Project description:Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome were significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population. Please note that the data from the comparable cohort of patients in the USUS data was published as supplemental material of PMID: 22760045 but not submitted to GEO The 'patient_info.txt' contains 12 clinical, 7 immunological and 3 microbiological variables for each patient.

Project description:BackgroundThe seamounts Ses Olives (SO), Ausias March (AM) and Emile Baudot (EB) at the Mallorca Channel (Balearic Islands, western Mediterranean), are poorly explored areas containing rich and singular sponge communities. Previous works have shown a large heterogeneity of habitats, including rhodolith beds, rocky, gravel and sandy bottoms and steeped slopes. This diversity of habitats provides a great opportunity for improving the knowledge of the sponges from Mediterranean seamounts.MethodsSponges were collected during several surveys carried out by the Balearic Center of the Spanish Institute of Oceanography at the Mallorca Channel seamounts. Samples were obtained using a beam-trawl, rock dredge and remote operated vehicle. Additional samples were obtained from fishing grounds of the Balearic Islands continental shelf, using the sampling device GOC-73. Sponges were identified through the analysis of morphological and molecular characters.ResultsA total of 60 specimens were analyzed, from which we identified a total of 19 species. Three species and one genus are new to science: Foraminospongia balearica gen. nov. sp. nov., Foraminospongia minuta gen. nov. sp. nov. and Paratimea massutii sp. nov. Heteroxya cf. beauforti represents the first record of the genus Heteroxya in the Mediterranean Sea. Additionally, this is the second report of Axinella spatula and Haliclona (Soestella) fimbriata since their description. Moreover, the species Petrosia (Petrosia) raphida, Calyx cf. tufa and Lanuginella pupa are reported for the first time in the Mediterranean Sea. Petrosia (Strongylophora) vansoesti is reported here for the first time in the western Mediterranean Sea. Haliclona (S.) fimbriata is reported here for the first time in the north-western Mediterranean Sea. Hemiasterella elongata is reported here for the second time in the Mediterranean Sea. The species Melonanchora emphysema, Rhabdobaris implicata, Polymastia polytylota, Dragmatella aberrans, Phakellia ventilabrum and Pseudotrachya hystrix are reported for first time off Balearic Islands. Following the Sponge Barcoding project goals, we have sequenced the Cytochrome Oxidase subunit I (COI) and the 28S ribosomal fragment (C1-D2 domains) for Foraminospongia balearica sp. nov., Foraminospongia minuta sp. nov., H. cf. beauforti and C. cf. tufa, and the COI for Paratimea massuti sp. nov. We also provide a phylogenetic analysis to discern the systematic location of Foraminospongia gen. nov., which, in accordance to skeletal complement, is placed in the Hymerhabdiidae family. A brief biogeographical discussion is provided for all these species, with emphasis on the sponge singularity of SO, AM and the EB seamounts and the implications for their future protection.

Project description:Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome were significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population. Please note that the data from the comparable cohort of patients in the USUS data was published as supplemental material of PMID: 22760045 but not submitted to GEO The 'patient_info.txt' contains 12 clinical, 7 immunological and 3 microbiological variables for each patient. The G2 PhyloChip microarray platform (commercially available from Second Genome, Inc.) was used to profile bacteria in lower airway samples from 60 subjects

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New genera, species and records of Phaneropterinae (Orthoptera, Phaneropteridae) from sub-Saharan Africa.

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New genera, species and records of Phaneropterinae (Orthoptera, Phaneropteridae) from sub-Saharan Africa.

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