Domination of Filamentous Anoxygenic Phototrophic Bacteria and Prediction of Metabolic Pathways in Microbial Mats from the Hot Springs of Al Aridhah.

Microbial mats in hot springs form a dynamic ecosystem and support the growth of diverse communities with broad-ranging metabolic capacity. In this study, we used 16S rRNA gene amplicon sequencing to analyse microbial communities in mat samples from two hot springs in Al Aridhah, Saudi Arabia. Putative metabolic pathways of the microbial communities were identified using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt). Filamentous anoxygenic phototrophic bacteria associated with phylum Chloroflexi were abundant (> 50 %) in both hot springs at 48 °C. Chloroflexi were mainly represented by taxa Chloroflexus followed by Roseiflexus. Cyanobacteria of genus Arthrospira constituted 3.4 % of microbial mats. Heterotrophic microorganisms were mainly represented by Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Archaea were detected at a lower relative abundance (< 1 %). Metabolic pathways associated with membrane transport, carbon fixation, methane metabolism, amino acid biosynthesis, and degradation of aromatic compounds were commonly found in microbial mats of both hot springs. In addition, pathways for production of secondary metabolites and antimicrobial compounds were predicted to be present in microbial mats. In conclusion, microbial communities in the hot springs of Al Aridhah were composed of diverse bacteria, with taxa of Chloroflexus being dominant.

Salt in stools is associated with obesity, gut halophilic microbiota and Akkermansia muciniphila depletion in humans.

BACKGROUND/OBJECTIVES: High salt intake has been linked to several diseases including obesity and an increased risk of death; however, fecal salinity and the ability of salt to alter the gut microbiota, which was recently identified as an instrumental factor for health and disease, remains poorly explored. METHODS/SUBJECTS: We analyzed the fecal samples of 1326 human individuals for salinity by refractometry, 572 for gut microbiota by culturomics, and 164 by 16S rRNA-targeted metagenomics. Geographical origin, age, gender, and obesity were tested as predictors of fecal salinity and halophilic diversity. All halophilic isolates were characterized by taxonogenomics and their genome sequenced. RESULTS: Fecal salinity was associated with obesity independently of geographical origin, gender, and age. The first 2 human-associated halophilic archaeal members were isolated along with 64 distinct halophilic species, including 21 new species and 41 known in the environment but not in humans. No halophiles grow in less than 1.5% salinity. Above this threshold, the richness of the halophilic microbiota was correlated with fecal salinity (r = 0.58, p < 0.0001). 16S metagenomics linked high fecal salinity to decreased diversity (linear regression, p < .035) and a depletion in anti-obesity Akkermansia muciniphila and Bifidobacterium, specifically B. longum and B. adolescentis. Genomics analysis suggested that halophilic microbes are not only transient passengers but may be residents of the human gut. CONCLUSIONS: High salt levels are associated with alteration of the gut microbial ecosystem and halophilic microbiota, as discovered during this study. Further studies should clarify if the gut microbiota alterations associated with high salt levels and the human halophilic microbiota could be causally related to human disease, such as obesity.

Amotosalen and ultraviolet A light efficiently inactivate MERS-coronavirus in human platelet concentrates.

OBJECTIVE: This study aimed to assess the efficacy of the INTERCEPT™ Blood System [amotosalen/ultraviolet A (UVA) light] to reduce the risk of Middle East respiratory syndrome-Coronavirus (MERS-CoV) transmission by human platelet concentrates. BACKGROUND: Since 2012, more than 2425 MERS-CoV human cases have been reported in 27 countries. The infection causes acute respiratory disease, which was responsible for 838 deaths in these countries, mainly in Saudi Arabia. Viral genomic RNA was detected in whole blood, serum and plasma of infected patients, raising concerns of the safety of blood supplies, especially in endemic areas. METHODS: Four apheresis platelet units in 100% plasma were inoculated with a clinical MERS-CoV isolate. Spiked units were then treated with amotosalen/UVA to inactivate MERS-CoV. Infectious and genomic viral titres were quantified by plaque assay and quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR). Inactivated samples were successively passaged thrice on Vero E6 cells to exclude the presence of residual replication-competent viral particles in inactivated platelets. RESULTS: Complete inactivation of MERS-CoV in spiked platelet units was achieved by treatment with Amotosalen/UVA light with a mean log reduction of 4·48 ± 0·3. Passaging of the inactivated samples in Vero E6 showed no viral replication even after nine days of incubation and three passages. Viral genomic RNA titration in inactivated samples showed titres comparable to those in pre-treatment samples. CONCLUSION: Amotosalen and UVA light treatment of MERS-CoV-spiked platelet concentrates efficiently and completely inactivated MERS-CoV infectivity (>4 logs), suggesting that such treatment could minimise the risk of transfusion-related MERS-CoV transmission.

Isolation, diversity, and biotechnological potential of rhizo- and endophytic bacteria associated with mangrove plants from Saudi Arabia.

Marine bacteria have been exceptional sources of halotolerant enzymes since decades. The aim of the present study was to isolate bacteria producing hydrolytic enzymes from seven different mangroves collected from the coastal area of Thuwal, Jeddah, Saudi Arabia, and to further screen them for other enzymatic and antifungal activities. We have isolated 46 different rhizo- and endophytic bacteria from the soil, roots, and leaves of the mangroves using different enzymatic media. These bacterial strains were capable of producing industrially important enzymes (cellulase, protease, lipase, and amylase). The bacteria were screened further for antagonistic activity against fungal pathogens. Finally, these bacterial strains were identified on the basis of the16S rDNA sequence. Taxonomic and phylogenetic analysis revealed 95.9-100% sequence identity to type strains of related species. The dominant phylum was Gammaproteobacteria (γ-Proteobacteria), which comprised 10 different genera - Erwinia, Vibrio, Psychrobacter, Aidingimonas, Marinobacter, Chromohalobacter, Halomonas, Microbulbifer, and Alteromonas. Firmicutes was the second dominant phylum, which contained only the genus Bacillus. Similarly, only Isoptericola belonged to Actinobacteria. Further these enzyme-producing bacteria were tested for the production of other enzymes. Most of the active strains showed cellulytic and lipolytic activities. Several were also active against fungal pathogens. Our results demonstrated that the mangroves represent an important source of potentially active bacteria producing enzymes and antifungal metabolites (bioactive products). These bacteria are a source of novel halophilic enzymes and antibiotics that can find industrial and medicinal use.

Growth factors in relation to obesity, food habits, and microbiota among healthy Saudis: preliminary results.

OBJECTIVE: Obesity is a serious problem among Saudis because of the country's affluent lifestyle. Obesity is associated with various metabolic disorders and characterized by low-grade inflammation that leads to the release of pro-inflammatory cytokines, human growth factors (GFs), lipids, aberrant adipokines, and other chemokines from adipose tissue. The objective of this study is to delineate the effects of GFs on microbiota and their relationship to body mass index (BMI) and food habits. SUBJECTS AND METHODS: In a cross-sectional study, 32 randomly selected participants (16 males and 16 females) were enrolled in a survey covering their sociodemographic information, medical history, lifestyle, and dietary practices. The information on diet, health condition, food and drink intake habits were examined under four distinct BMI categories: normal, underweight, overweight, and obese. The participants' serum samples were analyzed for the various GFs using a human magnetic 30-plex panel multiplex assay. Bioinformatics analysis was performed to investigate which bacterial taxa are enriched and to predict the functional profiles of the samples. RESULTS: Correlational studies revealed sex-based differences between GFs and microbiota. Females exhibited a significant correlation between epidermal GF (EGF) and Proteobacteria, whereas males showed a significant correlation between fibroblast GF-basic and Actinobacteria. Interestingly, a combined analysis of both sexes showed a significant correlation between EGF and vascular endothelial GF with Firmicutes. The data in the underweight group revealed a correlation between granulocyte colony-stimulating factor (G-CSF) and hepatocyte GF with Firmicutes. In the obese group, a correlation was found between G-CSF and Actinobacteria. CONCLUSIONS: Our results identified links between GFs, microbiota, and BMI in a Saudi cohort. The insights from this preliminary study will contribute to the predictive diagnosis of obesity. However, further research involving a larger cohort will be necessary to understand the mechanistic aspects of these GFs to provide biomarkers of potential obesity.

Efficient inactivation of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in human apheresis platelet concentrates with amotosalen and ultraviolet A light.

OBJECTIVES: The detection of SARS-CoV-2 RNA in blood and platelet concentrates from asymptomatic donors, and the detection of viral particles on the surface and inside platelets during in vitro experiments, raised concerns over the potential risk for transfusion-transmitted-infection (TTI). The objective of this study was to assess the efficacy of the amotosalen/UVA pathogen reduction technology for SARS-CoV-2 in human platelet concentrates to mitigate such potential risk. MATERIAL AND METHODS: Five apheresis platelet units in 100% plasma were spiked with a clinical SARS-CoV-2 isolate followed by treatment with amotosalen/UVA (INTERCEPT Blood System), pre- and posttreatment samples were collected as well as untreated positive and negative controls. The infectious viral titer was assessed by plaque assay and the genomic titer by quantitative RT-PCR. To exclude the presence of infectious particles post-pathogen reduction treatment below the limit of detection, three consecutive rounds of passaging on permissive cell lines were conducted. RESULTS: SARS-CoV-2 in platelet concentrates was inactivated with amotosalen/UVA below the limit of detection with a mean log reduction of>3.31±0.23. During three consecutive rounds of passaging, no viral replication was detected. Pathogen reduction treatment also inhibited nucleic acid detection with a log reduction of>4.46±0.51 PFU equivalents. CONCLUSION: SARS-CoV-2 was efficiently inactivated in platelet concentrates by amotosalen/UVA treatment. These results are in line with previous inactivation data for SARS-CoV-2 in plasma as well as MERS-CoV and SARS-CoV-1 in platelets and plasma, demonstrating efficient inactivation of human coronaviruses.

Bacterial contamination of Saudi "one" Riyal paper notes.

Fomites are inanimate objects that are capable of absorbing, harboring and transmitting infectious microorganisms. Paper currency, an exchangeable fomite, is constantly subjected to contamination. This study investigated bacterial contamination on the Saudi one Riyal paper note. Two hundred one Riyal bills (100 4th version and 100 5th version) were collected in the city of Jeddah for examination. The notes were examined for bacterial contamination using blood agar and MacConkey agar. Eighty-eight percent of the notes were contaminated with mixed (>or=2 types) bacterial growth. All 4th version notes had mixed bacterial growth: gram-positive bacilli (79%), coagulase-negative staphylococci (75%), Staphylococcus aureus (38%), Klebsiella spp (21%), Pseudomonas spp (19%), Escherichia coli (9%), viridans group streptococci (VGS) (8%), and non-hemolytic streptococci (4%). Seventy-six percent of the newer 5th version notes had mixed bacterial growth: gram-positive bacilli (68%), coagulase-negative staphylococci (64%), S. aureus (13%), Klebsiella spp (9%), Pseudomonas spp (5%), E. coli (2%) and VGS (2%). These results indicate the Saudi one Riyal paper note is commonly contaminated with bacteria, and may act as a vehicle for the transmission of potentially pathogenic bacteria. The more the bill had been handled the greater the contamination was.

Draft genome sequence of a multidrug-resistant emerging pathogenic isolate of Vibrio alginolyticus from the Red Sea.

The marine ecosystem is a growing reservoir of antimicrobial-resistant bacteria, and thus an emerging risk to human health. In this study, we report the first draft genome sequence of multidrug-resistant Vibrio alginolyticus strain OS1T-47, isolated from an offshore site in the Red Sea. The draft genome of V. alginolyticus OS1T-47 is 5 157 150 bp in length and has DNA G + C content of 44.83%. Strain OS1T-47 possesses 22 antimicrobial resistance genes, including those associated with multidrug-resistant efflux pumps.

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.

First complete genome sequence of circulating dengue virus serotype 3 in Jeddah, Saudi Arabia.

Here we report the first full-length genome sequence of dengue virus serotype 3 (DENV-3) from a strain isolated from a patient in Jeddah, Saudi Arabia, in 2014. The genome consists of 10 635 bp and shows close similarity to circulating genotype III isolates from Singapore, suggesting possible importation, most probably during religious pilgrimages to Saudi Arabia.

'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_airT (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.

'Pseudomonas saudiphocaensis' sp. nov., a new bacterial species isolated from currency notes collected during the Hajj pilgrimage in 2012 at Makkah, Saudi Arabia.

We report here the main characteristics of 'Pseudomonas saudiphocaensis' strain 20_BNT (CSUR P1224), a new species of the Pseudomonas genus that was isolated from currency notes collected during the Hajj pilgrimage in 2012 at Makkah, Saudi Arabia.

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 '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.

'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_airT (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.

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.

'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.

'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_airτ (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.

'Jeotgalicoccus 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 'Jeotgalicoccus saudimassiliensis' strain 13MG44_airT (CSUR P1221), a new species of the Jeotgalicoccus genus that was isolated from air samples in the city environment of Makkah, Saudi Arabia, during the pilgrim period of Hajj 2012.