Journal Article
- Core gut microbiota in Jinhua pigs and its correlation with strain, farm and weaning age
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Hua Yang , Yingping Xiao , Junjun Wang , Yun Xiang , Yujie Gong , Xueting Wen , Defa Li
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J. Microbiol. 2018;56(5):346-355. Published online May 2, 2018
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DOI: https://doi.org/10.1007/s12275-018-7486-8
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Abstract
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Gut microbial diversity and the core microbiota of the Jinhua
pig, which is a traditional, slow-growing Chinese breed with
a high body-fat content, were examined from a total of 105
fecal samples collected from 6 groups of pigs at 3 weaning
ages that originated from 2 strains and were raised on 3 different
pig farms. The bacterial community was analyzed following
high-throughput pyrosequencing of 16S rRNA genes,
and the fecal concentrations of short-chain fatty acids (SCFAs)
were measured by gas chromatograph. Our results showed
that Firmicutes and Bacteroidetes were the dominant phyla,
and Lactobacillus, Streptococcus, Clostridium, SMB53, and
Bifidobacterium were the most abundant genera. Fifteen predominant
genera present in every Jinhua pig sample constituted
a phylogenetic core microbiota and included the probiotics
Lactobacillus and Bifidobacterium, and the SCFAproducing
bacteria Clostridium, Prevotella, Bacteroides, Coprococcus,
Roseburia, Ruminococcus, Blautia, and Butyricicoccus.
Comparisons of the microbiota compositions and
SCFA concentrations across the 6 groups of pigs demonstrated
that genetic background and weaning age affected the
structure of the gut microbiota more significantly than the
farm. The relative abundance of the core genera in the pigs,
including Lactobacillus, Clostridium, Prevotella, Bacteroides,
Roseburia, Ruminococcus, Blautia, and Butyricicoccus varied
dramatically in pigs among the 2 origins and 3 weaning
ages, while Oscillospira, Megasphaera, Parabacteroides, and
Corynebacterium differed among pigs from different farms.
Interestingly, there was a more significant influence of strain
and weaning age than of rearing farm on the SCFA concentrations.
Therefore, strain and weaning age appear to be the
more important factors shaping the intestinal microbiome
of pigs.
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DOI: https://doi.org/10.1007/s12275-014-3380-1
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Abstract
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The lytic bacteriaphage (phage) A2 was isolated from human dental plaques along with its bacterial host. The virus was found to have an icosahedron-shaped head (60±3 nm), a sheathed and rigid long tail (~175 nm) and was categorized into the family Siphoviridae of the order Caudovirales, which are dsDNA viral family, characterised by their ability to infect bacteria and are nonenveloped with a noncontractile tail. The isolated phage contained a linear dsDNA genome having 31,703 base pairs of unique sequence, which were sorted into three contigs and 12 single sequences. A latent period of 25 minutes and burst size of 24±2 particles was determined for the virus. Bioinformatics approaches were used to identify ORFs in the genome. A phylogenetic analysis confirmed the species inter-relationship and its placement in the family.
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Jing Ping Zhu , Xian Li , Shi Du
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DOI: https://doi.org/10.1007/s12275-012-1418-9
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Abstract
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Based on sequence analyses of phycocyanin intergenic spacers
(PC-IGS) from Microcystis, Anabaena, Aphanizomenon,
and Planktothrix (Oscillatoria) strains, a genus-specific probe
pair TF/TR was designed, and a sandwich hybridization assay
was established to quantitatively detect Microcystis. Through
BLAST and cyanobacterial culture tests, TF/TR was demonstrated
to be specific for Microcystis. A calibration curve
for the sandwich hybridization assay was established, and
the lowest detected concentration was 100 cell/ml. Laboratory
and field samples were analyzed with both sandwich hybridization
assay and microscopy. The biotic and abiotic
components of the samples were of little disturbance to the
sandwich hybridization assay. The results showed no distinct
difference between the two methods. In this study, a sandwich
hybridization assay was established to detect Microcystis,
providing an alternative to traditional microscopic, morphology-
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Jagadeesan Premanandh , Balakrishnan Priya , Ivanka Teneva , Balik Dzhambazov , Dharmar Prabaharan , Lakshmanan Uma
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Abstract
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Molecular characterization of ten marine cyanobacterial isolates belonging to the order Oscillatoriales was carried out using the phycocyanin locus (cpcBA-IGS) and the 16S-23S internally transcribed spacer region. DNA sequences from the phycocyanin operon discriminated ten genotypes, which corresponded to seven morphotypes identified by traditional microscopic analysis. The cpcB coding region revealed 17% nucleotide variation, while cpcA exhibited 29% variation across the studied species. Phylogenetic analyses support the conclusion that the Phormidium and Leptolyngbya genera are not monophyletic. The nucleotide variations were heterogeneously distributed with no or minimal informative nucleotides. Our results suggest that the discriminatory power of the phycocyanin region varies across the cyanobacterial species and strains. The DNA sequence analysis of the 16S-23S internally transcribed spacer region also supports the polyphyletic nature of the studied oscillatorian cyanobacteria. This study demonstrated that morphologically very similar strains might differ genotypically. Thus, molecular approaches comprising different gene regions in combination with morphological criteria may provide better taxonomical resolution of the order Oscillatoriales.
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Hyun-Jung Kim , Yong-Keel Choi , Byung-Re Min
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J. Microbiol. 2001;39(4):265-272.
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Abstract
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Variation within the intergenic spacer (IGS) of the ribosomal DNA gene for twenty-two strains of F. oxysporum and its formae speciales was examined by PCR, coupled with RFLP analysis. The length of the amplified IGS region was about 2.6 kb in all strains except F. oxysporum f. sp. cucumerinum from Korea and F. oxysporum f. sp. niveum. Those two strains were 2.5 kb long. Restriction digestion of IGS-RFLP regions by EcoRI, NruI, HincII, SalI, SmaI, BglII, HindIII, XhoI, and KpnI gave rise to nine IGS haplotypes among all strains. Cluster analysis based on the presence or absence of comigrating restriction fragments show the two groups based on 44% genetic similarity. These results demonstrated that analysis of IGS showed some difference within and between F. oxysporum formae speciales.