Mahdi Ghanbari

Phylogenetic diversity and biological activity of culturable Actinobacteria isolated from freshwater fish gut microbiota

The diversity of Actinobacteria isolated from the gut microbiota of two freshwater fish species namely Schizothorax zarudnyi and Schizocypris altidorsalis was investigated employing classical cultivation techniques, repetitive sequence-based PCR (rep-PCR), partial and full 16S rDNA sequencing followed by phylogenetic analysis. A total of 277 isolates were cultured by applying three different agar media. Based on rep-PCR profile analysis a subset of 33 strains was selected for further phylogenetic investigations, antimicrobial activity testing and diversity analysis of secondary-metabolite biosynthetic genes. The identification based on 16S rRNA gene sequencing revealed that the isolates belong to eight genera distributed among six families. At the family level, 72% of the 277 isolates belong to the family Streptomycetaceae. Among the non-streptomycetes group, the most dominant group could be allocated to the family of Pseudonocardiaceae followed by the members of Micromonosporaceae. Phylogenetic analysis clearly showed that many of the isolates in the genera Streptomyces, Saccharomonospora, Micromonospora, Nocardiopsis, Arthrobacter, Kocuria, Microbacterium and Agromyces formed a single and distinct cluster with the type strains. Notably, there is no report so far about the occurrence of these Actinobacteria in the microbiota of freshwater fish. Of the 33 isolates, all the strains exhibited antibacterial activity against a set of tested human and fish pathogenic bacteria. Then, to study their associated potential capacity to synthesize diverse bioactive natural products, diversity of genes associated with secondary-metabolite biosynthesis including PKS I, PKS II, NRPS, the enzyme PhzE of the phenazine pathways, the enzyme dTGD of 6-deoxyhexoses glycosylation pathway, the enzyme Halo of halogenation pathway and the enzyme CYP in polyene polyketide biosynthesis were investigated among the isolates. All the strains possess at least two types of the investigated biosynthetic genes, one-fourth of them harbours more than four. This study demonstrates the significant diversity of Actinobacteria in the fish gut microbiota and its potential to produce biologically active compounds.

The intestinal microbiota of piglets fed with wheat bran variants as characterised by 16S rRNA next-generation amplicon sequencing

ABSTRACT The intestinal microbiota of piglets fed with a Control diet low in dietary fibre and modified wheat bran variants as an additional source of insoluble dietary fibre was characterised. In this context, variances in the microbiota of three different gut segments were assessed. Wheat bran was either included in its native form or modified by fermentation and extrusion before added at 150 g/kg to a basal diet for 48 piglets (12 animals per treatment). Total DNA was extracted from digesta samples from the jejunum, the end of the ileum and the colon ascendens. Samples were prepared accordingly for subsequent sequencing with the Illumina MiSeq. The obtained results revealed distinct location-specific differences in microbial composition. While Firmicutes were most predominant in all three gut segments, Bacteroidetes were additionally found in the colon at high abundance. The parameters of alpha and beta diversity analysis showed significant differences (p < 0.01) between the colon and the other two gut segments. Specialised bacterial groups like Prevotella and Ruminococcaceae were among the most predominant ones found in the colon, as they possess cellulolytic properties to degrade (at least partially) non-starch polysaccharides, while their abundance was negligible in the jejunum and the ileum. Conversely, the genera Lactobacillus, Bifidobacterium and Veillonella, for example, were among the most predominant groups in the jejunum and ileum, while in the colon they were hardly found. Although statistical taxonomical evaluation, following p-value correction, did not reveal pronounced differences in abundance related to bran modification, alpha and beta diversity analysis showed an influence regarding the various feeding strategies applied. Based on these findings, a more in-depth view on intestinal microbial composition within the gastrointestinal tract of young pigs fed with low- and high-fibre diets was generated.

Long-term effects of water pH changes on hematological parameters in the common carp (Cyprinus carpio L.)

The aim of this study was to examine the effects of water pH changes on certain hematological parameters of fingerlings of common carp ( Cyprinus carpio ), in water with different pH (acidic and alkaline). Fingerlings of common carp were subjected to acidic (pH 5.5 and 6.5) and alkaline (pH 8.0, 8.5 and 9.0) water for 21 days. Control groups were maintained at neutral pH. The result showed that exposure to both acidic and alkaline water exerted stress on fish and considerably affected the hematology of fingerlings of common carp. Cytological study revealed that such swollen erythrocytes with centrally located swollen nucleus and also immature erythrocytes were observed in fingerlings exposed to pH 8.5 - 9.0. Exposure to the two extreme pHs (pH 5.5 and 9.0) caused significant reductions (P < 0.05) in total erythrocyte count (TEC) in common carp. A significant reduction (P < 0.05) in the hemoglobin content was observed at the two extreme pHs 5.5 and 9.0. The total leukocyte count (TLC) was reduced at pH 5.5, but only after a brief increase at pH 6.5. Alkaline range also experienced a reduction in TLCs at pH 8.0 and underwent further reduction with increased pH. Blood glucose was significantly higher (P < 0.05) in fingerlings exposed to both acidic and alkaline waters and the increase was proportional to the degree of pH change. Serum protein levels were also significantly reduced (P < 0.05) following exposure of the fingerlings to both acidic and alkaline conditions. The changes in hematological parameters of the fingerlings of common carp indicated that the change in water pH might have caused the ion regulatory and acid–base disturbances originating at the gill leading to the altered internal pH, electrolyte and osmotic balances that imply an increase in energy consumption to restore homeostasis instead of other physiological functions, weight gain and growth.

Lactic Acid Bacteria and Their Bacteriocins: A Promising Approach to Seafood Biopreservation

© 2013 Ghanbari and Jami, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Lactic Acid Bacteria and Their Bacteriocins: A Promising Approach to Seafood Biopreservation

Celeribacter persicus sp. nov., a polycyclic-aromatic-hydrocarbon-degrading bacterium isolated from mangrove soil.

A Gram-stain-negative, mesophilic bacterial strain, designated SBU1T, which degrades polycyclic aromatic hydrocarbons was isolated from the sediments of the mangrove forests of Nayband Bay in the Iranian Persian Gulf during a bioremediation experiment. The 16S rRNA gene sequence of strain SBU1T exhibited highest similarities with Celeribacter indicus P73T (98.52%) and Celeribacter neptunius H 14T (97.05%). Phylogenetic analysis, based on 16S rRNA gene sequences, demonstrated that strain SBU1T fell within a cluster consisting of the type strains of species of the genus Celeribacter and formed a stable clade with C. indicus P73T in trees generated with three algorithms. The fatty acid profile of strain SBU1T consisted of the major fatty acids C18:1ω7c/ω6c and C18:1ω7c 11-methyl. The major compounds in the polar lipid profile were one phosphatidylglycerol and four unidentified phospholipids. The quinone system exclusively comprised ubiquinone (Q-10). The DNA G+C content was 60.4 mol%. A combination of phylogenetic analysis, DNA-DNA hybridization estimation, average nucleotide identity results and differential phenotypic and chemotaxonomic characteristics demonstrated that strain SBU1T could be distinguished from its close relatives. Therefore, strain SBU1T is considered to represent a novel species of the genus Celeribacter for which the name Celeribacter persicus sp. nov. is proposed. The type strain is SBU1T (=MCCC 1A00672T=DSM 100434T).

Selection of Lactobacillus Species from Intestinal Microbiota of Fish for Their Potential Use as Biopreservatives

© 2013 Ghanbari et al., licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Selection of Lactobacillus Species from Intestinal Microbiota of Fish for Their Potential Use as Biopreservatives