• The Plant Pathology Journal
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• v.38 no.6
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• pp.583-592
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• 2022

Root-knot nematode disease is a widespread and catastrophic disease of tobacco. However, little is known about the relationship between rhizosphere bacterial community and root-knot nematode disease. This study used 16S rRNA gene sequencing and PICRUSt to assess bacterial community structure and function changes in rhizosphere soil from Meloidogyne incognita-infected tobacco plants. We studied the rhizosphere bacterial community structure of M. incognita-infected and uninfected tobacco plants through a paired comparison design in two regions of tobacco planting area, Yuxi and Jiuxiang of Yunnan Province, southwest China. According to the findings, M. incognita infection can alter the bacterial population in the soil. Uninfested soil has more operational taxonomic unit numbers and richness than infested soil. Principal Coordinate Analysis revealed clear separations between bacterial communities from infested and uninfested soil, indicating that different infection conditions resulted in significantly different bacterial community structures in soils. Firmicutes was prevalent in infested soil, but Chloroflexi and Acidobacteria were prevalent in uninfested soil. Sphingomonas, Streptomyces, and Bradyrhizobium were the dominant bacteria genera, and their abundance were higher in infested soil. By PICRUSt analysis, some metabolism-related functions and signal transduction functions of the rhizosphere bacterial community in the M. incognita infection-tobacco plants had a higher relative abundance than those uninfected. As a result, rhizosphere soils from tobacco plants infected with M. incognita showed considerable bacterial community structure and function alterations.

• Journal of Microbiology and Biotechnology
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• v.26 no.12
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• pp.2141-2147
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• 2016

As one of the most complex human-associated microbial habitats, the oral cavity harbors hundreds of bacteria. Halitosis is a prevalent oral condition that is typically caused by bacteria. The aim of this study was to analyze the microbial communities and predict functional profiles in supragingival plaque from healthy individuals and those with halitosis. Ten preschool children were enrolled in this study; five with halitosis and five without. Supragingival plaque was isolated from each participant and 16S rRNA gene pyrosequencing was used to identify the microbes present. Samples were primarily composed of Actinobacteria, Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, and Candidate phylum TM7. The ${\alpha}$ and ${\beta}$ diversity indices did not differ between healthy and halitosis subjects. Fifteen operational taxonomic units (OTUs) were identified with significantly different relative abundances between healthy and halitosis plaques, and included the phylotypes of Prevotella sp., Leptotrichia sp., Actinomyces sp., Porphyromonas sp., Selenomonas sp., Selenomonas noxia, and Capnocytophaga ochracea. We suggest that these OTUs are candidate halitosis-associated pathogens. Functional profiles were predicted using PICRUSt, and nine level-3 KEGG Orthology groups were significantly different. Hub modules of co-occurrence networks implied that microbes in halitosis dental plaque were more highly conserved than microbes of healthy individuals' plaque. Collectively, our data provide a background for the oral microbiota associated with halitosis from supragingival plaque, and help explain the etiology of halitosis.

• Journal of Microbiology and Biotechnology
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• v.29 no.2
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• pp.292-296
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• 2019

Soils amended for long-term with high levels of compost demonstrated greater abundance of bacterial members of the phylum Bacteroidetes whereas a decreasing trend in the relative abundance of phylum Acidobacteria was noted with increasing levels of compost. Metabolic profiles predicted by PICRUSt demonstrated differences in functional responses of the bacterial community according to the treatments. Soils amended with lower compost levels were characterized by abundance of genes encoding enzymes contributing to membrane transport and cell growth whereas genes encoding enzymes related to protein folding and transcription were enriched in soils amended with high levels of compost. Thus, the results of the current study provide extensive evidence of the influence of different compost levels on bacterial diversity and community structure in paddy soils.

• Journal of Marine Life Science
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• v.8 no.1
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• pp.43-49
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• 2023

This study applied a metagenomic analysis of the penguins' gut microbiome from fecal samples of Adélie Penguin (Pygoscelis adeliae) and Emperor Penguin (Aptenodytes forsteri) living along the Ross Sea, Antarctica. As a result of taxonomic analysis, 7 phyla and 18 families were mainly present in the gut microbiome of Adélie and Emperor penguins. To assess microbial diversity, we performed alpha diversity and OTU abundance analyses. It was confirmed that the Adélie Penguin's gut microbial species had a higher diversity than Emperor Penguin's. Based on the Beta diversity analysis using PCoA, differences were observed in the clustering between Adélie and Emperor penguins, respectively. Through the KEGG pathway analysis using PICRUSt, the nucleoside and nucleotide biosynthesis pathway was the most prevalent in Adélie and Emperor penguins. This study enabled a comparison and analysis of the composition and diversity of the gut microbiome in Adélie and Emperor Penguins. It could be utilized for future research related to penguin feeding habits and could serve as a foundation for analyzing the gut microbiomes of various other Antarctic organisms.

• Journal of Microbiology and Biotechnology
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• v.30 no.9
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• pp.1355-1366
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• 2020

Sediment bacterial communities are critical to the biogeochemical cycle in river ecosystems, but our understanding of the relationship between sediment bacterial communities and their specific input streams in rivers remains insufficient. In this study, we analyzed the sediment bacterial community structure in a local river receiving discharge of urban domestic sewage by applying Illumina MiSeq high-throughput sequencing. The results showed that the bacterial communities of sediments samples of different pollution types had similar dominant phyla, mainly Proteobacteria, Actinobacteria, Chloroflexi and Firmicutes, but their relative abundances were different. Moreover, there were great differences at the genus level. For example, the genus Bacillus showed statistically significant differences in the hotel site. The clustering of bacterial communities at various sites and the dominant families (i.e., Nocardioidaceae, and Sphingomonadaceae) observed in the residential quarter differed from other sites. This result suggested that environmentally induced species sorting greatly influenced the sediment bacterial community composition. The bacterial co-occurrence patterns showed that the river bacteria had a nonrandom modular structure. Microbial taxonomy from the same module had strong ecological links (such as the nitrogenium cycle and degradation of organic pollutants). Additionally, PICRUSt metabolic inference analysis showed the most important function of river bacterial communities under the influence of different types of domestic sewage was metabolism (e.g., genes related to xenobiotic degradation predominated in residential quarter samples). In general, our results emphasize that the adaptive changes and interactions in the bacterial community structure of river sediment represent responses to different exogenous pollution sources.

• Food Science of Animal Resources
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• v.41 no.4
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• pp.701-714
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• 2021

In this study, the microbial community succession and the protein hydrolysis of donkey meat during refrigerated (4℃) storage were investigated. 16S rDNA sequencing method was used to analyze the bacteria community structure and succession in the level of genome. Meanwhile, the volatile base nitrogen (TVB-N) was measured to evaluate the degradation level of protein. After sorting out the sequencing results, 1,274,604 clean data were obtained, which were clustered into 2,064 into operational taxonomic units (OTUs), annotated to 32 phyla and 527 genus. With the prolonging of storage time, the composition of microorganism changed greatly. At the same time, the diversity and richness of microorganism decreased and then increased. During the whole storage period, Proteobacteria was the dominant phyla, and the Photobacterium, Pseudompnas, and Acinetobacter were the dominant genus. According to correlation analysis, it was found that the abundance of these dominant bacteria was significantly positively correlated with the variation of TVB-N. And Pseudomonas might play an important role in the production of TVB-N during refrigerated storage of donkey meat. The predicted metabolic pathways, based on PICRUSt analysis, indicated that amino metabolism in refrigerated donkey meat was the main metabolic pathways. This study provides insight into the process involved in refrigerated donkey meat spoilage, which provides a foundation for the development of antibacterial preservative for donkey meat.

• Journal of Microbiology and Biotechnology
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• v.32 no.12
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• pp.1561-1572
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• 2022

Plastic pollution has been recognized as a serious environmental problem, and microbial degradation of plastics is a potential, environmentally friendly solution to this. Here, we analyzed and compared microbial communities on waste plastic films (WPFs) buried for long periods at four landfill sites with those in nearby soils to identify microbes with the potential to degrade plastics. Fourier-transform infrared spectroscopy spectra of these WPFs showed that most were polyethylene and had signs of oxidation, such as carbon-carbon double bonds, carbon-oxygen single bonds, or hydrogen-oxygen single bonds, but the presence of carbonyl groups was rare. The species richness and diversity of the bacterial and fungal communities on the films were generally lower than those in nearby soils. Principal coordinate analysis of the bacterial and fungal communities showed that their overall structures were determined by their geographical locations; however, the microbial communities on the films were generally different from those in the soils. For the pulled data from the four landfill sites, the relative abundances of Bradyrhizobiaceae, Pseudarthrobacter, Myxococcales, Sphingomonas, and Spartobacteria were higher on films than in soils at the bacterial genus level. At the species level, operational taxonomic units classified as Bradyrhizobiaceae and Pseudarthrobacter in bacteria and Mortierella in fungi were enriched on the films. PICRUSt analysis showed that the predicted functions related to amino acid and carbohydrate metabolism and xenobiotic degradation were more abundant on films than in soils. These results suggest that specific microbial groups were enriched on the WPFs and may be involved in plastic degradation.

• Animal Bioscience
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• v.36 no.1
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• pp.63-74
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• 2023

Objective: The objective of this study was to investigate the effects of feeding active dry yeast (ADY) and yeast culture (YC) on fecal bacterial community in finishing bulls fed high-concentrate diets in the same experimental environment. Methods: Forty-five healthy finishing cattle (Simmental×Chinese Luxi yellow bulls; 24 months; 505±29 kg) were randomly divided into three groups: i) CON group (control group, only fed basal diet), ii) ADY group (fed basal diet + active dry yeast), and iii) YC group (fed basal diet + yeast culture). At the end of the trial, nine rectum fecal samples were randomly selected from each group for bacterial DNA sequencing. Results: There was no difference among groups about alpha diversity indices (all p>0.05), including ACE, Chao 1, Shannon, and Simpson indices. Principal component analysis and non-metric multidimensional scaling analysis showed a high similarity among three groups. Compared with CON group, ADY and YC groups had greater relative abundance of c_Clostridia, o_Oscillospirales, and f_Oscillospiraceae, but lesser relative abundance of g_Megasphaera, and s_Megasphaera_elsdenii (all p<0.01). And, the relative abundances of p_Firmicutes (p = 0.03), s_Prevotella_sp (p = 0.03), o_Clostridiales (p<0.01), g_Clostridium (p<0.01), f_Caloramatoraceae (p<0.01), and f_Ruminococcaceae (p = 0.04) were increased in the ADY group. The PICRUSt2 prediction results showed that the metabolic pathways had no significant differences among groups (p>0.05). Besides, the relative abundance of c_Clostridia (r = 0.42), and f_Oscillospiraceae (r = 0.40) were positively correlated to average daily gain of finishing bulls (p<0.05). Conclusion: Both of ADY and YC had no effect on diversity of fecal bacteria in finishing bulls, but the supplementation of ADY and YC can improve the large intestinal function in finishing bulls by increasing the abundance of cellulolytic bacteria and altering the abundance of lactic acid-utilizing bacteria.

• Journal of Applied Biological Chemistry
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• v.61 no.2
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• pp.165-172
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• 2018

Due to the recent economic development, the diet style has become more and more westernized in Korea, which increased the concern of our well-beings. Our well-beings are also associated with the gut microbiota which vary depending on the dietary intake. In this study, we compared gut microbiome shifted by two diets: high-fat diets (HFD) and low-fiber diet (LFD) based on 16S rRNA gene sequences using MiSeq. Compared to the control diet, LFD and HFD treatments significantly decreased species richness, while there was no difference in species evenness. Both diet treatments significantly increased the relative abundance of the Proteobacteria (p<0.05), especially the genus Sutterella. Bacteroidetes was significantly decreased in HFD groups, where the family S24-7 was decreased most. On the other hand, significant difference between HFD and LFD was seen among Firmicutes, where the abundance of family Lachnospiraceae was lower in LFD groups (p<0.05). PICRUSt-based metabolic difference analyses showed LFD treatment significantly decreased metabolisms of amino acid, carbohydrate and methane (p<0.01). In contrast, HFD significantly increased amino acid metabolism (p<0.05). Glycan biosynthesis and metabolism were significantly increased in both treatment groups (p<0.01). Our results suggest that long-term unbalanced dietary intakes induce gut dysbiosis, leading to metabolic and colonic disorders.

• Journal of Microbiology and Biotechnology
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• v.28 no.11
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• pp.1883-1895
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• 2018

Alcohol dependence is a global public health problem, yet the mechanisms of alcohol dependence are incompletely understood. The traditional view has been that ethanol alters various neurotransmitters and their receptors in the brain and causes the addiction. However, an increasing amount of experimental evidence suggests that gut microbiota also influence brain functions via gut-to-brain interactions, and may therefore induce the development of alcohol use disorders. In this study, a rat model of alcohol dependence and withdrawal was employed, the gut microbiota composition was analyzed by high-throughput 16S rRNA gene sequencing, and the metagenome function was predicted by PICRUSt software. The results suggested that chronic alcohol consumption did not significantly alter the diversity and richness of gut microbiota in the jejunum and colon, but rather markedly changed the microbiota composition structure in the colon. The phyla Bacteroidetes and eight genera including Bacteroidales S24-7, Ruminococcaceae, Parabacteroides, Butyricimonas, et al were drastically increased, however the genus Lactobacillus and gauvreauii in the colon were significantly decreased in the alcohol dependence group compared with the withdrawal and control groups. The microbial functional prediction analysis revealed that the proportions of amino acid metabolism, polyketide sugar unit biosynthesis and peroxisome were significantly increased in the AD group. This study demonstrated that chronic alcohol consumption has a dramatic effect on the microbiota composition structure in the colon but few effects on the jejunum. Inducement of colonic microbiota dysbiosis due to alcohol abuse seems to be a factor of alcohol dependence, which suggests that modulating colonic microbiota composition might be a potentially new target for treating alcohol addiction.