Microbial community composition in Brazilian stored diesel fuel of varying sulfur content, using high-throughput sequencing

In order to investigate the tolerance of an anoxic-oxic (A/O) process for the changing of refractory organics in electroplating wastewater, optimize the technological parameters, and reveal the microbial characteristics, a pilot-scale A/O process was carried out and the microbial community composition was analyzed by high-throughput sequencing. The results indicated that a better tolerance was achieved for sodium dodecyl benzene sulfonate, and the removal efficiencies of organic matter, ammonia nitrogen (NH4+-N), and total nitrogen (TN) were 82.87%, 66.47%, and 53.28% with the optimum hydraulic retention time (HRT), internal circulation and dissolved oxygen (DO) was 12 h, 200% and 2–3 mg/L, respectively. Additionally, high-throughput sequencing results demonstrated that Proteobacteria and Bacteroidetes were the dominant bacteria phylum, and the diversity of the microbial community in the stable-state period was richer than that in the start-up period.

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A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities

10.1101/2020.11.13.370387 ◽

2020 ◽

Author(s):

Justin P. Shaffer ◽

Clarisse Marotz ◽

Pedro Belda-Ferre ◽

Cameron Martino ◽

Stephen Wandro ◽

...

Keyword(s):

Microbial Community ◽

High Throughput ◽

High Throughput Sequencing ◽

Limit Of Detection ◽

Sequence Data ◽

Rna Virus ◽

Microbial Community Composition ◽

Rna Extraction ◽

Acid Extraction ◽

Dna And Rna

AbstractOne goal among microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused by the RNA virus SARS-CoV-2, has highlighted a gap in traditional DNA-based protocols, including the high-throughput methods we previously established as field standards. To enable simultaneous SARS-CoV-2 and microbial community profiling, we compare the relative performance of two total nucleic acid extraction protocols and our previously benchmarked protocol. We included a diverse panel of environmental and host-associated sample types, including body sites commonly swabbed for COVID-19 testing. Here we present results comparing the cost, processing time, DNA and RNA yield, microbial community composition, limit of detection, and well-to-well contamination, between these protocols.Accession numbersRaw sequence data were deposited at the European Nucleotide Archive (accession#: ERP124610) and raw and processed data are available at Qiita (Study ID: 12201). All processing and analysis code is available on GitHub (github.com/justinshaffer/Extraction_test_MagMAX).Methods summaryTo allow for downstream applications involving RNA-based organisms such as SARS-CoV-2, we compared the two extraction protocols designed to extract DNA and RNA against our previously established protocol for extracting only DNA for microbial community analyses. Across 10 diverse sample types, one of the two protocols was equivalent or better than our established DNA-based protocol. Our conclusion is based on per-sample comparisons of DNA and RNA yield, the number of quality sequences generated, microbial community alpha- and beta-diversity and taxonomic composition, the limit of detection, and extent of well-to-well contamination.

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High-throughput sequence-based analysis of milk kefir indicate an alteration in microbial community composition over time

Clinical Nutrition ESPEN ◽

10.1016/j.clnesp.2020.09.815 ◽

2020 ◽

Vol 40 ◽

pp. 675-676

Author(s):

P.G. Brasiel ◽

T. Costa de Almeida ◽

N. Lins de Andrade ◽

L. da Roza Corguinha ◽

B. Siqueira Lima da Silva ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

High Throughput ◽

Microbial Community Composition ◽

Over Time

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Effects of Andrographolide on Mouse Intestinal Microflora Based on High-Throughput Sequence Analysis

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.702885 ◽

2021 ◽

Vol 8 ◽

Author(s):

Haigang Wu ◽

Xian Wu ◽

Li Huang ◽

Chongmei Ruan ◽

Jinni Liu ◽

...

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

High Throughput ◽

High Throughput Sequencing ◽

Bacterial Resistance ◽

Microbial Community Composition ◽

Intestinal Flora ◽

Sequencing Analysis ◽

Beneficial Bacteria ◽

Intestinal Microbes

The intestinal flora is a micro-ecosystem that is closely linked to the overall health of the host. We examined the diversity and abundance of intestinal microorganisms in mice following the administration of andrographolide, a component of the Chinese medical herb Andrographis paniculata. Administration of andrographolide produces multiple beneficial effects including anti-inflammatory, antiviral and antibacterial effects but whether it directly influences the gut microbiota is not known. This study investigated whether the oral administration of andrographolide influences the intestinal microbiota and was compared with amoxicillin treatment as a positive control and water only as a negative control. We examined 21 cecal samples and conducted a high-throughput sequencing analysis based on V3-V4 variable region of the 16S rDNA genes. We found that the diversity and abundance of mouse gut microbiota decreased in direct proportion with the amoxicillin dose whereas andrographolide administration did not affect intestinal microbial community structure. The composition of intestinal microbes following andrographolide treatment was dominated by the Firmicutes while Bacteroidetes dominated the amoxicillin treatment group compared with the negative controls. Specifically, the f__Lachnospiraceae_ Unclassified, Lachnospiraceae_ NK4A136_group and Ruminococcaceae_ UCG-014 were enriched with andrographolide administration while Bacteroides, Klebsiella and Escherichia-Shigella significantly increased in the amoxicillin test groups. Amoxicillin administration altered the microbial community composition and structure by increasing the proportion of pathogenic to beneficial bacteria whereas andrographolide administration led to increases in the proportions and abundance of beneficial bacteria. This study provides a theoretical basis for finding alternatives to antibiotics to decrease bacterial resistance and restore intestinal floral imbalances.

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Predominance of methanogens over methanotrophs contributes to high methane emissions in rewetted fens

10.5194/bg-2018-184 ◽

2018 ◽

Cited By ~ 1

Author(s):

Xi Wen ◽

Viktoria Unger ◽

Gerald Jurasinski ◽

Franziska Koebsch ◽

Fabian Horn ◽

...

Keyword(s):

Microbial Community ◽

16S Rdna ◽

Community Composition ◽

High Throughput Sequencing ◽

Quantitative Polymerase Chain Reaction ◽

Microbial Community Composition ◽

Methane Emissions ◽

Methane Cycling ◽

Methane Fluxes ◽

Northeastern Germany

Abstract. The rewetting of drained peatlands alters peat geochemistry and often leads to sustained elevated methane emission. Although this methane is produced entirely by microbial activity, the distribution and abundance of methane-cycling microbes in rewetted peatlands, especially in fens, is rarely described. In this study, we compare the community composition and abundance of methane-cycling microbes in relation to peat porewater geochemistry in two rewetted fens in northeastern Germany, a coastal brackish fen and a freshwater riparian fen, with known high methane fluxes. We utilized 16S rDNA high-throughput sequencing and quantitative polymerase chain reaction on 16S rDNA, mcrA, and pmoA genes to determine microbial community composition and the abundance of total bacteria, methanogens, and methanotrophs. Electrical conductivity was more than three times higher in the coastal fen than in the riparian fen, averaging 5.3 and 1.5 mS cm−1, respectively. Porewater concentrations of terminal electron acceptors varied within and among the fens. This was also reflected in similarly high intra- and inter-site variations of microbial community composition. Despite these differences in environmental conditions and electron acceptor availability, we found a low abundance of methanotrophs and a high abundance of methanogens, represented in particular by Methanosaetaceae, in both fens. This suggests that rapid re/establishment of methanogens and slow re/establishment of methanotrophs contributes to prolonged increased methane emissions following rewetting.

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