Characterization of activity and microbial diversity of typical types of Daqu for traditional Chinese vinegar

Abstract Objective: Currently the majority of non-culturable microbes in sea water are yet to be discovered, Nanopore offers a solution to overcome the challenging tasks to identify the genomes and complex composition of oceanic microbiomes. In this study we evaluate the utility of Oxford Nanopore Technologies (ONT) sequencing to characterize microbial diversity in seawater from multiple locations. We compared the microbial species diversity of retrieved environmental samples from two different locations and time points.Results: With only three ONT flow cells we were able to identify thousands of organisms, including bacteriophages, from which a large part at species level. It was possible to assemble genomes from environmental samples with Flye. In several cases this resulted in >1 Mbp contigs and in the particular case of a Thioglobus singularis species it even produced a near complete genome. k-mer analysis reveals that a large part of the data represents species of which close relatives have not yet been deposited to the database. These results show that our approach is suitable for scalable genomic investigations such as monitoring oceanic biodiversity and provides a new platform for education in biodiversity.

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Characterization of fungus microbial diversity in healthy and diarrheal yaks in Gannan region of Tibet Autonomous Prefecture

Acta Tropica ◽

10.1016/j.actatropica.2018.02.017 ◽

2018 ◽

Vol 182 ◽

pp. 14-26 ◽

Cited By ~ 8

Author(s):

Kun Li ◽

Khalid Mehmood ◽

Hui Zhang ◽

Xiong Jiang ◽

Muhammad Shahzad ◽

...

Keyword(s):

Microbial Diversity

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Characterization of the pathoimmunology of necrotizing enterocolitis reveals novel therapeutic opportunities

Nature Communications ◽

10.1038/s41467-020-19400-w ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Steven X. Cho ◽

Ina Rudloff ◽

Jason C. Lao ◽

Merrin A. Pang ◽

Rimma Goldberg ◽

...

Keyword(s):

Microbial Diversity ◽

Preterm Infants ◽

Necrotizing Enterocolitis ◽

Lymphoid Cells ◽

Immune Homeostasis ◽

Blood Monocytes ◽

Type 3 ◽

Lower Birthweight ◽

Novel Therapeutic

AbstractNecrotizing enterocolitis (NEC) is a severe, currently untreatable intestinal disease that predominantly affects preterm infants and is driven by poorly characterized inflammatory pathways. Here, human and murine NEC intestines exhibit an unexpected predominance of type 3/TH17 polarization. In murine NEC, pro-inflammatory type 3 NKp46−RORγt+Tbet+ innate lymphoid cells (ILC3) are 5-fold increased, whereas ILC1 and protective NKp46+RORγt+ ILC3 are obliterated. Both species exhibit dysregulation of intestinal TLR repertoires, with TLR4 and TLR8 increased, but TLR5-7 and TLR9-12 reduced. Transgenic IL-37 effectively protects mice from intestinal injury and mortality, whilst exogenous IL-37 is only modestly efficacious. Mechanistically, IL-37 favorably modulates immune homeostasis, TLR repertoires and microbial diversity. Moreover, IL-37 and its receptor IL-1R8 are reduced in human NEC epithelia, and IL-37 is lower in blood monocytes from infants with NEC and/or lower birthweight. Our results on NEC pathomechanisms thus implicate type 3 cytokines, TLRs and IL-37 as potential targets for novel NEC therapies.

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Microbial Diversity of Chromium-Contaminated Soils and Characterization of Six Chromium-Removing Bacteria

Environmental Management ◽

10.1007/s00267-016-0675-5 ◽

2016 ◽

Vol 57 (6) ◽

pp. 1319-1328 ◽

Cited By ~ 25

Author(s):

Zhiguo He ◽

Yuting Hu ◽

Zhen Yin ◽

Yuehua Hu ◽

Hui Zhong

Keyword(s):

Microbial Diversity ◽

Contaminated Soils

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Microbial diversity characterization of seawater in a pilot study using Oxford Nanopore Technologies long-read sequencing

10.21203/rs.3.rs-17068/v1 ◽

2020 ◽

Author(s):

Michael Liem ◽

A.J.G. Regensburg-Tuïnk ◽

C.V. Henkel ◽

H.P. Spaink

Keyword(s):

Microbial Diversity ◽

Environmental Samples ◽

Sea Water ◽

Flow Cells ◽

Oxford Nanopore ◽

Challenging Tasks ◽

Long Read ◽

Close Relatives ◽

Oxford Nanopore Technologies

Abstract Objective Currently the majority of non-culturable microbes in sea water are yet to be discovered, Nanopore offers a solution to overcome the challenging tasks to identify the genomes and complex composition of oceanic microbiomes. In this study we evaluate the utility of Oxford Nanopore Technologies (ONT) sequencing to characterize microbial diversity in seawater from multiple locations. We compared the microbial species diversity of retrieved environmental samples from two different locations and time points. Results With only three ONT flow cells we were able to identify thousands of organisms, including bacteriophages, from which a large part at species level. It was possible to assemble genomes from environmental samples with Flye. In several cases this resulted in >1 Mbp contigs and in the particular case of a Thioglobus singularis species it even produced a near complete genome. k-mer analysis reveals that a large part of the data represents species of which close relatives have not yet been deposited to the database. These results show that our approach is suitable for scalable genomic investigations such as monitoring oceanic biodiversity and provides a new platform for education in biodiversity.

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