scholarly journals Characterization of the Microbial Communities in Rumen Fluid Inoculated Reactors for the Biogas Digestion of Wheat Straw

2017 ◽  
Vol 9 (2) ◽  
pp. 243 ◽  
Author(s):  
Ke Li ◽  
Haoran Zhu ◽  
Yajie Zhang ◽  
Hongxun Zhang
Keyword(s):  
Microbial Communities ◽  
Wheat Straw ◽  
Rumen Fluid ◽  
Biogas Digestion

scholarly journals Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn’s Disease

2016 ◽  
Vol 2 (5) ◽  
pp. 563-566.e5 ◽  
Author(s):  
Chandra Sekhar Pedamallu ◽  
Ami S. Bhatt ◽  
Susan Bullman ◽  
Sharyle Fowler ◽  
Samuel S. Freeman ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Microbial Communities

scholarly journals Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal Microbiota

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 405
Author(s):  
Anna Matysiak ◽  
Michal Kabza ◽  
Justyna A. Karolak ◽  
Marcelina M. Jaworska ◽  
Malgorzata Rydzanicz ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Ocular Surface ◽  
Molecular Techniques ◽  
Corneal Tissue ◽  
Rna Seq ◽  
Microbiome Composition ◽  
Viral Sequences ◽  
Pcr Techniques ◽  
Unmapped Reads

The ocular microbiome composition has only been partially characterized. Here, we used RNA-sequencing (RNA-Seq) data to assess microbial diversity in human corneal tissue. Additionally, conjunctival swab samples were examined to characterize ocular surface microbiota. Short RNA-Seq reads, obtained from a previous transcriptome study of 50 corneal tissues, were mapped to the human reference genome GRCh38 to remove sequences of human origin. The unmapped reads were then used for taxonomic classification by comparing them with known bacterial, archaeal, and viral sequences from public databases. The components of microbial communities were identified and characterized using both conventional microbiology and polymerase chain reaction (PCR) techniques in 36 conjunctival swabs. The majority of ocular samples examined by conventional and molecular techniques showed very similar microbial taxonomic profiles, with most of the microorganisms being classified into Proteobacteria, Firmicutes, and Actinobacteria phyla. Only 50% of conjunctival samples exhibited bacterial growth. The PCR detection provided a broader overview of positive results for conjunctival materials. The RNA-Seq assessment revealed significant variability of the corneal microbial communities, including fastidious bacteria and viruses. The use of the combined techniques allowed for a comprehensive characterization of the eye microbiome’s elements, especially in aspects of microbiota diversity.

Characterization of degradation products from alkaline wet oxidation of wheat straw

2002 ◽  
Vol 82 (1) ◽  
pp. 15-26 ◽  
Author(s):  
Helene B Klinke ◽  
Birgitte K Ahring ◽  
Anette S Schmidt ◽  
Anne Belinda Thomsen
Keyword(s):  
Wheat Straw ◽  
Degradation Products ◽  
Wet Oxidation

Molecular characterization of microbial communities in deep coal seam groundwater of northern Japan

Geobiology ◽  
2007 ◽  
Vol 5 (4) ◽  
pp. 423-433 ◽  
Author(s):  
S. SHIMIZU ◽  
M. AKIYAMA ◽  
T. NAGANUMA ◽  
M. FUJIOKA ◽  
M. NAKO ◽  
...  
Keyword(s):  
Coal Seam ◽  
Microbial Communities ◽  
Molecular Characterization ◽  
Northern Japan

Characterization of microbial communities and fungal metabolites on field grown strawberries from organic and conventional production

2013 ◽  
Vol 160 (3) ◽  
pp. 313-322 ◽  
Author(s):  
Birgit Jensen ◽  
Inge M.B. Knudsen ◽  
Birgitte Andersen ◽  
Kristian Fog Nielsen ◽  
Ulf Thrane ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Fungal Metabolites ◽  
Conventional Production

scholarly journals Future Climate Alters Pathogens-Microbiome Co-occurrence Networks in Wheat Straw Residues during Decomposition

Proceedings ◽  
2021 ◽  
Vol 66 (1) ◽  
pp. 22
Author(s):  
Sara Fareed Mohamed Wahdan ◽  
François Buscot ◽  
Witoon Purahong
Keyword(s):  
Network Analysis ◽  
Microbial Communities ◽  
Wheat Straw ◽  
Pathogenic Fungi ◽  
Future Climate ◽  
Plant Residues ◽  
Plant Pathogenic Fungi ◽  
Plant Growth Promoting Bacteria ◽  
Ambient Conditions ◽  
Ecological Functions

The return of plant residues to the ground is used to promote soil carbon sequestration, improve soil structure, reduce evaporation, and help to fix additional carbon dioxide in the soil. The microbial communities with diverse ecological functions that colonize plant residues during decomposition are expected to be highly dynamic. We aimed to characterize microbial communities colonizing wheat straw residues and their ecological functions during the early phase of straw decomposition. The experiment, run in Central Germany, was conducted in a conventional farming system under both ambient conditions and a future climate scenario expected in 50–70 years from now. We used MiSeq illumina sequencing and network analysis of bacterial 16S rRNA and fungal ITS genes. Our results show that future climate alters the dynamics of bacterial and fungal communities during decomposition. We detected various microbial ecological functions within wheat straw residues such as plant growth-promoting bacteria, N-fixing bacteria, saprotrophs, and plant pathogenic fungi. Interestingly, plant pathogenic fungi dominated (~87% of the total sequences) within the wheat residue mycobiome under both ambient and future climate conditions. Therefore, we applied co-occurrence network analysis to predict the potential impacts of climate change on the interaction between pathogenic community and other bacterial and fungal microbiomes. The network under ambient climate consisted of 91 nodes and 129 correlations (edges). The highest numbers of connections were detected for the pathogens Mycosphaerella tassiana and Neosetophoma rosigena. The network under future climate consisted of 100 nodes and 170 correlations. The highest numbers of connections were detected for the pathogens Pseudopithomyces rosae and Gibellulopsis piscis. We conclude that the future climate significantly changes the interactions between plant pathogenic fungi and other microorganisms during the early phrase of decomposition.

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

2018 ◽  
Vol 17 (1) ◽  
pp. 37-49 ◽  
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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