• Asian-Australasian Journal of Animal Sciences
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• v.30 no.11
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• pp.1515-1528
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• 2017

The gastrointestinal (GI) tract, including the rumen and the other intestinal segments of cattle, harbors a diverse, complex, and dynamic microbiome that drives feed digestion and fermentation in cattle, determining feed efficiency and output of pollutants. This microbiome also plays an important role in affecting host health. Research has been conducted for more than a century to understand the microbiome and its relationship to feed efficiency and host health. The traditional cultivation-based research elucidated some of the major metabolism, but studies using molecular biology techniques conducted from late 1980's to the late early 2000's greatly expanded our view of the diversity of the rumen and intestinal microbiome of cattle. Recently, metagenomics has been the primary technology to characterize the GI microbiome and its relationship with host nutrition and health. This review addresses the main methods/techniques in current use, the knowledge gained, and some of the challenges that remain. Most of the primers used in quantitative real-time polymerase chain reaction quantification and diversity analysis using metagenomics of ruminal bacteria, archaea, fungi, and protozoa were also compiled.

• Biomedical Science Letters
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• v.24 no.4
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• pp.292-304
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• 2018

Microbes is becoming increasingly forensic possibility as a consequence of advances in massive parallel sequencing (MPS) and bioinformatics. Human DNA typing is the best identifier, but it is not always possible to extract a full DNA profile namely its degradation and low copy number, and it may have limitations for identical twins. To overcome these unsatisfactory limitations, forensic potential for bacteria found in evidence could be used to differentiate individuals. Prokaryotic cells have a cell wall that better protects the bacterial nucleoid compared to the cell membrane of eukaryotic cells. Humans have an extremely diverse microbiome that may prove useful in determining human identity and may even be possible to link the microbes to the person responsible for them. Microbial composition within the human microbiome varies across individuals. Therefore, MPS of human microbiome could be used to identify biological samples from the different individuals, specifically for twins and other cases where standard DNA typing doses not provide satisfactory results due to degradation of human DNA. Microbial forensics is a new discipline combining forensic science and microbiology, which can not to replace current STR analysis methods used for human identification but to be complementary. Among the fields of microbial forensics, this paper will briefly describe information on the current status of microbiome research such as metagenomic code, salivary microbiome, pubic hair microbiome, microbes as indicators of body fluids, soils microbes as forensic indicator, and review microbial forensics as the feasibility of microbiome-based human identification.

• Journal of Species Research
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• v.10 no.1
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• pp.46-56
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• 2021

Diatoms have been used in examining water quality and environmental change in freshwater systems. Here, we analyzed molecular profiling of seasonal diatoms in the Han River, Korea, using the hypervariable region of 18S V1-V3 rRNA and pyrosequencing. Physicochemical data, such as temperature, DO, pH, and nutrients showed the typical seasonal pattern in a temperate region. In addition, cell counts and chlorophyll-a, were recorded at high levels in spring compared to other seasons, due to the diatom bloom. Metagenomic analysis showed a seasonal variation in the phytoplankton community composition, with diatoms as the most frequently detected in spring (83.8%) and winter (69.7%). Overall, diatom genera such as Stephanodiscus, Navicula, Cyclotella, and Discostella were the most frequent in the samples. However, a large number of unknown Thalassiosirales diatoms were found in spring (35.5%) and winter (36.3%). Our molecular profiling revealed a high number of diatom taxa compared to morphological observation. This is the first study of diatoms in the Han River using molecular approaches, providing a valuable reference for future study on diatoms-basis environmental molecular monitoring and ecology.

• Journal of Korean Dental Science
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• v.16 no.1
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• pp.35-46
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• 2023

Purpose: Culture-based methods for microbiological diagnosis and antibiotic susceptibility tests have limitations in the management of orofacial infections. We aimed to profile pus microbiota and identify antibiotic resistance genes (ARGs) using a culture-independent approach. Materials and Methods: Genomic DNA samples extracted from the pus specimens of two patients with orofacial abscesses were subjected to shotgun sequencing on the NovaSeq system. Taxonomic profiling and prediction of ARGs were performed directly from the metagenomic raw reads. Result: Taxonomic profiling revealed obligate anaerobic polymicrobial communities associated with infections of odontogenic origins: the microbial community of Patient 1 consisted of one predominant species (Prevotella oris 74.6%) with 27 minor species, while the sample from Patient 2 contained 3 abundant species (Porphyromonas endodontalis 33.0%; P. oris 31.6%; and Prevotella koreensis 13.4%) with five minor species. A total of 150 and 136 putative ARGs were predicted in the metagenome of each pus sample. The coverage of most predicted ARGs was less than 10%, and only the CfxA2 gene identified in Patient 1 was covered 100%. ARG analysis of the seven assembled genome/metagenome datasets of P. oris revealed that strain C735 carried the CfxA2 gene. Conclusion: A metagenomics-based approach is useful to profile predominantly anaerobic polymicrobial communities but needs further verification for reliable ARG detection.

• Journal of Animal Science and Technology
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• v.64 no.6
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• pp.1144-1172
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• 2022

Salmonella enterica serovar Typhimurium isolate HJL777 is a virulent bacterial strain in pigs. The high rate of salmonella infection are at high risk of non-typhoidal salmonella gastroenteritis development. Salmonellosis is most common in young pigs. We investigated changes in gut microbiota and biological function in piglets infected with salmonella via analysis of rectal fecal metagenome and intestinal transcriptome using 16S rRNA and RNA sequencing. We identified a decrease in Bacteroides and increase in harmful bacteria such as Spirochaetes and Proteobacteria by microbial community analysis. We predicted that reduction of Bacteroides by salmonella infection causes proliferation of salmonella and harmful bacteria that can cause an intestinal inflammatory response. Functional profiling of microbial communities in piglets with salmonella infection showed increasing lipid metabolism associated with proliferation of harmful bacteria and inflammatory responses. Transcriptome analysis identified 31 differentially expressed genes. Using gene ontology and Innate Immune Database analysis, we identified that BGN, DCN, ZFPM2 and BPI genes were involved in extracellular and immune mechanisms, specifically salmonella adhesion to host cells and inflammatory responses during infection. We confirmed alterations in gut microbiota and biological function during salmonella infection in piglets. Our findings will help prevent disease and improve productivity in the swine industry.

• Journal of Microbiology and Biotechnology
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• v.28 no.9
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• pp.1517-1526
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• 2018

Investigating bacterial diversity and its metabolic capabilities is crucial for interpreting the ecological patterns in a desert environment and assessing the presence of exploitable microbial resources. In this study, we evaluated the spatial heterogeneity of physicochemical parameters, soil bacterial diversity and metabolic adaptation at meter scale. Soil samples were collected from two quadrats of a desert (Thar Desert, India) with a hot, arid climate, very little rainfall and extreme temperatures. Analysis of physico-chemical parameters and subsequent variance analysis (p-values < 0.05) revealed that sulfate, potassium and magnesium ions were the most variable between the quadrats. Microbial diversity of the two quadrats was studied using Illumina bar-coded sequencing by targeting V3-V4 regions of 16S rDNA. As for the results, 702504 high-quality sequence reads, assigned to 173 operational taxonomic units (OTUs) at species level, were examined. The most abundant phyla in both quadrats were Actinobacteria (38.72%), Proteobacteria (32.94%), and Acidobacteria (9.24%). At genus level, Gaiella represented highest prevalence, followed by Streptomyces, Solirubrobacter, Aciditerrimonas, Geminicoccus, Geodermatophilus, Microvirga, and Rubrobacter. Between the quadrats, significant difference (p-values < 0.05) was found in the abundance of Aciditerrimonas, Geodermatophilus, Geminicoccus, Ilumatobacter, Marmoricola, Nakamurella, and Solirubrobacter. Metabolic functional mapping revealed diverse biological activities, and was significantly correlated with physicochemical parameters. The results revealed spatial variation of ions, microbial abundance and functional attributes in the studied quadrats, and patchy nature in local scale. Interestingly, abundance of the biotechnologically important phylum Actinobacteria, with large proposition of unclassified species in the desert, suggested that this arid environment is a promising site for bioprospection.

• Journal of Microbiology and Biotechnology
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• v.22 no.3
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• pp.301-310
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• 2012

Prosopis juliflora and Parthenium hysterophorus are the two arid, exotic weeds of India that are characterized by distinct, profuse growth even in nutritionally poor soils and environmentally stressed conditions. Owing to the exceptional growth nature of these two plants, they are believed to harbor some novel bacterial communities with wide adaptability in their rhizosphere. Hence, in the present study, the bacterial communities associated with the rhizosphere of Prosopis and Parthenium were characterized by clonal 16S rRNA gene sequence analysis. The culturable microbial counts in the rhizosphere of these two plants were higher than bulk soils, possibly influenced by the root exudates of these two plants. The phylogenetic analysis of V1_V2 domains of the 16S rRNA gene indicated a wider range of bacterial communities present in the rhizosphere of these two plants than in bulk soils and the predominant genera included Acidobacteria, Gammaproteobacteria, and Bacteriodetes in the rhizosphere of Prosopis, and Acidobacteria, Betaproteobacteria, and Nitrospirae in the Parthenium rhizosphere. The diversity of bacterial communities was more pronounced in the Parthenium rhizosphere than in the Prosopis rhizosphere. This culture-independent bacterial analysis offered extensive possibilities of unraveling novel microbes in the rhizospheres of Prosopis and Parthenium with genes for diverse functions, which could be exploited for nutrient transformation and stress tolerance in cultivated crops.

• The Plant Pathology Journal
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• v.37 no.6
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• pp.619-631
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• 2021

Alfalfa mosaic virus (AMV), an economically important pathogen, is present worldwide with a very wide host range. This work reports for the first time the infection of Vinca minor and Wisteria sinensis with AMV using RNA sequencing and reverse transcription polymerase chain reaction confirmation. De novo assembly and annotating of contigs revealed that RNA1, RNA2, and RNA3 genomic fragments consist of 3,690, 2,636, and 2,057 nucleotides (nt) for IR-VM and 3,690, 2,594, and 2,057 nt for IR-WS. RNA1 and RNA3 segments of IR-VM and IR-WS closely resembled those of the Chinese isolate HZ, with 99.23-99.26% and 98.04-98.09% nt identity, respectively. Their RNA2 resembled that of Canadian isolate CaM and American isolate OH-2-2017, with 97.96-98.07% nt identity. The P2 gene revealed more nucleotide diversity compared with other genes. Genes in the AMV genome were under dominant negative selection during evolution, and the P1 and coat protein (CP) proteins were subject to the strongest and weakest purifying selection, respectively. In the population genetic analysis based on the CP gene sequences, all 107 AMV isolates fell into two main clades (A, B) and isolates of clade A were further divided into three groups with significant subpopulation differentiation. The results indicated moderate genetic variation within and no clear geographic or genetic structure between the studied populations, implying moderate gene flow can play an important role in differentiation and distribution of genetic diversity among populations. Several factors have shaped the genetic structure and diversity of AMV: selection, recombination/reassortment, gene flow, and random processes such as founder effects.

• Journal of Animal Science and Technology
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• v.65 no.4
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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.

• International Journal of Industrial Entomology and Biomaterials
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• v.48 no.1
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• pp.42-47
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• 2024

The value of silkworms as functional health food materials has increased, as has the interest in its disease control for stable production, and in the economic value of entomopathogenic microorganisms. In this study, we isolated and identified disease-causing fungi from white muscardine silkworms, and confirmed whether this strain could produce white muscardine silkworms. For the analysis of the cause of white muscardine disease in the infected silkworms, the fungi and prokaryotes causing the disease were identified, isolated, and identified using metagenome analysis. Metagenomic analysis detected a large amount of the fungus Metarhizium rileyi in silkworms, and a large amount of the bacterium Enterococcus mundtii, which was presumed to be the causative agent of the disease. For accurate identification of the fungi, these were purified by culture medium, and sequencing and phylogenetic tree analyses were performed using an internal transcribed spacer. As a result, M. rileyi, Cladosporium cladosporioides, and C. tenuissimum were identified. In general, M. rileyi is known to form green conidia, but in this study, white-yellow conidia were formed, indicating that the exact causative agent of the fungal disease cannot be estimated by diagnosing the symptoms. Thus, a diagnostic method is necessary for the continuously collection of required pathogens, and identifying their morphological and genetic characteristics.