Dataset Information

A reasonable correlation between cloacal and cecal microbiomes in broiler chickens.

ABSTRACT: Gut microbiota play an important role in animal health. For livestock, an understanding of the effect of husbandry interventions on gut microbiota helps develop methods that increase sustainable productivity, animal welfare, and food safety. Poultry microbiota of the mid-gut and hind-gut can only be investigated postmortem; however, samples from the terminal cloaca may be collected from live animals. This study tests whether cloacal microbiota reflect cecal microbiota in European broiler poultry by evaluating total and paired cecal and cloacal microbiomes from 47 animals. 16S amplicon libraries were constructed and sequenced with a MiSeq 250 bp PE read metric. The composition of cloacal and cecal microbiomes were significantly affected by the age and location of animals, but the effect was very small. Bacilli were relatively more abundant in ceca and Clostridia in cloaca. There was an overlap of 99.5% for the abundances and 59% for the types of taxa between cloacal and cecal communities, but the small fraction of rare nonshared taxa were sufficient to produce a signal for differentiation between cecal and cloacal communities. There was a significant positive correlation between specific taxa abundances in cloacal and cecal communities (Rho = 0.66, P = 2 × 10-16). Paired analyses revealed that cloacal communities were more closely related to cecal communities from the same individual than expected by chance. This study is in line with the only other study to evaluate the relationship between cecal and cloacal microbiomes in broiler poultry, but it extends previous findings by analyzing paired cecal-cloacal samples from the same birds and reveals that abundant bacterial taxa in ceca may be reasonably inferred by sampling cloaca. Together, the findings from Europe and Australasia demonstrate that sampling cloaca shows promise as a method to estimate cecal microbiota, and especially abundant taxa, from live broiler poultry in a manner which reduces cost and increases welfare for husbandry and research purposes.

SUBMITTER: Andreani NA

PROVIDER: S-EPMC7647853 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A reasonable correlation between cloacal and cecal microbiomes in broiler chickens.

Andreani Nadia A NA Donaldson Caroline J CJ Goddard Matthew M

Poultry science 20200826 11

Gut microbiota play an important role in animal health. For livestock, an understanding of the effect of husbandry interventions on gut microbiota helps develop methods that increase sustainable productivity, animal welfare, and food safety. Poultry microbiota of the mid-gut and hind-gut can only be investigated postmortem; however, samples from the terminal cloaca may be collected from live animals. This study tests whether cloacal microbiota reflect cecal microbiota in European broiler poultry ...[more]

PMID: 33142525

Similar Datasets

Project description:BackgroundApicomplexan protozoans of the genus Eimeria cause coccidiosis, one of the most economically relevant parasitic diseases in chickens. The lack of a complete understanding of molecular mechanisms in the host-parasite interaction limits the development of effective control measures. In the present study, RNA sequencing (RNA-Seq) was applied to investigate the host mRNA profiles of the cecal mucosa collected at day 5 post-infection with Eimeria maxima (EM).ResultsTotal RNA from cecal samples of the uninfected naïve control and the EM groups was used to make libraries, generating 354,924,372 and 356,229,250 usable reads, respectively, which were assembled into a total of 386,088 high-quality unigenes (transcripts) in Trinity software. RNA-Seq analysis of cecal samples in the two groups revealed 332 upregulated and 363 downregulated genes with significant differences (P ≤ 0.05), including several significant immune-related gene families, such as the major histocompatibility complex (MHC) class I alpha chain, granzyme A and immunoglobulin subtype genes among upregulated differentially expressed genes. In addition, a total of 60 clusters of differentiation (CD) molecular genes and 570 novel genes were found. The completeness of the assembled transcriptome was further assessed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, Gene ontology (GO), eggNOG and CAZy for gene annotation. The broad gene categories represented by the highly differentiated host genes suggested enrichment in immune responses, and downregulation in the metabolic pathway, MARK signaling pathway, vascular smooth muscle contraction, and proteins processing in endoplasmic reticulum after EM infection.ConclusionsEimeria maxima induced statistically significant differences in the cecal mucosal gene expression of infected chickens. These findings provide new insights into the host-parasite interaction and enhance our understanding of the molecular mechanism of avian coccidiosis.

Project description:The chicken gut microbiota plays an influential role in nutrient absorption and metabolism. A clear picture of microbiota succession can enhance host nutrition and disease resistance. This study investigated the cecal microbiota succession of broilers between 3 and 42 days after hatching using 16S rRNA gene sequencing and analyzed its potential association with intestinal nutrient metabolism. Microbiota structure differed significantly at different time points depending on the microbiota alpha-diversity or beta-diversity. Proteobacteria and Bacteroidetes promoted succession on days 3 to 7 and days 28 to 35, respectively. Firmicutes and Tenericutes maintained homeostasis on days 7 to 28 and days 35 to 42. Shigella, [Ruminococcus], Erysipelotrichaceae_Clostridium, and Coprobacillus promoted succession on days 3 to 7; Faecalibacterium modified microbial composition on days 7 to 14; Faecalibacterium and Bacteroides regulated microbial structure from days 21 to 28. The microbiota structure was relatively stable on days 14 to 21 and days 28 to 35. Spearman's correlation analysis indicated a positive correlation between Lactobacillus and villus height and crypt depth (P < 0.01). Faecalibacterium and Shigella were correlated with propionate, butyrate, and valerate concentrations (P < 0.01). Ruminococcus was correlated with sodium-glucose cotransporters 1 and cationic amino acid transporter 1 expression (P < 0.05). Erysipelotrichaceae_Clostridium and Shigella were positively correlated with serum levels of total cholesterol, tryglucerides, and high- and low-density lipoprotein cholesterol (P < 0.01). Bacteroides, Parabacteroides, Lactobacillus, and Shigella were correlated with serum VB6 levels (P < 0.01). Bacteroides, Erysipelotrichaceae_Clostridium, and Coprobacillus were correlated with the moisture content of cecal contents (P < 0.05). The identification of the microbiota in correlation with nutrient metabolism will promote microbial nutrition through microbiota intervention or nutritional regulation. IMPORTANCE The poultry industry has become a global leader in livestock farming over the past few decades. Poultry production has a large consumer market as an integrated industry producing high-protein foods. Establishing the association between microbiota and nutrient metabolism processes provides fresh insights for precise nutrient regulation. This study aimed to describe the development of cecal microbiota in broiler chickens throughout the production cycle and to assess the correlation of nutrient metabolism phenotypes with temporal changes in the microbiota. The results suggested that changes in cecal microbes with age partly explain changes in gut nutrient metabolic processes, and numerous microbes were significantly associated with the processes. Therefore, this study attempts to further find efficient ways of improving poultry production. One is to promote nutrient metabolism by identifying potential candidates for probiotics, and another is to foster the dominant colonization of the microbiota by regulating nutrient metabolism.

Project description:Dietary deoxynivalenol (DON) impairs the intestinal functions and performance in broiler chickens, whereas little is known about the effect of DON on the gastrointestinal microbiota. This study evaluated the impact of graded levels of dietary DON contamination on the cecal bacterial microbiota, their predicted metabolic abilities and short-chain fatty acid (SCFA) profiles in chickens. In using a single oral lipopolysaccharide (LPS) challenge we further assessed whether an additional intestinal stressor would potentiate DON-related effects on the cecal microbiota. Eighty 1-day-old chicks were fed diets with increasing DON concentrations (0, 2.5, 5, and 10 mg DON per kg diet) for 5 weeks and were sampled after half of the chickens received an oral LPS challenge (1 mg LPS/kg bodyweight) 1 day before sampling. The bacterial composition was investigated by Illumina MiSeq sequencing of the V3-5 region of the 16S rRNA gene. DON-feeding decreased (p < 0.05) the cecal species richness (Chao1) and evenness (Shannon) compared to the non-contaminated diet. The phyla Firmicutes and Proteobacteria tended to linearly increase and decrease with increasing DON-concentrations, respectively. Within the Firmicutes, DON decreased the relative abundance of Oscillospira, Clostridiaceae genus, Clostridium, and Ruminococcaceae genus 2 (p < 0.05), whereas it increased Clostridiales genus 2 (p < 0.05). Moreover, increasing DON levels linearly decreased a high-abundance Enterobacteriaceae genus and an Escherichia/Shigella-OTU (p < 0.05). Changes in the bacterial composition and their imputed metagenomic capabilities may be explained by DON-related changes in host physiology and cecal nutrient availability. The oral LPS challenge only decreased the abundance of an unassigned Clostridiales genus 2 (p = 0.03). Increasing dietary concentrations of DON quadratically increased the cecal total SCFA and butyrate concentration (p < 0.05), whereas a DON × LPS interaction indicated that LPS mainly increased cecal total SCFA, butyrate, and acetate concentrations in chickens fed the diets that were not contaminated with DON. The present findings showed that even the lowest level of dietary DON contamination had modulatory effects on chicken's cecal bacterial microbiota composition and diversity, whereas the additional oral challenge with LPS did not potentiate DON effects on the cecal bacterial composition.

Project description:Background:The relationship between diet and intestinal microbiota and mucin composition appears to be fundamental for poultry gut health. The effects of insect meal (whose role as alternative feed ingredient is now well recognized) on gut microbiota and mucin composition have recently been reported in Tenebrio molitor-fed free-range and broiler chickens, but no data are currently available for Hermetia illucens (HI)-fed broilers. The present study evaluated the effects of dietary HI meal inclusion on cecal microbiota and intestinal mucin composition of broiler chickens. Results:A total of 256 male broiler chickens were allotted to 4 dietary treatments (control diet [C] and 5%, 10% and 15% HI meal inclusion, with 8 replicate pens/treatment and 8 birds/pen) and slaughtered at 35?d of age (2 animals/pen, 16 birds/diet). The cecal microbiota assessment by 16S rRNA amplicon based sequencing showed lower alpha diversity in HI15 chickens (Shannon, P?<?0.05) and higher beta diversity (Adonis and ANOSIM, P?<?0.001) in birds fed HI diets than C. Furthermore, HI15 birds displayed significant increase of the relative abundance of Proteobacteria phylum (False Discovery Rate [FDR]?<? 0.05) when compared to HI10. L-Ruminococcus (Ruminococcus from Lachnospiraceae family), Faecalibacterium, Blautia and Clostridium genera were found to be characteristic of HI5 cecal microbiota (FDR?<?0.05), while broiler chickens fed HI10 and HI15 diets were characterized (FDR?<?0.05) by Lactobacillus and Ruminococcus (HI10) and Bacteroides, Roseburia and Helicobacter genera (HI15). Periodic-acid Schiff, Alcian Blue pH?2.5 and high iron diamine staining on small and large intestine also demonstrated lower mucin staining intensity in the intestinal villi of HI10 and HI15 birds than C (P?<?0.05). Conclusions:Dietary HI meal utilization at low inclusion levels (i.e., 5%) positively influenced either the cecal microbiota or the gut mucin dynamics in terms of selection of potentially beneficial bacteria and increase in villi mucins. However, high inclusion levels (in particular the 15%) may have a negative influence in terms of partial reduction of microbial complexity, reduction of potentially beneficial bacteria, selection of bacteria with mucolytic activity and decrease in villi mucins.

Dataset Information

A reasonable correlation between cloacal and cecal microbiomes in broiler chickens.

Publications

A reasonable correlation between cloacal and cecal microbiomes in broiler chickens.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets