Extensive Profiling of a Complex Microbial Community by High-Throughput Sequencing

ABSTRACT Complex microbial communities remain poorly characterized despite their ubiquity and importance to human and animal health, agriculture, and industry. Attempts to describe microbial communities by either traditional microbiological methods or molecular methods have been limited in both scale and precision. The availability of genomics technologies offers an unprecedented opportunity to conduct more comprehensive characterizations of microbial communities. Here we describe the application of an established molecular diagnostic method based on the chaperonin-60 sequence, in combination with high-throughput sequencing, to the profiling of a microbial community: the pig intestinal microbial community. Four libraries of cloned cpn60 sequences were generated by two genomic DNA extraction procedures in combination with two PCR protocols. A total of 1,125 cloned cpn60 sequences from the four libraries were sequenced. Among the 1,125 cloned cpn60 sequences, we identified 398 different nucleotide sequences encoding 280 unique peptide sequences. Pairwise comparisons of the 398 unique nucleotide sequences revealed a high degree of sequence diversity within the library. Identification of the likely taxonomic origins of cloned sequences ranged from imprecise, with clones assigned to a taxonomic subclass, to precise, for cloned sequences with 100% DNA sequence identity with a species in our reference database. The compositions of the four libraries were compared and differences related to library construction parameters were observed. Our results indicate that this method is an alternative to 16S rRNA sequence-based studies which can be scaled up for the purpose of performing a potentially comprehensive assessment of a given microbial community or for comparative studies.

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Effects of Distinct Revegetation Methods on Growth and Microbial Properties of Vallisneria natans

Water ◽

10.3390/w12051294 ◽

2020 ◽

Vol 12 (5) ◽

pp. 1294

Author(s):

Ning Wang ◽

Qi Li ◽

Mengqi Jiang ◽

Weizhen Zhang ◽

Hao Zhang ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

High Throughput ◽

Water Purification ◽

High Throughput Sequencing ◽

Rhizosphere Soil ◽

Soil Microbial Communities ◽

Agar Gel ◽

Vallisneria Natans ◽

Significant Difference

This study investigated the effects of the mud-sinking (MS) method, agar gel-sinking (AS) method and agar gel-sinking with artificial aquatic mat (ASA) method on the growth, physiological characteristics, water purification capacity, and associated microbial community of the different organs of Vallisneria natans (V. natans). Results showed that the growth of agar-based growth (group AS and ASA) were more effective than the mud-wrapped method (group MS), exhibiting longer length, higher fresh weight and biomass of agar-based V. natans with the artificial aquatic mat (group ASA) being higher than those of other groups. MS caused a stress response in the oxidative system, which then inhibited photosynthesis. Results of water quality measurements showed that the three planting methods positively affected water purification without significant differences (p > 0.05). Besides, there was no significant difference (p > 0.05) between the microbial communities in terms of the roots and those found in rhizosphere soils in the MS group with high throughput sequencing. Meanwhile, the addition of agar in the AS and ASA groups increased the diversity of rhizosphere soil microbial communities and reduced the diversity of root microbial communities. Microbial community compositions in the rhizosphere soil and root differed significantly (p < 0.05). High throughput sequencing and scanning electron microscopy (SEM) also revealed that the biofilm on the surfaces were different, with Proteobacteria and Cyanophyta consistently dominating. This study provides new insights on the more effective revegetation methods of V. natans, researched the environmental impact of the addition of agar, and provides some theoretical support for the revegetation of submerged macrophytes under ecological restoration.

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Study of Periplaneta Americana Microbial Community Structure and Diversity by 16S rRNA High-Throughput Sequencing

Sustainability in Environment ◽

10.22158/se.v2n4p350 ◽

2017 ◽

Vol 2 (4) ◽

pp. 350

Author(s):

Zhuang Zhi Chen ◽

Xiu Mei Wu ◽

Yong Mei Shen ◽

Cheng Gong Li ◽

Kai Ge Xu ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

16S Rrna ◽

Microbial Communities ◽

High Throughput ◽

Microbial Community Structure ◽

Periplaneta Americana ◽

High Throughput Sequencing ◽

Shannon Index

Objective: The present study probes into the microbial community structure in Periplaneta americana under different breeding conditions, using 16S rRNA high-throughput sequencing technique, in the hope of finding the microbial community structure in Periplaneta americana and their diversity under different breeding conditions. Methods: In this study, we extract the microbial metagenomic DNA of 5 groups of Periplaneta americana which under different breeding conditions. Using lllumina Miseq sequencing platform, two-terminal sequencing of V3-V4 regions of 16S rRNA were sequenced; diversity of community structure was analyzed using the softwares such as fastqc, QIIME, PyNAST, fasttree and R language.Results: Shannon index of samples in SG group was lower than that of the other four groups, significantly lower than that of DB group (P<0.05), but not significantly different from other groups. This suggested that the intake of a mixed fodder with high sugar, high fat and high protein by Periplaneta americana can reduce the diversity of microbial communities. Our findings showed that breeding intervention with different fodders may cause differences in the contents of Bacteroidetes, Proteobacteria and Firmicutes in Periplaneta americana. Results showed that long-term intake of lots of sucrose and fat may increase the proportion of Bacteroidetes in Periplaneta americana; and long-term intake of lots of sucrose may reduce the proportion of Proteobacteria in Periplaneta americana; and long-term intake of lots of fat may reduce the proportion of Firmicutes in Periplaneta americana. Two major dominant bacterial genera in all samples were Blattabacterium and Rickettsiella. But different feeding interventions can change the proportions of Blattabacterium and Rickettsiella.Conclusion: Periplaneta americana has a complex microbial community structure. Different feeding conditions may change the microbial community structure of Periplaneta americana. An important bacterial genus in Periplaneta americana, Blattabacterium is positively correlated with the intake of sucrose- and fat-rich fodder. In the breeding process of Periplaneta americana, adding sucrose and fat to fodder may increase the content and proportion of Blattabacterium in microbial communities.

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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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High-throughput sequencing analysis of microbial community diversity in response to indica and japonica bar-transgenic rice paddy soils

PLoS ONE ◽

10.1371/journal.pone.0222191 ◽

2019 ◽

Vol 14 (9) ◽

pp. e0222191 ◽

Cited By ~ 1

Author(s):

Meidan He ◽

Jiachao Zhang ◽

Linbo Shen ◽

Lixin Xu ◽

Wenjie Luo ◽

...

Keyword(s):

Microbial Community ◽

Transgenic Rice ◽

High Throughput ◽

High Throughput Sequencing ◽

Rice Paddy ◽

Paddy Soils ◽

Community Diversity ◽

Sequencing Analysis ◽

Microbial Community Diversity ◽

Rice Paddy Soils

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Diversity of microbial communities in hot springs of Sri Lanka as revealed by 16S rRNA gene high-throughput sequencing analysis

Gene ◽

10.1016/j.gene.2021.146103 ◽

2021 ◽

pp. 146103

Author(s):

Dilini Sadeepa ◽

Kosala Sirisena ◽

Pathmalal M. Manage

Keyword(s):

Sri Lanka ◽

16S Rrna ◽

16S Rrna Gene ◽

Microbial Communities ◽

High Throughput ◽

High Throughput Sequencing ◽

Hot Springs ◽

Rrna Gene ◽

Sequencing Analysis

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Analysis of Microbial Community Structure and Volatile Compounds in the Pit Mud Used for Manufacturing Taorong-type Baijiu Based on High-Throughput Sequencing

10.21203/rs.3.rs-1097837/v1 ◽

2021 ◽

Author(s):

Yanbo Liu ◽

Mengxiao Sun ◽

Pei Hou ◽

Wenya Wang ◽

Xiangkun Shen ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Qualitative Analysis ◽

Volatile Compounds ◽

High Throughput ◽

Microbial Community Structure ◽

High Throughput Sequencing ◽

Solid Phase ◽

Gas Chromatography Mass Spectrometry ◽

Pit Mud

Abstract In this study, the pit mud used in manufacturing Taorong-type Baijiu was collected from the upper, middle, lower and bottom layers of pits in Henan Yangshao Liquor Co., LTD. Besides, high-throughput sequencing (HTS) technology was adopted to analyze the microbial community structure of the pit mud. In addition, the volatile compounds in the pit mud were subjected to preliminarily qualitative analysis through headspace-solid phase microextraction (HS-SPME) and gas chromatography-mass spectrometry (GC-MS). The results of HTS demonstrated that there were 5, 3, 5 and 5 dominant bacterial phyla (including 11, 11, 9 and 8 dominant bacterial genera) and 3, 3, 3 and 3 dominant fungal phyla (including 4, 7, 7 and 5 dominant fungal genera) in the pit mud from F-S (upper), G-Z (middle), H-X (lower) and I-D (bottom), respectively. The qualitative analysis results of volatile compounds demonstrated that a total of 78 kinds of volatile compounds were detected in the pit mud, including 46, 45, 39 and 49 kinds in the pit mud from F-S, G-Z, H-X and I-D, respectively. Ester and acid were the two main components in the pit mud. Meanwhile, the correlation between microorganisms and main volatile compounds in the pit mud was analyzed. Moreover, Lentimicrobium, Syner-01 and Blvii28_wastewater-sludge group were found for the first time in the pit mud used for manufacturing Taorong-type Baijiu. The findings of this study could provide a theoretical foundation for improving the quality of pit mud and the flavor of Taorong-type Baijiu.

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Assessing high-throughput environmental DNA extraction methods for meta-barcode characterization of aquatic microbial communities

Journal of Water and Health ◽

10.2166/wh.2018.108 ◽

2018 ◽

Vol 17 (1) ◽

pp. 37-49 ◽

Cited By ~ 6

Author(s):

Abdolrazagh Hashemi Shahraki ◽

Subba Rao Chaganti ◽

Daniel Heath

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

High Throughput ◽

Environmentally Friendly ◽

Environmental Dna ◽

Magnetic Bead ◽

Extraction Methods ◽

Environmental Research ◽

Rrna Gene

Abstract The characterization of microbial community dynamics using genomic methods is rapidly expanding, impacting many fields including medical, ecological, and environmental research and applications. One of the biggest challenges for such studies is the isolation of environmental DNA (eDNA) from a variety of samples, diverse microbes, and widely variable community compositions. The current study developed environmentally friendly, user safe, economical, and high throughput eDNA extraction methods for mixed aquatic microbial communities and tested them using 16 s rRNA gene meta-barcoding. Five different lysis buffers including (1) cetyltrimethylammonium bromide (CTAB), (2) digestion buffer (DB), (3) guanidinium isothiocyanate (GITC), (4) sucrose lysis (SL), and (5) SL-CTAB, coupled with four different purification methods: (1) phenol-chloroform-isoamyl alcohol (PCI), (2) magnetic Bead-Robotic, (3) magnetic Bead-Manual, and (4) membrane-filtration were tested for their efficacy in extracting eDNA from recreational freshwater samples. Results indicated that the CTAB-PCI and SL-Bead-Robotic methods yielded the highest genomic eDNA concentrations and succeeded in detecting the core microbial community including the rare microbes. However, our study recommends the SL-Bead-Robotic eDNA extraction protocol because this method is safe, environmentally friendly, rapid, high-throughput and inexpensive.

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Characterization of the Fecal Microbiota Using High-Throughput Sequencing Reveals a Stable Microbial Community during Storage

PLoS ONE ◽

10.1371/journal.pone.0046953 ◽

2012 ◽

Vol 7 (10) ◽

pp. e46953 ◽

Cited By ~ 119

Author(s):

Ian M. Carroll ◽

Tamar Ringel-Kulka ◽

Jennica P. Siddle ◽

Todd R. Klaenhammer ◽

Yehuda Ringel

Keyword(s):

Microbial Community ◽

High Throughput ◽

High Throughput Sequencing ◽

Fecal Microbiota

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Novel Approach to Study the Diversity of Soil Microbial Communities in Qatar

University of the Future: Re-Imagining Research and Higher Education ◽

10.29117/quarfe.2020.0025 ◽

2020 ◽

Author(s):

Jane Oja ◽

Sakeenah Adenan ◽

Abdel-Fattah Talaat ◽

Juha Alatalo

Keyword(s):

Microbial Communities ◽

High Throughput ◽

Mycorrhizal Fungi ◽

High Throughput Sequencing ◽

Soil Microbial Communities ◽

Arbuscular Mycorrhizal ◽

Soil Microbial ◽

Fungal Abundance ◽

Novel Approach ◽

Soil Climate

A broad diversity of microorganisms can be found in soil, where they are essential for nutrient cycling and energy transfer. Recent high-throughput sequencing methods have greatly advanced our knowledge about how soil, climate and vegetation variables structure the composition of microbial communities in many world regions. However, we are lacking information from several regions in the world, e.g. Middle-East. We have collected soil from 19 different habitat types for studying the diversity and composition of soil microbial communities (both fungi and bacteria) in Qatar and determining which edaphic parameters exert the strongest influences on these communities. Preliminary results indicate that in overall bacteria are more abundant in soil than fungi and few sites have notably higher abundance of these microbes. In addition, we have detected some soil patameters, which tend to have reduced the overall fungal abundance and enhanced the presence of arbuscular mycorrhizal fungi and N-fixing bacteria. More detailed information on the diversity and composition of soil microbial communities is expected from the high-throughput sequenced data.

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