scholarly journals Uterine Microbiota Progression from Calving until Establishment of Metritis in Dairy Cows

2015 ◽  
Vol 81 (18) ◽  
pp. 6324-6332 ◽  
Author(s):  
Soo Jin Jeon ◽  
Achilles Vieira-Neto ◽  
Mohanathas Gobikrushanth ◽  
Rodolfo Daetz ◽  
Rodolfo D. Mingoti ◽  
...  
Keyword(s):  
Dairy Cows ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Heat Map ◽  
Content Type ◽  
Illumina Miseq Platform ◽  
Uterine Health ◽  
Miseq Platform ◽  
The 16S Rrna Gene

ABSTRACTThe objective of this study was to evaluate the progression of the uterine microbiota from calving until establishment of metritis. Uterine swabs (n= 72) collected at 0, 2, and 6 ± 2 days postpartum (dpp) from 12 metritic and 12 healthy cows were used for metagenomic sequencing of the 16S rRNA gene on the Illumina MiSeq platform. A heat map showed that uterine microbiota was established at calving. The microbiota changed rapidly from 0 to 6 ± 2 dpp, with a decrease in the abundance ofProteobacteriaand an increase in the abundance ofBacteroidetesandFusobacteria, which were dominant in metritic cows. Uterine microbiota composition was shared; however, metritic and healthy cows could be discriminated using relative abundance of bacterial genera at 0, 2, and 6 ± 2 dpp.Bacteroideswas the main genus associated with metritis because it was the only genus that showed significantly greater abundance in cows with metritis. As the abundance ofBacteroidesorganisms increased, the uterine discharge score, a measure of uterine health, worsened.Fusobacteriumwas also an important genus associated with metritis becauseFusobacteriumabundance increased asBacteroidesabundance increased and the uterine discharge score worsened as the abundance increased. The correlation with uterine discharge score and the correlation withBacteroidesorFusobacteriumshowed that other bacteria, such asHelcoccocus,Filifactor, andPorphyromonas, were also associated with metritis. There were also bacteria associated with uterine health, such as “CandidatusBlochmannia,”Escherichia,Sneathia, andPedobacter.

scholarly journals Faecal Microbiota of Dogs Offered a Vegetarian Diet with or without the Supplementation of Feather Meal and either Cornmeal, Rye or Fermented Rye: A Preliminary Study

2020 ◽  
Vol 8 (9) ◽  
pp. 1363
Author(s):  
Julia Hankel ◽  
Amr Abd El-Wahab ◽  
Richard Grone ◽  
Birgit Keller ◽  
Eric Galvez ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Hypervariable Region ◽  
Illumina Miseq ◽  
Vegetarian Diet ◽  
Rrna Gene ◽  
Feather Meal ◽  
Illumina Miseq Platform ◽  
Faecal Samples ◽  
Miseq Platform ◽  
Preliminary Study

Anthropomorphism of dogs has affected feeding and the choice of components present in diets for dogs. Conflicting trends are present: raw or vegetarian appear more prevalent. Animal-derived proteins seem to have unfavourable impacts on intestinal microflora by decreasing the presence of Bacteroidetes. This preliminary study evaluates whether effects of diets with animal proteins on intestinal microbiota can be compensated by the addition of certain carbohydrates to dog diet. Eight female beagles were included in a cross-over study and fed a vegetarian diet or the same diet supplemented with feather meal (2.7%) and either 20% of cornmeal, fermented or non-fermented rye (moisture content of the diets about 42%). A 16S rRNA gene amplification was performed within the hypervariable region V4 on faecal samples and sequenced with the Illumina MiSeq platform. The Firmicutes/Bacteroidetes ratio tended to shift to the advantage of Firmicutes when feather meal and cornmeal were added (Firmicutes/Bacteroidetes ratio of 5.12 compared to 2.47 when offered the vegetarian diet) and tended to switch back to the advantage of Bacteroidetes if rye: fermented (2.17) or not (1.03) was added. The addition of rye might have the potential to compensate possible unfavourable effects of diets with animal proteins on intestinal microbiota of dogs.

scholarly journals Resolving microbial microdiversity with high accuracy full length 16S rRNA Illumina sequencing

2014 ◽  
Author(s):  
Catherine Burke ◽  
Aaron E Darling
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Single Molecule ◽  
Illumina Miseq ◽  
Full Length ◽  
Rrna Gene ◽  
Variable Regions ◽  
Phylogenetic Resolution ◽  
Miseq Platform ◽  
The 16S Rrna Gene

We describe a method for sequencing full-length 16S rRNA gene amplicons using the high throughput Illumina MiSeq platform. The resulting sequences have about 100-fold higher accuracy than standard Illumina reads and are chimera filtered using information from a single molecule dual tagging scheme that boosts the signal available for chimera detection. We demonstrate that the data provides fine scale phylogenetic resolution not available from Illumina amplicon methods targeting smaller variable regions of the 16S rRNA gene.

scholarly journals Ultrahigh-Throughput Multiplexing and Sequencing of >500-Base-Pair Amplicon Regions on the Illumina HiSeq 2500 Platform

mSystems ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Johanna B. Holm ◽  
Michael S. Humphrys ◽  
Courtney K. Robinson ◽  
Matthew L. Settles ◽  
Sandra Ott ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sequence Data ◽  
Microbial Community Composition ◽  
Pcr Amplification ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Illumina Hiseq ◽  
Illumina Miseq Platform ◽  
Miseq Platform

ABSTRACT Amplification, sequencing, and analysis of the 16S rRNA gene affords characterization of microbial community composition. As this tool has become more popular and amplicon-sequencing applications have grown in the total number of samples, growth in sample multiplexing is becoming necessary while maintaining high sequence quality and sequencing depth. Here, modifications to the Illumina HiSeq 2500 platform are described which produce greater multiplexing capabilities and 300-bp paired-end reads of higher quality than those produced by the current Illumina MiSeq platform. To improve the feasibility and flexibility of this method, a 2-step PCR amplification protocol is also described that allows for targeting of different amplicon regions, and enhances amplification success from samples with low bacterial bioburden. IMPORTANCE Amplicon sequencing has become a popular and widespread tool for surveying microbial communities. Lower overall costs associated with high-throughput sequencing have made it a widely adopted approach, especially for projects that necessitate sample multiplexing to eliminate batch effect and reduced time to acquire data. The method for amplicon sequencing on the Illumina HiSeq 2500 platform described here provides improved multiplexing capabilities while simultaneously producing greater quality sequence data and lower per-sample cost relative to those of the Illumina MiSeq platform without sacrificing amplicon length. To make this method more flexible for various amplicon-targeted regions as well as improve amplification from low-biomass samples, we also present and validate a 2-step PCR library preparation method.

scholarly journals Methanogenic Population and CH4Production in Swedish Dairy Cows Fed Different Levels of Forage

2012 ◽  
Vol 78 (17) ◽  
pp. 6172-6179 ◽  
Author(s):  
R. Danielsson ◽  
A. Schnürer ◽  
V. Arthurson ◽  
J. Bertilsson
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dairy Cows ◽  
Rflp Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Methanobrevibacter Ruminantium ◽  
Gene Libraries ◽  
Swedish Dairy ◽  
The 16S Rrna Gene

ABSTRACTMethanogenic community structure, methane production (CH4), and volatile fatty acid (VFA) profiles were investigated in Swedish dairy cows fed a diet with a forage/concentrate ratio of 500/500 or 900/100 g/kg of dry matter (DM) of total DM intake (DMI). The rumen methanogenic population was evaluated using terminal restriction fragment length polymorphism (T-RFLP) analysis, 16S rRNA gene libraries, and quantitative real-time PCR (qRT-PCR). Mean CH4yields did not differ (P> 0.05) between diets, being 16.9 and 20.2 g/kg DMI for the 500/500 and 900/100 diets, respectively. The T-RFLP analysis revealed that populations differed between individual cows and that each individual population responded differently to the diets. The 16S rRNA gene libraries revealed thatMethanobrevibacterspp. dominated for both diets. CH4production was positively correlated with a dominance of sequences representing T-RFs related toMethanobrevibacter thaueri,Methanobrevibacter millerae, andMethanobrevibacter smithiirelative toMethanobrevibacter ruminantiumandMethanobrevibacter olleyae. Total numbers of methanogens and total numbers ofMethanobacterialeswere significantly higher with the 500/500 diet (P< 0.0004 andP< 0.002, respectively). However, no relationship was found between CH4production and total number of methanogens. No differences were seen in total VFA, propionic acid, or acetic acid contents, but the molar proportion of butyric acid in the rumen was higher for the 500/500 diet than for the 900/100 diet (P< 0.05). Interestingly, the results also revealed that a division of the identified methanogenic species into two groups, suggested in the work of King et al. (E. E. King, R. P. Smith, B. St-Pierre, and A. D. G. Wright, Appl. Environ. Microbiol.77:5682–5687, 2011), increased the understanding of the variation in CH4production between different cows.

scholarly journals Ultra-high throughput multiplexing and sequencing of >500 bp amplicon regions on the Illumina HiSeq 2500 platform

2018 ◽  
Author(s):  
Johanna B. Holm ◽  
Michael S. Humphrys ◽  
Courtney K. Robinson ◽  
Matthew L. Settles ◽  
Sandra Ott ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Microbial Community Composition ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Illumina Hiseq ◽  
Illumina Miseq Platform ◽  
Miseq Platform

AbstractAmplification, sequencing and analysis of the 16S rRNA gene affords characterization of microbial community composition. As this tool has become more popular and amplicon-sequencing applications have grown in the total number of samples, growth in sample multiplexing is becoming necessary while maintaining high sequence quality and sequencing depth. Here, modifications to the Illumina HiSeq 2500 platform are described which produce greater multiplexing capabilities and 300 bp paired-end reads of higher quality than produced by the current Illumina MiSeq platform. To improve the feasibility and flexibility of this method, a 2-Step PCR amplification protocol is also described that allows for targeting of different amplicon regions, thus improving amplification success from low bacterial bioburden samples.ImportanceAmplicon sequencing has become a popular and widespread tool for surveying microbial communities. Lower overall costs associated with high throughput sequencing have made it a widely-adopted approach, especially for projects which necessitate sample multiplexing to eliminate batch effect and reduced time to acquire data. The method for amplicon sequencing on the Illumina HiSeq 2500 platform described here provides improved multiplexing capabilities while simultaneously producing greater quality sequence data and lower per sample cost relative to the Illumina MiSeq platform, without sacrificing amplicon length. To make this method more flexible to various amplicon targeted regions as well as improve amplification from low biomass samples, we also present and validate a 2-Step PCR library preparation method.

scholarly journals Draft Genome Sequence of Bacillus subtilis subsp. subtilis MD 32, Isolated from the Korean Fermented Food Kimchi

2021 ◽  
Vol 10 (3) ◽  
Author(s):  
Ji-Young Lee ◽  
Gyu-Sung Cho ◽  
Charles M. A. P. Franz ◽  
Dae-Ook Kang
Keyword(s):  
Bacillus Subtilis ◽  
Draft Genome ◽  
Noncoding Rnas ◽  
Gc Content ◽  
Illumina Miseq ◽  
Fermented Food ◽  
Content Type ◽  
Illumina Miseq Platform ◽  
Miseq Platform ◽  
Subtilis Subsp

ABSTRACT Bacillus subtilis subsp. subtilis MD 32 was isolated from kimchi. The strain was sequenced using an Illumina MiSeq platform, and the genome size was 4,238,856 bp with a GC content of 43.41 mol%. The genome encoded 4,396 proteins, with 45 tRNAs, 6 rRNAs, and 5 noncoding RNAs.

scholarly journals Optimized Protocol for Simple Extraction of High-Quality Genomic DNA from Clostridium difficile for Whole-Genome Sequencing

2015 ◽  
Vol 53 (7) ◽  
pp. 2329-2331 ◽  
Author(s):  
James Heng Chiak Sim ◽  
Victoria Anikst ◽  
Akshar Lohith ◽  
Nader Pourmand ◽  
Niaz Banaei
Keyword(s):  
Clostridium Difficile ◽  
Genomic Dna ◽  
Illumina Miseq ◽  
High Quality ◽  
Content Type ◽  
Illumina Miseq Platform ◽  
Optimized Protocol ◽  
High Quality Sequence ◽  
Miseq Platform ◽  
Simple Extraction

Successful sequencing of theClostridium difficilegenome requires high-quality genomic DNA (gDNA) as the starting material. gDNA extraction using conventional methods is laborious. We describe here an optimized method for the simple extraction ofC. difficilegDNA using the QIAamp DNA minikit, which yielded high-quality sequence reads on the Illumina MiSeq platform.

scholarly journals An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform

Microbiome ◽  
2014 ◽  
Vol 2 (1) ◽  
pp. 6 ◽  
Author(s):  
Douglas W Fadrosh ◽  
Bing Ma ◽  
Pawel Gajer ◽  
Naomi Sengamalay ◽  
Sandra Ott ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Illumina Miseq Platform ◽  
Miseq Platform ◽  
Rrna Gene Sequencing

scholarly journals Draft Genome Sequences of Two Novel Salmonella enterica subsp. enterica Strains Isolated from Low-Moisture Foods with Applications in Food Safety Research

2018 ◽  
Vol 6 (13) ◽  
Author(s):  
Devon R. Radford ◽  
Carlos G. Leon-Velarde ◽  
Shu Chen ◽  
Amir M. Hamidi Oskouei ◽  
Sampathkumar Balamurugan
Keyword(s):  
Salmonella Enterica ◽  
De Novo ◽  
Draft Genome ◽  
Illumina Miseq ◽  
Consensus Method ◽  
Genome Sequences ◽  
Content Type ◽  
Illumina Miseq Platform ◽  
Safety Research ◽  
Miseq Platform

ABSTRACT The genomes of two strains of Salmonella enterica subsp. enterica serovar Cubana and serovar Muenchen, isolated from dry hazelnuts and chia seeds, respectively, were sequenced using the Illumina MiSeq platform, assembled de novo using the overlap-layout-consensus method, and aligned to their respective most identical sequence genome scaffolds using MUMMER and BLAST searches.

scholarly journals Complete Genome Sequence of Listeria monocytogenes DFPST0073, Isolated from Imported Mexican Soft Cheese

2018 ◽  
Vol 6 (23) ◽  
Author(s):  
Joelle K. Salazar ◽  
Lauren J. Gonsalves ◽  
Kristin M. Schill ◽  
Maria Sanchez Leon ◽  
Nathan Anderson ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Complete Genome Sequence ◽  
Genome Annotation ◽  
Prokaryotic Genome ◽  
Illumina Miseq ◽  
Annotation Pipeline ◽  
Content Type ◽  
Illumina Miseq Platform ◽  
Soft Cheese ◽  
Miseq Platform

ABSTRACT The genome of Listeria monocytogenes strain DFPST0073, isolated from imported fresh Mexican soft cheese in 2003, was sequenced using the Illumina MiSeq platform. Reads were assembled using SPAdes, and genome annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline.

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