Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes

Study information

Reviewed Marked as Reviewed by Svetlana up on 2024-12-16

study design

laboratory experiment

Citation

PMID PubMed identifier for scientific articles.

31759120

DOI Digital object identifier for electronic documents.

10.1016/j.ygeno.2019.11.011

URI

Authors

Kumar H, Park W, Lim D, Srikanth K, Kim JM, Jia XZ, Han JL, Hanotte O, Park JE, Oyola SO

Journal

Genomics

Year

2020

Keywords:

Antibiotic resistant gene., CAZy, Indigenous chicken, KEGG, LEfSe, Microbiome, eggNOG

We analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m). Through metagenomic analysis we found that microbial populations were mainly dominated by Bacteroidetes and Firmicutes. We identified 2210 common genes in the two groups. LEfSe showed that the distribution of Coprobacter, Geobacter, Cronobacter, Alloprevotella, and Dysgonomonas were more abundant in AF than AM. Analyses using KEGG, eggNOG, and CAZy databases indicated that the pathways of metabolism, genetic information processing, environmental information processing, and cellular process were significantly enriched. Functional abundance was found to be associated with the nutrient absorption and microbial localization of indigenous chickens. We also investigated antibiotic resistant genes and found antibiotics like LSM, cephalosporin, and tetracycline were significantly more abundant in AF than AM.

Experiment 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-12-16

Curated date: 2024/11/06

Curator: Tosin

Revision editor(s): Tosin

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: Caecum Blind intestine,Blindgut,Caeca,Caecum,Ceca,Cecum,Intestinum caecum,Intestinum crassum caecum,Intestinum crassum cecum,caecum

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Restricted to specific location localized,Restricted to specific location,restricted to specific location

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Amhara (AM) highland region

Group 1 name Corresponds to the case (exposed) group for case-control studies: Afar (AF) lowland region

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Afar (AF) is a low altitude region known for active volcanic eruptions and receives relatively limited rainfall (Dulecha, 730 m above sea level).

Group 0 sample size Number of subjects in the control (unexposed) group: 5

Group 1 sample size Number of subjects in the case (exposed) group: 5

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

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

Signature 1

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Curated date: 2024/11/06

Curator: Tosin

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Source: Figure S2

Description: Taxonomic annotation of microorganisms in AF (Afar: lowland) and AM (Amhara: highland) regions through Linear Discriminant Analysis, identifying taxa with significant differences between the two regions.

Abundance in Group 1: increased abundance in Afar (AF) lowland region

NCBI	Quality Control	Links
Alistipes sp. CHKCI003
Alloprevotella
Bacteroides caecimuris
Bacteroides eggerthii
Bacteroides sp. 3_1_13
Bacteroides sp. CAG:443
Bacteroides sp. CAG:661
Bacteroides sp. CAG:714
Barnesiella sp. An22
Bifidobacterium pullorum subsp. saeculare
Coprobacter
Coprobacter secundus
Cronobacter
Cronobacter sakazakii
Desulfuromonadales
Dysgonomonadaceae
Dysgonomonas
Dysgonomonas capnocytophagoides
Flavonifractor sp. An92
Geobacter
Geobacteraceae
Parabacteroides sp. CAG:409
Phocaeicola barnesiae
Phocaeicola coprocola
Phocaeicola coprocola CAG:162
Phocaeicola plebeius
Prevotella sp. P2-180
Subdoligranulum variabile
[Eubacterium] cellulosolvens
uncultured Bacteroides sp.
uncultured Dysgonomonas sp.

Revision editor(s): Tosin

Signature 2

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Curated date: 2024/11/08

Curator: Tosin

Revision editor(s): Tosin

Source: Figure S2

Description: Taxonomic annotation of microorganisms in AF (Afar: lowland) and AM (Amhara: highland) regions through Linear Discriminant Analysis, identifying taxa with significant differences between the two regions.

Abundance in Group 1: decreased abundance in Afar (AF) lowland region

NCBI	Quality Control	Links
Alistipes sp. An54
Bacteroides cellulosilyticus
Bacteroides eggerthii CAG:109
Bacteroides sp. 3_1_40A
Bacteroides sp. An279
Bacteroides sp. CAG:1060
Bacteroides sp. CAG:462
Bacteroides sp. CAG:702
Bacteroidia bacterium 43-41
Blautia producta
Blautia sp. An46
Burkholderia
Burkholderiaceae
Burkholderiales
Clostridiales bacterium 59_14
Clostridiales bacterium CHKCI006
Enterocloster citroniae
Faecalibacterium
Faecalibacterium prausnitzii
Faecalibacterium sp. An121
Faecalibacterium sp. An122
Faecalibacterium sp. An192
Prevotella sp. HUN102
Faecalibacterium sp. An58
Faecalibacterium sp. An77
Holdemania
Holdemania filiformis
Lachnoclostridium sp. An138
Megasphaera
Megasphaera elsdenii
Negativicutes
Parabacteroides johnsonii
Parabacteroides sp. Marseille-P3160
Prevotella sp. CAG:1058
Prevotella sp. CAG:1124
Prevotella sp. CAG:1185
Prevotella sp. CAG:617
Prevotella sp. CAG:924
Veillonellales
Xylanibacter rarus