), NA1 group (800 mg/kg NA in concentrate diet) and NA2 group (1,200 mg/kg NA in concentrate diet). All animals were fed a 60% concentrate diet and 40% dried rice straw for a 120-day feeding experiment. Results: Supplemental NA not only enhanced the apparent nutrient digestibility of acid detergent fiber (p<0.01), but also elevated the rumen acetate and total volatile fatty acid concentrations (p<0.05). 16S rRNA gene sequencing analysis of rumen microbiota revealed that dietary NA changed the diversity of rumen microbiota (p<0.05) and the abundance of bacterial taxa in the rumen. The relative abundances of eight Erysipelotrichales taxa, five Ruminococcaceae taxa, and five Sphaerochaetales taxa were decreased by dietary NA (p<0.05). However, the relative abundances of two taxa belonging to Roseburia faecis were increased by supplemental 800 mg/kg NA, and the abundances of seven Prevotella taxa, three Paraprevotellaceae taxa, three Bifidobacteriaceae taxa, and two operational taxonomic units annotated to Fibrobacter succinogenes were increased by 1,200 mg/kg NA in diets. Furthermore, the correlation analysis found significant correlations between the concentrations of volatile fatty acids in the rumen and the abundances of bacterial taxa, especially Prevotella. Conclusion: The results from this study suggest that dietary NA plays an important role in regulating apparent digestibility of acid detergent fiber, acetate, total volatile fatty acid concentrations, and the composition of rumen microbiota.

• Journal of Microbiology and Biotechnology
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• 제33권11호
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• pp.1428-1436
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• 2023

The three Gram-negative, catalase- and oxidase-positive bacterial strains RS43^T, HBC28, and HBC61^T, were isolated from fresh water and subjected to a polyphasic study. Comparison of 16S rRNA gene sequence initially indicated that strains RS43^T, HBC28, and HBC61^T were closely related to species of genus Curvibacter and shared the highest sequence similarity of 98.14%, 98.21%, and 98.76%, respectively, with Curvibacter gracilis 7-1^T. Phylogenetic analysis based on genome sequences placed all strains within the genus Curvibacter. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the three strains and related type strains supported their recognition as two novel genospecies in the genus Curvibacter. Comparative genomic analysis revealed that the genus possessed an open pangenome. Based on KEGG BlastKOALA analyses, Curvibacter species have the potential to metabolize benzoate, phenylacetate, catechol, and salicylate, indicating their potential use in the elimination of these compounds from the water systems. The results of polyphasic characterization indicated that strain RS43^T and HBC61^T represent two novel species, for which the name Curvibacter microcysteis sp. nov. (type strain RS43^T =KCTC 92793^T=LMG 32714^T) and Curvibacter cyanobacteriorum sp. nov. (type strain HBC61^T =KCTC 92794^T=LMG 32713^T) are proposed.

• 한국미생물·생명공학회지
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• 제51권4호
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• pp.403-415
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• 2023

This study aimed to isolate and identify L-(+)-lactic acid-producing bacteria from tree barks collected in Thailand and evaluate the potential strain as probiotics. Twelve strains were isolated and characterized phenotypically and genotypically. The strains exhibited a rod-shaped morphology, high-temperature tolerance, and the ability to ferment different sugars into lactic acid. Based on 16S rRNA gene analysis, all strains were identified as belonging to Weizmannia coagulans. Among the isolated strains, BKMTCR2-2 demonstrated exceptional lactic acid production, with 96.41% optical purity, 2.33 g/l of lactic acid production, 1.44 g/g of lactic acid yield (per gram of glucose consumption), and 0.0049 g/l/h of lactic acid productivity. This strain also displayed a wide range of pH tolerance, suggesting suitability for the human gastrointestinal tract and potential probiotic applications. The whole-genome sequence of BKMTCR2-2 was assembled using a hybridization approach that combined long and short reads. The genomic analysis confirmed its identification as W. coagulans and safety assessments revealed its non-pathogenic attribute compared to type strains and commercial probiotic strains. Furthermore, this strain exhibited resilience to acidic and bile conditions, along with the presence of potential probiotic-related genes and metabolic capabilities. These findings suggest that BKMTCR2-2 holds promise as a safe and effective probiotic strain with significant lactic acid production capabilities.

• Journal of Animal Science and Technology
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• 제66권2호
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• pp.340-352
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• 2024

This study measured the potential changes of the microbiota in the gastrointestinal tract and energy and nutrient digestibility by supplemental bacteriophages in pigs. Twelve castrated male pigs (initial mean body weight = 29.5 ± 2.3 kg) were surgically cannulated using T-cannula. The animals were housed individually in pens equipped with a feeder and a nipple waterer. The pigs were allotted to 1 of 3 experimental diets in a quadruplicated 3 × 2 Latin square design with 3 experimental diets, 2 periods, and 12 pigs resulting in 8 replicates per diet. The 3 diets were a control mainly based on corn and soybean meal with no antibiotics or bacteriophages, a diet containing 0.1% antibiotics, and a diet containing 0.2% bacteriophages. On day 5 of the experimental period, feces were collected and on days 6 and 7, ileal digesta were collected. Genomic DNA for bacteria were extracted from the ileal digesta and feces and the V4 region of the 16S rRNA gene was amplified. The ileal and fecal digestibility of energy, dry matter, organic matter, crude protein, and fiber was unaffected by dietary antibiotics or bacteriophages. At the phylum level, the supplemental antibiotic or bacteriophage tended to result in a higher proportion of Firmicutes (p = 0.059) and a lower proportion of Bacteroidetes (p = 0.099) in the ileal digesta samples compared with the control group with no difference between the antibiotic and bacteriophage groups. At the genus level, the supplemental antibiotic or bacteriophage tended to result in a higher proportion of Lactobacillus (p = 0.062) and a lower proportion of Bacteroides (p = 0.074) and Streptococcus (p = 0.088) in the ileal digesta compared with the control group with no difference between the antibiotic and bacteriophage groups. In the feces, supplemental antibiotics or bacteriophages reduced the proportion of Bifidobacterium compared with the control group (p = 0.029) with no difference between the antibiotic and bacteriophage groups. Overall, supplemental antibiotics and bacteriophages showed positive effect on the microbiota of in the ileal digesta without largely affecting energy or nutrient digestibility, with no differences between the antibiotic and bacteriophage groups in growing pigs.

• The Plant Pathology Journal
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• 제40권4호
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• pp.346-357
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• 2024

This study was carried out to screen the antifungal activity against Colletotrichum acutatum, Colletotrichum dematium, and Colletotrichum coccodes. Bacterial isolate GP-P8 from pepper soil was found to be effective against the tested pathogens with an average inhibition rate of 70.7% in in vitro dual culture assays. 16S rRNA gene sequencing analysis result showed that the effective bacterial isolate as Bacillus siamensis. Biochemical characterization of GP-P8 was also performed. According to the results, protease and cellulose, siderophore production, phosphate solubilization, starch hydrolysis, and indole-3-acetic acid production were shown by the GP-P8. Using specific primers, genes involved in the production of antibiotics, such as iturin, fengycin, difficidin, bacilysin, bacillibactin, surfactin, macrolactin, and bacillaene were also detected in B. siamensis GP-P8. Identification and analysis of volatile organic compounds through solid phase microextraction/gas chromatography-mass spectrometry (SPME/GC-MS) revealed that acetoin and 2,3-butanediol were produced by isolate GP-P8. In vivo tests showed that GP-P8 significantly reduced the anthracnose disease caused by C. acutatum, and enhanced the growth of pepper plant. Reverse transcription polymerase chain reaction analysis of pepper fruits revealed that GP-P8 treated pepper plants showed increased expression of immune genes such as CaPR1, CaPR4, CaNPR1, CaMAPK4, CaJA2, and CaERF53. These results strongly suggest that GP-P8 could be a promising biocontrol agent against pepper anthracnose disease and possibly a pepper plant growth-promoting agent.