{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T01:11:08Z","timestamp":1780449068950,"version":"3.54.1"},"reference-count":38,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2020,2,28]],"date-time":"2020-02-28T00:00:00Z","timestamp":1582848000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004351","name":"Sultan Qaboos University","doi-asserted-by":"publisher","award":["[number: IG\/AGR\/ANVS\/15\/02]"],"award-info":[{"award-number":["[number: IG\/AGR\/ANVS\/15\/02]"]}],"id":[{"id":"10.13039\/501100004351","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>The objective of this study was to assess the relative abundance of bacteria microflora in different segments of the gastrointestinal tract (duodenum, jejunum, ilium, and cecum) of indigenous (local Omani) and commercial (Cobb 500) chicken strains. Birds were raised under an intensive management system fed a nonmedicated corn-soybean meal diet from Day 0\u201335 days of age. Using 16S rDNA-based analysis the study showed that in both breeds of birds Bacilli were the most abundant class of bacteria in the duodenum, jejunum, and ileum. Local Omani chickens had significantly higher numbers of Clostridia at most time periods. Actinobacteria were found in higher numbers and reached 54.9% of the bacteria in the jejunum at Day 35 in Cobb 500 versus only 5.42% in the Omani chickens. The bacterial microbiota relative abundance differed significantly (p &lt; 0.05) across different intestinal segments of the two strains, suggesting that each region developed its own bacterial community and the relative abundances of these were quite different.<\/jats:p>","DOI":"10.3390\/ani10030391","type":"journal-article","created":{"date-parts":[[2020,3,2]],"date-time":"2020-03-02T07:35:30Z","timestamp":1583134530000},"page":"391","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Diversity of Intestinal Bacterial Microbiota of Indigenous and Commercial Strains of Chickens Using 16S rDNA-Based Analysis"],"prefix":"10.3390","volume":"10","author":[{"given":"Waleed","family":"Al-Marzooqi","sequence":"first","affiliation":[{"name":"Department of Animal and Veterinary Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, P.O. Box 34, Al-Khoud 123, Oman"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zeyana A.S.","family":"Al-Maskari","sequence":"additional","affiliation":[{"name":"Department of Animal and Veterinary Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, P.O. Box 34, Al-Khoud 123, Oman"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaadhia","family":"Al-Kharousi","sequence":"additional","affiliation":[{"name":"Department of Animal and Veterinary Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, P.O. Box 34, Al-Khoud 123, Oman"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eugene H.","family":"Johnson","sequence":"additional","affiliation":[{"name":"Department of Animal and Veterinary Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, P.O. Box 34, Al-Khoud 123, Oman"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yasmin","family":"El Tahir","sequence":"additional","affiliation":[{"name":"Department of Animal and Veterinary Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, P.O. Box 34, Al-Khoud 123, Oman"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,2,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1035s","DOI":"10.1093\/ajcn\/69.5.1035s","article-title":"Developmental microbial ecology of the neonatal gastrointestinal tract","volume":"69","author":"Mackie","year":"1999","journal-title":"Am. J. Clin. Nutr."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1030","DOI":"10.1093\/ps\/82.6.1030","article-title":"Effects of dietary fructooligosaccharide on digestive enzyme activities, intestinal microflora and morphology of male broilers","volume":"82","author":"Xu","year":"2003","journal-title":"Poult. Sci."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"421","DOI":"10.4141\/A05-049","article-title":"The gastrointestinal microbiota and its role in monogastric nutrition and health with an emphasis on pigs: Current understanding, possible modulations, and new technologies for ecological studies","volume":"85","author":"Richards","year":"2005","journal-title":"Can. J. Anim. Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1574-6968.2002.tb11051.x","article-title":"Diversity and phylogenetic analysis of bacteria in the mucosa of chicken ceca and comparison with bacteria in the cecal lumen","volume":"208","author":"Gong","year":"2002","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1007\/s00248-002-2015-y","article-title":"Spatial and temporal variation of the intestinal bacterial community in commercially raised broiler chickens during growth","volume":"44","author":"Keuzenkamp","year":"2002","journal-title":"Microb. Ecol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1093\/ps\/83.7.1093","article-title":"Microflora ecology of the chicken intestine using 16S ribosomal DNA primers","volume":"83","author":"Sklan","year":"2004","journal-title":"Poult. Sci."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"5656","DOI":"10.1128\/AEM.67.12.5656-5667.2001","article-title":"Percent G + C profiling accurately reveals diet-related differences in the gastrointestinal microbial community of broiler chickens","volume":"67","author":"Apajalahti","year":"2001","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"5918","DOI":"10.1128\/AEM.68.12.5918-5924.2002","article-title":"Effects of dietary fat source and subtherapeutic levels of antibiotic on the bacterial community in the ileum of broiler chickens at various ages","volume":"68","author":"Knarreborg","year":"2002","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"6816","DOI":"10.1128\/AEM.69.11.6816-6824.2003","article-title":"Diversity and succession of the intestinal bacterial community of the maturing broiler chicken","volume":"69","author":"Lu","year":"2003","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"174","DOI":"10.3923\/ijps.2019.174.180","article-title":"Comparative evaluation of growth performance, meat quality and intestinal development of indigenous and commercial chicken strains","volume":"18","author":"Johnson","year":"2019","journal-title":"Int. J. Poult. Sci."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1614","DOI":"10.3382\/ps.2010-00747","article-title":"Evaluation of the bacterial community and intestinal development of different genetic lines of chickens","volume":"89","author":"Lumpkins","year":"2010","journal-title":"Poult. Sci."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"410s","DOI":"10.1093\/ajcn\/73.2.410s","article-title":"Molecular assessment of intestinal microflora","volume":"73","author":"Tannock","year":"2001","journal-title":"Am. J. Clin. Nutr."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1111\/j.1348-0421.2002.tb02709.x","article-title":"Phylogenetic analysis of caecal microbiota in chicken by the use of 16S rDNA clone libraries","volume":"46","author":"Lan","year":"2002","journal-title":"Microbiol. Immunol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1100","DOI":"10.1093\/ps\/82.7.1100","article-title":"Poultry digestive microflora biodiversity as indicated by denaturing gradient gel electrophoresis","volume":"82","author":"Hume","year":"2003","journal-title":"Poult. Sci."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1242","DOI":"10.1093\/ps\/82.8.1242","article-title":"Composition of microbiota in content and mucus from cecae of broiler chickens as measured by fluorescent in situ hybridization with group-specific, 16S rRNA-targeted oligonucleotide probes","volume":"82","author":"Zhu","year":"2003","journal-title":"Poult. Sci."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fmicb.2016.00484","article-title":"Metataxonomic and metagenomic approaches vs. culture-based techniques for clinical pathology","volume":"7","author":"Hilton","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref_17","unstructured":"Federation of Animal Science Societies (2010). Guide for the Care and Use of Agricultural Animals in Research and Teaching, Federation of Animal Science Societies."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nat. Methods"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2957","DOI":"10.1093\/bioinformatics\/btr507","article-title":"FLASH: Fast length adjustment of short reads to improve genome assemblies","volume":"27","author":"Magoc","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","article-title":"Search and clustering orders of magnitude faster than BLAST","volume":"26","author":"Edgar","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_21","first-page":"1","article-title":"Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples","volume":"5","author":"James","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1387","DOI":"10.3382\/ps\/pew372","article-title":"Microbial Community Mapping in Intestinal Tract of Broiler Chicken","volume":"5","author":"Xiao","year":"2017","journal-title":"Poult. Sci."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1080\/17450390701556817","article-title":"Indigenous bacteria and bacterial metabolic products in the gastrointestinal tract of broiler chickens","volume":"5","author":"Rehman","year":"2007","journal-title":"Arch. Anim. Nutr."},{"key":"ref_24","first-page":"1138","article-title":"Quantitative analysis of the intestinal bacterial community in one to three-week-old commercially reared broiler chickens fed conventional or antibiotic-free vegetable-based diets","volume":"102","author":"Wise","year":"2007","journal-title":"J. Appl. Microbiol."},{"key":"ref_25","first-page":"1","article-title":"Development of digestive function in neonatal poultry: Physiological limitations and potential","volume":"15","author":"Ravindran","year":"2003","journal-title":"Proc. Aust. Poultry Sci. Symp."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"229","DOI":"10.2141\/jpsa.39.229","article-title":"Review on chicken intestinal villus histological alterations related with intestinal function","volume":"39","author":"Yamauchi","year":"2002","journal-title":"J. Poult. Sci."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1080\/00071660903247182","article-title":"Growth performance and intestinal histology in broiler chickens fed with dietary chitosan","volume":"50","author":"Khambualai","year":"2009","journal-title":"Br. Poult. Sci."},{"key":"ref_28","first-page":"1","article-title":"Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses","volume":"7","author":"Sieo","year":"2015","journal-title":"Gut Pathog."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1093\/ps\/85.7.1151","article-title":"Microbial community composition of the ileum and cecum of broiler chickens as revealed by molecular and culture-based techniques","volume":"85","author":"Bjerrum","year":"2006","journal-title":"Poult. Sci."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1111\/j.1574-6941.2006.00193.x","article-title":"16S rRNA gene-based analysis of mucosa-associated bacterial community and phylogeny in the chicken gastrointestinal tracts: From crops to ceca","volume":"59","author":"Gong","year":"2007","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1217","DOI":"10.3382\/ps.2010-00653","article-title":"Quantificationof Faecalibacteriumprausnitzii- and Subdoligranulumvariabile-like bacteria in the cecum of chickens by real-time PCR","volume":"89","author":"Lund","year":"2010","journal-title":"Poult. Sci."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1152\/ajpregu.1996.271.4.R1085","article-title":"Kinetics of hexose uptake by the small and large intestine of the chicken","volume":"271","author":"Amat","year":"1996","journal-title":"Am. J. Physiol. Regul. Integr. Comp. Physiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"299S","DOI":"10.1093\/ajcn\/55.1.299s","article-title":"Physiology and pathophysiology of intestinal absorption","volume":"55","author":"Caspary","year":"1992","journal-title":"Am. J. Clin. Nutr."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"4799","DOI":"10.1128\/AEM.65.11.4799-4807.1999","article-title":"Direct analysis of genes encoding 16S rRnA from complex communities reveals many novel molecular species within the human gut","volume":"65","author":"Suau","year":"1999","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"3651","DOI":"10.1099\/00221287-148-11-3651","article-title":"Analysis of 16S libraries of mouse gastrointestinal microflora reveal a large new group of mouse intestinal bacteria","volume":"148","author":"Salzman","year":"2002","journal-title":"Microbiology"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"5868","DOI":"10.1128\/AEM.00165-11","article-title":"Identification and characterization of potential performance-related gut microbiotas in broiler chickens across various feeding trials","volume":"77","author":"Torok","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"e46923","DOI":"10.7554\/eLife.46923","article-title":"Consistent and correctable bias in metagenomic sequencing measurements","volume":"8","author":"McLaren","year":"2019","journal-title":"Elife"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1217","DOI":"10.5713\/ajas.15.0026","article-title":"Metagenomic Analysis of Chicken Gut Microbiota for Improving Metabolism and Health of Chickens\u2014A Review","volume":"9","author":"Choi","year":"2015","journal-title":"Asian-Australas J. Anim. Sci."}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/10\/3\/391\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T09:02:27Z","timestamp":1760173347000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/10\/3\/391"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,2,28]]},"references-count":38,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2020,3]]}},"alternative-id":["ani10030391"],"URL":"https:\/\/doi.org\/10.3390\/ani10030391","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,2,28]]}}}