{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T15:03:48Z","timestamp":1778857428709,"version":"3.51.4"},"reference-count":49,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2024,9,23]],"date-time":"2024-09-23T00:00:00Z","timestamp":1727049600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Science, Technology &amp; Innovation Funding Authority (STDF), Egypt","award":["LEAP-Agri 326"],"award-info":[{"award-number":["LEAP-Agri 326"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>The animal gastrointestinal tract contains a complex microbiome whose composition ultimately reflects the co-evolution of microorganisms with their animal host and their host\u2019s environment. This study aimed to gain insights into the adaptation of the microbiota of local Egyptian cattle to three different ecosystems (Upper Egypt, Middle Egypt, and Lower Egypt) distributed across 11 governorates (with an average of 12 animals per governorate) using amplicon sequencing. We analyzed the microbiota from 136 fecal samples of local Egyptian cattle through a 16S rRNA gene sequencing approach to better understand the fecal microbial diversity of this breed which developed under different ecosystems. An alpha diversity analysis showed that the fecal microbiota of the Egyptian cattle was not significantly diverse across areas, seasons, sexes, or farm types. Meanwhile, microbiota data revealed significant differences in richness among age groups (p = 0.0018). The microbial community differed significantly in the distribution of its relative abundance rather than in richness across different ecosystems. The taxonomic analysis of the reads identified Firmicutes and Actinobacteriota as the dominant phyla, accounting for over 93% of the total bacterial community in Egyptian cattle. Middle Egypt exhibited a different microbial community composition compared to Upper and Lower Egypt, with a significantly higher abundance of Firmicutes and Euryarchaeota and a lower abundance of Actinobacteriota in this region than the other two ecosystems. Additionally, Middle Egypt had a significantly higher relative abundance of the Methanobacteriaceae family and the Methanobrevibacter genera than Lower and Upper Egypt. These results suggest a difference in the adaptation of the fecal microbial communities of Egyptian cattle raised in Middle Egypt. At the genus level, eleven genera were significantly different among the three ecosystems including Bacillus, DNF00809, Kandleria, Lachnospiraceae_NK3A20_group, Methanobrevibacter, Mogibacterium, Olsenella, Paeniclostridium, Romboutsia, Turicibacter, and UCG-005. These significant differences in microbiota composition may impact the animal\u2019s adaptation to varied environments.<\/jats:p>","DOI":"10.3390\/ani14182752","type":"journal-article","created":{"date-parts":[[2024,9,24]],"date-time":"2024-09-24T03:49:46Z","timestamp":1727149786000},"page":"2752","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Gut Microbiota Diversity of Local Egyptian Cattle Managed in Different Ecosystems"],"prefix":"10.3390","volume":"14","author":[{"given":"Hadeer M.","family":"Aboshady","sequence":"first","affiliation":[{"name":"Department of Animal Production, Faculty of Agriculture, Cairo University, Giza 12613, Egypt"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0204-2223","authenticated-orcid":false,"given":"Asimenia","family":"Gavriilidou","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0480-0959","authenticated-orcid":false,"given":"Nasser","family":"Ghanem","sequence":"additional","affiliation":[{"name":"Department of Animal Production, Faculty of Agriculture, Cairo University, Giza 12613, Egypt"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8793-9659","authenticated-orcid":false,"given":"Mohamed A.","family":"Radwan","sequence":"additional","affiliation":[{"name":"Department of Animal Production, Faculty of Agriculture, Cairo University, Giza 12613, Egypt"}]},{"given":"Ahmed","family":"Elnahas","sequence":"additional","affiliation":[{"name":"Animal Production Department, Faculty of Agriculture, Sohag University, Sohag 82524, Egypt"}]},{"given":"Rania","family":"Agamy","sequence":"additional","affiliation":[{"name":"Department of Animal Production, Faculty of Agriculture, Cairo University, Giza 12613, Egypt"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0380-2338","authenticated-orcid":false,"given":"Nadia H.","family":"Fahim","sequence":"additional","affiliation":[{"name":"Department of Animal Production, Faculty of Agriculture, Cairo University, Giza 12613, Egypt"}]},{"given":"Mohamed H.","family":"Elsawy","sequence":"additional","affiliation":[{"name":"Department of Cattle, Animal Production Research Institute, Agriculture Research Center, Dokki, Giza 12618, Egypt"}]},{"given":"Al-Moataz Bellah M.","family":"Shaarawy","sequence":"additional","affiliation":[{"name":"Department of Cattle, Animal Production Research Institute, Agriculture Research Center, Dokki, Giza 12618, Egypt"}]},{"given":"Ahmed M.","family":"Abdel-Hafeez","sequence":"additional","affiliation":[{"name":"Department of Cattle, Animal Production Research Institute, Agriculture Research Center, Dokki, Giza 12618, Egypt"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6350-6373","authenticated-orcid":false,"given":"Juha","family":"Kantanen","sequence":"additional","affiliation":[{"name":"Natural Resources Institute Finland, 31600 Jokioinen, Finland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2278-7089","authenticated-orcid":false,"given":"Catarina","family":"Ginja","sequence":"additional","affiliation":[{"name":"CIISA, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisboa, Portugal"},{"name":"CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO, Associate Laboratory, BIOPOLIS Program in Genomics, Biodiversity and Land Planning, University of Porto, 4485-661 Vair\u00e3o, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1275-4558","authenticated-orcid":false,"given":"Mahlako L.","family":"Makgahlela","sequence":"additional","affiliation":[{"name":"Agricultural Research Council, Animal Production, Private Bag X2, Irene 0062, South Africa"},{"name":"Department of Animal, Wildlife and Grassland Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9301, South Africa"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4873-6637","authenticated-orcid":false,"given":"Donald R.","family":"Kugonza","sequence":"additional","affiliation":[{"name":"School of Agricultural Sciences, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3679-4685","authenticated-orcid":false,"given":"Rayner","family":"Gonzalez-Prendes","sequence":"additional","affiliation":[{"name":"Animal Breeding and Genomics, Wageningen University & Research, 6700 AH Wageningen, The Netherlands"}]},{"given":"Richard P. M. A.","family":"Crooijmans","sequence":"additional","affiliation":[{"name":"Animal Breeding and Genomics, Wageningen University & Research, 6700 AH Wageningen, The Netherlands"}]}],"member":"1968","published-online":{"date-parts":[[2024,9,23]]},"reference":[{"key":"ref_1","unstructured":"Food and Agriculture Organisation (FAO) (2011). 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