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Differences of Gut Microbiota in the Freshwater Blackworm (Lumbriculus variegatus: Oligochaeta) in Two Different Habitat Conditions.

ABSTRACT: The distribution of organisms is governed by their habitat condition. We analyzed bacterial communities in the gut of the blackworm Lumbriculus variegatus by pyrosequencing of the extracted intestinal metagenomic DNA. Blackworms were collected from two sampling sites with differences in irradiance and riparian vegetation, where site GP7 was covered by riparian vegetation and site GP8 was exposed to sunlight. We obtained the filtered 6414 reads from three samples of each site. At GP7, 271 OTUs were identified, including 32 OTUs unique to the site, whereas at GP8, 238 OTUs were identified, including 22 unique OTUs. Among them, 18 OTUs were shared between both sites. The phylum Proteobacteria was a major component contributing 67.84% and 64.05% of sequences at sites GP7 and GP8, respectively, while each remaining phylum contributed less than 10% at both sites. The two sites differed in microbial community composition and KEGG-indicated biochemical pathways. Community indices such as species richness and Shannon diversity were higher at site GP7 than at GP8. Meanwhile, the abundance of Cyanobacteria was significantly higher at site GP8, while site GP7 showed a greater proportion of genes for membrane transport and carbohydrate metabolism, reflecting differences in food resources.

SUBMITTER: Kim PS

PROVIDER: S-EPMC8508024 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description: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.

Dataset Information

Differences of Gut Microbiota in the Freshwater Blackworm (Lumbriculus variegatus: Oligochaeta) in Two Different Habitat Conditions.

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