Pyrosequencing reveals sponge specific bacterial communities in marine sponges of Red Sea, Saudi Arabia

Bacterial communities of marine sponges are believed to be an important partner for host survival but remain poorly studied. Sponges show difference in richness and abundance of microbial population inhabiting them. Three marine sponges belonging to the species of Pione vastifica, Siphonochalina siphonella and Suberea mollis were collected from Red sea in Jeddah and were investigated using high throughput sequencing. Highly diverse communities containing 105 OTUs were identified in S. mollis host. Only 61 and 43 OTUs were found in P. vastifica and S. siphonella respectively. We identified 10 different bacterial phyla and 31 genera using 27,356 sequences. Most of the OTUs belong to phylum Proteobacteria (29%–99%) comprising of Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria where later two were only detected in HMA sponge, S. mollis. A number of 16S rRNA sequences (25%) were not identified to phylum level and may be novel taxa. Richness of bacterial community and Shannon, Simpson diversity revealed that sponge S. mollis harbors high diversity compared to other two LMA sponges. Dominance of Proteobacteria in sponges may indicate an ecological significance of this phylum in the Red sea sponges. These differences in bacterial composition may be due to difference in location site or host responses to environmental conditions. To the best of our knowledge, the microbial communities of these sponges have never been studied before and this is first attempt to unravel bacterial diversity using PCR-based 454-pyrosequencing method.

Chromosomal Micro-aberration in a Saudi Family with Juvenile Myoclonic Epilepsy

BACKGROUND AND OBJECTIVE

Epilepsy is etiologically and genetically complex neurological disorder affecting millions of people worldwide. Juvenile myoclonic epilepsy (JME) is the most common epilepsy syndrome that starts in the teen age group commonly between ages 12, 18, and lasts till adulthood. One out of fourteen people with epilepsy suffers with JME. Myoclonic seizures and muscle twitching or uncontrolled jerking are the most common type of seizures in the people suffering with JME.

METHOD

To observe the novel CNVs involved in JME, we investigated a Saudi family with nine siblings including one male and one female affected members. In this study we used high density whole genome Agilent sure print G3 Hmn CGH 2x 400K array-CGH chips. Our results showed CNVs including the amplifications and deletions in different chromosomal regions in the patients as compared to the normal members of the family. Amplifications were observed in the chromosome 22 cytoband 22q11.23 with LDL receptor related protein 5 like (LRP5L), Immunoglobulin Lambda-Like Polypeptide 3 (IGLL3) and crystallin beta B2 pseudogene (CRYBB2P) genes respectively whereas the deletions were observed in the chromosomal regions 4q22.2 with Glutamate receptor, ionotropic, delta 2 (GRID2) as potential gene cytoband 1p31.1 with potential Neuronal Growth Regulator 1 gene (NEGR1) gene in this region and NME/NM23 family member (NME7) gene cytoband 1q24. Moreover, the array CGH resulting in deletions and duplication were also validated by using primer for simple PCR or also by using quantitative real time PCR analysis. We found deletions and duplication in JME patients in our study for the first time in Saudi population.

RESULTS & CONCLUSION

The findings in this study suggest that the array-CGH may be considered as a first line of genetic testing for diagnosis of epilepsy unless strong evidence is presented for a monogenic syndrome. The use of high throughput technique in this study will help to identify novel mechanisms underlying epileptic disorder in order to lower the burden of epilepsy in Saudi Arabia.

Comparison of the gut microbiota of obese individuals from different geographic origins

Few studies have examined the interaction of human geography, microbial community structure and obesity. We tested obese adult volunteers from France, Saudi Arabia, French Polynesia and from a traditional population in the village of Trois-Sauts in French Guiana by sequencing the V3-V4 region. We also sequenced homemade fermented cachiri beers that were obtained from the traditional Amazonian population and are highly consumed by this population. We found that French and Saudis had significantly less richness and biodiversity in their gut microbiota than Amazonians and Polynesians (p <0.05). Principle coordinate analysis of the overall composition of the genera communities revealed that the microbiomes of Amazonians clustered independently from the other obese individuals. Moreover, we found that Amazonians presented significantly stricter anaerobic genera than the Saudis, French and Polynesians (p < 0.001). Polynesians presented significantly lower relative abundance of Lactobacillus sp. than French (p 0.01) and Saudis (p 0.05). Treponema berlinense and Treponema succinifaciens were only present in the gut microbiome of Amazonians. The cachiri beers presented significantly more bacterial species in common with the gut microbiome of Amazonians (p < 0.005). Obese individuals with different origins present modifications in their gut microbiota, and we provide evidence that the cachiri beers influenced the gut microbiome of Amazonians.

Treponema species enrich the gut microbiota of traditional rural populations but are absent from urban individuals

There is a significant gap in our knowledge of the microbe-host relationship between urban and traditional rural populations. We conducted a large-scale study to examine the gut microbiota of different traditional rural and urban lifestyles in human populations. Using high-throughput 16S ribosomal RNA gene amplicon sequencing, we tested urban French, Saudi, Senegalese, Nigerian and Polynesian individuals as well as individuals living in traditional rural societies, including Amazonians from French Guiana, Congolese Pygmies, Saudi Bedouins and Algerian Tuaregs. The gut microbiota from individuals living in traditional rural settings clustered differently and presented significantly higher diversity than those of urban populations (p 0.01). The bacterial taxa identified by class analysis as contributing most significantly to each cluster were Phascolarctobacterium for traditional rural individuals and Bifidobacterium for urban individuals. Spirochaetae were only present in the gut microbiota of individuals from traditional rural societies, and the gut microbiota of all traditional rural populations was enriched with Treponema succinifaciens. Cross-transmission of Treponema from termites or swine to humans or the increased use of antibiotics in nontraditional populations may explain why Treponema is present only in the gut microbiota of traditional rural populations.

Culturomics-Based Taxonomic Diversity of Bacterial Communities in the Hot Springs of Saudi Arabia

Hot springs are natural habitats for thermophilic microorganisms and provide a significant opportunity for bioprospecting thermostable biomolecules. However, the scientific community has only a fragmented understanding of the microbial diversity and composition in these biotopes. In this study, bacterial diversity in sediment samples from six hot springs of Saudi Arabia was investigated using an improved culture-dependent approach. High-throughput MALDI-TOF MS (matrix assisted laser desorption/ionization mass spectrometry) and 16S rRNA genes sequencing were used for the identification of purified isolates. Most of the hot springs had a neutral pH and a temperature range of 45-89°C. Relatively higher colony-forming units (1.9 ± 0.45 × 10⁴) were observed with 60°C incubation of an 89°C sediment sample from the hot spring at Ain al Harra1. Among the 536 purified isolates, 6 novel candidate species were found, and the remaining isolates represented 139 distinct species. Several species, such as Bacillus cereus, Bacillus subtilis, and Bacillus schlegelii, were ubiquitous in the hot springs sampled, but 102 of the identified species were uniquely distributed among the hot springs. Sixteen of the isolated thermophilic bacteria, including Geobacillus kaustophilus, Thermus oshimai, and Brevibacillus thermoruber, grew at ≥60°C. In addition, 21 species exhibited hydrolytic enzymatic activity. Most of these species belonged to Bacillus and Brevibacillus. Overall, this study contributes to global knowledgebase on bacterial communities by comprehensively profiling culture-based bacterial diversity in the hot springs of Saudi Arabia. Further studies are required for investigating bacteria from hot springs by a metagenomic approach.

Bacteria From Marine Sponges: A Source of New Drugs

BACKGROUND

Sponges are rich source of bioactive natural products synthesized by the symbiotic bacteria belonging to different phyla. Due to a competition for space and nutrients the marine bacteria associated with sponges could produce more antibiotic substances. To explore the proactive potential of marine microbes extensive research has been done. These bioactive metabolites have some unique properties that are pharmaceutically important.

METHODS

For this review, we have performed a non-systematic search of the available literature though various online search engines. This review provides an insight that how majority of active metabolites have been identified from marine invertebrates of which sponges predominate.

RESULTS

Sponges harbor abundant and diverse microorganisms, which are the sources of a range of marine bioactive metabolites. From sponges and their associated microorganisms, approximately 5,300 different natural compounds are known. Current research on sponge-microbe interaction and their active metabolites has become a focal point for many researchers. Various active metabolites derived from sponges are now known to be produced by their symbiotic microflora.

CONCLUSION

In this review, we attempt to report the latest studies regarding capability of bacteria from sponges as producers of bioactive metabolite. Moreover, these sponge associated bacteria are an important source of different enzymes of industrial significance. In present review, we will address some novel approaches for discovering marine metabolites from bacteria that have the greatest potential to be used in clinical treatments.

Detection of genetic alterations in gastric cancer patients from Saudi Arabia using comparative genomic hybridization (CGH)

Background

The present study was conducted to discover genetic imbalances such as DNA copy number variations (CNVs) associated with gastric cancer (GC) and to examine their association with different genes involved in the process of gastric carcinogenesis in Saudi population.

Methods

Formalin-fixed paraffin-embedded (FFPE) tissues samples from 33 gastric cancer patients and 15 normal gastric samples were collected. Early and late stages GC samples were genotyped and CNVs were assessed by using Illumina HumanOmni1-Quad v.1.0 BeadChip.

Results

Copy number gains were more frequent than losses throughout all GC samples compared to normal tissue samples. The mean number of the altered chromosome per case was 64 for gains and 40 for losses, and the median aberration length was 679115bp for gains and 375889bp for losses. We identified 7 high copy gain, 52 gains, 14 losses, 32 homozygous losses, and 10 copy neutral LOHs (loss of heterozygosities). Copy number gains were frequently detected at 1p36.32, 1q12, 1q22, 2p11.1, 4q23-q25, 5p12-p11, 6p21.33, 9q12-q21.11, 12q11-q12, 14q32.33, 16p13.3, 17p13.1, 17q25.3, 19q13.32, and losses at 1p36.23, 1p36.32, 1p32.1, 1q44, 3q25.2, 6p22.1, 6p21.33, 8p11.22, 10q22.1, 12p11.22, 14q32.12 and 16q24.2. We also identified 2 monosomy at chromosome 14 and 22, 52 partially trisomy and 22 whole chromosome 4 neutral loss of heterozygosities at 13q14.2-q21.33, 5p15.2-p15.1, 5q11.2-q13.2, 5q33.1-q34 and 3p14.2-q13.12. Furthermore, 11 gains and 2 losses at 1p36.32 were detected for 11 different GC samples and this region has not been reported before in other populations. Statistical analysis confirms significant association of H. pylori infection with T4 stage of GC as compare to control and other stages.

Conclusions

We found that high frequency of copy number gains and losses at 1p36.23, 1p32.1, 1p36.32, 3q25.2, 6p21.33 and 16q24.2 may be common events in gastric cancer. While novel CNVs at 1p36.32 harbouring PRDM16, TP73 and TP73-AS1 genes showed 11 gains and 2 losses for 11 different GC cases and this region is not reported yet in Database of Genomic Variants may be specific to Saudi population.

Anaerococcus jeddahensis sp. nov., a New Bacterial Species Isolated From Healthy Nomadic Bedouin Woman From Saudi Arabia

An understanding of the microbial diversity of the human body has generated significant interest in recent years. With the advent of MALDI-TOF mass spectrometry, high-speed sequencing, and the rebirth of microbial culture, knowledge of human microbiota is growing. Using culturomics, a strategy to explore the microbial diversity of samples, coupled with a taxono-genomic strategy, we isolated a new bacterium named Anaerococcus jeddahensis sp. nov. strain SB3^T. This strain was isolated from the stool sample of a healthy nomadic Bedouin woman from Saudi Arabia. Here, we describe the characteristics of this organism, and the complete genome sequence and annotation. Strain SB3^T is a Gram-positive obligate anaerobic coccus which is non-motile and non-spore forming. Fatty acid analysis shows that the major fatty acid is by far hexadecanoic acid (C16:0; 52%). Its genome is 1,903,534 bp long and has 29.70 mol% of G+C content. It contains 1756 protein-coding genes and 53 RNA genes. These results show that strategy provides a better understanding of the microorganism and that is a good methodology for microbial identification and characterization.

Microbial Flora Associated with the Halophyte-Salsola imbricate and Its Biotechnical Potential

Halophytes are associated with the intertidal forest ecosystem of Saudi Arabia and seemingly have an immense potential for yielding useful and important natural products. In this study we have aimed to isolate and characterize the endophytic and rhizospheric bacterial communities from the halophyte, Salsola imbricata, In addition these bacterial strains were identified and selected strains were further studied for bioactive secondary metabolites. At least 168 rhizspheric and endophytic bacteria were isolated and of these 22 were active antagonists against the oomycetous fungal plant pathogens, Phytophthora capsici and Pythium ultimum. Active cultures were mainly identified with molecular techniques (16S r DNA) and this revealed 95.7–100% sequence similarities with relevant type strains. These microorgansims were grouped into four major classes: Actinobacteria, Firmicutes, β-Proteobacteria, and γ-Proteobacteria. Production of fungal cell wall lytic enzymes was detected mostly in members of Actinobacteria and Firmicutes. PCR screening for type I polyketide synthases (PKS-I), type II polyketide synthases (PKS-II) and nonribosomal peptide synthetases (NRPS) revealed 13 of the 22 strains (59%) were positive for at least one of these important biosynthetic genes that are known to be involved in the synthesis of important antibiotics. Four bacterial strains of Actinobacteria with potential antagonistic activity including two rhizobacteria, EA52 (Nocardiopsis sp.), EA58 (Pseudonocardia sp.) and two endophytic bacteria Streptomyces sp. (EA65) and Streptomyces sp. (EA67) were selected for secondary metabolite analyses using LC-MS. As a result, the presence of different bioactive compounds in the culture extracts was detected some of which are already reported for their diverse biological activities including antibiotics such as Sulfamethoxypyridazine, Sulfamerazine, and Dimetridazole. In conclusion, this study provides an insight into antagonistic bacterial population especially the Actinobacteria from S. imbricata, producing antifungal metabolites of medical significance and characterized taxonomically in future.

Description of 'Blautia phocaeensis' sp. nov. and 'Lachnoclostridium edouardi' sp. nov., isolated from healthy fresh stools of Saudi Arabia Bedouins by culturomics

We report here the main characteristics of 'Blautia phocaeensis' strain Marseille-P3441 sp. nov. and 'Lachnoclostridium edouardi' strain Marseille-P3397 sp. nov., that were isolated from a faecal specimen of a 42-year-old female Saudi Bedouin. We used a bacterial culturomics approach combined with taxono-genomics.

Description of 'Beduinibacterium massiliense' gen. nov., sp. nov., 'Massilimaliae massiliensis' gen. nov., sp. nov., 'Provencibacterium massiliense' gen. nov., sp. nov. and 'Oscilibacter massiliensis' sp. nov., isolated from a faecal specimen of a 19-year-old healthy Saudi Arabian Bedouin by culturomics

We report here the main characteristics of 'Beduinibacterium massiliense' strain Marseille-P3337T gen. nov., sp. nov., 'Massilimaliae massiliensis' Marseille-P2963T gen. nov., sp. nov., 'Provencibacterium massiliense' Marseille-P2780T gen. nov., sp. nov. and 'Oscilibacter massiliensis' Marseille-P2778T sp. nov., all isolated from the stool of a Bedouin from Saudi Arabia. We used a bacterial culturomics approach combined with taxonogenomics.

Description of 'Arabia massiliensis' gen. nov., sp. nov., 'Gordonibacter massiliensis' sp. nov., and 'Bacilliculturomica massiliensis' gen. nov., sp. nov., isolated from a faecal specimen of a 50-year-old Saudi Bedouin woman

We report here the main characteristics of 'Arabia massiliensis' strain Marseille-P3078T gen. nov., sp. nov., 'Gordonibacter massiliensis' Marseille-P2775T sp. nov. and 'Bacilliculturomica massiliensis' strain Marseille-P3303 gen. nov., sp. nov. The culturomics approach combined with taxonogenomics was used to characterize these strains, which were all isolated from a faecal specimen of a 50-year-old Saudi Bedouin woman.

Diversity of antagonistic bacteria isolated from medicinal plant Peganum harmala L

The antimicrobial activity of plant extract of Peganum harmala, a medicinal plant has been studied already. However, knowledge about bacterial diversity associated with different parts of host plant antagonistic to different human pathogenic bacteria is limited. In this study, bacteria were isolated from root, leaf and fruit of plant. Among 188 bacterial isolates isolated from different parts of the plant only 24 were found to be active against different pathogenic bacteria i.e. Escherichia coli, Methicillin-resistant Staphylococcus aureus (MRSA), Enterococcus faecium, Enterococcus faecalis and Pseudomonas aeruginosa. These active bacterial isolates were identified on the basis of 16S rRNA gene analysis. Total population of bacteria isolated from plant was high in root, following leaf and fruit. Antagonistic bacteria were also more abundant in root as compared to leaf and fruit. Two isolates (EA5 and EA18) exhibited antagonistic activity against most of the targeted pathogenic bacteria mentioned above. Some isolates showed strong inhibition for one targeted pathogenic bacterium while weak or no inhibition for others. Most of the antagonistic isolates were active against MRSA, following E. faecium, P. aeruginosa, E. coli and E. faecalis. Taken together, our results show that medicinal plants are good source of antagonistic bacteria having inhibitory effect against clinical bacterial pathogens.

Metformin attenuate PTZ-induced apoptotic neurodegeneration in human cortical neuronal cells

Objective:

Seizures are one of the neurodegenerative disorders of human being. Metformin has antioxidant properties and commonly used as an oral antidiabetic drug. The current study was aimed to observe the neuroprotective effect of metformin against PTZ-induced apoptotic neurodegeneration in human cortical neuronal cell culture.

Methods:

To observe that exposure of pentylenetetrazol (PTZ) at the dose of (30mM) for 30 minutes induced neuronal cell death by activation of caspase-3 in human cortical neuronal 2 (HCN-2) cell line. While the metformin at the dose of (20mM) along with PTZ for 30 minutes showed neuroprotection against PTZ-induced neuronal cell loss by MTT assay and Western blot analysis.

Results:

The results of this study showed that PTZ-induced neuronal cell death by activation of pro apoptotic proteins caspase-3 and 9 whereas the exposure of metformin showed its protective effect against neuronal loss in HCN-2 cell line. Finally, our results showed that exposure of metformin can prevent the harmful effect induced by PTZ in neuronal cells cultures.

Conclusions:

Our finding suggest that metformin exposure attenuates PTZ-induced neuronal cell death may act as a safe therapeutics and neuroprotective agent for the treatment of neuronal loss as result of seizure.

Detection and Genotyping of Helicobacter pylori among Gastric ulcer and Cancer Patients from Saudi Arabia

BACKGROUND AND OBJECTIVES

Helicobacter pylori (H. pylori) infection is cause of several gastrointestinal diseases in humans. Virulence genes of H. pylori are associated with severity of disease and vary geographically. The aim of present study was to detect H. pylori in formalin-fixed paraffin-embedded (FFPE) tissues and further investigate prevalence of babA_2, cagA, iceA1_, iceA2, vacA s1/s2 and vacA m1/m2 genotypes in H. pylori from gastric cancer (GC) and gastric ulcer (GU) patients' biopsy samples.

METHODS

We used FFPE tissues of 35 GC and 10 GU patients' biopsy samples. Using Polymerase Chain Reaction (PCR), detection of H. pylori strain was performed by using specific primers targeting 16S rRNA and ureC encodes for phosphoglucosamine mutase genes. We have identified different virulence genes of H. pylori by PCR.

RESULTS

Of all the 45 samples tested, 20 GC and all 10 GU samples were positive for identification of H. pylori using specific genes (16S rRNA and ureC). The prevalence of babA₂ (100%) was significantly higher in GC as compared to GU (40%) samples. The rate of virulence genes vacAs1 was higher in both GU 8 (80%) and GC (100%).

CONCLUSIONS

Our study finds that vacAs1am1 and babA₂ are most prominent genotypes and may play role in development of Gastric cancer.

Comparative bacterial community analysis in relatively pristine and anthropogenically influenced mangrove ecosystems on the Red Sea

Mangrove habitats are ecologically important ecosystems that are under severe pressure worldwide because of environmental changes and human activities. In this study, 16S rRNA gene amplicon deep-sequencing was used to compare bacterial communities in Red Sea mangrove ecosystems at anthropogenically influenced coastal sites with those at a relatively pristine island site. In total, 32 phyla were identified from the mangrove rhizospheres, with Proteobacteria predominating at each of the studied sites; however, the relative abundance was significantly decreased at the coastal sites (Mastorah, MG-MS; Ar-Rayis, MG-AR) compared with the pristine island site near Dhahban (MG-DBI). The phyla Actinobacteria, Firmicutes, Acidobacteria, Chloroflexi, Spirochetes, and Planctomycetes were present at a relative abundance of >1% at the MG-MS and MG-AR sites, but their concentration was <1% at the MG-DBI site. A total of 1659 operational taxonomic units (OTUs) were identified at the species level, and approximately 945 OTUs were shared across the different sampling sites. Multivariate principal coordinate data analysis separated the MG-DBI site from the MG-AR and MG-MS cluster. Specific bacterial taxa were enriched at each location, and in particular, the genera Pseudoalteromonas and Cobetia were predominantly identified in the MG-DBI site compared with the anthropogenically influenced coastal sites.

'Arthrobacter saudimassiliensis' sp. nov. a new bacterial species isolated from air samples in the urban environment of Makkah, Saudi Arabia

We report here the main characteristics of ‘Arthrobacter saudimassiliensis’ strain 11W110_air^T (CSUR P1223), a new species of the Arthrobacter genus that was isolated from air samples in the city environment of Makkah, Saudi Arabia, during the pilgrim period of Hajj 2012.

'Lysinibacillus saudimassiliensis' sp. nov., a new bacterial species isolated from air samples in the urban environment of Makkah, Saudi Arabia

We report here the main characteristics of 'Lysinibacillus saudimassiliensis' strain 13S34_air^τ (CSUR = P1222), a new species of the Lysinibacillus genus that was isolated from air samples in the city environment of Makkah, Saudi Arabia, during the pilgrim period of Hajj 2012.

Microbial Culturomics to Map Halophilic Bacterium in Human Gut: Genome Sequence and Description of Oceanobacillus jeddahense sp. nov

Culturomics is a new omics subspecialty to map the microbial diversity of human gut, coupled with a taxono-genomic strategy. We report here the description of a new bacterial species using microbial culturomics: strain S5T, (= CSUR P1091=DSM 28586) isolated from a stool specimen of a 25-year-old obese patient from Saudi Arabia. The strain S5T was a Gram-positive, strictly aerobic rod, which was motile by a polar flagellum, spore-forming, and exhibited catalase and oxidase activities. It grows optimally at 37°C, with a pH of 7.5 and 10% of NaCl. 16S rRNA gene-based identification revealed that strain S5T has 98.6% 16S rRNA sequence similarity with the reference O. oncorhynchi, phylogenetically the closest validated Oceanobacillus species. Here, we further describe the phenotypic characteristics of this organism and its complete genome sequence and annotation. The 5,388,285 bp long genome exhibits a G+C content of 37.24% and contains 5109 protein-coding genes and 198 RNA genes. Based on the characteristics reported here, we propose classifying this novel bacterium as representative of a new species belonging to the genus Oceanobacillus, Oceanobacillus jeddahense sp. nov. In a broader context, it is noteworthy that halophilic bacteria have long been overlooked in the human gut, and their role in human health and disease has not yet been investigated. This study thus further underscores the usefulness of the culturomics approach exploring the bacterial diversity of the gut.

'Pseudomonas saudimassiliensis' sp. nov. a new bacterial species isolated from air samples in the urban environment of Makkah, Saudi Arabia

We report here the main characteristics of ‘Pseudomonas saudimassiliensis’ strain 12M76_air^T (CSUR P1220), a new species of the Pseudomonas genus that was isolated from air samples in the city environment of Makkah, Saudi Arabia, during the pilgrim period of Hajj 2012.

'Halomonas saudii' sp. nov., a new bacterial species isolated from marine plant Halocnemum strobilaceum

We report here the main characteristics of 'Halomonas saudii' strain Saudii DR2 (CSUR P2512), a new species of the Halomonas genus that was isolated from a rhizosphere of Halocnemum strobilaceum in April 2015.