The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the Gallus gallus microbiota

Study information

Needs review

study design

laboratory experiment

Citation

PMID PubMed identifier for scientific articles.

33138790

DOI Digital object identifier for electronic documents.

10.1186/s12866-020-02001-4

URI

Authors

Feye KM, Swaggerty CL, Kogut MH, Ricke SC, Piva A, Grilli E

Journal

BMC microbiology

Year

2020

Keywords:

Botanicals, Ileum, Jejunum, Microbiota, Microencapsulated, Organic acids

BACKGROUND: Microencapsulated organic acids and botanicals have the potential to develop into important tools for the poultry industry. A blend of organic acids and botanicals (AviPlus®P) has previously shown to reduce Salmonella and Campylobacter in chickens; however, changes to the microbiota of the jejunum and ileum have not been evaluated. Microbiota diversity is linked to, but not correlated with, the efficacy of natural products; therefore, understanding the effects on the microbiota is necessary for evaluating their potential as an antibiotic alternative. RESULTS: Ileal and jejunal segments from control and supplement-fed chickens (300 and 500 g/metric ton [MT]) were subjected to alpha diversity analysis including Shannon's diversity and Pielou's Evenness. In both analytics, the diversity in the ileum was significantly decreased compared to the jejunum irrespective of treatment. Similarly, beta diversity metrics including Bray-Curtis dissimilarity index and Weighted Unifrac Distance Matrix, were significant (Q < 0.05) for both tissue and treatments comparisons. Alpha and beta diversity analytics indicated compartmentalization effects between the ileum and jejunum. Additionally, analysis of communities in the microbiota (ANCOM) analysis showed Lactobacilliaceae predominated the total operational taxonomic units (OTU), with a stepwise increase from 53% in the no treatment control (NTC) to 56% in the 300 g/MT and 67% in the 500 g/MT group. Staphylococcaceae were 2% in NTC and 2 and 0% in 300 and 500 g/MT groups. Enterobacteriaceae decreased in the 500 g/MT (31%) and increased in the 300 g/MT (37%) compared to the NTC (35%). Aerococcaceae was 0% for both doses and 7% in NTC. Ruminococcaceae were 0% in NTC and 2 and 1% in the 300 and 500 g/MT. These changes in the microbial consortia were statistically (Q < 0.05) associated with treatment groups in the jejunum that were not observed in the ileum. Least discriminant analysis effect size (LEfSE) indicated different changes directly corresponding to treatment. Enterobacteriaceae demonstrated a stepwise decrease (from NTC onward) while Clostridiaceae, were significantly increased in the 500 g/MT compared to NTC and 300 g/MT (P < 0.05). CONCLUSION: The bioactive site for the microencapsulated blend of organic acids and botanicals was the jejunum, and dietary inclusion enhanced the GIT microbiota and may be a viable antibiotic alternative for the poultry industry.

Experiment 1

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Curated date: 2024/03/25

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Revision editor(s): Omojokunoluwatomisin, Nityasinghal 14

Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled. Contact us to have more species added.: Gallus gallus

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Ileum Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,ileum

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Chicken with no AviPlus®P. (0 g/MT)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Chickens feed with 300 g/MT

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Chickens feed with 300 g/MT of AviPlus®P.

Group 0 sample size Number of subjects in the control (unexposed) group: 5

Group 1 sample size Number of subjects in the case (exposed) group: 5

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V2

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Alpha Diversity

Pielou Quantifies how equal the community is numerically: decreased

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Experiment 2

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: chicken with no AviPlus®P. (0 g/MT)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Chicken feed with 500 g/MT

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Chickens feed with 500 g/MT of AviPlus®P.

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically: decreased

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Experiment 3

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Chickens feed with 300 g/MT

Group 1 name Corresponds to the case (exposed) group for case-control studies: Chickens feed with 500 g/MT

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Chickens feed with 500 g/MT of AviPlus®P.

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically: decreased

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Experiment 4

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Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Jejunum Intestinum jejunum,Mid-intestine,Middle intestine,Jejunum,jejunum

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Chicken with no AviPlus®P. (0 g/MT)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Chickens feed with 300 g/MT

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Chickens that were fed with 300 g/MT of AviPlus®P.

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: centered log-ratio

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

Alpha Diversity

Pielou Quantifies how equal the community is numerically: increased

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Signature 1

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Source: Figure 4 and text

Description: Differential abundance of taxa as per the LEfSE analysis.

Abundance in Group 1: increased abundance in Chickens feed with 300 g/MT

NCBI	Quality Control	Links
unclassified Oscillospiraceae

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Signature 2

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Source: Figure 4 and text

Description: Differential abundance of taxa as per the LEfSE analysis.

Abundance in Group 1: decreased abundance in Chickens feed with 300 g/MT

NCBI	Quality Control	Links
Aerococcaceae
Enterobacterales
Enterobacteriaceae
Gammaproteobacteria

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Experiment 5

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Chicken feed with 300g/MT

Group 1 name Corresponds to the case (exposed) group for case-control studies: Chickens feed with 500 g/MT

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Chickens that were fed with 500 g/MT of AviPlus®P.