Delayed access to feed early post-hatch affects the development and maturation of gastrointestinal tract microbiota in broiler chickens

Abstract

Background: The first two weeks of post-hatch (PH) growth in broilers (meat-type birds) are critical for gut development and microbiota colonization. In the current broiler production system, chicks may not receive feed and water for 24 to 72 h due to variations in hatching time and hatchery management. Post-hatch feed delay affects body weight, feed efficiency, mortality, and gut development. The goal of this study was to investigate changes in the microbiome in broiler chickens early PH and the effect of delayed access to feed on the microbiota.

Results: Chicks either received feed and water immediately after hatch or access to feed was delayed for 48 h to mimic commercial hatchery settings (treatment, TRT). Both groups were sampled (n = 6) at -48, 0, 4 h, and 1 (24 h), 2 (48 h), 3 (72 h), 4 (96 h), 6 (144 h), 8 (192 h), 10 (240 h), 12 (288 h) and 14 (336 h) days PH. Ileal (IL) and cecal (CE) epithelial scrapings (mucosal bacteria, M) and digesta (luminal bacteria, L) were collected for microbiota analysis. Microbiota was determined by sequencing the V3-V4 region of bacterial 16S rRNA and analyzed using QIIME2. The microbiota of early ileal and cecal samples were characterized by high abundance of unclassified bacteria. Among four bacterial populations (IL-L, IL-M, CE-L, CE-M), IL-M was the least affected by delayed access to feed early PH. Both alpha and beta diversities were affected by delayed access to feed PH in IL-L, CE-M and CE-L. However, the development effect was more pronounced. In all four bacterial populations, significant changes due to developmental effect (time relative to hatch) was observed in taxonomic composition, with transient changes of bacterial taxa during the first two weeks PH. Delayed access to feed has limited influence on bacterial composition with only a few genera and species affected in all four bacterial populations. Predicted function based on 16S rRNA was also affected by delayed access to feed PH with most changes in metabolic pathway richness observed in IL-L, CE-L and CE-M.

Conclusions: These results show transient changes in chicken microbiota biodiversity during the first two weeks PH and indicate that delayed access to feed affects microbiota development. Proper microbiota development could be an important factor in disease prevention and antibiotic use in broiler chickens. Moreover, significant differences in response to delayed access to feed PH between luminal and mucosal bacterial populations strongly suggests the need for separate analysis of these two populations.

Keywords: 16S; Ceca; Chicken; Delayed access to feed; Ileum; Microbiota.

Fig. 1

Taxonomic profile [relative abundance (%)] in ileal (IL, a-b) and cecal (CE, c-d) bacterial populations at the genus and species level in embryo (-48 h), chicks at hatch (0 h) and 4 h post-hatch. Uncl – unclassified bacterial reads, Low Abundant Reads (LAR). 4 h post-hatch chicks have access to feed (F) or do not have access to feed (NF)

Fig. 2

Effect of delay in feed access for the first 48 h post-hatch on alpha diversity indices (a) number of amplicon sequence variants (ASV), (b) Shannon index, (c) Richness and (d) Evenness in ileal luminal bacterial population from day 1 (24 h) through day 14 (336 h) post-hatch. When the interaction between time and treatment was significant, only significant (P < 0.05) differences between fed (F) and not fed (NF) groups for a single age are shown as indicated by asterisk. When the interaction between time and treatment was not significant, only significant (P < 0.05) main effects (time and treatment) are presented and significant differences between groups are indicated by lines

Fig. 3

Effect of delay in feed access for the first 48 h post-hatch on alpha diversity indices (a) number of amplicon sequence variants (ASV), (b) Shannon index, (c) Richness and (d) Evenness in cecal luminal bacterial population from day 1 (24 h) through day 14 post-hatch. When the interaction between time and treatment was significant, only significant (P < 0.05) differences between fed (F) and not fed (NF) group are shown as indicated by asterisk

Fig. 4

Effect of delay in feed access for the first 48 h post-hatch on alpha diversity indices (a) number of amplicon sequence variants (ASV), (b) Shannon index, (c) Richness and (d) Evenness in cecal mucosal bacterial population from day 1 (24 h) through day 14 (336 h) post-hatch. When the interaction between time and treatment was significant, only significant (P < 0.05) differences between fed (F) and not fed (NF) group are shown as indicated by asterisk

Fig. 5

Effect of delay in feed access for the first 48 h post-hatch on beta diversity of ileal luminal bacterial population from day 1 (24 h) through day 14 (336 h) post-hatch using the Principal Coordinate analysis (PCoA) based on the Unweighted UniFrac distances between specific groups. Panel (a) shows PCoA for all samples while (b-g) panels depict differences between treatment groups at (b) day (d) 1 and 2, (c) d 3; (d) d 4, (e) d 6, (f) d 8 and (g) d 10 post-hatch. F – chicks fed immediately post-hatch; NF – chicks without access to feed for the first 48 h post-hatch

Fig. 6

Effect of delay in feed access for the first 48 h post-hatch on beta diversity of cecal luminal bacterial population from day 1 (24 h) through day 14 (336 h) post-hatch using the Principal Coordinate analysis (PCoA) based on the Unweighted UniFrac distances between groups. Panel (a) shown PCoA for all samples while (b-g) panels depict differences between specific treatment groups at (b) day (d) 1, (c) d 2; (d) d 3, (e) d 4, (f) d 6 and (g) d 8 post-hatch. F – chicks feed immediately post-hatch; NF – chicks without access to feed for the first 48 h post-hatch

Fig. 7

Effect of delay in feed access for the first 48 h post-hatch on beta diversity of cecal mucosal bacterial population from day 1 (24 h) through day 14 (336 h) post-hatch using the Principal Coordinate analysis (PCoA) based on the Unweighted UniFrac distances between groups. Panel (a) shown PCoA for all samples while (b-g) panels depict differences between specific treatment groups at (b) day (d) 1, (c) d 2; (d) d 3, (e) d 4, (f) d 6 and (g) d 8 post-hatch. F – chicks feed immediately post-hatch; NF – chicks without access to feed for the first 48 h post-hatch

Fig. 8

Effect of delay in feed access for the first 48 h post-hatch on relative bacterial abundance (%) in ileal luminal (IL-L, a-d) and mucosal (IL-M, e–f) bacterial populations from day 1 (24 h) through day 14 (336 h) post-hatch at genus and species level. Taxonomic profile of chicken IL-L at (a) genus and (c) species level. Effect of delayed access to feed early post-hatch on (b) Clostridium and (d) Clostridium perfringens level in IL-L. Taxonomic profile of chicken IL-M at (e) genus and (h) species level. Effect of delayed access to feed early post-hatch on (f) Low Abundant Reads (LAR) and (g) Klebsiella level in IL-M. Asterisk denote statistically significant (P < 0.05) differences between fed (F) and not-fed (NF) chickens

Fig. 9

Effect of delay in feed access for the first 48 h post-hatch on relative bacterial abundance (%) in cecal luminal (CE-L, a-c) and mucosal (CE-M, d-g) bacterial populations day 1 (24 h) through day 14 (336 h) post-hatch at genus and species level. Taxonomic profile of chicken CE-L at (a) genus and (c) species level. Effect of delayed access to feed early post-hatch on (b) Klebsiella level in CE-L. Taxonomic profile of chicken CE-M at (d) genus and (h) species level. Effect of delayed access to feed early post-hatch on (e) Unclassified bacteria (Uncl), (f) Anaerotruncus and (g) Klebsiella level in CE-M. Asterisks denote statistically significant differences between fed (F) and not-fed (NF) chickens (P < 0.05)

Fig. 10

Effect of delay in feed access for the first 48 h post-hatch on differentially abundant bacterial taxa as determined by Linear Discriminant Analysis (LDA) effect size (LEfSe) analysis in ileal luminal (IL-L, a) and mucosal (IL-M, b), and cecal luminal (CE-L, c) and mucosal (CE-M, d) bacterial population 2 or 3 days post-hatch. F-chicken immediately fed after hatch, NF – chicken with 48 h delayed access to feed