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Molecular Systematics and Conservation Genetics
Institute Of Ecology and Biological Resources
Systematics (Taxonomy), Molecular Biology and Bioinformatics
S. Nguyen, Shahbaz Raza, Loan Thi Ta, Lan Anh Thi Le, C. T. Ho and T. Unno
Applied Biological Chemistry, ISSN: 24680834, eISSN: 24680842, Published: December 2022
In this study, we use high-throughput sequencing-based metagenomic methods to investigate the differences in seasonal structures of the bacterial community and the abundance and diversity of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in both shrimp ponds and river water samples downstream of the Day River, Ninh Binh, Vietnam. The structure of the central bacterial community, ARGs, and MGEs was found to be regardless of the seasons and locations. The predominant phyla found in all samples was Proteobacteria , Bacteroidetes, and Actinobacteria . Multi-drug resistance (MDR) genes and transposases are the most dominant ARG types and MGEs, respectively. Our data showed a higher abundance of bacterial communities, ARGs, and MGEs in the river water during the rainy season. There is a significant correlation between the abundance of ARGs, MGEs, and environmental factors. Our results indicate that water environments containing ARGs/MGEs carrying bacteria pose a risk to shrimp and human health, especially during the rainfall-polluted water season.
ANH D. NGUYEN, SON G. NGUYEN, and KATSUYUKI EGUCHI
Zootaxa, ISSN: 11755326, eISSN: 11755334, Volume: 4927, Pages: 257-264, Published: 12 February 2021 Magnolia Press
A new pill millipede, Rhopalomeris nagao sp. nov., is described from Vietnam. It is recognized by the following combination of characters: antennal tip with numerous sensory cones; telopods with short prefemoral and femoral trichosteles, with long, straight and acute tuberculiform femoral process, and with shorter lobuliform tibial process; syncoxial lobe being slightly concave medially, syncoxial horns being longer than lobe. A fragment of the cytochrome c oxidase subunit I (COI) gene is also provided for the new species. The K2P genetic distance of the COI between the new species and other Vietnamese glomeridans is from 10.7% to 16.9%. Two genera, Hyperglomeris and Hyleoglomeris, are considered to be non-monophyletic, but more data and samples will be needed for confirmation.
Dinh Nguyen, Loan Ho, and Son Nguyen
Biodiversity Data Journal, ISSN: 13142836, eISSN: 13142828, Pages: 1-11, Published: 2021 Pensoft Publishers
The genus Charaea Baly is distributed in the eastern Palaearctic, Himalayas, China and adjacent countries of the Oriental Region. Currently, 59 species of the genus Charaea have been recorded. The species of Charaea is characterised with a robust tubular aedeagus that terminates with a more or less distinct apical process with the Charaea coomani group having an internal sac with long sharp lateral sclerites. Up to now, 13 species of this group have been described in the Oriental Region, four of which are found in Vietnam. Charaea dinhcuongisp. nov. is described as a new species, based on specimens collected from Phu Quoc Island in southern Vietnam. Colour photographs of habitus and body details and DNA barcode sequences are presented. An identification key is provided for all Vietnamese species from the Charaea coomani group.
Van The Pham, Robert D. Kloppenburg, Leonid V. Averyanov, Giang Son Nguyen, Hoang Tuan Nguyen, Tuan Anh Le, and Van Canh Nguyen
Pakistan Journal of Botany, ISSN: 05563321, Pages: 291-295, Published: February 2020 Pakistan Journal of Botany
Hoya lamthanhiae V.T. Pham & Kloppenb. is described and illustrated. The molecular data is provided; this species was found in Dak Lak province, southern Vietnam. Diagnostic features of the new species are a milky latex lithophytic vine and pure white with red-purple centre flowers. The described species clearly differs from closely related H. hainanensis in number of characters: a leaf blade shortly attenuated and wavy margins at the base, a hairy abaxial leaf surface, a bigger calyx with few sparse hairs or glabrous, a bigger corolla with acute lobe, shorter pollinia, as well as molecular characters.
Raffles Bulletin of Zoology, eISSN: 02172445, Pages: 96-109, Published: 2018
Son G. Nguyen, Jungman Kim, Robin B. Guevarra, Ji-Hoon Lee, Eungpil Kim, Su-il Kim, and Tatsuya Unno
Food and Function, ISSN: 20426496, eISSN: 2042650X, Pages: 4193-4201, Published: October 2016 Royal Society of Chemistry (RSC)
We investigated the anti-obesity effects of the potential prebiotic, laminarin, on mice fed a high-fat diet.
Jungman Kim, Robin Becina Guevarra, Son Giang Nguyen, Ji-Hoon Lee, Dong Kee Jeong, and Tatsuya Unno
Journal of Microbiology and Biotechnology, ISSN: 10177825, eISSN: 17388872, Pages: 876-882, Published: May 2016 Journal of Microbiology and Biotechnology
Tylosin has been used as a livestock feed additive and antibiotic growth promoter for many years. However, the mode of action by which tylosin enhances animal growth is unclear. We used high-throughput sequencing of 16S rRNA genes to investigate the effects of tylosin as a feed additive on swine gut microbiota. No significant difference in the rate of weight increase was observed between control and tylosin-treated pigs during a 10-week feeding trial. However, tylosin-treated pigs showed rapid increases in the relative abundance of the phylum Firmicutes. Increases in Firmicutes species are associated with (so-called) obese-type gut microbiota. The abundance of species of four families of the phylum Firmicutes (Streptococcaceae, Peptococcaceae, Peptostreptococcaceae, and Clostridiaceae) correlated positively with host weight gain. The abundance of Streptococcaceae family bacteria was least affected by tylosin treatment. Distribution analysis of operational taxonomic units (OTUs) showed that both control and tylosin-treated pigs exhibited similar OTU alterations during growth. However, the tylosin-treated group showed distinctive alterations in gut microbiota when the host weighed approximately 60 kg, whereas similar alterations occurred at around 80 kg in the control group. Our results suggest that use of tylosin accelerates maturation of swine gut microbiota rather than altering its composition.
Son G. Nguyen, Cuong Tu Ho, Ji-Hoon Lee, and Tatsuya Unno
Korean Journal of Microbiology, ISSN: 04402413, eISSN: 23839902, Pages: 157-165, Published: 2016 The Microbiological Society of Korea
Under flooded rice fields, methanogens produce methane which comes out through rice stalks, thus rice fields are known as one of the anthropogenic sources of atmospheric methane. Studies have shown that use of manure increases amount of methane emission from rice. To investigate mechanisms by which manure boosts methane emission, comparative soil metagenomics between inorganically (NPK) and pig manure fertilized paddy soils (PIG) were conducted. Results from taxonomy analysis showed that more abundant methanogens, methanotrophs, methylotrophs, and acetogens were found in PIG than in NPK. In addition, BLAST results indicated more abundant carbohydrate mabolisetm functional genes in PIG. Among the methane metabolism related genes, PIG sample showed higher abundance of methyl-coenzyme M reductase (mcrB/mcrD/mcrG) and trimethylamine-corrinoid protein Co-methyltransferase (mttB) genes. In contrast, genes that down regulate methane emission, such as trimethylamine monooxygenase (tmm) and phosphoserine/homoserine phosphotransferase (thrH), were observed more in NPK sample. In addition, more methanotrophic genes (pmoB /amoB / mxaJ ), were found more abundant in PIG sample. Identifying key genes related to methane emission and methane oxidation may provide fundamental information regarding to mechanisms by which use of manure boosts methane emission from rice. The study presented here characterized molecular variation in rice paddy, introduced by the use of pig manure.
Tatsuya Unno, Jungman Kim, Yumi Kim, Son G. Nguyen, Robin B. Guevarra, Gee Pyo Kim, Ji-Hoon Lee, and Michael J. Sadowsky
Science of the Total Environment, ISSN: 00489697, eISSN: 18791026, Volume: 532, Pages: 337-343, Published: November 01, 2015 Elsevier BV
Groundwater is the sole source of potable water on Jeju Island in the Republic of (South) Korea. Groundwater is also used for irrigation and industrial purposes, and it is severely impacted by seawater intrusion in coastal areas. Consequently, monitoring the intrusion of seawater into groundwater on Jeju is very important for health and environmental reasons. A number of studies have used hydrological models to predict the deterioration of groundwater quality caused by seawater intrusion. However, there is conflicting evidence of intrusion due to complicated environmental influences on groundwater quality. Here we investigated the use of next generation sequencing (NGS)-based microbial community analysis as a way to monitor groundwater quality and detect seawater intrusion. Pristine groundwater, groundwater from three coastal areas, and seawater were compared. Analysis of the distribution of bacterial species clearly indicated that the high and low salinity groundwater differed significantly with respect to microbial composition. While members of the family Parvularculaceae were only identified in high salinity water samples, a greater percentage of the phylum Actinobacteria was predominantly observed in pristine groundwater. In addition, we identified 48 shared operational taxonomic units (OTUs) with seawater, among which the high salinity groundwater sample shared a greater number of bacterial species with seawater (6.7%). In contrast, other groundwater samples shared less than 0.5%. Our results suggest that NGS-based microbial community analysis of groundwater may be a useful tool for monitoring groundwater quality and detect seawater intrusion. This technology may also provide additional insights in understanding hydrological dynamics.
Son G. Nguyen, Robin B. Guevarra, Jungman Kim, Cuong T. Ho, Mai V. Trinh, and Tatsuya Unno
Water, Air, and Soil Pollution, ISSN: 00496979, eISSN: 15732932, Volume: 226, Published: 29 September 2015 Springer Science and Business Media LLC
Methane production by methanogenic microbes under anaerobic condition is affected by the types of fertilizers, which determine carbon availability, used in rice fields. In addition, irrigation management controls oxygen availability in soil. Thus, irrigation management and types of fertilizers are major driving forces for methane emission in rice fields. While these factors affect paddy microbial communities over the course of cultivation, little is known about the effects of fertilizers and irrigation conditions on initial paddy microbial communities. In this study, we investigated the initial impacts of fertilizers and irrigation systems on paddy microbial communities and methane emission. At early stages of rice cultivation (2 weeks after transplanting 15-day-old rice seedlings), a high amount of methane was emitted from rice fertilized with swine manure. In addition, pre-transplantation flooding increased methane emission by 30 %. Although these conditions did not affect the overall paddy soil microbial communities, 126 operational taxonomic units (OTUs) were found to be significantly more abundant in paddy soils fertilized with swine manure. These OTUs included archaeal methanogenic species and bacterial substrate providers for biomethane production. Shared-OTU analysis with swine fecal microbial communities indicated swine manure as the origin of key methane-producing microbes. In conclusion, the applications of swine manure and permanent flooding irrigation introduce active methane producers and enhance methane emission, respectively, and should therefore be avoided.
Jungman Kim, Son G. Nguyen, Robin B. Guevarra, Iljoo Lee, and Tatsuya Unno
Archives of Microbiology, ISSN: 03028933, eISSN: 1432072X, Volume: 197, Pages: 753-759, Published: 25 August 2015 Springer Science and Business Media LLC
Recent obesity studies in humans and rodents have suggested that host weight gain is significantly associated with energy harvesting efficiency which is regulated by gut microbiota. Antibiotic growth promoters have been banned as feed additives in many countries. In this study, we aimed to provide knowledge of swine fecal microbiota by analyzing bacterial 16S rRNA gene sequences. Our results showed that swine fecal bacterial composition varied at each growth stage. Bacteroidetes decreased as the swine gained weight and unclassified genera significantly increased at later growth stages. Operational taxonomic unit (OTU) distribution analysis showed that the bacterial community difference was most significant between growers and finishers, while analysis of shared OTUs indicated a greater proportion of common species between growers and finishers. The differential abundance test between growers and finishers detected that nearly half of the species were shared OTUs, suggesting that differential abundance of each bacterial species predominantly controls bacterial community differences. Although functions of these bacteria are yet to be identified, understanding differences in fecal microbiota between each growth stage will provide additional insights for further studies related to swine gut microbiota.
Robin B. Guevarra, Jungman Kim, Son G. Nguyen, and Tatsuya Unno
Journal of Applied Biological Chemistry, ISSN: 19760442, Pages: 369-375, Published: 2015 Korean Society for Applied Biological Chemistry
Meat from black pigs (BP) is in high demand compared with that from modern white pig (WP) breeds such as Landrace pigs owing to its high quality. However, the growth rate of black pigs is slower than that of white pig breeds. We investigated differences in the fecal microbial composition between white and black pigs to explore whether these breeds differed in the composition of their gut microbial communities. The swine gut microbiota was investigated using Illumina`s MiSeq-based sequencing technology by targeting the V4 region of the 16S rRNA gene. Our results showed that the composition of the gut microbiota was significantly different between the two pig breeds. While the composition of the WP microbiota shifted according to the growth stage, fewer shifts in composition were observed for the BP gut microbiota. In addition, the WP gut microbiota showed a higher Firmicutes/Bacteroidetes ratio compared with that of BP. A high ratio between these phyla was previously reported as an obesity-linked microbiota composition. Moreover, the WP microbiota contained a significantly higher abundance of cellulolytic bacteria, suggesting a possibility of higher fiber digestion efficiency in WP compared to BP. These findings may be important factors affecting growth performance and energy-harvesting capacities in pigs. Our findings of differences in the gut microbiota composition between the two breeds may provide new leads to understand growth rate variation across pig breeds.
Jungman Kim, Robin B. Guevarra, Son G. Nguyen, and Tatsuya Unno
Korean Journal of Microbiology, ISSN: 04402413, Pages: 81-85, Published: 2015 The Microbiological Society of Korea
Since the banning of antibiotic growth promoters (AGPs), the death of livestock has been increased, thus there is a strong demand for AGP-alternatives. Modulation of gut microbiota has been reported to affect host physiological functions and suggested to be a novel approach for developing AGP-alternatives. However, little has been understood about livestock gut microbiota compared to that of humans. We conducted preliminary study provide fundamental information regarding to regional differences in swine gut microbiota. Swine fecal samples were obtained from farms in Jeju (n=40), Gwangju (n=28), and Haenam (n=30). MiSeq was used to sequence 16S rRNA V4 region, and Mothur pipeline (Schloss et al., 2009) was used for data processing. A total of 5,642,125 reads were obtained and 3,868,143 reads were remained after removing erroneous reads. Analysis of taxonomic composition at the phylum level indicated greater abundance of Firmicutes among Jeju swine, and cluster analysis of distribution of operational taxonomic units also showed regional differences among swine gut microbiota. In addition, correlation analysis between non-metric multidimensional scaling and abundance of phyla suggested that the phyla Actinobacter, Verrucomicrobia, Firmicutes, and Fibrobacteres were driving factors for the regional differences. Livestock gut microbiota may be affected by diet and practices in farms. Our results indicated significant regional differences in swine gut microbiota, suggesting that future livestock gut microbiota studies should be designed with the regional differences in mind.
Tatsuya Unno, Jungman Kim, Robin B. Guevarra, and Son G. Nguyen
Journal of Microbiology and Biotechnology, ISSN: 10177825, eISSN: 17388872, Pages: 431-438, Published: 2015 Journal of Microbiology and Biotechnology
Ever since the ban on antibiotic growth promoters (AGPs), the livestock death rate has increased owing to pathogenic bacterial infections. There is a need of developing AGP alternatives; however, the mechanisms by which AGP enhances livestock growth performance are not clearly understood. In this study, we fed 3-week-old swine for 9 weeks with and without AGPs containing chlortetracycline, sulfathiazole, and penicillin to investigate the effects of AGPs on swine gut microbiota. Microbial community analysis was done based on bacterial 16S rRNA genes using MiSeq. The use of AGP showed no growth promoting effect, but inhibited the growth of potential pathogens during the early growth stage. Our results showed the significant increase in species richness after the stabilization of gut microbiota during the post-weaning period (4-week-old). Moreover, the swine gut microbiota was divided into four clusters based on the distribution of operational taxonomic units, which was significantly correlated to the swine weight regardless of AGP treatments. Taxonomic abundance analysis indicated a negative correlation between host weight and the abundance of the family Prevotellaceae species, but showed positive correlation to the abundance of the family Spirochaetaceae, Clostridiaceae_1, and Peptostreptococcaeae species. Although no growth performance enhancement was observed, the use of AGP inhibited the potential pathogens in the early growth stage of swine. In addition, our results indicated the ecological succession of swine gut microbiota according to swine weight. Here, we present a characterization of swine gut microbiota with respect to the effects of AGPs on growth performance.