• Microbiology and Biotechnology Letters
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• v.44 no.2
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• pp.171-179
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• 2016

Recent succession of soil microorganisms and vegetation has occurred in the glacier foreland, because of glacier thawing. In this study, whole microbial communities, including bacteria, archaea, and eukaryotes, from the glacier foreland of Midtre Lovénbreen in Svalbard were analyzed by metagenome sequencing, using the Ion Torrent Personal Genome Machine (PGM) platform. Soil samples were collected from two research sites (ML4 and ML7), with different exposure times, from the ice. A total of 2,798,108 and 1,691,859 reads were utilized for microbial community analysis based on the metagenomic sequences of ML4 and ML7, respectively. The relative abundance of microbial communities at the domain level showed a high proportion of bacteria (about 86−87%), whereas archaeal and eukaryotic communities were poorly represented by less than 1%. The remaining 12% of the sequences were found to be unclassified. Predominant bacterial groups included Proteobacteria (40.3% from ML4 and 43.3% from ML7) and Actinobacteria (22.9% and 24.9%). Major groups of Archaea included Euryarchaeota (84.4% and 81.1%), followed by Crenarchaeota (10.6% and 13.1%). In the case of eukaryotes, both ML4 and ML7 samples showed Ascomycota (33.8% and 45.0%) as the major group. These findings suggest that metagenome analysis using the Ion Torrent PGM platform could be suitably applied to analyze whole microbial community structures, providing a basis for assessing the relative importance of predominant groups of bacterial, archaeal, and eukaryotic microbial communities in the Arctic glacier foreland of Midtre Lovénbreen, with high resolution.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.21 no.7
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• pp.312-320
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• 2020

The objective of the study was to undertake a phylogenetic diversity census of ruminal archaea based on a meta-analysis of 16S rRNA gene sequences that were publicly available in the Ribosomal Database Project. A total of 8,416 sequences were retrieved from the Ribosomal Database Project (release 11, update 5) and included in the construction of a taxonomy tree. Species-level operational taxonomic units (OTUs) were analyzed at a 97% sequence similarity by using the QIIME program. Of the 8,416 sequences, 8,412 were classified into one of three phyla; however, the remaining four sequences could not be classified into a known phylum. The Euryarchaeota phylum was predominant and accounted for 99.8% of the archaeal sequences examined. Among the Euryarchaeota, 65.4% were assigned to Methanobrevibacter, followed by Methanosphaera (10.4%), Methanomassillicoccus (10.4%), Methanomicrobium (7.9%), Methanobacterium (1.9%), Methanimicrococcus (0.5%), Methanosarcina (0.1%), and Methanoculleus (0.1%). The 7,544 sequences that had been trimmed to the V2 and V3 regions clustered into 493 OTUs. Only 17 of those 493 OTUs were dominant groups and accounted for more than 1% of the 7,544 sequences. These results can help guide future research into the dominant ruminal methanogens that significantly contribute to methane emissions from ruminants, research that may lead to the development of anti-methanogenic compounds that inhibit these methanogens regardless of diet or animal species.

• Korean Journal of Microbiology
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• v.48 no.2
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• pp.125-133
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• 2012

Anaerobic digestion is an alternative method to digest food wastes and to produce methane that can be used as a renewable energy source. We investigated bacterial and archaeal community structures in a three-stage methane production process using food wastes with concomitant wastewater treatment. The three-stage methane process is composed of semianaerobic hydrolysis/acidogenic, anaerobic acidogenic, and strictly anaerobic methane production steps in which food wastes are converted methane and carbon dioxide. The microbial diversity was determined by the nucleotide sequences of 16S rRNA gene library and quantitative real-time PCR. The major eubacterial population of the three-stage methane process was belonging to VFA-oxidizing bacteria. The archaeal community consisted mainly of two species of hydrogenotrophic methanogen (Methanoculleus). Family Picrophilaceae (Order Thermoplasmatales) was also observed as a minor population. The predominance of hydrogenotrophic methanogen suggests that the main degradation pathway of this process is different from the classical methane production systems that have the pathway based on acetogenesis. The domination of hydrogenotrophic methanogen (Methanoculleus) may be caused by mesophilic digestion, neutral pH, high concentration of ammonia, short HRT, and interaction with VFA-oxidizing bacteria (Tepidanaerobacter etc.).

• Journal of Life Science
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• v.23 no.10
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• pp.1295-1303
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• 2013

According to facts revealed up until the present, there are a total of 68 known phyla on earth, including 55 phyla of bacteria and 13 phyla of archaea. The human large intestine has 9 phyla of microorganisms, which is a relatively lower diversity compared to the general environments of soil or sea. The diversity of intestinal microorganisms is affected by the characteristics of the host (genetic background, sex, age, immune system, and gut motility), the diet (non-digestible carbohydrates, fat, prebiotics, probiotics), and the intake of antibiotics, which in turn have an effect on energy storage processes, gene expressions, and even metabolic diseases like obesity. Probiotics are referred to as living microorganisms that improve the intestinal microbiota and contribute to the health of the host; in addition, probiotics usually comprise lactic acid bacteria. Recently, bacteriotherapy using probiotics has been utilized to treat sicknesses like diarrhea and irritable bowel syndrome. Prebiotics are a food ingredient which can selectively adjust intestinal microorganisms and which comprise inulin, fructooligosaccharides, galactooligosaccharides, and lactulose. In recent days, attention has been paid to the use of dietary cellulose in the large intestine and the production of short chain fatty acids (short-chain fatty acids) in relation to obesity and anticancer. More research into microorganisms in the large intestine is necessary to identify specific microorganism species, which are adjusted by diverse non-digestible carbohydrates, prebiotics, and probiotics in the large intestine and to understand the connection between sicknesses and metabolites like short chain fatty acids produced by these microorganism species.

• Journal of Life Science
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• v.27 no.4
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• pp.435-441
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• 2017

Perchlorate ($ClO_4^-$) is an emerging contaminant detected in soil, groundwater, and surface water. Previous study revealed bacterial community in the enrichment culture tdegraded perchlorate using elemental sulfur as an electron donor. Quantitative and qualitative molecular methods were employed in this study to investigate archaeal community in the enrichment culture. Real-time qPCR showed that archaeal 16S rRNA gene copy number in the culture was about 1.5% of bacterial 16S rRNA gene copy number. This suggested that less archaea were adapted to the environment of the enrichment culture and bacteria were dominant. DGGE banding pattern revealed that archaeal community profile of the enrichment culture was different from that of the activated sludge used as an inoculum for the enrichment culture. The most dominant DGGE band of the enrichment culture was affiliated with Methanococci. Further research is necessary to investigate metabolic role of the dominant archaeal population to better understand microbial community in the perchlorate-reducing enrichment culture.

• Journal of Animal Science and Technology
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• v.62 no.6
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• pp.801-811
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• 2020

The main objective of this in vitro study was to evaluate red ginseng byproduct (RGP) as a protein resource and its effects on rumen fermentation characteristics, microflora, CO2, and CH4 production in ruminants. Four treatments for in vitro fermentation using buffered rumen fluid over a 48 h incubation period were used: 1, RGP; 2, corn gluten feed (CGF); 3, wheat gluten (WG); and 4, corn germ meal. In vitro dry matter digestibility (IVDMD), in vitro neutral detergent fiber digestibility (IVNDFD), in vitro crude protein digestibility (IVCPD), volatile fatty acids, pH, and ammonia nitrogen (NH3-N) were estimated after 48 h incubation. Gas production was investigated after 3, 6, 12, 24, 36 and 48 h. The CO2 and CH4 were evaluated after 12, 24, 36, and 48 h. A significant difference in total gas production and CO2 emissions was observed (p < 0.01) at all incubation times. CH4 production in RGP were higher (p < 0.05) than that in other treatments but a higher CH4 portion in the total gas production was observed in WG (p < 0.05) at 48 h incubation. The IVDMD, IVNDFD, and IVCPD of RGP was lower than those of other conventional ingredients (p < 0.01). The RGP had the lowest NH3-N value among the treatments (p < 0.01). The RGP also had the lowest total VFA concentration (p < 0.01), but presented the highest acetate proportion and acetate to propionate ratio among the treatments (both, p < 0.01). The abundance of Prevotella ruminicola was higher in RGP than in WG (p < 0.01), whereas RGP has lower methanogenic archaea (p < 0.01). In conclusion, based on the nutritive value, IVDMD, low NH3-N, and decreased methanogenic archaea, RGP inclusion as a protein source in ruminant diets can be an option in replacing conventional feed sources.

• Journal of Life Science
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• v.32 no.3
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• pp.249-255
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• 2022

Metabolism is essential for survival and reproduction, and there is a metabolic pathways entry in the clusters of orthologous groups of proteins (COGs) database, updated in 2020. In this study, the metabolic pathways of 1309 prokaryotes were analyzed using COGs. There were 822 COGs associated with 63 metabolic pathways, and the mean for each taxon was between 200.50 (mollicutes) and 527.07 (cyanobacteria) COGs. The metabolic pathway composition ratio (MPCR) was defined as the number of COGs present in one genome in relation to the total number of COGs constituting each metabolic pathway, and the number of pathways with 100% MPCR ranged from 0 to 26 in each prokaryote. Among 1309 species, the 100% MPCR pathways included murein biosynthesis associated with cell wall synthesis (922 species); glycine cleavage (918); and ribosomal 30S subunit synthesis (903). The metabolic pathways with 0% MPCR were those involving photosystem I (1263 species); archaea/vacuolar-type ATP synthase (1028); and Na⁺-translocation NADH dehydrogenase (976). Depending on the prokaryote, three to 49 metabolic pathways could not be performed at all. The sequence of most highly conserved metabolic pathways was ribosome 30S subunit synthesis (96.1% of 1309 species); murein biosynthesis (86.8%); arginine biosynthesis (80.4%); serine biosynthesis (80.3%); and aminoacyl-tRNA synthesis (82.2%). Protein and cell wall synthesis have been shown to be important metabolic pathways in prokaryotes, and the results of this study of COGs related to such pathways can be utilized in, for example, the development of antibiotics and artificial cells.

• Biotechnology and Bioprocess Engineering:BBE
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• v.4 no.1
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• pp.21-25
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• 1999

Two low-salt complex media, bactopeptone and desalted yeast extract, were used for high density cultivation of the hyperthermophilic archaeon Sulfolobus solfataricus (DSM 1617). Bactopeptone, which has low mineral ion content among various complex media, was good for cell growth in batch cultures; the maximal cell density in bactopeptone was comparable to that in yeast extract. However, cell growth was rather poor when bactopeptone was added by the fed-batch procedure. Since several vitamins are deficient in abctopeptone, the effect of vitamins on cell growth was examined. Among the vitamins tested, pyridoxine was found to improve the growth rate of S. solfataricus. To reduce the growth inhibition caused by mineral ions, yeast extract was dialyzed against distilled water and then fed-batch cultures were carried out using a fed medium containing desalted yeast extract. Although the concentrations of mineral ions in yeast extract were significantly lowered by the dialysis whether low molecular weight solutes in yest extract are crucial for cell growth, we investigated the effect of trehalose, a most abundant compatible solute in yeast extract, on the growth pattern. Cell densities were increased and the length of the lag phase was markedly shortened by the presence of trehalose, indicating that trehalose plays an important role in the growth of S. solfataricus.

• KSBB Journal
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• v.26 no.3
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• pp.237-242
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• 2011

As a number of archaea are ubiquitously found in non-extreme habitats, elucidation of their functional roles becomes currently an emerging issue. However, most of them are unable to grow in pure culture and so it remains to be established. In order to find genes lacking in the genome of an ammonia-oxidizing archaeon (AOA), we here report on the comparative analyses of an AOA genome with those of experimentally or theoretically established minimal genomes for independent growth. We assessed the genes lacking in AOA using logic of clusters of orthologous groups (COG), remote homology, consensus sequence weight matrix, function-based motif or domain, and then further excluded genes encoding hypothetical orarchaea-specific proteins. The results of these combination analyses revealed 19 candidate genes lacking in the genome of an AOA. Thus, our results provide a possibility of inducing independent growth of AOA when supplemented with product (s) of the lacking gene (s), and also give a chance for finding new proteins with novel sequence or structure space even if the predicted lacking-genes will be found using another algorithms or biochemical studies.

• Journal of Animal Reproduction and Biotechnology
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• v.34 no.3
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• pp.157-165
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• 2019

This study was conducted to analyze the diversity census of fecal microbiome in horses using meta-analysis of equine 16S rRNA gene sequences that are available in the Ribosomal Database Project (RDP; Release 11, Update 5). The search terms used were "horse feces (or faeces)" and "equine feces (or faeces)". A total of 842 sequences of equine feces origin were retrieved from the RDP database, where 744 sequences were assigned to 10 phyla placed within Domain Bacteria. Firmicutes (n = 391) and Bacteroidetes (n = 203) were the first and the second dominant phyla, respectively, followed by Verrucomicrobia (n = 58), Proteobacteria (n = 30) and Fibrobacteres (n = 24). Clostridia (n = 319) was the first dominant class placed within Bacteroidetes while Bacteroidia (n = 174) was the second dominant class placed within Bacteroidetes. The remaining 98 sequences were assigned to phylum Euryarchaeota placed within Domain Archaea, where 74 sequences were assigned to class Methanomicrobia. The current results will improve understanding of the diversity of fecal microbiome in horses and may be used to further analyze equine fecal microbiome in future studies.