Cigarette Smoking Modulation of Saliva Microbial Composition and Cytokine Levels

Tobacco use has been implicated as an immunomodulator in the oral cavity and contributes to the development of oral cancer. In the present study, we investigated the effects of cigarette smoking on bacterial diversity and host responses compared to healthy nonsmoking controls. Saliva samples were collected from eighteen smokers and sixteen nonsmoking individuals by passive drool. The 16S rRNA gene was used to characterize the salivary microbiome by using the Illumina MiSeq platform. Cytokine and chemokine expression analyses were performed to evaluate the host response. Significant differences in cytokine and chemokine expression levels of MDC, IL-10, IL-5, IL-2, IL-4, IL-7, adrenocorticotropic hormone (ACTH), insulin, and leptin were observed between smokers and nonsmokers. Taxonomic analyses revealed differences between the two groups, and some bacterial genera associated with the smokers group had correlations with hormones and cytokines identified as statistically different between smokers and nonsmokers. These factors have been associated with inflammation and carcinogenesis in the oral cavity. The data obtained may aid in the identification of the interactions between the salivary microbiome, host inflammatory responses, and metabolism in smokers.

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Descriptive Bacterial and Fungal Characterization of Propolis Using Ultra-High-Throughput Marker Gene Sequencing

Insects ◽

10.3390/insects10110402 ◽

2019 ◽

Vol 10 (11) ◽

pp. 402 ◽

Cited By ~ 1

Author(s):

Jose F. Garcia-Mazcorro ◽

Jorge R. Kawas ◽

Alicia G. Marroquin-Cardona

Keyword(s):

Apis Mellifera ◽

Marker Gene ◽

Illumina Miseq ◽

Rrna Gene ◽

Microbial Composition ◽

Microbial World ◽

Bacterial Microbiota ◽

Miseq Platform ◽

Marker Gene Sequencing

Bees harbor microorganisms that are important for host health, physiology, and survival. Propolis helps modulate the immune system and health of the colony, but little information is available about its microbial constituents. Total genomic DNA from samples of natural propolis from Apis mellifera production hives from four locations in Mexico were used to amplify a region of the 16S rRNA gene (bacteria) and the internal transcriber spacer (fungi), using PCR. The Illumina MiSeq platform was used to sequence PCR amplicons. Extensive variation in microbial composition was observed between the propolis samples. The most abundant bacterial group was Rhodopila spp. (median: 14%; range: 0.1%–27%), a group with one of the highest redox potential in the microbial world. Other high abundant groups include Corynebacterium spp. (median: 8.4%; 1.6%–19.5%) and Sphingomonas spp. (median: 5.9%; 0.03%–14.3%), a group that has been used for numerous biotechnological applications because of its biodegradative capabilities. Bacillus and Prevotella spp. alone comprised as much as 88% (53% and 35%, respectively) of all bacterial microbiota in one sample. Candida (2%–43%), Acremonium (0.03%–25.2%), and Aspergillus (0.1%–43%) were among the most abundant fungi. The results contribute to a better understanding of the factors associated with the health of Apis mellifera production hives.

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PSIX-6 Gastrointestinal microbiome of calves fed solid diets containing different levels and sources of NDF

Journal of Animal Science ◽

10.1093/jas/skaa278.729 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 418-419

Author(s):

Gercino F Virgínio Júnior ◽

Milaine Poczynek ◽

Ana Paula Silva ◽

Ariany Toledo ◽

Amanda Cezar ◽

...

Keyword(s):

Illumina Miseq ◽

Diversity Indices ◽

Dairy Calves ◽

Rrna Gene ◽

Gastrointestinal Microbiome ◽

Fecal Microbiome ◽

Miseq Platform ◽

Holstein Calves ◽

Ad Libitum ◽

Different Levels

Abstract Different levels and sources of NDF can modify the gastrointestinal microbiome. This study evaluated 18 Holstein calves housed in not-bedded suspended individual cages and fed one of three treatments: 22NDF - conventional starter containing 22% NDF (n = 7); 31NDF - starter with 31% NDF, replacing part of the corn by soybean hull (n = 6); and 22NDF+H - conventional starter with 22% NDF plus coast-cross hay ad libitum (n = 5). All animals received 4 L of milk replacer daily (24% CP; 18.5% fat; diluted to 12.5% solids), divided into two meals, being weaned at 8th week of age. After weaning, animals were housed in tropical shelters, fed with the respective solid diet and coast-cross hay ad libitum for all treatments. To evaluate the microbiome, ruminal fluid samples were collected using a modified Geishauser oral probe at weeks 2, 4, 6, 8 and 10, two hours after the morning feeding, and fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8 and 10. The microbial community was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene that was amplified by PCR and sequenced by the Illumina MiSeq platform. Ruminal microbiome had no differences in diversity for the effects of weeks, treatments or interaction of both factors (Table 1). In feces, the diversity indices and evenness were higher for 22NDF+H when compared to 22NDF, with no difference for 31NDF. All indices were significantly affected by calves age. At birth, calves had the greatest diversity and richness. Week 1 and 2 had less evenness and diversity. Bacteroidota, Firmicutes_A and Firmicutes_C were the most abundant phylum in rumen and feces. The supply of hay was only effective in modifying the fecal microbiome of dairy calves, suggesting a resilience in the ruminal microbiome.

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Influence of Agaricus Bisporus Establishment and Fungicidal Treatments on Casing Soil Metataxonomy During Mushroom Cultivation

10.21203/rs.3.rs-956209/v1 ◽

2021 ◽

Author(s):

Maria Luisa Tello ◽

Rebeca Lavega ◽

Margarita Pérez ◽

Antonio J. Pérez ◽

Michael Thon ◽

...

Keyword(s):

Agaricus Bisporus ◽

Illumina Miseq ◽

Biological Efficiency ◽

Its2 Region ◽

Rrna Gene ◽

Mushroom Cultivation ◽

Microbial Composition ◽

Mycelium Growth ◽

Bacterial Phyla ◽

The Impact

Abstract The cultivation of edible mushroom is an emerging sector with a potential yet to be discovered. Unlike plants, it is a less developed agriculture where many studies are lacking to optimize the cultivation. Mushrooms are a source of resources still to be revealed, which have applications not only in food, but in many other sectors such as health, industry and biotechnology. Mushroom cultivation consists of the development of selective substrates through composting where the mushroom grows via solid fermentation process. In case of Agaricus bisporus, the compost fully colonized by mycelium hardly produces mushrooms and it is necessary to apply a casing layer with certain physical, chemical and biological characteristics to shift from the vegetative mycelium to the reproductive one, where the native microbiota plays crucial roles. Currently, the industry faces a challenge to substitute the actual peat based casing materials due to the limited natural resources and the impact on the peatlands where peat is extracted.In this work we have employed high-throughput techniques by next generation sequencing to screen the microbial structure of casing soil employed in mushroom cultivation while sequencing V3-V4 of the 16S rRNA gene for bacteria and the ITS2 region of rRNA for fungi in an Illumina MiSeq. In addition, the microbiome dynamics and evolution (bacterial and fungal communities) in peat based casing along the process of incubation of Agaricus bisporus have been studied, while comparing the effect of fungicidal treatment (Chlorothalonil and Metrafenone). Statistically significant changes in populations of bacteria and fungi were observed. Microbial composition differed significantly based on incubation day, changing radically from the original communities to a specific microbial composition adapted to enhance the A. bisporus mycelium growth. Chlorothalonil treatment seems to delay casing colonization by A. bisporus. Proteobacteria and Bacteroidota appeared as the most dominant bacterial phyla. We observed a great change in the structure of the bacteria populations between day 0 and the following days. Fungi populations changed more gradually, A. bisporus displacing the rest of the species as the cultivation cycle progresses. A better understanding of the microbial communities in the casing will hopefully allow us to increase the biological efficiency during production as well as possibly help us to have a clearer view of the microbial community-pathogen relationships as they are directly related to disease development.

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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

Microorganisms ◽

10.3390/microorganisms8091363 ◽

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.

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A Plant Growth-Promoting Microbial Soil Amendment Dynamically Alters the Strawberry Root Bacterial Microbiome

Scientific Reports ◽

10.1038/s41598-019-53623-2 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 3

Author(s):

Siwen Deng ◽

Heidi M.-L. Wipf ◽

Grady Pierroz ◽

Ted K. Raab ◽

Rajnish Khanna ◽

...

Keyword(s):

Bacterial Community ◽

Soil Amendment ◽

Bacterial Community Composition ◽

Illumina Miseq ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Bacterial Microbiome ◽

Plant Growth Promoting ◽

Miseq Platform ◽

Soil Rhizosphere

AbstractDespite growing interest in utilizing microbial-based methods for improving crop growth, much work still remains in elucidating how beneficial plant-microbe associations are established, and what role soil amendments play in shaping these interactions. Here, we describe a set of experiments that test the effect of a commercially available soil amendment, VESTA, on the soil and strawberry (Fragaria x ananassa Monterey) root bacterial microbiome. The bacterial communities of the soil, rhizosphere, and root from amendment-treated and untreated fields were profiled at four time points across the strawberry growing season using 16S rRNA gene amplicon sequencing on the Illumina MiSeq platform. In all sample types, bacterial community composition and relative abundance were significantly altered with amendment application. Importantly, time point effects on composition are more pronounced in the root and rhizosphere, suggesting an interaction between plant development and treatment effect. Surprisingly, there was slight overlap between the taxa within the amendment and those enriched in plant and soil following treatment, suggesting that VESTA may act to rewire existing networks of organisms through an, as of yet, uncharacterized mechanism. These findings demonstrate that a commercial microbial soil amendment can impact the bacterial community structure of both roots and the surrounding environment.

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PSIX-1 Fecal microbiome of dairy calves fed with fresh or frozen maternal colostrum or colostrum powder

Journal of Animal Science ◽

10.1093/jas/skaa278.730 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 419-419

Author(s):

Gercino F Virgínio Júnior ◽

Cristiane Tomaluski ◽

Ana Paula Silva ◽

Sophia Dondé ◽

Horácio Montenegro ◽

...

Keyword(s):

Bacterial Colonization ◽

Illumina Miseq ◽

Well Being ◽

Diversity Indices ◽

Dairy Calves ◽

Rrna Gene ◽

Fecal Samples ◽

Fecal Microbiome ◽

Bacteria Growth ◽

Miseq Platform

Abstract Besides the importance for passive immune transfer, the supply of colostrum accelerates the bacterial colonization of the calf small intestine by providing nutrients, that will function as bacteria growth substrate, as well being a microorganism inoculum source. However, it is not known whether the effect is maintained when the calves are fed with frozen colostrum or colostrum powder. The present work evaluated 15 Holstein calves housed in tropical shelters, fed one of the colostrum sources: I – fresh colostrum from the dam (n = 5), II – frozen colostrum and III – colostrum powder, a dose of 150g of IgG (n = 5). Animals fed with fresh or frozen colostrum received a corresponding volume 10% of its birth weight of high-quality colostrum (IgG > 50g / L). All animals were fed within 4h after birth. From the second meal, calves received 6 L of liquid diet, divided into two meals, being weaned at the 8th week of age. After weaning, calves were grouped housed, and fed with starter and coast-cross hay ad libitum. To evaluate the microbiome, fecal samples were collected at birth and at weeks 1, 2, 4, 8 and 10. The microbial community was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene that was amplified by PCR and sequenced by the Illumina MiSeq platform. There was no treatment effect for the diversity indices, evenness and richness. Simpson’s diversity and evenness had no effect for weeks. Weeks 1 and 2 had less Shannon’ diversity. Richness was higher for week 0. Analyzing the relative abundance, 31 phyla were identified in the fecal samples, the most abundant being Bacteriodota, Firmicutes_A, Proteobacterias, Fusobacteriota and Firmicutes. Different sources of colostrum can be used to feed dairy calves, without affecting the diversity in the colonization of the intestinal tract.

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

10.1101/010967 ◽

2014 ◽

Cited By ~ 5

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.

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Intestinal Microbiota of Fattening Pigs Offered Non-Fermented and Fermented Liquid Feed with and without the Supplementation of Non-Fermented Coarse Cereals

Microorganisms ◽

10.3390/microorganisms8050638 ◽

2020 ◽

Vol 8 (5) ◽

pp. 638 ◽

Cited By ~ 2

Author(s):

Sebastian Bunte ◽

Richard Grone ◽

Birgit Keller ◽

Christoph Keller ◽

Eric Galvez ◽

...

Keyword(s):

Hypervariable Region ◽

Illumina Miseq ◽

Rrna Gene ◽

Bacterial Composition ◽

Operational Taxonomic Units ◽

Liquid Feed ◽

Faecal Samples ◽

Genus Lactobacillus ◽

Miseq Platform ◽

Small And Large Intestine

Introducing high numbers of lactic acid bacteria into the gastrointestinal tract of pigs via fermented liquid feed (FLF) could have an impact on intestinal bacterial ecosystems. Twenty piglets were allocated into four groups and fed a botanically identical liquid diet that was offered either non-fermented (twice), fully fermented or partially fermented but supplemented with 40% of non-fermented coarse cereals. Microbiota studies were performed on the small and large intestine digesta and faecal samples. A 16S rRNA gene amplification was performed within the hypervariable region V4 and sequenced with the Illumina MiSeq platform. R (version 3.5.2) was used for the statistical analyses. The digesta of the small intestines of pigs fed FLF were dominated by Lactobacillaceae (relative abundance up to 95%). In the colonic contents, the abundance of Lactobacillaceae was significantly higher only in the pigs fed the FLF supplemented with non-fermented coarse cereals. Additionally, the digesta of the small and large intestines as well as in the faeces of the pigs fed the FLF supplemented with non-fermented coarse cereals were significantly enriched for two operational taxonomic units (OTUs) belonging to the genus Lactobacillus and Bifidobacterium. The FLF supplemented with non-fermented coarse cereals had probiotic and prebiotic-like impacts on the intestinal and faecal bacterial composition of pigs.

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Modulation of cytokine patterns and microbiome during pregnancy in IBD

Gut ◽

10.1136/gutjnl-2019-318263 ◽

2019 ◽

Vol 69 (3) ◽

pp. 473-486 ◽

Cited By ~ 11

Author(s):

Janine van der Giessen ◽

Dana Binyamin ◽

Anna Belogolovski ◽

Sigal Frishman ◽

Kinneret Tenenbaum-Gavish ◽

...

Keyword(s):

Dynamic Modelling ◽

Late Pregnancy ◽

Intestinal Microbiome ◽

Rrna Gene ◽

Healthy Controls ◽

Serum Samples ◽

Microbial Composition ◽

Intestinal Microbiology ◽

Microbiome Diversity ◽

Cytokine Levels

ObjectivePregnancy may affect the disease course of IBD. Both pregnancy and IBD are associated with altered immunology and intestinal microbiology. However, to what extent immunological and microbial profiles are affected by pregnancy in patients with IBD remains unclear.DesignFaecal and serum samples were collected from 46 IBD patients (31 Crohn’s disease (CD) and 15 UC) and 179 healthy controls during first, second and third trimester of pregnancy, and prepregnancy and postpartum for patients with IBD. Peripheral blood cytokine profiles were determined by ELISA, and microbiome analysis was performed by sequencing the V4 region of the bacterial 16S rRNA gene.ResultsProinflammatory serum cytokine levels in patients with IBD decrease significantly on conception. Reduced interleukin (IL)-10 and IL-5 levels but increased IL-8 and interferon (IFN)γ levels compared with healthy controls were seen throughout pregnancy, but cytokine patterns remained stable during gestation. Microbial diversity in pregnant patients with IBD was reduced compared with that in healthy women, and significant differences existed between patients with UC and CD in early pregnancy. However, these microbial differences were no longer present during middle and late pregnancy. Dynamic modelling showed considerable interaction between cytokine and microbial composition.ConclusionSerum proinflammatory cytokine levels markedly improve on conception in pregnant patients with IBD, and intestinal microbiome diversity of patients with IBD normalises during middle and late pregnancy. We thus conclude that pregnancy is safe and even potentially beneficial for patients with IBD.

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

mSystems ◽

10.1128/msystems.00029-19 ◽

2019 ◽

Vol 4 (1) ◽

Cited By ~ 17

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.

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