Insights into the bacterial communities of Nile tilapia – core members and intergenerational transfer

Doctoral thesis (PhD) – Nord University, 2022publishedVersio

Intergenerational transfer of persistent bacterial communities in female Nile tilapia

5openInternationalInternational coauthor/editorResident microbial communities that can support various host functions play a key role in their development and health. In fishes, microbial symbionts are vertically transferred from the parents to their progeny. Such transfer of microbes in mouthbrooder fish species has not been reported yet. Here, we employed Nile tilapia (Oreochromis niloticus) to investigate the vertical transmission of microbes across generations using a 16S rRNA amplicon sequencing approach, based on the presence of bacteria in different generations. Our analysis revealed that the core microbiome in the buccal cavity and posterior intestine of parents shapes the gut microbiome of the progeny across generations. We speculate that the route of this transmission is via the buccal cavity. The identified core microbiome bacteria, namely Nocardioides, Propionibacterium, and Sphingomonas have been reported to play an essential role in the health and development of offspring. These core microbiome members could have specific functions in fish, similar to mammals.openAbdelhafiz, Yousri; Fernandes, Jorge M. O.; Donati, Claudio; Pindo, Massimo; Kiron, ViswanathAbdelhafiz, Y.; Fernandes, J.M.O.; Donati, C.; Pindo, M.; Kiron, V

Gracilaria gracilis and Nannochloropsis oceanica, singly or in combination, in diets alter the intestinal microbiota of European seabass (Dicentrarchus labrax)

publishedVersio

Macroalga-derived alginate oligosaccharide alters intestinal bacteria of atlantic salmon

Prebiotics are substrates intended to sculpt gut microbial communities as they are selectively utilized by the microorganisms to exert beneficial health effects on hosts. Macroalga-derived oligosaccharides are candidate prebiotics, and herein, we determined the effects of Laminaria sp.-derived alginate oligosaccharide (AlgOS) on the distal intestinal microbiota of Atlantic salmon (Salmo salar). Using a high-throughput 16S rRNA gene amplicon sequencing technique, we investigated the microbiota harbored in the intestinal content and mucus of the fish offered feeds supplemented with 0.5 and 2.5% AlgOS. We found that the prebiotic shifts the intestinal microbiota profile; alpha diversity was significantly reduced with 2.5% AlgOS while with 0.5% AlgOS the alteration occurred without impacting the bacterial diversity. Beta diversity analysis indicated the significant differences between control and prebiotic-fed groups. The low supplementation level of AlgOS facilitated the dominance of Proteobacteria (including Photobacterium phosphoreum, Aquabacterium parvum, Achromobacter insolitus), and Spirochaetes (Brevinema andersonii) in the content or mucus of the fish, and few of these bacteria (Aliivibrio logei, A. parvum, B. andersonii, A. insolitus) have genes associated with butyrate production. The results indicate that the low inclusion of AlgOS can plausibly induce a prebiotic effect on the distal intestinal microbiota of Atlantic salmon. These findings can generate further interest in the potential of macroalgae-derived oligosaccharides for food and feed applications.publishedVersio

Insights into the bacterial communities of Nile tilapia – core members and intergenerational transfer

Doctoral thesis (PhD) – Nord University, 2022publishedVersio

Whole genome sequencing and functional features of a novel biosurfactant-producing Bacillus subtilis UMX-103 / Yousri Abdelmutalab Ahmed Abdelhafiz

The genus Bacillus is a Gram-positive, aerobic, endospore-forming, rod-shaped bacterium commonly found in the environment that have important industrial, medical, agriculture and environmental values. This study characterized a novel biosurfactant producing bacterial strain UMX-103 which was isolated from a hydrocarbon contaminated site in Terengganu, Malaysia. An integration of both genomics and biochemical approaches were conducted to analyse the biosurfactant production by the strain UMX-103. Determination of biosurfactant production by the strain was conducted using five different assays including; Hemolytic assay, Oil spreading test, Drop-collapse assay, Emulsification assay and Surface tension measurements. The surface tension test showed that the strain is able to lower surface tension up to (26.4 ± 0.02 mN/m). UMX-103 also showed positive results in the other assays. Whole Genome Sequence analysis revealed the genetic contents and genes involved in biosurfactant production. The whole genome was assembled using a combination of both de novo and reference-guided assembly methods. The genome size of UMX-103 is 4,234,627 bp with 4399 genes comprising of 4301 protein-coding genes and 98 RNA genes. The mapping results showed 93.44% of genome similarity with B. subtilis strain 168. The functional annotation analysis revealed present of surfactin biosynthetic gene cluster. This gene cluster belongs to the Non-ribosomal Peptide Synthetase (NRPS) family, which is one of the microbial surfactant groups. A total of 25 genes were identified that involved in biosurfactants production. Among these genes, 14 genes were involved in surfactin biosynthesis and while the remaining genes were involved in surfactin regulation. The comparative genomics and Pangenome analysis of UMX-103 with other Bacillus sp. highlighted unique features of this strain, especially relating to the biosurfactant gene cluster

Power play of commensal bacteria in the buccal cavity of female Nile Tilapia

Fish are widely exposed to higher microbial loads compared to land and air animals. It is known that the microbiome plays an essential role in the health and development of the host. The oral microbiome is vital in females of different organisms, including the maternal mouthbrooding species such as Nile tilapia (Oreochromis niloticus). The present study reports for the first time the microbial composition in the buccal cavity of female and male Nile tilapia reared in a recirculating aquaculture system. Mucus samples were collected from the buccal cavity of 58 adult fish (∼1 kg), and 16S rRNA gene amplicon sequencing was used to profile the microbial communities in females and males. The analysis revealed that opportunistic pathogens such as Streptococcus sp. were less abundant in the female buccal cavity. The power play of certain bacteria such as Acinetobacter, Acidobacteria (GP4 and GP6), and Saccharibacteria that have known metabolic advantages was evident in females compared to males. Association networks inferred from relative abundances showed few microbe–microbe interactions of opportunistic pathogens in female fish. The findings of opportunistic bacteria and their interactions with other microbes will be valuable for improving Nile tilapia rearing practices. The presence of bacteria with specific functions in the buccal cavity of female fish points to their ability to create a protective microbial ecosystem for the offspring

Macroalga-derived alginate oligosaccharide alters intestinal bacteria of atlantic salmon

Prebiotics are substrates intended to sculpt gut microbial communities as they are selectively utilized by the microorganisms to exert beneficial health effects on hosts. Macroalga-derived oligosaccharides are candidate prebiotics, and herein, we determined the effects of Laminaria sp.-derived alginate oligosaccharide (AlgOS) on the distal intestinal microbiota of Atlantic salmon (Salmo salar). Using a high-throughput 16S rRNA gene amplicon sequencing technique, we investigated the microbiota harbored in the intestinal content and mucus of the fish offered feeds supplemented with 0.5 and 2.5% AlgOS. We found that the prebiotic shifts the intestinal microbiota profile; alpha diversity was significantly reduced with 2.5% AlgOS while with 0.5% AlgOS the alteration occurred without impacting the bacterial diversity. Beta diversity analysis indicated the significant differences between control and prebiotic-fed groups. The low supplementation level of AlgOS facilitated the dominance of Proteobacteria (including Photobacterium phosphoreum, Aquabacterium parvum, Achromobacter insolitus), and Spirochaetes (Brevinema andersonii) in the content or mucus of the fish, and few of these bacteria (Aliivibrio logei, A. parvum, B. andersonii, A. insolitus) have genes associated with butyrate production. The results indicate that the low inclusion of AlgOS can plausibly induce a prebiotic effect on the distal intestinal microbiota of Atlantic salmon. These findings can generate further interest in the potential of macroalgae-derived oligosaccharides for food and feed applications