scholarly journals Metagenomic Analysis Identifies Sex-Related Cecal Microbial Gene Functions and Bacterial Taxa in the Quail

2021 ◽  
Vol 8 ◽  
Author(s):  
Jing-E Ma ◽  
Xin-Wei Xiong ◽  
Ji-Guo Xu ◽  
Ji-Shang Gong ◽  
Jin Li ◽  
...  
Keyword(s):  
Japanese Quail ◽  
Growth Promotion ◽  
Genetic Selection ◽  
Antibiotic Resistance Genes ◽  
Microbial Species ◽  
Female Quail ◽  
Gene Catalog ◽  
Gene Functions ◽  
Microbial Genes ◽  
Microbiome Data

Background: Japanese quail (Coturnix japonica) are important and widely distributed poultry in China. Researchers continue to pursue genetic selection for heavier quail. The intestinal microbiota plays a substantial role in growth promotion; however, the mechanisms involved in growth promotion remain unclear.Results: We generated 107.3 Gb of cecal microbiome data from ten Japanese quail, providing a series of quail gut microbial gene catalogs (1.25 million genes). We identified a total of 606 main microbial species from 1,033,311 annotated genes distributed among the ten quail. Seventeen microbial species from the genera Anaerobiospirillum, Alistipes, Barnesiella, and Butyricimonas differed significantly in their abundances between the female and male gut microbiotas. Most of the functional gut microbial genes were involved in metabolism, primarily in carbohydrate transport and metabolism, as well as some active carbohydrate-degrading enzymes. We also identified 308 antibiotic-resistance genes (ARGs) from the phyla Bacteroidetes, Firmicutes and Euryarchaeota. Studies of the differential gene functions between sexes indicated that abundances of the gut microbes that produce carbohydrate-active enzymes varied between female and male quail. Bacteroidetes was the predominant ARG-containing phylum in female quail; Euryarchaeota was the predominant ARG-containing phylum in male quail.Conclusion: This article provides the first description of the gene catalog of the cecal bacteria in Japanese quail as well as insights into the bacterial taxa and predictive metagenomic functions between male and female quail to provide a better understanding of the microbial genes in the quail ceca.

Estrogenic effects of the enantiomers of o,p′-DDT in Japanese quail

1977 ◽  
Vol 55 (3) ◽  
pp. 562-568 ◽  
Author(s):  
W. A. McBlain ◽  
V. Lewin ◽  
F. H. Wolfe
Keyword(s):  
Japanese Quail ◽  
Glycogen Content ◽  
Weight Increase ◽  
Immature Female ◽  
Estrogenic Effects ◽  
Female Quail ◽  
Wet Weight ◽  
Sensitive Parameters

Immature female Japanese quail were given three daily intraperitoneal injections of (±)-o,p′-DDT, (−)-o,p′-DDT, or (+)-o,p′-DDT. Seventy-two hours after the first injection the oviducts were excised and the estrogen-sensitive parameters, oviducal wet weight and oviducal glycogen content, were measured. The levo enantiomer of o,p′-DDT was a more active estrogen than the dextro form in the immature female quail. The differing estrogenic activities of the o,p′-DDT enantiomers apparently were not the result of a differential transport within the birds. A dietary dose of 200 ppm of (±)-o,p′-DDT was not estrogenic in immature female quail when administered for 3 or 7 days. Neither enantiomer of o,p′-DDT was able to offset a light-stimulated testicular wet weight increase in male Japanese quail.

scholarly journals Effects on the Ileal Microbiota of Phosphorus and Calcium Utilization, Bird Performance, and Gender in Japanese Quail

Animals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 885 ◽  
Author(s):  
Daniel Borda-Molina ◽  
Christoph Roth ◽  
Angélica Hérnandez-Arriaga ◽  
Daniel Rissi ◽  
Solveig Vollmar ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Japanese Quail ◽  
Body Weight Gain ◽  
Sensu Stricto ◽  
Microbiota Composition ◽  
Feed Conversion ◽  
Core Microbiome ◽  
Entire Cohort ◽  
Enteropathogenic Bacteria ◽  
Female Quail

In this study, we aimed to investigate the ileum digesta of a large cohort of Japanese quail fed the same diet, with similar environmental conditions. We also address how P utilization (PU), Ca utilization (CaU), and bird performance (feed intake (FI), feed conversion (FC), and body weight gain (BWG)) modify intestinal microbiota of male and female quail. Despite the great number of samples analyzed (760), a core microbiome was composed of five bacteria. The Unc. Lactobacillus, Unc. Clostridaceae 1, Clostridium sensu stricto, Escherichia coli, and Streptococcus alactolyticus were detected in all samples and contributed to more than 70% of the total community. Depending on the bird predisposition for PU, CaU, FI, BWG, and FC, those species were present in higher or lower abundances. There was a significant gender effect on the ileal microbial community. While females had higher abundances of Lactobacillus, males were more colonized by Streptococcus alactolyticus. The entire cohort was highly colonized by Escherichia coli (8%–15%), an enteropathogenic bacteria. It remains unclear, if microbiota composition followed the mechanisms that caused different PU, CaU, FI, FC, and BWG or if the change in microbiota composition and function caused the differences in PU, CaU, and performance traits.

Color Preferences in Quail Chicks: Generalization of the Effects of Genetic Selection

Behaviour ◽  
1978 ◽  
Vol 65 (1-2) ◽  
pp. 263-269 ◽  
Author(s):  
Kovach Joseph K.
Keyword(s):  
Japanese Quail ◽  
Genetic Selection ◽  
Coturnix Japonica ◽  
Selected Lines ◽  
Color Preferences ◽  
Selection For ◽  
Different Color ◽  
Color Combinations

Japanese quail (C. coturnix japonica) were artificially selected for early preferences of blue over red and red over blue. Subjects were drawn from the 2nd and 8th generations of the selected lines and were tested for color choices by five different color pairs, in addition to the blue-red pair used for selection. Eight generations of selection for choices between blue and red modified choice responses to all color combinations. Maximum preferences were not shown in the selected choices between blue and red, but in the choice of green over red in the subjects from the line selected for preference of blue and in the choice of yellow over blue in the subjects from the line selected for preference of red.

scholarly journals MAAWf: A Multifunctional and Visual Tool for Microbiomic Data Analyses

2019 ◽  
Author(s):  
Sibo Zhu ◽  
Tao Sun ◽  
Chengkai Zhu ◽  
Tao Qing ◽  
Yanfeng Jiang ◽  
...  
Keyword(s):  
Computing Time ◽  
Antibiotic Resistance Genes ◽  
Automated Analysis ◽  
Rrna Gene ◽  
Analysis Tool ◽  
Command Line ◽  
16S Sequencing ◽  
Alpha And Beta Diversity ◽  
Analysis Workflow ◽  
Microbiome Data

Abstract Background: Microbiomic research has grown in popularity in recent decades. The widespread use of next-generation sequencing technologies, including 16S rRNA gene-based and metagenomic shotgun-based methods, has produced a wealth of microbiome data. At present, most software and analysis workflows for analysis and processing of microbiomic data are command line-based, which requires considerable computing time and makes interaction difficult. Results: To provide a command-line free, multifunctional, user interface friendly and online/local deployable microbiome analysis tool, we developed Microbiome Automated Analysis Workflows (MAAWf). MAAWf is composed of a whole metagenomic shotgun workflow (WMS) and a 16S Sequencing Workflow. The WMS analysis workflow assesses taxonomy, protein-coding genes, metabolic pathways, carbohydrate-active enzymes (CAZy) and antibiotic resistance genes (ARGs). The 16S ribosomal RNA (rRNA) analysis workflow counts and clusters operational taxonomic units (OTUs), estimates alpha- and beta-diversity and inter-group differences, and performs functional analysis. We also compared MAAWf with other commonly avaiable analysis tools using two public datasets. The MAAWf pipeline was established using the Ubuntu 16.04.6 LTS kernel with primary sequence files such as FASTQ format and taxonomic format such as OTU or BIOM formats. Following analysis of public 16S and WMS datasets, MAAWf obtained similar results to DIAMOND-MEGAN6, MG-RAST, DADA2 and QIIME2, but the running time was much shorter. Conclusions: MAAWf is a visual, integrated, rapid analysis tool that enables remote and local computing of microbiome data.

A novel deep learning method for predictive modeling of microbiome data

2020 ◽  
Author(s):  
Ye Wang ◽  
Tathagata Bhattacharya ◽  
Yuchao Jiang ◽  
Xiao Qin ◽  
Yue Wang ◽  
...  
Keyword(s):  
Deep Learning ◽  
Phylogenetic Tree ◽  
Human Microbiome ◽  
Prediction Method ◽  
Disease Diagnosis ◽  
Research Field ◽  
Correlation Structure ◽  
Learning Method ◽  
Microbial Species ◽  
Microbiome Data

Abstract With the development and decreasing cost of next-generation sequencing technologies, the study of the human microbiome has become a rapid expanding research field, which provides an unprecedented opportunity in various clinical applications such as drug response predictions and disease diagnosis. It is thus essential and desirable to build a prediction model for clinical outcomes based on microbiome data that usually consist of taxon abundance and a phylogenetic tree. Importantly, all microbial species are not uniformly distributed in the phylogenetic tree but tend to be clustered at different phylogenetic depths. Therefore, the phylogenetic tree represents a unique correlation structure of microbiome, which can be an important prior to improve the prediction performance. However, prediction methods that consider the phylogenetic tree in an efficient and rigorous way are under-developed. Here, we develop a novel deep learning prediction method MDeep (microbiome-based deep learning method) to predict both continuous and binary outcomes. Conceptually, MDeep designs convolutional layers to mimic taxonomic ranks with multiple convolutional filters on each convolutional layer to capture the phylogenetic correlation among microbial species in a local receptive field and maintain the correlation structure across different convolutional layers via feature mapping. Taken together, the convolutional layers with its built-in convolutional filters capture microbial signals at different taxonomic levels while encouraging local smoothing and preserving local connectivity induced by the phylogenetic tree. We use both simulation studies and real data applications to demonstrate that MDeep outperforms competing methods in both regression and binary classifications. Availability and Implementation: MDeep software is available at https://github.com/lichen-lab/MDeep Contact:[email protected]

Increased Responding to Female Stimuli as a Result of Sexual Experience: Tests of Mechanisms of Learning

1992 ◽  
Vol 45 (2b) ◽  
pp. 139-157 ◽  
Author(s):  
Michael Domjan ◽  
Chana Akins ◽  
Danny H. Vandergriff
Keyword(s):  
Japanese Quail ◽  
Instrumental Conditioning ◽  
Sexual Experience ◽  
Mammalian Species ◽  
Contextual Cues ◽  
Female Quail

Sexual experience increases the response of males to stimuli provided by female conspecifics in a variety of species. The mechanisms of learning involved in this type of phenomenon were explored in two experiments with Japanese quail. The results indicated that instrumental conditioning with copulatory opportunity is not necessary for the acquisition of responding to female cues, and responding is not facilitated by learning about the location of the female. However, the response of males to female stimuli (as well as to arbitrary stimuli associated with access to a female) was enhanced by the presence of sexually conditioned contextual cues. Substantial levels of responding also occurred to female stimuli in a context where the subjects never encountered a female quail before. This latter outcome is consistent with the possibility that stimuli from a female become directly associated with sexual reinforcement during the course of sexual experience. Similar forms of learning may be involved in the effects of sexual experience on the response of mammalian species to female odours.

scholarly journals Fat absorption and deposition in Japanese quail (Coturnix coturnix japonica) fed a high fat diet

2013 ◽  
Vol 84 (1) ◽  
Author(s):  
Mhlengi M. Magubane ◽  
Busisani W. Lembede ◽  
Kennedy H. Erlwanger ◽  
Eliton Chivandi ◽  
Janine Donaldson
Keyword(s):  
Japanese Quail ◽  
Lipid Content ◽  
High Fat Diet ◽  
Lipid Absorption ◽  
Thigh Muscle ◽  
Standard Diet ◽  
High Fat ◽  
Muscle Lipid ◽  
Coturnix Coturnix ◽  
Female Quail

Dietary fat contributes significantly to the energy requirements of poultry. Not all species are able to increase their absorptive capacity for fats in response to a high fat diet. The effects of a high fat diet (10% canola oil) on the lipid absorption and deposition in the liver, breast and thigh muscles of male and female Japanese quail were investigated. Thirty-eight Japanese quail (Coturnix coturnix japonica) were randomly divided into a high fat diet (HFD) and a standard diet (STD) group. The birds were fed the diets for seven weeks after which half of the birds were subjected to oral fat loading tests (OFLT) with plant oils containing long-chain and medium-chain triglycerides. The remaining birds were included for the lipid deposition measurements. Thereafter the birds were euthanised, blood samples were collected and liver, breast and thigh muscle lipid deposition was determined. Female quail on both diets had significantly higher plasma triglyceride concentrations (p < 0.05) compared with their male counterparts. No significant differences in plasma triglyceride concentrations were observed after the OFLTs. Female quail had significantly heavier liver masses compared with the males but there was no significant difference in the liver lipid content per gram liver mass. Female quail on the HFD had higher lipid content (p < 0.05) in the breast muscle compared with their male counterparts whilst male quail on the HFD had higher lipid content (p < 0.05) in the thigh muscle in comparison with both males and females on the standard diet. Dietary supplementation with 10% canola oil did not alter gastrointestinal tract lipid absorption, but it caused differences between the sexes in muscle lipid accumulation, the physiological significance of which requires further investigation.

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