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:Pastoral systems are the dominant livestock production system in arid and semiarid regions of sub-Saharan Africa (SSA). They are often the only form of agriculture that can be practiced due to unfavorable climate and soil fertility levels that prevent crop cultivation. Pastoralism can have negative impacts on the environment, including land degradation, greenhouse gas emissions and other gases to the atmosphere, soil erosion, water pollution and biodiversity loss. Here, we review the current knowledge on nitrogen (N) cycling, storage, and loss pathways, with an emphasis on identification of N emission hotspots. Our review reports a large uncertainty in the amount of N lost as ammonia from excreta and manure storage, as well as N losses via nitrate and DON leaching. We also found that another major N loss pathway (18%), soil N2 emissions, has not yet been measured. In order to summarize the available information, we use a virtual pastoral farm, with characteristics and management practices obtained from a real farm, Kapiti Research Station in Kenya. For outlining N flows at this virtual farm, we used published data, data from global studies, satellite imagery and geographic information system (GIS) tools. Our results show that N inputs in pastoral systems are dominated by atmospheric N deposition (˜80%), while inputs due to biological nitrogen fixation seems to play a smaller role. A major N loss pathway is nitrogen leaching (nitrate > DON) from pastures (33%). Cattle enclosures (bomas), where animals are kept during night, represent N emissions hotspots, representing 16% of the total N losses from the system. N losses via ammonia volatilization and N2 O were four and three orders of magnitude higher from bomas than from the pasture, respectively. Based on our results, we further identify future research requirements and highlight the urgent need for experimental data collection to quantify nitrogen losses from manure in animal congregation areas. Such information is needed to improve our understanding on N cycling in pastoral systems in semiarid regions and to provide practical recommendations for managers that can help with decision-making on management strategies in pastoral systems in semiarid savannas.

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

Dataset Information

Livestock enclosures in drylands of Sub-Saharan Africa are overlooked hotspots of N₂O emissions.

Publications

Livestock enclosures in drylands of Sub-Saharan Africa are overlooked hotspots of N<sub>2</sub>O emissions.

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