Characterization of the microbial diversity in yacon spontaneous fermentation at 20°C

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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Isolation and characterization of lactic acid bacteria and yeasts from the Brazilian grape sourdough

Brazilian Journal of Pharmaceutical Sciences ◽

10.1590/s1984-82502014000200011 ◽

2014 ◽

Vol 50 (2) ◽

pp. 321-327 ◽

Cited By ~ 9

Author(s):

Krischina Singer Aplevicz ◽

Jaciara Zarpellon Mazo ◽

Eunice Cassanego Ilha ◽

Andréia Zilio Dinon ◽

Ernani Sebastião Sant´Anna

Keyword(s):

Lactic Acid ◽

Lactic Acid Bacteria ◽

Bakery Products ◽

Spontaneous Fermentation ◽

Isolation And Characterization ◽

Genotypic Characterization ◽

Sequencing Method ◽

Microorganism Identification ◽

Niagara Rosada

Sourdough is a mixture of flour and water fermented by lactic acid bacteria and yeast, with a large use in bakery products. This study was developed with Brazilian grape (Niagara rosada) sourdough obtained from spontaneous fermentation. The aim of this work was to characterize genotypic and phenotypically lactic acid bacteria and yeasts isolated from sourdough. The phenotypic identification for bacteria and yeasts was performed by using the kit API50CHL and 20CAUX and the genotypic characterization was performed by sequencing method. A total of four isolated strains were analyzed in this study. Two of these strains were phenotypically and genotypic identified as Lactobacillus paracasei and one as Saccharomyces cerevisiae. Another sample phenotypically identified as Candida pelliculosa did not show the same identity by sequencing. It shows the need to use phenotypic and genotypic characterization associated for the correct microorganism identification.

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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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Technological Feature Assessment of Lactic Acid Bacteria Isolated from Cricket Powder’s Spontaneous Fermentation as Potential Starters for Cricket-Wheat Bread Production

Foods ◽

10.3390/foods9091322 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1322

Author(s):

Viola Galli ◽

Manuel Venturi ◽

Niccolò Pini ◽

Lisa Granchi

Keyword(s):

Lactic Acid ◽

Lactic Acid Bacteria ◽

Wheat Bread ◽

Aminopeptidase Activity ◽

Spontaneous Fermentation ◽

Baked Goods ◽

Isolation And Characterization ◽

Enterococcus Spp ◽

Bread Production

The bacterial community profile of cricket powder highlighted the presence of four main genera: Bacteroides spp., Parabacteroides spp., Lactococcus spp., and Enterococcus spp. The spontaneous fermentation of cricket powder allowed for the isolation and characterization of seven lactic acid bacteria strains belonging to six species: Latilactobacillus curvatus, Lactiplantibacillus plantarum, Latilactobacillus sakei, Lactococcus garvieae, Weissella confusa, and Enterococcus durans. The strains were characterized and selected according to different technological properties. L. plantarum CR L1 and L. curvatus CR L13 showed the best performance in terms of general aminopeptidase activity, acidification, and growth rate in MRS broth and in dough with cricket powder and wheat flour, as well as robustness during consecutive backslopping. Thus, they were used as starter-mixed to produce sourdough to manufacture bread fortified with 20% cricket powder. The addition of cricket powder led to a significant increase of protein (up to 94%) and lipid content, from 0.7 up to 6 g/100 g of bread. Spontaneous fermentation represents a source of microbial diversity that can be exploited in order to obtain potential starters for food with innovative ingredients. Edible insects powder can be successfully added in leavened baked goods to enhance their nutritional value.

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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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