scholarly journals 77 Responses to alfalfa supplementation in mice

2019 ◽  
Vol 97 (Supplement_2) ◽  
pp. 45-46
Author(s):  
Krysten Fries-Craft ◽  
Justin Anast ◽  
Stephan Schmitz-Esser ◽  
Elizabeth A Bobeck
Keyword(s):  
Amplicon Sequencing ◽  
Chloroform Extract ◽  
Citrobacter Rodentium ◽  
Sequencing Data ◽  
Discrimination Analysis ◽  
16S Rrna Amplicon Sequencing ◽  
Linear Discrimination ◽  
Alfalfa Hay ◽  
Cytokine Analysis ◽  
System 2

Abstract Anecdotal evidence suggests health benefits from feeding late cutting alfalfa to non-ruminants, but there is a lack of published literature to support these claims. The objective was to compare early (1st) and late (5th) cutting alfalfa as ground hay, aqueous, or chloroform-extracted hay in combination with a gastrointestinal challenge to understand the effect of supplementation form and cutting on the overall health, microbiome, and immune system of mice. 163 C57BL/6J mice were housed for 35 d (Innovive system; 2–4 mice/cage) and fed treatments that consisted of an 18% protein rodent diet (alfalfa-free control), or control supplemented with 1st or 5th cutting 9% ground alfalfa hay, 0.25% aqueous extract (AAE), or 0.25% chloroform extract (CAE). After a 14 d enrichment period, 6 mice/treatment were euthanized for baseline tissue and digesta sampling, and remaining mice were orally gavaged with 2x1010 CFU Citrobacter rodentium. On d18, 22, 28, and 35, 4 mice/treatment were euthanized for sampling. Body weight (BW) and feed intake (FI) were recorded, 13 serum cytokines were measured, and changes in the microbial communities were analyzed using 16S rRNA amplicon sequencing. Data were analyzed using PROC MIXED and linear discrimination analysis effect size (LEfSe), with significance at P ≤ 0.05. No BW differences were observed between treatments at the key timepoints (P > 0.05). Mice fed hay diets ate 16% more per day during the enrichment period (P = 0.03), 19% more from d14–18 (P = 0.001), and 17% more from d18–22 (P = 0.03) versus mice fed AAE. Citrobacter rodentium infection was confirmed via MiSeq in colon digesta. Significant shifts in microbial taxa were observed in mice fed alfalfa hay regardless of cutting (P < 0.05). Cytokine analysis, flow cytometry, and microbiome analysis is ongoing. Preliminary results show that alfalfa form significantly impacts FI and microbiome while cutting impacts weight (P < 0.05).

scholarly journals Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Caitlin M. Singleton ◽  
Francesca Petriglieri ◽  
Jannie M. Kristensen ◽  
Rasmus H. Kirkegaard ◽  
Thomas Y. Michaelsen ◽  
...  
Keyword(s):  
16S Rrna ◽  
Wastewater Treatment Plants ◽  
In Situ Hybridisation ◽  
Amplicon Sequencing ◽  
Rrna Genes ◽  
Fluorescence In Situ Hybridisation ◽  
Sequencing Data ◽  
High Quality ◽  
16S Rrna Amplicon Sequencing ◽  
Long Read

AbstractMicroorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with >13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.

scholarly journals Dramatic differences in gut bacterial densities help to explain the relationship between diet and habitat in rainforest ants

2017 ◽  
Author(s):  
Jon G Sanders ◽  
Piotr Lukasik ◽  
Megan E Frederickson ◽  
Jacob A Russell ◽  
Ryuichi Koga ◽  
...  
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
Tropical Rainforest ◽  
Amplicon Sequencing ◽  
Sequencing Data ◽  
Lowland Tropical Forest ◽  
16S Rrna Amplicon Sequencing ◽  
Microbial Symbionts ◽  
Microbial Symbiosis ◽  
Diversity Profiles

AbstractAbundance is a key parameter in microbial ecology, and important to estimates of potential metabolite flux, impacts of dispersal, and sensitivity of samples to technical biases such as laboratory contamination. However, modern amplicon-based sequencing techniques by themselves typically provide no information about the absolute abundance of microbes. Here, we use fluorescence microscopy and quantitative PCR as independent estimates of microbial abundance to test the hypothesis that microbial symbionts have enabled ants to dominate tropical rainforest canopies by facilitating herbivorous diets, and compare these methods to microbial diversity profiles from 16S rRNA amplicon sequencing. Through a systematic survey of ants from a lowland tropical forest, we show that the density of gut microbiota varies across several orders of magnitude among ant lineages, with median individuals from many genera only marginally above detection limits. Supporting the hypothesis that microbial symbiosis is important to dominance in the canopy, we find that the abundance of gut bacteria is positively correlated with stable isotope proxies of herbivory among canopy-dwelling ants, but not among ground-dwelling ants. Notably, these broad findings are much more evident in the quantitative data than in the 16S rRNA sequencing data. Our results help to resolve a longstanding question in tropical rainforest ecology, and have broad implications for the interpretation of sequence-based surveys of microbial diversity.

scholarly journals A core salivary microbiome shows the high prevalence of bacterial members yet variability across human populations

2021 ◽  
Author(s):  
Xinwei Ruan ◽  
Jiaqiang Luo ◽  
Pangzhen Zhang ◽  
Kate Howell
Keyword(s):  
Meta Analysis ◽  
Geographic Location ◽  
Amplicon Sequencing ◽  
Human Saliva ◽  
Independent Study ◽  
Human Populations ◽  
Sequencing Data ◽  
The Core ◽  
16S Rrna Amplicon Sequencing ◽  
The Impact

Human saliva contains diverse bacterial communities, reflecting human health status, dietary patterns and contributing to variability in the sensory perception of food. Many descriptions of salivary microbiome diversity compare commonalities and differences with reference to a diseased state, but the composition of healthy saliva has not been described. Here, we use a meta-analysis approach to define and explore the core membership of the human salivary microbial community by collecting and re-analysing raw 16S rRNA amplicon sequencing data from 47 studies with 2206 saliva samples. We found 68 core bacterial taxa that were consistently detected. Differences induced by various host intrinsic and behaviour factors, including gender, age, geographic location, tobacco usage, and alcohol consumption, were evident. The core of the salivary microbiome was verified by collecting and analysing saliva in an independent study, and this analysis showed that the impact of geographic variation is likely due to diet.

scholarly journals Machine Learning-assisted Identification of Bioindicators Predicts Medium-chain Carboxylate Production Performance of an Anaerobic Mixed Culture

2020 ◽  
Author(s):  
Bin Liu ◽  
Heike Sträuber ◽  
Joao Saraiva ◽  
Hauke Harms ◽  
Sandra Godinho Silva ◽  
...  
Keyword(s):  
Machine Learning ◽  
16S Rrna ◽  
Retention Time ◽  
Hydraulic Retention Time ◽  
Amplicon Sequencing ◽  
Production Performance ◽  
Chain Elongation ◽  
Sequencing Data ◽  
Medium Chain ◽  
16S Rrna Amplicon Sequencing

Abstract Background: The ability to quantitatively predict ecophysiological functions of microbial communities provides an important step to engineer microbiota for desired functions related to specific biochemical conversions. Here, we present the quantitative prediction of medium-chain carboxylate production in two continuous anaerobic bioreactors from 16S rRNA gene dynamics in enrichment cultures. Results: By progressively shortening the hydraulic retention time from 8 days to 2 days with different temporal schemes in both bioreactors operated for 211 days, we achieved higher productivities and yields of the target products n-caproate and n-caprylate. The datasets generated from each bioreactor were applied independently for training and testing in machine learning. A predictive model was generated by employing the random forest algorithm using 16S rRNA amplicon sequencing data. More than 90% accuracy in the prediction of n-caproate and n-caprylate productivities was achieved. Four inferred bioindicators belonging to the genera Olsenella, Lactobacillus, Syntrophococcus and Clostridium IV suggest their relevance to the higher carboxylate productivity at shorter hydraulic retention time. The recovery of metagenome-assembled genomes of these bioindicators confirmed their genetic potential to perform key steps of medium-chain carboxylate production.Conclusions: Shortening the hydraulic retention time of the continuous bioreactor systems allows to shape the communities with desired chain elongation functions. Using machine-learning, we demonstrated that 16S rRNA amplicon sequencing data can be used to predict bioreactor process performance quantitatively and accurately. Characterising and harnessing bioindicators holds promise to manage reactor microbiota towards selection of the target processes. Our mathematical framework is transferrable to other ecosystem processes and 3 microbial systems where community dynamics is linked to key functions. The general methodology can be adapted to data types of other functional categories such as genes, transcripts, proteins or metabolites.

scholarly journals Bioinformatics Analysis of Oral, Vaginal, and Rectal Microbial Profiles during Pregnancy: A Pilot Study on the Bacterial Co-Residence in Pregnant Women

2021 ◽  
Vol 9 (5) ◽  
pp. 1027
Author(s):  
Megumi Fudaba ◽  
Tomonori Kamiya ◽  
Daisuke Tachibana ◽  
Masayasu Koyama ◽  
Naoko Ohtani
Keyword(s):  
Preterm Labor ◽  
Bacterial Species ◽  
Bacterial Genome ◽  
Amplicon Sequencing ◽  
Bioinformatic Analysis ◽  
Lactobacillus Species ◽  
Sequencing Data ◽  
Associated Bacteria ◽  
16S Rrna Amplicon Sequencing ◽  
Threatened Preterm Labor

Preterm birth (PTB) and threatened preterm labor (TPL), an important pre-PTB state, are major obstetric complications during pregnancy. However, their triggers have not been fully elucidated. The vagina is dominated by Lactobacillus species (categorized as community state types; CSTs I, II, III, and V) or by mixed anaerobes (CST IV). An abundance of the latter is associated with bacterial vaginosis (BV) and BV-triggered PTB/TPL. To identify factors that influence the diversity of vaginal microbiota associated with BV and CST IV (BV-type) bacterial profile, we performed a bioinformatic analysis of the microbial taxa using 16S rRNA amplicon sequencing data of bacterial genome in oral, vaginal, and rectal samples collected from 58 pregnant Japanese women. Interestingly, common residence of BV-associated bacteria in the vagina and rectum was individually detected in the CST IV (non-Lactobacillus dominated) group by species-level Spearman correlation coefficient analysis, suggesting that the rectum acts as a reservoir of BV-associated bacterial species in the CST IV group. The current study provides evidence of bacterial co-residence in vagina and rectum in the non-Lactobacillus dominated group, which could be targeted to reduce the risk of preterm incidence in pregnancy.

scholarly journals NanoRTax, a real-time pipeline for taxonomic and diversity analysis of nanopore 16S rRNA amplicon sequencing data

2021 ◽  
Author(s):  
Héctor Rodriguez-Perez ◽  
Laura Ciuffreda ◽  
Carlos Flores
Keyword(s):  
16S Rrna ◽  
Real Time ◽  
Amplicon Sequencing ◽  
Sequencing Data ◽  
Real Time Analysis ◽  
16S Rrna Amplicon Sequencing ◽  
Oxford Nanopore ◽  
Long Read ◽  
Cost Efficient ◽  
User Friendly

Abstract The study of microbial communities and their applications have been leveraged by the advances in sequencing techniques and bioinformatics tools. The Oxford Nanopore Technologies long read sequencing by nanopores provides a portable and cost-efficient platform for sequencing assays opening the possibility of its application outside specialized environments and real-time analysis of data. To complement the existing efficient library preparation protocol with a streamlined analytic workflow, here we present NanoRTax, a nextflow pipeline for nanopore 16S rRNA amplicon data that features state-of-art taxonomic classification tools and real-time capability. The pipeline is paired with a web-based visual interface to enable user-friendly inspections of the experiment in progress.

scholarly journals Retinitis pigmentosa is associated with shifts in the gut microbiome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Oksana Kutsyr ◽  
Lucía Maestre-Carballa ◽  
Mónica Lluesma-Gomez ◽  
Manuel Martinez-Garcia ◽  
Nicolás Cuenca ◽  
...  
Keyword(s):  
Retinitis Pigmentosa ◽  
Gut Microbiome ◽  
Functional Decline ◽  
Retinal Disease ◽  
Photoreceptor Cells ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Alpha And Beta Diversity ◽  
Potential Biomarker

AbstractThe gut microbiome is known to influence the pathogenesis and progression of neurodegenerative diseases. However, there has been relatively little focus upon the implications of the gut microbiome in retinal diseases such as retinitis pigmentosa (RP). Here, we investigated changes in gut microbiome composition linked to RP, by assessing both retinal degeneration and gut microbiome in the rd10 mouse model of RP as compared to control C57BL/6J mice. In rd10 mice, retinal responsiveness to flashlight stimuli and visual acuity were deteriorated with respect to observed in age-matched control mice. This functional decline in dystrophic animals was accompanied by photoreceptor loss, morphologic anomalies in photoreceptor cells and retinal reactive gliosis. Furthermore, 16S rRNA gene amplicon sequencing data showed a microbial gut dysbiosis with differences in alpha and beta diversity at the genera, species and amplicon sequence variants (ASV) levels between dystrophic and control mice. Remarkably, four fairly common ASV in healthy gut microbiome belonging to Rikenella spp., Muribaculaceace spp., Prevotellaceae UCG-001 spp., and Bacilli spp. were absent in the gut microbiome of retinal disease mice, while Bacteroides caecimuris was significantly enriched in mice with RP. The results indicate that retinal degenerative changes in RP are linked to relevant gut microbiome changes. The findings suggest that microbiome shifting could be considered as potential biomarker and therapeutic target for retinal degenerative diseases.

scholarly journals Bacterial Diversity of Breast Milk in Healthy Spanish Women: Evolution from Birth to Five Years Postpartum

Nutrients ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 2414
Author(s):  
Laura Sanjulián ◽  
Alexandre Lamas ◽  
Rocío Barreiro ◽  
Alberto Cepeda ◽  
Cristina A. Fente ◽  
...  
Keyword(s):  
Breast Milk ◽  
16S Rrna ◽  
Human Milk ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Maternal Body Mass Index ◽  
16S Rrna Amplicon Sequencing ◽  
Spanish Women ◽  
Calcium Magnesium ◽  
Abundant Genus

The objective of this work was to characterize the microbiota of breast milk in healthy Spanish mothers and to investigate the effects of lactation time on its diversity. A total of ninety-nine human milk samples were collected from healthy Spanish women and were assessed by means of next-generation sequencing of 16S rRNA amplicons and by qPCR. Firmicutes was the most abundant phylum, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. Accordingly, Streptococcus was the most abundant genus. Lactation time showed a strong influence in milk microbiota, positively correlating with Actinobacteria and Bacteroidetes, while Firmicutes was relatively constant over lactation. 16S rRNA amplicon sequencing showed that the highest alpha-diversity was found in samples of prolonged lactation, along with wider differences between individuals. As for milk nutrients, calcium, magnesium, and selenium levels were potentially associated with Streptococcus and Staphylococcus abundance. Additionally, Proteobacteria was positively correlated with docosahexaenoic acid (DHA) levels in breast milk, and Staphylococcus with conjugated linoleic acid. Conversely, Streptococcus and trans-palmitoleic acid showed a negative association. Other factors such as maternal body mass index or diet also showed an influence on the structure of these microbial communities. Overall, human milk in Spanish mothers appeared to be a complex niche shaped by host factors and by its own nutrients, increasing in diversity over time.

Advantage of 16S rRNA amplicon sequencing in Helicobacter pylori diagnosis

Helicobacter ◽  
2021 ◽  
Author(s):  
Boldbaatar Gantuya ◽  
Hashem B. El Serag ◽  
Batsaikhan Saruuljavkhlan ◽  
Dashdorj Azzaya ◽  
Takashi Matsumoto ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
16S Rrna ◽  
Amplicon Sequencing ◽  
16S Rrna Amplicon Sequencing
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