Characterization of microbial communities in the chicken oviduct and the origin of chicken embryo gut microbiota

Study information

Reviewed Marked as Reviewed by Folakunmi on 2024-4-12

study design

laboratory experiment

Citation

PMID PubMed identifier for scientific articles.

DOI Digital object identifier for electronic documents.

10.1038/s41598-019-43280-w

URI

https://doi.org/10.1038/s41598-019-43280-w

Authors

Choi In-Soo, La Tae-Min, Lee Hong-Jae, Lee Joong-Bok, Lee Sangwon, Park Seung-Yong, Song Chang-Seon

Journal

Scientific reports

Year

2019

Pages:

6838

First page:

1

Keywords:

Metagenomics, Metagenomics

The transferred microbiota from mother to baby constitutes the initial infant gastrointestinal microbiota and has an important influence on the development and health of infants in human. However, the reproductive tract microbiota of avian species and its inheritance have rarely been studied. We aimed to characterize the microbial community in the chicken reproductive tract and determine the origin of the chicken embryo gut microbiota. Microbiota in four different portions of chicken oviduct were determined using 16S rRNA metagenomic approach with the IonTorrent platform. Additionally, we analyzed the mother hen’s magnum and cloaca, descendent egg, and embryo gut microbiota. The microbial composition and relative abundance of bacterial genera were stable throughout the entire chicken reproductive tract, without significant differences between the different parts of the oviduct. The chicken reproductive tract showed a relatively high abundance of Lactobacillus species. The number of bacterial species in the chicken reproductive tract significantly increased following sexual maturation. Core genera analysis detected 21 of common genera in the maternal magnum and cloaca, descendent egg shell, egg white, and embryo gut. Some elements of the maternal oviduct microbiota appear to be transferred to the embryo through the egg white and constitute most of the embryo gut bacterial population.

Experiment 1

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Reviewed Marked as Reviewed by Folakunmi on 2024-4-12

Curated date: 2024/03/08

Curator: KwennB

Revision editor(s): KwennB, Rahila, Folakunmi

Subjects

Location of subjects: South Korea

Host species Species from which microbiome was sampled. Contact us to have more species added.: Gallus gallus

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Oviduct Female reproductive tracts,Ovarian duct,Ovarian tube,Oviducts,Tuba uterina,Tuba uterinae,Tubular parts of female reproductive system,Uterine tube,Oviduct,oviduct

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Developmental stage development stage,developmental_stage,life cycle stage,Developmental stage,developmental stage

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Immature hen magnum sample (23 weeks-old)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Mature hen magnum sample

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Magnum samples of 34 weeks-old laying SPF hens

Group 0 sample size Number of subjects in the control (unexposed) group: 8

Group 1 sample size Number of subjects in the case (exposed) group: 16

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V2-V9

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Ion Torrent

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: centered log-ratio

Statistical test: ANCOM

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: increased

Signature 1

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Reviewed Marked as Reviewed by Folakunmi on 2024-4-12

Curated date: 2024/03/11

Curator: KwennB

Revision editor(s): KwennB, Ayibatari, Rahila, Folakunmi

Source: Figure 2.

Description: ANCOM differential abundance mature and immature hen magnum groups.

Abundance in Group 1: increased abundance in Mature hen magnum sample

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Flavobacterium
Megamonas

Revision editor(s): KwennB, Ayibatari, Rahila, Folakunmi

Signature 2

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Reviewed Marked as Reviewed by Folakunmi on 2024-4-12

Curated date: 2024/03/13

Curator: KwennB

Revision editor(s): KwennB, Ayibatari, Rahila, Folakunmi

Source: Figure 2.

Description: ANCOM differential abundance between the mature and immature hen magnum groups.

Abundance in Group 1: decreased abundance in Mature hen magnum sample

NCBI	Quality Control	Links
Bradyrhizobium
unclassified Bradyrhizobiaceae
unclassified Nocardiaceae
Unclassified 0319-6G20Unclassified 0319-6G20

Revision editor(s): KwennB, Ayibatari, Rahila, Folakunmi