{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T14:15:15Z","timestamp":1783692915490,"version":"3.55.0"},"reference-count":39,"publisher":"MDPI AG","issue":"14","license":[{"start":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T00:00:00Z","timestamp":1783641600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100008111","name":"Hainan Provincial Key R&D Program","doi-asserted-by":"publisher","award":["ZDYF2025XDNY080"],"award-info":[{"award-number":["ZDYF2025XDNY080"]}],"id":[{"id":"10.13039\/501100008111","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008111","name":"Hainan Provincial Key R&D Program","doi-asserted-by":"publisher","award":["ZDYF2024YJGG003-5"],"award-info":[{"award-number":["ZDYF2024YJGG003-5"]}],"id":[{"id":"10.13039\/501100008111","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Hainan Academy of Agricultural Sciences","award":["HAAS2025MLXXQ01"],"award-info":[{"award-number":["HAAS2025MLXXQ01"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Early-life dietary transition is a critical window for gut microbiota assembly and intestinal maturation in squabs. This study compared the overall artificial-feeding system using a lactic acid bacteria-fermented diet (AF) with a parent-feeding system (PF) during 18\u201325 days of age. Because AF differed from PF in both diet exposure and feeding ecology, including manual feeding, absence of parental feeding and crop milk, altered feeding rhythm, and potential loss of parental microbial transmission, the objective was to characterize associations between the two systems rather than to isolate the effect of fermentation alone. Squabs were assigned to AF or PF for 7 days. Microbial communities in the duodenum, jejunum, ileum, and rectum were profiled by 16S rRNA sequencing, and body size traits, organ indices, jejunal morphology, muscle histology, serum biochemical indicators, and muscle composition were assessed. The AF system, characterized by lower pH, a higher acid value, and detectable lactic acid bacteria in the feed, was associated with higher alpha diversity in multiple segments and distinct beta-diversity profiles relative to PF. Across intestinal regions, lactobacilli-related genera were enriched, with Limosilactobacillus consistently identified as the most discriminant genus and, together with Lactobacillus, occupying central positions in exploratory co-occurrence networks. AF was also associated with a greater jejunal villus height and villus height-to-crypt depth ratio, larger muscle fiber dimensions, higher intramuscular fat content with increased levels of selected polyunsaturated fatty acids, altered lipid-related serum indicators, and higher organ indices, including the bursa of Fabricius. PICRUSt2 further suggested differences in predicted functional potential related to carbohydrate, amino acid, lipid, and cofactor\/vitamin metabolism, although these outputs represent inference from 16S data rather than directly measured functions. Collectively, the AF system was associated with a lactobacilli-centered, tract-wide microbial signature and coordinated intestinal, muscular, and lipid-related phenotypes in squabs, but the findings should not be interpreted as evidence for fermentation alone.<\/jats:p>","DOI":"10.3390\/ani16142145","type":"journal-article","created":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T13:16:28Z","timestamp":1783689388000},"page":"2145","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The Artificial-Feeding System with a Lactic Acid Bacteria-Fermented Diet, Compared with Parent Feeding, Is Associated with Tract-Wide Microbiota Shifts and Coordinated Developmental Indices in Squabs"],"prefix":"10.3390","volume":"16","author":[{"given":"Qijun","family":"Liang","sequence":"first","affiliation":[{"name":"Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinquan","family":"Xi","sequence":"additional","affiliation":[{"name":"Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shihong","family":"Liu","sequence":"additional","affiliation":[{"name":"Haikou Coconut Pigeon Delicacy Breeding Co., Ltd., Haikou 571100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tieshan","family":"Xu","sequence":"additional","affiliation":[{"name":"Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinli","family":"Zheng","sequence":"additional","affiliation":[{"name":"Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shudai","family":"Lin","sequence":"additional","affiliation":[{"name":"College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lizhi","family":"Lu","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zongxi","family":"Cao","sequence":"additional","affiliation":[{"name":"Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9847-3097","authenticated-orcid":false,"given":"Asmaa Taha Yaseen","family":"Kishawy","sequence":"additional","affiliation":[{"name":"Department of Nutrition and Clinical Nutrition, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44500, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lihong","family":"Gu","sequence":"additional","affiliation":[{"name":"Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"108","DOI":"10.4161\/gmic.26945","article-title":"Intestinal microbiome of poultry and its interaction with host and diet","volume":"5","author":"Pan","year":"2014","journal-title":"Gut Microbes"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/s40104-018-0310-9","article-title":"Strategies to modulate the intestinal microbiota and their effects on nutrient utilization, performance, and health of poultry","volume":"10","author":"Yadav","year":"2019","journal-title":"J. Anim. Sci. Biotechnol."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Schokker, D., Veninga, G., Vastenhouw, S.A., Bossers, A., de Bree, F.M., Kaal-Lansbergen, L.M., Rebel, J.M., and Smits, M.A. (2015). Early life microbial colonization of the gut and intestinal development differ between genetically divergent broiler lines. BMC Genom., 16.","DOI":"10.1186\/s12864-015-1646-6"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1093\/nutrit\/nuv039","article-title":"Potential role of the intestinal microbiota in programming health and disease","volume":"73","author":"Goulet","year":"2015","journal-title":"Nutr. Rev."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1268","DOI":"10.1080\/19490976.2020.1747335","article-title":"Gut microbiota derived metabolites contribute to intestinal barrier maturation at the suckling-to-weaning transition","volume":"11","author":"Beaumont","year":"2020","journal-title":"Gut Microbes"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"102681","DOI":"10.1016\/j.psj.2023.102681","article-title":"Chemical composition of pigeon crop milk and factors affecting its production: A review","volume":"102","author":"Jin","year":"2023","journal-title":"Poult. Sci."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Wang, L., Zhu, J., Xie, P., and Gong, D. (2023). Pigeon during the Breeding Cycle: Behaviors, Composition and Formation of Crop Milk, and Physiological Adaptation. Life, 13.","DOI":"10.3390\/life13091866"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e0189221","DOI":"10.1128\/spectrum.01892-21","article-title":"Intestinal Immune Development Is Accompanied by Temporal Deviation in Microbiota Composition of Newly Hatched Pigeon Squabs","volume":"10","author":"Xu","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1186\/s40168-020-00896-9","article-title":"Maternal gut microbes shape the early-life assembly of gut microbiota in passerine chicks via nests","volume":"8","author":"Chen","year":"2020","journal-title":"Microbiome"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.aninu.2019.11.004","article-title":"Dietary fiber and chicken microbiome interaction: Where will it lead to?","volume":"6","author":"Mahmood","year":"2020","journal-title":"Anim. Nutr."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/2049-1891-6-4","article-title":"Fermented liquid feed for pigs: An ancient technique for the future","volume":"6","author":"Missotten","year":"2015","journal-title":"J. Anim. Sci. Biotechnol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.aninu.2018.11.001","article-title":"Recent advances in fermented feeds towards improved broiler chicken performance, gastrointestinal tract microecology and immune responses: A review","volume":"5","author":"Sugiharto","year":"2019","journal-title":"Anim. Nutr."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Dittoe, D.K., Ricke, S.C., and Kiess, A.S. (2018). Organic Acids and Potential for Modifying the Avian Gastrointestinal Tract and Reducing Pathogens and Disease. Front. Vet. Sci., 5.","DOI":"10.3389\/fvets.2018.00216"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2782","DOI":"10.1099\/ijsem.0.004107","article-title":"A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae","volume":"70","author":"Zheng","year":"2020","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1007\/s00253-012-4407-3","article-title":"The immunomodulatory effects of lactic acid bacteria for improving immune functions and benefits","volume":"96","author":"Tsai","year":"2012","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Dempsey, E., and Corr, S.C. (2022). Lactobacillus spp. for Gastrointestinal Health: Current and Future Perspectives. Front. Immunol., 13.","DOI":"10.3389\/fimmu.2022.840245"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1186\/s40168-021-01040-x","article-title":"Joint contributions of the gut microbiota and host genetics to feed efficiency in chickens","volume":"9","author":"Wen","year":"2021","journal-title":"Microbiome"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Shehata, A.M., Paswan, V.K., Attia, Y.A., Abdel-Moneim, A.E., Abougabal, M.S., Sharaf, M., Elmazoudy, R., Alghafari, W.T., Osman, M.A., and Farag, M.R. (2021). Managing Gut Microbiota through In Ovo Nutrition Influences Early-Life Programming in Broiler Chickens. Animals, 11.","DOI":"10.3390\/ani11123491"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1002\/ar.1104","article-title":"Luminal morphology of the avian lower intestine: Evidence supporting the importance of retrograde peristalsis for water conservation","volume":"263","author":"Casotti","year":"2001","journal-title":"Anat. Rec."},{"key":"ref_20","first-page":"762","article-title":"Morphology of rectum in broiler chicken and domestic fowl: Notability of retrograde peristalsis for water preservation","volume":"46","author":"Moghaddam","year":"2018","journal-title":"J. Appl. Anim. Res."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/0003-2697(84)90307-5","article-title":"Amino acid analysis by reverse-phase high-performance liquid chromatography: Precolumn derivatization with phenylisothiocyanate","volume":"136","author":"Heinrikson","year":"1984","journal-title":"Anal. Biochem."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet. J."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1186\/s40168-018-0470-z","article-title":"Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2\u2032s q2-feature-classifier plugin","volume":"6","author":"Bokulich","year":"2018","journal-title":"Microbiome"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools","volume":"41","author":"Quast","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"R60","DOI":"10.1186\/gb-2011-12-6-r60","article-title":"Metagenomic biomarker discovery and explanation","volume":"12","author":"Segata","year":"2011","journal-title":"Genome Biol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1038\/s41587-020-0548-6","article-title":"PICRUSt2 for prediction of metagenome functions","volume":"38","author":"Douglas","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Ratsika, A., Codagnone, M.C., O\u2019Mahony, S., Stanton, C., and Cryan, J.F. (2021). Priming for Life: Early Life Nutrition and the Microbiota-Gut-Brain Axis. Nutrients, 13.","DOI":"10.3390\/nu13020423"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"101570","DOI":"10.1016\/j.psj.2021.101570","article-title":"Effects of different probiotic fermented feeds on production performance and intestinal health of laying hens","volume":"101","author":"Lv","year":"2022","journal-title":"Poult. Sci."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Peng, W., Talpur, M.Z., Zeng, Y., Xie, P., Li, J., Wang, S., Wang, L., Zhu, X., Gao, P., and Jiang, Q. (2022). Influence of fermented feed additive on gut morphology, immune status, and microbiota in broilers. BMC Vet. Res., 18.","DOI":"10.1186\/s12917-022-03322-4"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Vemuri, R., Martoni, C.J., Kavanagh, K., and Eri, R. (2022). Lactobacillus acidophilus DDS-1 Modulates the Gut Microbial Co-Occurrence Networks in Aging Mice. Nutrients, 14.","DOI":"10.20944\/preprints202202.0208.v1"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"237921","DOI":"10.1155\/2013\/237921","article-title":"The role of cell surface architecture of lactobacilli in host-microbe interactions in the gastrointestinal tract","volume":"2013","author":"Sengupta","year":"2013","journal-title":"Mediat. Inflamm."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1016\/j.resmic.2010.03.001","article-title":"Importance of lactobacilli in food and feed biotechnology","volume":"161","author":"Giraffa","year":"2010","journal-title":"Res. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Reicher, N., Melkman-Zehavi, T., Dayan, J., and Uni, Z. (2020). It\u2019s All About Timing: Early Feeding Promotes Intestinal Maturation by Shifting the Ratios of Specialized Epithelial Cells in Chicks. Front. Physiol., 11.","DOI":"10.3389\/fphys.2020.596457"},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Yin, Y., Liao, Y., Li, J., Pei, Z., Wang, L., Shi, Y., Peng, H., Tan, Y., Li, C., and Bai, H. (2023). Lactobacillus plantarum GX17 benefits growth performance and improves functions of intestinal barrier\/intestinal flora among yellow-feathered broilers. Front. Immunol., 14.","DOI":"10.3389\/fimmu.2023.1195382"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Niu, J.L., Zhang, J., Wei, L.Q., Zhang, W.J., and Nie, C.X. (2019). Effect of Fermented Cottonseed Meal on the Lipid-Related Indices and Serum Metabolic Profiles in Broiler Chickens. Animals, 9.","DOI":"10.3390\/ani9110930"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/j.aninu.2022.09.003","article-title":"Fermented mixed feed alters growth performance, carcass traits, meat quality and muscle fatty acid and amino acid profiles in finishing pigs","volume":"12","author":"Liu","year":"2023","journal-title":"Anim. Nutr."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"e0021424","DOI":"10.1128\/msystems.00214-24","article-title":"Lactobacillus-derived protoporphyrin IX and SCFAs regulate the fiber size via glucose metabolism in the skeletal muscle of chickens","volume":"9","author":"Cai","year":"2024","journal-title":"mSystems"}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/14\/2145\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T13:30:20Z","timestamp":1783690220000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/14\/2145"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,10]]},"references-count":39,"journal-issue":{"issue":"14","published-online":{"date-parts":[[2026,7]]}},"alternative-id":["ani16142145"],"URL":"https:\/\/doi.org\/10.3390\/ani16142145","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,10]]}}}