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Mycobacterium avium Subspecies paratuberculosis Infection Modifies Gut Microbiota under Different Dietary Conditions in a Rabbit Model.

Arrazuria R, Elguezabal N, Juste RA, Derakhshani H, Khafipour E - Front Microbiol (2016)

Bottom Line: Mycobacterium avium subspecies paratuberculosis (MAP) the causative agent of paratuberculosis, produces a chronic granulomatous inflammation of the gastrointestinal tract of ruminants.A lower abundance of Proteobacteria in the cecal content of infected animals fed the high fiber diet and also lower abundance of Bacteroidetes in the sacculus rotundus of infected animals fed the regular diet were observed.Based on OPLS-DA analysis, we observed that some bacteria repeatedly appear to be positively associated with infection in different samples under different diets (families Dehalobacteriaceae, Coriobacteriaceae, and Mogibacteriaceae; genus Anaerofustis).

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Health, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario Derio, Spain.

ABSTRACT
Mycobacterium avium subspecies paratuberculosis (MAP) the causative agent of paratuberculosis, produces a chronic granulomatous inflammation of the gastrointestinal tract of ruminants. It has been recently suggested that MAP infection may be associated with dysbiosis of intestinal microbiota in ruminants. Since diet is one of the key factors affecting the balance of microbial populations in the digestive tract, we intended to evaluate the effect of MAP infection in a rabbit model fed a regular or high fiber diet during challenge. The composition of microbiota of the cecal content and the sacculus rotundus was studied in 20 New Zealand white female rabbits. The extracted DNA was subjected to paired-end Illumina sequencing of the V3-V4 hypervariable region of the 16S rRNA gene for microbiota analysis. Microbial richness (Chao1) in the cecal content was significantly increased by MAP infection in regular diet rabbits (p = 0.0043) and marginally increased (p = 0.0503) in the high fiber group. Analysis of beta-diversity showed that MAP infection produces deeper changes in the microbiota of sacculus rotundus than in the cecal content. A lower abundance of Proteobacteria in the cecal content of infected animals fed the high fiber diet and also lower abundance of Bacteroidetes in the sacculus rotundus of infected animals fed the regular diet were observed. Based on OPLS-DA analysis, we observed that some bacteria repeatedly appear to be positively associated with infection in different samples under different diets (families Dehalobacteriaceae, Coriobacteriaceae, and Mogibacteriaceae; genus Anaerofustis). The same phenomenon was observed with some of the bacteria negatively associated with MAP infection (genera Anaerostipes and Coprobacillus). However, other groups of bacteria (Enterobacteriaceae family and ML615J-28 order) were positively associated with infection in some circumstances and negatively associated with infection in others. Data demonstrate that MAP infection and diet changes do interact and result in shifts in the microbiota of the cecal content and sacculus rotundus of rabbits.

No MeSH data available.


Related in: MedlinePlus

Cecal content diversity analysis.(A) Cecal content microbiota rarefaction curve generated using Chao1 richness estimator. Samples have been rarified at an even depth of 24,500 sequences per sample. Error bars indicate the 95% confidence intervals. (B) Cecal content alpha-diversity; richness (Chao1) and diversity (Shannon and Simpson) indices box plot.
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Figure 2: Cecal content diversity analysis.(A) Cecal content microbiota rarefaction curve generated using Chao1 richness estimator. Samples have been rarified at an even depth of 24,500 sequences per sample. Error bars indicate the 95% confidence intervals. (B) Cecal content alpha-diversity; richness (Chao1) and diversity (Shannon and Simpson) indices box plot.

Mentions: Following quality control and removal of chimeric reads, an average of 40,986 (SD = 12,744) high quality sequences were obtained for cecal content samples and used for downstream analyses. Analyses of microbial communities revealed differences in richness (Chao1) between infected and control animals (Figure 2A). The RI animals presented higher richness values than RC (6873 ± 481 vs. 5313 ± 651; p = 0.0043; Figure 2B). An increasing trend was also observed in the Chao1 richness estimates of HFI compared to HFC group (6274 ± 1299 vs. 4434 ± 1273; p = 0.0503). However, the Shannon and Simpson indices were not significantly different between infected and control animals in any of the diet groups.


Mycobacterium avium Subspecies paratuberculosis Infection Modifies Gut Microbiota under Different Dietary Conditions in a Rabbit Model.

Arrazuria R, Elguezabal N, Juste RA, Derakhshani H, Khafipour E - Front Microbiol (2016)

Cecal content diversity analysis.(A) Cecal content microbiota rarefaction curve generated using Chao1 richness estimator. Samples have been rarified at an even depth of 24,500 sequences per sample. Error bars indicate the 95% confidence intervals. (B) Cecal content alpha-diversity; richness (Chao1) and diversity (Shannon and Simpson) indices box plot.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4815054&req=5

Figure 2: Cecal content diversity analysis.(A) Cecal content microbiota rarefaction curve generated using Chao1 richness estimator. Samples have been rarified at an even depth of 24,500 sequences per sample. Error bars indicate the 95% confidence intervals. (B) Cecal content alpha-diversity; richness (Chao1) and diversity (Shannon and Simpson) indices box plot.
Mentions: Following quality control and removal of chimeric reads, an average of 40,986 (SD = 12,744) high quality sequences were obtained for cecal content samples and used for downstream analyses. Analyses of microbial communities revealed differences in richness (Chao1) between infected and control animals (Figure 2A). The RI animals presented higher richness values than RC (6873 ± 481 vs. 5313 ± 651; p = 0.0043; Figure 2B). An increasing trend was also observed in the Chao1 richness estimates of HFI compared to HFC group (6274 ± 1299 vs. 4434 ± 1273; p = 0.0503). However, the Shannon and Simpson indices were not significantly different between infected and control animals in any of the diet groups.

Bottom Line: Mycobacterium avium subspecies paratuberculosis (MAP) the causative agent of paratuberculosis, produces a chronic granulomatous inflammation of the gastrointestinal tract of ruminants.A lower abundance of Proteobacteria in the cecal content of infected animals fed the high fiber diet and also lower abundance of Bacteroidetes in the sacculus rotundus of infected animals fed the regular diet were observed.Based on OPLS-DA analysis, we observed that some bacteria repeatedly appear to be positively associated with infection in different samples under different diets (families Dehalobacteriaceae, Coriobacteriaceae, and Mogibacteriaceae; genus Anaerofustis).

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Health, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario Derio, Spain.

ABSTRACT
Mycobacterium avium subspecies paratuberculosis (MAP) the causative agent of paratuberculosis, produces a chronic granulomatous inflammation of the gastrointestinal tract of ruminants. It has been recently suggested that MAP infection may be associated with dysbiosis of intestinal microbiota in ruminants. Since diet is one of the key factors affecting the balance of microbial populations in the digestive tract, we intended to evaluate the effect of MAP infection in a rabbit model fed a regular or high fiber diet during challenge. The composition of microbiota of the cecal content and the sacculus rotundus was studied in 20 New Zealand white female rabbits. The extracted DNA was subjected to paired-end Illumina sequencing of the V3-V4 hypervariable region of the 16S rRNA gene for microbiota analysis. Microbial richness (Chao1) in the cecal content was significantly increased by MAP infection in regular diet rabbits (p = 0.0043) and marginally increased (p = 0.0503) in the high fiber group. Analysis of beta-diversity showed that MAP infection produces deeper changes in the microbiota of sacculus rotundus than in the cecal content. A lower abundance of Proteobacteria in the cecal content of infected animals fed the high fiber diet and also lower abundance of Bacteroidetes in the sacculus rotundus of infected animals fed the regular diet were observed. Based on OPLS-DA analysis, we observed that some bacteria repeatedly appear to be positively associated with infection in different samples under different diets (families Dehalobacteriaceae, Coriobacteriaceae, and Mogibacteriaceae; genus Anaerofustis). The same phenomenon was observed with some of the bacteria negatively associated with MAP infection (genera Anaerostipes and Coprobacillus). However, other groups of bacteria (Enterobacteriaceae family and ML615J-28 order) were positively associated with infection in some circumstances and negatively associated with infection in others. Data demonstrate that MAP infection and diet changes do interact and result in shifts in the microbiota of the cecal content and sacculus rotundus of rabbits.

No MeSH data available.


Related in: MedlinePlus