Unveiling the Kadaknath Gut Microbiome: Early Growth Phase Spatiotemporal Diversity
The early growth phase is a critical period for the development of the chicken gut microbiome. In this study, the spatiotemporal diversity of the gastrointestinal microbiota, shifts in taxonomic composition, and relative abundances of the main bacterial taxa were characterized in Kadaknath, a high-v...
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2025-02-01
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| author | Amruta Nair Swapnil Prakash Doijad Mangesh Vasant Suryavanshi Anwesha Dey Satya Veer Singh Malik Bas E. Dutilh Sukhadeo Baliram Barbuddhe |
| author_facet | Amruta Nair Swapnil Prakash Doijad Mangesh Vasant Suryavanshi Anwesha Dey Satya Veer Singh Malik Bas E. Dutilh Sukhadeo Baliram Barbuddhe |
| author_sort | Amruta Nair |
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| description | The early growth phase is a critical period for the development of the chicken gut microbiome. In this study, the spatiotemporal diversity of the gastrointestinal microbiota, shifts in taxonomic composition, and relative abundances of the main bacterial taxa were characterized in Kadaknath, a high-value indigenous Indian chicken breed, using sequencing of the V3–V4 region 16S rRNA gene. To assess microbiome composition and bacterial abundance shifts, three chickens per growth phase (3, 28, and 35 days) were sampled, with microbiota analyzed from three gut regions (crop, small intestine, and ceca) per bird. The results revealed <i>Firmicutes</i> as the most abundant phylum and <i>Lactobacillus</i> as the dominant genus across all stages. <i>Lactobacillus</i> was particularly abundant in the crop at early stages (3 and 28 days), while the ceca exhibited a transition towards the dominance of genus <i>Phocaeicola</i> by day 35. Microbial richness and evenness increased with age, reflecting microbiome maturation, and the analyses of the microbial community composition revealed distinct spatiotemporal differences, with the ceca on day 35 showing the highest differentiation. Pathogen analysis highlighted a peak in poultry-associated taxa <i>Campylobacter</i>, <i>Staphylococcus</i>, and <i>Clostridium paraputrificum</i> in 3-day-old Kadaknath, particularly in the small intestine, underscoring the vulnerability of early growth stages. These findings provide critical insights into age-specific microbiome development and early life-stage susceptibility to pathogens, emphasizing the need for targeted interventions to optimize poultry health management and growth performance. |
| format | Article |
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| institution | Kabale University |
| issn | 2036-7481 |
| language | English |
| publishDate | 2025-02-01 |
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| series | Microbiology Research |
| spelling | doaj-art-7b0393408b5046d88bbff2cb913f80d02025-08-20T03:43:31ZengMDPI AGMicrobiology Research2036-74812025-02-011635410.3390/microbiolres16030054Unveiling the Kadaknath Gut Microbiome: Early Growth Phase Spatiotemporal DiversityAmruta Nair0Swapnil Prakash Doijad1Mangesh Vasant Suryavanshi2Anwesha Dey3Satya Veer Singh Malik4Bas E. Dutilh5Sukhadeo Baliram Barbuddhe6ICAR-National Meat Research Institute, Hyderabad 500092, IndiaInstitute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07745 Jena, GermanyDepartment of Cardiovascular and Metabolic Sciences, Cleveland Clinic—Lerner Research Institute, Cleveland, OH 44106, USADepartment of Forest, West Bengal Zoo Authority, Kolkata 700106, IndiaDivision of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Bareilly 243122, IndiaInstitute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07745 Jena, GermanyICAR-National Meat Research Institute, Hyderabad 500092, IndiaThe early growth phase is a critical period for the development of the chicken gut microbiome. In this study, the spatiotemporal diversity of the gastrointestinal microbiota, shifts in taxonomic composition, and relative abundances of the main bacterial taxa were characterized in Kadaknath, a high-value indigenous Indian chicken breed, using sequencing of the V3–V4 region 16S rRNA gene. To assess microbiome composition and bacterial abundance shifts, three chickens per growth phase (3, 28, and 35 days) were sampled, with microbiota analyzed from three gut regions (crop, small intestine, and ceca) per bird. The results revealed <i>Firmicutes</i> as the most abundant phylum and <i>Lactobacillus</i> as the dominant genus across all stages. <i>Lactobacillus</i> was particularly abundant in the crop at early stages (3 and 28 days), while the ceca exhibited a transition towards the dominance of genus <i>Phocaeicola</i> by day 35. Microbial richness and evenness increased with age, reflecting microbiome maturation, and the analyses of the microbial community composition revealed distinct spatiotemporal differences, with the ceca on day 35 showing the highest differentiation. Pathogen analysis highlighted a peak in poultry-associated taxa <i>Campylobacter</i>, <i>Staphylococcus</i>, and <i>Clostridium paraputrificum</i> in 3-day-old Kadaknath, particularly in the small intestine, underscoring the vulnerability of early growth stages. These findings provide critical insights into age-specific microbiome development and early life-stage susceptibility to pathogens, emphasizing the need for targeted interventions to optimize poultry health management and growth performance.https://www.mdpi.com/2036-7481/16/3/54gut microbiomeKadaknath<i>Lactobacillus</i>spatiotemporal variation |
| spellingShingle | Amruta Nair Swapnil Prakash Doijad Mangesh Vasant Suryavanshi Anwesha Dey Satya Veer Singh Malik Bas E. Dutilh Sukhadeo Baliram Barbuddhe Unveiling the Kadaknath Gut Microbiome: Early Growth Phase Spatiotemporal Diversity Microbiology Research gut microbiome Kadaknath <i>Lactobacillus</i> spatiotemporal variation |
| title | Unveiling the Kadaknath Gut Microbiome: Early Growth Phase Spatiotemporal Diversity |
| title_full | Unveiling the Kadaknath Gut Microbiome: Early Growth Phase Spatiotemporal Diversity |
| title_fullStr | Unveiling the Kadaknath Gut Microbiome: Early Growth Phase Spatiotemporal Diversity |
| title_full_unstemmed | Unveiling the Kadaknath Gut Microbiome: Early Growth Phase Spatiotemporal Diversity |
| title_short | Unveiling the Kadaknath Gut Microbiome: Early Growth Phase Spatiotemporal Diversity |
| title_sort | unveiling the kadaknath gut microbiome early growth phase spatiotemporal diversity |
| topic | gut microbiome Kadaknath <i>Lactobacillus</i> spatiotemporal variation |
| url | https://www.mdpi.com/2036-7481/16/3/54 |
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