Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia

Study information

Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

39044244

DOI Digital object identifier for electronic documents.

10.1186/s40168-024-01847-4

URI

Authors

Glendinning L, Jia X, Kebede A, Oyola SO, Park JE, Park W, Assiri A, Holm JB, Kristiansen K, Han J, Hanotte O

Journal

Microbiome

Year

2024

Keywords:

Agro-ecology, Chicken, Ethiopia, Metagenomics, Microbiota, Poultry

BACKGROUND: Scavenging indigenous village chickens play a vital role in sub-Saharan Africa, sustaining the livelihood of millions of farmers. These chickens are exposed to vastly different environments and feeds compared to commercial chickens. In this study, we analysed the caecal microbiota of 243 Ethiopian village chickens living in different altitude-dependent agro-ecologies. RESULTS: Differences in bacterial diversity were significantly correlated with differences in specific climate factors, topsoil characteristics, and supplemental diets provided by farmers. Microbiota clustered into three enterotypes, with one particularly enriched at high altitudes. We assembled 9977 taxonomically and functionally diverse metagenome-assembled genomes. The vast majority of these were not found in a dataset of previously published chicken microbes or in the Genome Taxonomy Database. CONCLUSIONS: The wide functional and taxonomic diversity of these microbes highlights their importance in the local adaptation of indigenous poultry, and the significant impacts of environmental factors on the microbiota argue for further discoveries in other agro-ecologies. Video Abstract.

Experiment 1

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Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/02/22

Curator: KateRasheed

Revision editor(s): KateRasheed

Subjects

Location of subjects: Ethiopia

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: Cecum mucosa Caecum mucosa,Caecum mucosa of organ,Caecum mucous membrane,Caecum organ mucosa,Cecal mucosa,Cecum mucosa of organ,Cecum mucous membrane,Cecum organ mucosa,Intestinum crassum caecum mucosa,Intestinum crassum caecum mucosa of organ,Intestinum crassum caecum mucous membrane,Intestinum crassum caecum organ mucosa,Mucosa of caecum,Mucosa of cecum,Mucosa of intestinum crassum caecum,Mucosa of organ of caecum,Mucosa of organ of cecum,Mucosa of organ of intestinum crassum caecum,Mucous membrane of caecum,Mucous membrane of cecum,Mucous membrane of intestinum crassum caecum,Organ mucosa of caecum,Organ mucosa of cecum,Organ mucosa of intestinum crassum caecum,Cecum mucosa,cecum mucosa

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Social environment measurement Social environment measurement,social environment measurement

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Enterotype 2 + Enterotype 3

Group 1 name Corresponds to the case (exposed) group for case-control studies: Enterotype 1

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Enterotype 1 refers to the Ethiopian chicken caecal microbiota from the gene catalogue, that was classified under Enterotype 1

Lab analysis

Sequencing type: WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: LEfSe

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

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 4

Signature 1

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Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/02/22

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Fig. 3C

Description: Differential enrichment of genera between enterotypes using LEfSe analysis

Abundance in Group 1: increased abundance in Enterotype 1

NCBI	Quality Control	Links
Alistipes
Treponema
Brachyspira
Mucispirillum
Muribaculum
Parabacteroides
Sutterella
Acidaminococcus
Akkermansia
Sphaerochaeta

Revision editor(s): KateRasheed

Experiment 2

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Curated date: 2025/02/22

Curator: KateRasheed

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Enterotype 1 + Enterotype 3

Group 1 name Corresponds to the case (exposed) group for case-control studies: Enterotype 2

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Enterotype 2 refers to the Ethiopian chicken caecal microbiota from the gene catalogue, that was classified under Enterotype 2.

Lab analysis

Statistical Analysis

Signature 2

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Curated date: 2025/02/23

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Source: Fig. 3C

Description: Differential enrichment of genera between enterotypes using LEfSe analysis

Abundance in Group 1: increased abundance in Enterotype 2

NCBI	Quality Control	Links
Azospirillum
Bacteroides
Blautia
Clostridium
Flavonifractor
Gemmiger
Lachnoclostridium
Merdimonas
Pseudoflavonifractor
Thomasclavelia

Revision editor(s): KateRasheed

Experiment 3

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Reviewed Marked as Reviewed by Svetlana up on 2025-3-17

Curated date: 2025/02/22

Curator: KateRasheed

Revision editor(s): KateRasheed

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Enterotype 1 + Enterotype 2

Group 1 name Corresponds to the case (exposed) group for case-control studies: Enterotype 3

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Enterotype 3 refers to the Ethiopian chicken caecal microbiota from the gene catalogue, that was classified under Enterotype 3. They were particularly distinct from enterotypes 1 and 2 and clearly dominated by Climate zone 1.