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Next-Generation Sequencing of the Microbial Community Profile In Free-Range Chicken (Gallus gallus domesticus) Cecum from East Nusa Tenggara Province: Microbial community profile in free-range chicken (Gallus gallus domesticus) cecum

Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences · Vol. 13 No. 2 (2023) · hlm. 349–358

DOI
10.11594/jtls.13.02.13
ISSN
2527-4376, 2087-5517
Terbit
2023-06-06
Penerbit
Journal of Tropical Life Science
Bahasa
eng
Lisensi
creativecommons.org/licenses/by-nc/4.0

Abstrak

Free-range chicken is livestock reared to support the humans' need for protein alongside its ritualistic use in traditional medicine to treat diseases. This study investigates the diversity of bacterial communities in the free-range chicken cecum reared in different East Nusa Tenggara Province localities comprising Sambi 1, Sambi 2 villages, Labuan Bajo, and Kupang City. The extracted chromosomal DNA was subjected to next-generation sequencing using the V3-V4 region primers. Results revealed that the Kupang chicken cecum had the highest total tags, while the Sambi 2 village recorded the lowest. Similarly, Sambi 2 chicken cecum exhibited the highest unique tags (6662) and OTUs number (1261), while the Kupang samples gave the lowest at 2550 and 745, respectively. The Shannon diversity index for bacterial diversity demonstrated that cecum samples from Labuan Bajo (5.679) were more diverse than Sambi 1 (5.378), Sambi 2 (5.653), and Kupang samples (3.77). The bacteria with the highest dominance index (0.935) was found in Sambi 2, while the lowest was observed in the Kupang samples (0.082). The three bacterial phyla showing the highest relative abundance were those from Sambi 1, Sambi 2, and Labuan Bajo cecum samples, comprising Firmicutes, Bacteroidota, and Actinobacteriota.Conversely, the Kupang samples showed an abundance of Firmicutes, Bacteroidota, and Campilobacterota, compared to the Lactobacillus-dominated Kupang, Sambi 1, and Sambi 2 chicken cecum samples. The highest relative abundance for Bifidobacterium occurred in Sambi 1 and Sambi 2 chicken cecum samples, the Kupang samples were Campylobacter dominated, and Olsenella was abundant in the Labuan Bajo samples. Intriguingly, the bacterial composition in the tested chicken cecum samples largely comprised beneficial bacteria such as the lactic acid bacteria group. This bacterial group can be further characterized for obtaining probiotic cultures that could improve the health of free-range chickens.

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  • University of Brawijaya
  • Universitas Katolik Widya Mandira
  • Universitas Nahdlatul Ulama Blitar
  • Universitas Maarif Hasyim Latif
  • North Carolina Agricultural and Technical State University
  • Lambung Mangkurat University
  • Universitas Halu Oleo
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Rekan penulisOrganisasiArtikel bersama
Catur RetnaningdyahUniversity of Brawijaya5
Adji Achmad Rinaldo FernandesUniversity of Brawijaya4
Amin Setyo LeksonoUniversity of Brawijaya4
Tri ArdyatiUniversity of Brawijaya3
Muhammad Fadhil AnshariUniversity of Brawijaya3
Muhaimin Rifa’iUniversity of Brawijaya3
Irfan MustafaUniversity of Brawijaya3
Nashi WidodoUniversity of Brawijaya2
Dwi Purno WidekdoUniversity of Brawijaya2
Nining HaryuniUniversitas Nahdlatul Ulama Blitar2
Hartutik HartutikUniversity of Brawijaya2
Sri WahjuningsihUniversity of Brawijaya2
Agung Putra PurwantoUniversity of Brawijaya1
Alifia Issabella MulyawatiUniversity of Brawijaya1
Elsa Mega SuryaniUniversitas Maarif Hasyim Latif1
Hikmah MaulidiyahUniversity of Brawijaya1
Salam Adnan IbrahimNorth Carolina Agricultural and Technical State University1
Wayan Firdaus MahmudyUniversity of Brawijaya1
Candra DewiUniversity of Brawijaya1
Solimun SolimunUniversity of Brawijaya1
Kurniatun HairiahUniversity of Brawijaya1
Depi NataliaUniversity of Brawijaya1
SOEJONO SOEJONOAfiliasi tidak diketahui1
Eko Rini IndrayatieLambung Mangkurat University1
Soemarno SoemarnoUniversity of Brawijaya1
Daru Setyo RiniUniversity of Brawijaya1
Donny HarisusenoUniversity of Brawijaya1
Chatarina Gradict SemiunUniversitas Katolik Widya Mandira1
Muhammad YusufUniversitas Halu Oleo1
Syahrul KurniawanUniversity of Brawijaya1
Yulia NurainiUniversity of Brawijaya1
Siska NurfitrianiUniversity of Brawijaya1
Durrotul InayahUniversity of Brawijaya1
Nia KurniawanUniversity of Brawijaya1
Syifa SaputraUniversity of Brawijaya1
Sefihara Paramitha SaktiUniversity of Brawijaya1

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Sumber metadata: OAI-PMH (metadata jurnal) http://jtrolis.ub.ac.id/index.php/jtrolis/oai, pertama di-harvest 9 Nov 2026, terakhir terlihat 9 Nov 2026.
Metadata asli (oai_dc) 
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	<dc:title xml:lang="en">Next-Generation Sequencing of the Microbial Community Profile In Free-Range Chicken (Gallus gallus domesticus) Cecum from East Nusa Tenggara Province: Microbial community profile in free-range chicken (Gallus gallus domesticus) cecum</dc:title>
	<dc:creator xml:lang="en">Lengur, Eufrasia Reneilda Arianti</dc:creator>
	<dc:creator xml:lang="en">Dwi Jatmiko, Yoga</dc:creator>
	<dc:creator xml:lang="en">Arisoesilaningsih, Endang</dc:creator>
	<dc:creator xml:lang="en">Widodo, Eko</dc:creator>
	<dc:subject xml:lang="en">Cecum</dc:subject>
	<dc:subject xml:lang="en">Diversity</dc:subject>
	<dc:subject xml:lang="en"> Firmicutes</dc:subject>
	<dc:subject xml:lang="en">Free-range chicken</dc:subject>
	<dc:subject xml:lang="en">Next-generation sequencing</dc:subject>
	<dc:description xml:lang="en">Free-range chicken is livestock reared to support the humans' need for protein alongside its ritualistic use in traditional medicine to treat diseases. This study investigates the diversity of bacterial communities in the free-range chicken cecum reared in different East Nusa Tenggara Province localities comprising Sambi 1, Sambi 2 villages, Labuan Bajo, and Kupang City. The extracted chromosomal DNA was subjected to next-generation sequencing using the V3-V4 region primers. Results revealed that the Kupang chicken cecum had the highest total tags, while the Sambi 2 village recorded the lowest. Similarly, Sambi 2 chicken cecum exhibited the highest unique tags (6662) and OTUs number (1261), while the Kupang samples gave the lowest at 2550 and 745, respectively. The Shannon diversity index for bacterial diversity demonstrated that cecum samples from Labuan Bajo (5.679) were more diverse than Sambi 1 (5.378), Sambi 2 (5.653), and Kupang samples (3.77). The bacteria with the highest dominance index (0.935) was found in Sambi 2, while the lowest was observed in the Kupang samples (0.082). The three bacterial phyla showing the highest relative abundance were those from Sambi 1, Sambi 2, and Labuan Bajo cecum samples, comprising Firmicutes, Bacteroidota, and Actinobacteriota.Conversely, the Kupang samples showed an abundance of Firmicutes, Bacteroidota, and Campilobacterota, compared to the Lactobacillus-dominated Kupang, Sambi 1, and Sambi 2 chicken cecum samples. The highest relative abundance for Bifidobacterium occurred in Sambi 1 and Sambi 2 chicken cecum samples, the Kupang samples were Campylobacter dominated, and Olsenella was abundant in the Labuan Bajo samples. Intriguingly, the bacterial composition in the tested chicken cecum samples largely comprised beneficial bacteria such as the lactic acid bacteria group. This bacterial group can be further characterized for obtaining probiotic cultures that could improve the health of free-range chickens.</dc:description>
	<dc:publisher xml:lang="en">Journal of Tropical Life Science</dc:publisher>
	<dc:date>2023-06-06</dc:date>
	<dc:type>info:eu-repo/semantics/article</dc:type>
	<dc:type>info:eu-repo/semantics/publishedVersion</dc:type>
	<dc:format>application/pdf</dc:format>
	<dc:identifier>https://jtrolis.ub.ac.id/index.php/jtrolis/article/view/2457</dc:identifier>
	<dc:identifier>10.11594/jtls.13.02.13</dc:identifier>
	<dc:source xml:lang="en">Journal of Tropical Life Science; Vol. 13 No. 2 (2023); 349-358</dc:source>
	<dc:source>2527-4376</dc:source>
	<dc:source>2087-5517</dc:source>
	<dc:language>eng</dc:language>
	<dc:relation>https://jtrolis.ub.ac.id/index.php/jtrolis/article/view/2457/654</dc:relation>
	<dc:rights xml:lang="en">Copyright (c) 2022 Journal of Tropical Life Science</dc:rights>
	<dc:rights xml:lang="en">https://creativecommons.org/licenses/by-nc/4.0</dc:rights>
</oai_dc:dc>