Diversity of Intestinal Microbiota in Coilia ectenes from Lake Taihu, China

AbstractTo investigate the community structure and species composition of intestinal microbiota in Coilia ectenes, sixty-seven samples were collected from Lake Taihu in China. The intestinal microbiota of the C. ectenes were identified by the V4 of the 16S ribosomal RNA gene using high-throughput sequencing. Furthermore, the water quality of different sampling sites was also evaluated. A total of 53 phyla and 730 classified genera were found in all the samples. The eight dominant phyla Planctomycetes, Firmicutes, Proteobacteria, Bacteroidetes, Cyanobacteria, Crenarchaeota, Actinobacteria, and Verrucomicrobia were included. The intestinal microbiota compositions of the C. ectenes obtained from the same location presented more similar profiles, and the intestinal microbiota compositions of the C. ectenes from different geographical locations showed considerable differences. The operational taxonomic units (OTUs) abundance of the intestinal microbiota was significantly correlated with both the concentrations of total nitrogen and chlorophyll-a of the aquatic environment (p<0.05). Geographical location was an important determinant for the fish’s intestinal microbiota composition. The intestinal microbiota of C. ectenes would be affected by the concentrations of total nitrogen and chlorophyll-a in the water. These findings achieve a basic understanding of fish’s gut microbiota, and are helpful for the protection of fish resources in Lake Taihu and provided the cornerstone to sustainable utlization of C. ectenes.

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Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding

MycoKeys ◽

10.3897/mycokeys.39.28109 ◽

2018 ◽

Vol 39 ◽

pp. 29-40 ◽

Cited By ~ 21

Author(s):

Sten Anslan ◽

R. Henrik Nilsson ◽

Christian Wurzbacher ◽

Petr Baldrian ◽

Leho Tedersoo ◽

...

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Computation Time ◽

Potential Effect ◽

Data Sets ◽

Sequencing Data ◽

Operational Taxonomic Units ◽

High Throughput Sequencing Data ◽

Recent Developments

Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.

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Personalized Hybrid Book Recommender

International Journal of Information Systems in the Service Sector ◽

10.4018/ijisss.2019070105 ◽

2019 ◽

Vol 11 (3) ◽

pp. 70-97

Author(s):

Hossein Arabi ◽

Vimala Balakrishnan

Keyword(s):

Personality Traits ◽

Root Mean Square ◽

Demographic Data ◽

Geographical Location ◽

Personalized Recommendation ◽

Mean Square ◽

Location Factor ◽

Root Mean Square Residual ◽

Geographical Locations

Personalized Recommendation Systems (RS) provide end users with suggestions about items that are likely to be of their interest based on users' details such as demographics, location, time, and emotion. In this article, a Personalized Hybrid Book Recommender (PHyBR) is presented, which integrates personality traits with users' demographic data and geographical location to improve the quality of recommendations. The Ten Item Personality Inventory (TIPI) was used to determine users' personality traits. PHyBR was evaluated using two metrics, that are, Standardized Root Mean Square Residual (SRMR) and Root Mean Square Error of Approximation (RMSEA). Both metrics revealed PHyBR outperforms the baseline models (without considering personality traits and geographical location factor) in terms of the recommendation accuracies. This study shows that users who are in the same geographical contexts intend to have similar preferences. Therefore, users' personality details along with their geographical locations can be used to provide improved personalized recommendations.

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Eutrophication study of twenty reservoirs in Taiwan

Water Science & Technology ◽

10.2166/wst.2001.0331 ◽

2001 ◽

Vol 44 (6) ◽

pp. 19-26 ◽

Cited By ~ 9

Author(s):

S. -P. Chang ◽

S. -M. Chuang

Keyword(s):

Water Quality ◽

Nutrient Limitation ◽

Chlorophyll A ◽

Total Nitrogen ◽

Secchi Disc ◽

Study Results ◽

Limiting Nutrient ◽

Nitrogen Concentrations ◽

North Latitude

Taiwan is an island off the southeastern coast of China with total area of roughly 36,000 km2. The geographic position of Taiwan is between 21° 45′ 25″ to 25° 56′ 31″ north latitude and 119° 18′ 3″ to 124° 34′ 30″ east longitude and includes both tropical and subtropical areas. The study was carried out at twenty main reservoirs in Taiwan area from 1994 to 1998. The study revealed that the water quality of most reservoirs gradually deteriorated during the study period. Total phosphorus concentrations over 60 μg/L were observed in 12.5% of these reservoirs in 1994, but in 22.2% of these reservoirs in 1998. Total nitrogen concentrations over 1.0 mg/L were observed in 37.5% of these reservoirs in 1994, but in 94.4% of these reservoirs in 1998. Secchi disc transparency below 2 m was observed in 75% of these reservoirs in 1994, but in 83.3% of these reservoirs in 1998. Chlorophyll a concentrations over 15 mg/m3 were observed in 12.5% of these reservoirs in 1994, but in 27.8% of these reservoirs in 1998. The TN:TP mass ratios (wt/wt) of all the studied reservoirs except Akungting Reservoir, Fongshan Reservoir, and Chengching Reservoir are higher than 16. The study results on nutrient limitation indicated that phosphorus is the primary limiting nutrient in Taiwan reservoirs except Akungting Reservoir, Fongshan Reservoir, and Chengching Reservoir.

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Modeling impacts of water transfers on alleviation of phytoplankton aggregation in Lake Taihu

Journal of Hydroinformatics ◽

10.2166/hydro.2014.023 ◽

2014 ◽

Vol 17 (1) ◽

pp. 149-162 ◽

Cited By ~ 13

Author(s):

Jiacong Huang ◽

Junfeng Gao ◽

Yinjun Zhang ◽

Yan Xu

Keyword(s):

Chlorophyll A ◽

Algal Blooms ◽

Lake Taihu ◽

Water Transfer ◽

Short Term ◽

Phytoplankton Distribution ◽

Spatially Distributed ◽

Transfer Strategies ◽

Chlorophyll A Distribution

A water transfer project has been ongoing since 2002 to alleviate severe phytoplankton aggregation in Lake Taihu. This study aimed to quantify the effectiveness of the water transfer project on alleviation of phytoplankton aggregation in Lake Taihu on a short-term scale. In this study, a spatially distributed hydrodynamic-phytoplankton model was used to predict the short-term (3–4 days) changes in phytoplankton distribution (represented by chlorophyll a) in Lake Taihu. Four simulations with different water transfer strategies were carried out based on this model. During the water transfer period, phytoplankton aggregation was alleviated in some areas, suggesting that the water transfer project has the potential to alleviate algal blooms on a short-term scale. However, the effectiveness of the water transfer project on alleviating severe algal blooms was strongly affected by other environmental factors (e.g. wind conditions, chlorophyll a distribution, and the amount and quality of the transfer water). This study demonstrates the success of the hydrodynamic-phytoplankton model in evaluating the contribution of the water transfer project to alleviation of phytoplankton aggregation. These evaluation results could assist managers in decision-making before conducting a water transfer plan in Lake Taihu.

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Effect of red algal bloom on growth and production of carps

Our Nature ◽

10.3126/on.v16i1.22122 ◽

2018 ◽

Vol 16 (1) ◽

pp. 48-54

Author(s):

Ram Bhajan Mandal ◽

Sunila Rai ◽

Madhav Kumar Shrestha ◽

Dilip Kumar Jha ◽

Narayan Prasad Pandit

Keyword(s):

Water Quality ◽

Body Weight ◽

Chlorophyll A ◽

Total Nitrogen ◽

Total Phosphorus ◽

Algal Bloom ◽

Total Dissolved Solids ◽

Dissolved Solids ◽

Aquaculture Farm ◽

Red Algal

An experiment was carried to assess the effect of red algal bloom on growth and production of carp, water quality and profit from carp for 120 days at Aquaculture Farm of Agriculture and Forestry University, Chitwan. The experiment included two treatments: carp polyculture in non-red pond and carp polyculture in red pond with algal bloom each with three replicates. Carp fingerlings were stocked at 1 fish/m2 and fed with pellet containing 24% CP at 3% body weight. Net yield of rohu was found significantly higher (p<0.05) in non-red ponds (0.38±0.01 t ha-1) than red ponds (0.24±0.05 t ha-1). Survival of rohu (84.9±1.4%), bighead (95.2±2.0%) and mrigal (88.1±14.4%) were also significantly higher (p<0.05) in non-red ponds than red ponds. Red algal bloom affected DO, nitrate and chlorophyll-a, nitrite, total nitrogen, total phosphorus, total dissolved solids and conductivity. However, overall carp production and profit from carp remained unaffected.

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New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

Microorganisms ◽

10.3390/microorganisms9030659 ◽

2021 ◽

Vol 9 (3) ◽

pp. 659

Author(s):

Elias Asimakis ◽

Panagiota Stathopoulou ◽

Apostolis Sapounas ◽

Kanjana Khaeso ◽

Costas Batargias ◽

...

Keyword(s):

Relative Abundance ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Mutual Exclusion ◽

Bacterial Composition ◽

Operational Taxonomic Units ◽

Host Diet ◽

Dominant Bacteria ◽

High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

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Extremely Halophilic Biohydrogen Producing Microbial Communities from High-Salinity Soil and Salt Evaporation Pond

Fuels ◽

10.3390/fuels2020014 ◽

2021 ◽

Vol 2 (2) ◽

pp. 241-252

Author(s):

Dyah Asri Handayani Taroepratjeka ◽

Tsuyoshi Imai ◽

Prapaipid Chairattanamanokorn ◽

Alissara Reungsang

Keyword(s):

Microbial Communities ◽

High Throughput ◽

High Throughput Sequencing ◽

High Salinity ◽

Amplicon Sequencing ◽

Spatial Proximity ◽

Lignocellulosic Waste ◽

Evaporation Pond ◽

Operational Taxonomic Units ◽

Determining Factor

Extreme halophiles offer the advantage to save on the costs of sterilization and water for biohydrogen production from lignocellulosic waste after the pretreatment process with their ability to withstand extreme salt concentrations. This study identifies the dominant hydrogen-producing genera and species among the acclimatized, extremely halotolerant microbial communities taken from two salt-damaged soil locations in Khon Kaen and one location from the salt evaporation pond in Samut Sakhon, Thailand. The microbial communities’ V3–V4 regions of 16srRNA were analyzed using high-throughput amplicon sequencing. A total of 345 operational taxonomic units were obtained and the high-throughput sequencing confirmed that Firmicutes was the dominant phyla of the three communities. Halanaerobium fermentans and Halanaerobacter lacunarum were the dominant hydrogen-producing species of the communities. Spatial proximity was not found to be a determining factor for similarities between these extremely halophilic microbial communities. Through the study of the microbial communities, strategies can be developed to increase biohydrogen molar yield.

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Exploring the plant environmental DNA diversity in soil from two sites on Deception Island (Antarctica, South Shetland Islands) using metabarcoding

Antarctic Science ◽

10.1017/s0954102021000274 ◽

2021 ◽

pp. 1-10

Author(s):

Micheline Carvalho-Silva ◽

Luiz Henrique Rosa ◽

Otávio H.B. Pinto ◽

Thamar Holanda Da Silva ◽

Diego Knop Henriques ◽

...

Keyword(s):

High Throughput Sequencing ◽

Crater Lake ◽

Environmental Dna ◽

Food Sources ◽

South Shetland Islands ◽

Deception Island ◽

Shetland Islands ◽

Operational Taxonomic Units ◽

First Time ◽

Impacted Site

Abstract The few Antarctic studies to date to have applied metabarcoding in Antarctica have primarily focused on microorganisms. In this study, for the first time, we apply high-throughput sequencing of environmental DNA to investigate the diversity of Embryophyta (Viridiplantae) DNA present in soil samples from two contrasting locations on Deception Island. The first was a relatively undisturbed site within an Antarctic Specially Protected Area at Crater Lake, and the second was a heavily human-impacted site in Whalers Bay. In samples obtained at Crater Lake, 84% of DNA reads represented fungi, 14% represented Chlorophyta and 2% represented Streptophyta, while at Whalers Bay, 79% of reads represented fungi, 20% represented Chlorophyta and < 1% represented Streptophyta, with ~1% of reads being unassigned. Among the Embryophyta we found 16 plant operational taxonomic units from three Divisions, including one Marchantiophyta, eight Bryophyta and seven Magnoliophyta. Sequences of six taxa were detected at both sampling sites, eight only at Whalers Bay and two only at Crater Lake. All of the Magnoliophyta sequences (flowering plants) represent species that are exotic to Antarctica, with most being plausibly linked to human food sources originating from local national research operator and tourism facilities.

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The intestinal microbiota, gastrointestinal environment and colorectal cancer: a putative role for probiotics in prevention of colorectal cancer?

AJP Gastrointestinal and Liver Physiology ◽

10.1152/ajpgi.00110.2011 ◽

2011 ◽

Vol 301 (3) ◽

pp. G401-G424 ◽

Cited By ~ 125

Author(s):

M. Andrea Azcárate-Peril ◽

Michael Sikes ◽

José M. Bruno-Bárcena

Keyword(s):

Colorectal Cancer ◽

Intestinal Microbiota ◽

Defense Mechanisms ◽

High Throughput Sequencing ◽

Safety Evaluation ◽

Health Benefit ◽

The United States ◽

Dietary Factors ◽

Colorectal Adenomas ◽

Food Allergies

Colorectal cancer (CRC) is the third most commonly diagnosed cancer in the United States, and, even though 5–15% of the total CRC cases can be attributed to individual genetic predisposition, environmental factors could be considered major factors in susceptibility to CRC. Lifestyle factors increasing the risks of CRC include elevated body mass index, obesity, and reduced physical activity. Additionally, a number of dietary elements have been associated with higher or lower incidence of CRC. In this context, it has been suggested that diets high in fruit and low in meat might have a protective effect, reducing the incidence of colorectal adenomas by modulating the composition of the normal nonpathogenic commensal microbiota. In addition, it has been demonstrated that changes in abundance of taxonomic groups have a profound impact on the gastrointestinal physiology, and an increasing number of studies are proposing that the microbiota mediates the generation of dietary factors triggering colon cancer. High-throughput sequencing and molecular taxonomic technologies are rapidly filling the knowledge gaps left by conventional microbiology techniques to obtain a comprehensive catalog of the human intestinal microbiota and their associated metabolic repertoire. The information provided by these studies will be essential to identify agents capable of modulating the massive amount of gut bacteria in safe noninvasive manners to prevent CRC. Probiotics, defined as “live microorganisms which, when administered in adequate amounts, confer a health benefit on the host” ( 219 ), are capable of transient modulation of the microbiota, and their beneficial effects include reinforcement of the natural defense mechanisms and protection against gastrointestinal disorders. Probiotics have been successfully used to manage infant diarrhea, food allergies, and inflammatory bowel disease; hence, the purpose of this review was to examine probiotic metabolic activities that may have an effect on the prevention of CRC by scavenging toxic compounds or preventing their generation in situ. Additionally, a brief consideration is given to safety evaluation and production methods in the context of probiotics efficacy.

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