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Marked differences in the prevalence of allergy between urban and rural environments have been well established. Certain microorganisms encountered in and around farming and rural surroundings can 'train' and modulate the human immune system to protect against certain infectious and non-communicable diseases, including allergies. Research from South Africa has indicated that drinking fermented cow's milk from a young age may protect against allergy even in a urban population. Lactic acid bacteria are important role-players in allergy protection and these organisms are abundant in fermented food products. The questions arise: Can people living in urban areas, at least to some extent, 'replicate' the allergy protective environment of rural people or at least compensate for a lack of exposure to protective organisms? And can they do so safely? In this review we focus on fermented milk and other fermented foods and elaborate on the allergy-protective microbiota favoured by fermentation. [ABSTRACT FROM AUTHOR]

Marula wine is produced from ripe fruits of the Sclerocarya birrea subspecies caffra tree through spontaneous fermentation. A few culture-based studies have shown that the fermentation is largely driven by yeasts, although, in the early stages, some lactic acid bacteria (LAB) and acetic acid bacteria may be detected. Some of the microbes may produce undesirable metabolites that lead to the spoilage and short shelf life of the wine. However, there is generally limited information on the microbial composition and its contribution to the chemical characteristics of the resultant marula wine. The aim of this study was to characterise the microbial population of marula wine from different localities in the Limpopo province, South Africa. MALDI-TOF and amplicon sequencing technique were used to identify microbial strains and to determine their diversity and changes in the different stages of fermentation. The phylogenetic relationships of LAB and S. cerevisiae were analysed using multilocus sequence typing. Bacterial species that were common in the different marula wines included Gluconobacter oxydans, Lactiplantibacillus plantarum, Levilactobacillus brevis, Lacitilactobacillus nagelii, Lentilactobacillus kefiri and Lentilactobacillus parabuchneri, and the yeasts were Hanseniaspora guiliermondii, Saccharomyces cerevisiae, Rhodotorula mucilaginosa and Pichia kudriavzevii. The MLST data indicated common microbiota from different marula wines with low intraspecific diversity, suggesting that the LAB and S. cerevisiae strains that are mainly responsible for the spontaneous fermentation of marula wine are similar irrespective of the geographical differences and production preferences. [ABSTRACT FROM AUTHOR]

Background: Endophytes are a rich source of novel, distinct, and applicable compounds of interest in agricultural, medical, cosmetic, and pharmaceutical industries. In this respect, they have been attracting growing interest in the past few years. Endophytes are defined as microorganisms such as bacteria and fungi which have a mutualistic relationship with their host plants without causing any harm to their host. In this study, we isolated and identified bacterial endophytes from Centella asiatica collected in Western Cape, South Africa. Results: Twenty bacterial endophytes were isolated from Centella asiatica and characterized by using morphological and molecular techniques. Based on molecular traits, the isolates were identified as Pseudomonas sp. strain SGM1, Pseudomonas sp. strain SGM2, Pseudomonas sp. strain SGM3, Pseudomonas sp. strain SGM4, Pseudomonas sp. strain SGM5, Pseudomonas sp. strain SGM6, Pseudomonas sp. strain SGM7, Novosphingobium sp. strain SGM8, Pseudomonas sp. strain SGM9, Pseudomonas sp. strain SGM10, Chryseobacterium sp. strain SGM11, Enterobacter sp. strain SGM12, Enterobacter sp. strain SGM13, Pseudomonas sp. strain SGM14, Enterobacter sp. strain SGM15, Enterobacter sp. strain SGM16, Agrobacterium sp. strain SGM17, Pantoea sp. strain SGM18, Paraburkholderia sp. strain SGM19, and Pseudomonas sp. strain SGM20. Pseudomonas genus was dominant with eleven isolates. Morphological trait results showed that all isolates were gram-negative rod-shaped bacteria. Conclusion: According to our understanding, this study revealed the first twenty endophytic bacteria isolated from Centella asiatica growing in the Western Cape Province, South Africa. Data obtained in the current study will increase the knowledge of the already existing microbial diversity associated with Centella asiatica. Further work is needed to evaluate the antioxidant and antibacterial activities in vitro and assess the growth and medicinal compounds of the identified endophytic bacteria in a laboratory scale bioreactors. [ABSTRACT FROM AUTHOR]

Purpose: The urinary tract is colonized by microbial communities that impact urinary health. Previous studies have suggested that the bacterial composition of the male urinary microbiota is related to STIs. This study assessed the bacterial composition of the urinary microbiome in South African MSM with and without C. trachomatis.This study used urine samples from MSM attending care at the King Edward VIII hospital and the Aurum Institute in Durban, South Africa. A total of 200 samples were tested for C. trachomatis infection using the Applied Biosystems™ TaqMan® Assays. Urinary microbiomes of 23 samples were characterized using 16 S rRNA (V3 and V4) gene sequencing on the Illumina MiSeq platform.Bacterial taxonomic analysis showed a high abundance of Streptococcus, Corynebacterium, and Staphylococcus in all the sequenced samples. Moreover, Prevotella and Lactobacillus were detected in urine samples of MSM. Alpha diversity metrics showed a slight increase in microbial diversity in C. trachomatis positive samples; however, this was not significant (ANOVA, P > 0.05). Principal coordinates analysis (PCoA) showed that the microbiome of C. trachomatis infected MSM was not clearly different from those uninfected. Distinct bacterial communities were not detected between positive and negative samples (PERMANOVA F1,22= 1.0284, R2 = 0.047%, P = 0.385).Most microbiome studies on MSM to date have focused on the gut microenvironment. Few studies, however, have provided data regarding the normal composition of the male urethral microbiomes or if these microbiomes are associated with male STIs. This study adds to the growing body of knowledge highlighting the urinary microbiome in MSM.Methods: The urinary tract is colonized by microbial communities that impact urinary health. Previous studies have suggested that the bacterial composition of the male urinary microbiota is related to STIs. This study assessed the bacterial composition of the urinary microbiome in South African MSM with and without C. trachomatis.This study used urine samples from MSM attending care at the King Edward VIII hospital and the Aurum Institute in Durban, South Africa. A total of 200 samples were tested for C. trachomatis infection using the Applied Biosystems™ TaqMan® Assays. Urinary microbiomes of 23 samples were characterized using 16 S rRNA (V3 and V4) gene sequencing on the Illumina MiSeq platform.Bacterial taxonomic analysis showed a high abundance of Streptococcus, Corynebacterium, and Staphylococcus in all the sequenced samples. Moreover, Prevotella and Lactobacillus were detected in urine samples of MSM. Alpha diversity metrics showed a slight increase in microbial diversity in C. trachomatis positive samples; however, this was not significant (ANOVA, P > 0.05). Principal coordinates analysis (PCoA) showed that the microbiome of C. trachomatis infected MSM was not clearly different from those uninfected. Distinct bacterial communities were not detected between positive and negative samples (PERMANOVA F1,22= 1.0284, R2 = 0.047%, P = 0.385).Most microbiome studies on MSM to date have focused on the gut microenvironment. Few studies, however, have provided data regarding the normal composition of the male urethral microbiomes or if these microbiomes are associated with male STIs. This study adds to the growing body of knowledge highlighting the urinary microbiome in MSM.Results: The urinary tract is colonized by microbial communities that impact urinary health. Previous studies have suggested that the bacterial composition of the male urinary microbiota is related to STIs. This study assessed the bacterial composition of the urinary microbiome in South African MSM with and without C. trachomatis.This study used urine samples from MSM attending care at the King Edward VIII hospital and the Aurum Institute in Durban, South Africa. A total of 200 samples were tested for C. trachomatis infection using the Applied Biosystems™ TaqMan® Assays. Urinary microbiomes of 23 samples were characterized using 16 S rRNA (V3 and V4) gene sequencing on the Illumina MiSeq platform.Bacterial taxonomic analysis showed a high abundance of Streptococcus, Corynebacterium, and Staphylococcus in all the sequenced samples. Moreover, Prevotella and Lactobacillus were detected in urine samples of MSM. Alpha diversity metrics showed a slight increase in microbial diversity in C. trachomatis positive samples; however, this was not significant (ANOVA, P > 0.05). Principal coordinates analysis (PCoA) showed that the microbiome of C. trachomatis infected MSM was not clearly different from those uninfected. Distinct bacterial communities were not detected between positive and negative samples (PERMANOVA F1,22= 1.0284, R2 = 0.047%, P = 0.385).Most microbiome studies on MSM to date have focused on the gut microenvironment. Few studies, however, have provided data regarding the normal composition of the male urethral microbiomes or if these microbiomes are associated with male STIs. This study adds to the growing body of knowledge highlighting the urinary microbiome in MSM.Conclusion: The urinary tract is colonized by microbial communities that impact urinary health. Previous studies have suggested that the bacterial composition of the male urinary microbiota is related to STIs. This study assessed the bacterial composition of the urinary microbiome in South African MSM with and without C. trachomatis.This study used urine samples from MSM attending care at the King Edward VIII hospital and the Aurum Institute in Durban, South Africa. A total of 200 samples were tested for C. trachomatis infection using the Applied Biosystems™ TaqMan® Assays. Urinary microbiomes of 23 samples were characterized using 16 S rRNA (V3 and V4) gene sequencing on the Illumina MiSeq platform.Bacterial taxonomic analysis showed a high abundance of Streptococcus, Corynebacterium, and Staphylococcus in all the sequenced samples. Moreover, Prevotella and Lactobacillus were detected in urine samples of MSM. Alpha diversity metrics showed a slight increase in microbial diversity in C. trachomatis positive samples; however, this was not significant (ANOVA, P > 0.05). Principal coordinates analysis (PCoA) showed that the microbiome of C. trachomatis infected MSM was not clearly different from those uninfected. Distinct bacterial communities were not detected between positive and negative samples (PERMANOVA F1,22= 1.0284, R2 = 0.047%, P = 0.385).Most microbiome studies on MSM to date have focused on the gut microenvironment. Few studies, however, have provided data regarding the normal composition of the male urethral microbiomes or if these microbiomes are associated with male STIs. This study adds to the growing body of knowledge highlighting the urinary microbiome in MSM. [ABSTRACT FROM AUTHOR]

Peatlands are complex wetland-like ecosystems that harbor diverse microbial communities. In this study, the microbial communities (fungal and actinobacterial) associated with an unimpacted peatland (Vankervelsvlei; VV), an impacted peatland (Goukou River system; GK), and a developing peatland (Nuwejaars River system; NR) were determined through ITS and 16S rRNA metataxonomic analyses. Unidentified Acidimicrobiales dominated in GK and NR, unidentified Intrasporangiaceae and Solirubobacterales in NR, and Corynebacterium, Propionibacterium, and Streptomyces species in VV. The fungal phyla, Ascomycota and Basidiomycota, dominated all three sites, and harbored unique fungal taxa belonging to a wide range of fungal guilds. Physicochemical properties of the peat collected from the three sites were analyzed in association with microbial community structures in order to determine which parameters acted as the main drivers for microbial diversity. BEST analysis (linking microbial diversity patterns to environmental variables) showed that nitrogen (N), aluminum (Al), phosphorus (P), and potassium (K) were the most significant physicochemical drivers of actinobacterial community structure, while iron (Fe) and humification were the environmental parameters that affected the fungal communities the most. In conclusion, this study has provided some insight into the fungal and actinobacterial communities associated with three South African peatlands and the main environmental drivers that influence these communities. [ABSTRACT FROM AUTHOR]

Microbial diversity in vineyards and in grapes has generated significant scientific interest. From a biotechnological perspective, vineyard and grape biodiversity has been shown to impact soil, vine, and grape health and to determine the fermentation microbiome and the final character of wine. Thus, an understanding of the drivers that are responsible for the differences in vineyard and grape microbiota is required. The impact of soil and climate, as well as of viticultural practices in geographically delimited areas, have been reported. However, the limited scale makes the identification of generally applicable drivers of microbial biodiversity and of specific microbial fingerprints challenging. The comparison and meta-analysis of different datasets is furthermore complicated by differences in sampling and in methodology. Here we present data from a wide-ranging coordinated approach, using standardized sampling and data generation and analysis, involving four countries with different climates and viticultural traditions. The data confirm the existence of a grape core microbial consortium, but also provide evidence for country-specific microbiota and suggest the existence of a cultivar-specific microbial fingerprint for Cabernet Sauvignon grape. This study puts in evidence new insight of the grape microbial community in two continents and the importance of both location and cultivar for the definition of the grape microbiome. [ABSTRACT FROM AUTHOR]

The Cape fynbos biome in South Africa is home to highly diverse and endemic shrub legumes, which include species of Aspalathus, Polhillia, Wiborgia and Wiborgiella. These species play a significant role in improving soil fertility due to their ability to fix N2. However, information regarding their microbiome is still unknown. Using the 16S rRNA Miseq illumina sequencing, this study assessed the bacterial community structure associated with the rhizospheres of Polhillia pallens, Polhillia brevicalyx, Wiborgia obcordata, Wiborgia sericea and Wiborgiella sessilifolia growing at different locations during the wet and dry seasons in the Cape fynbos. The results showed that the most dominant bacterial phylum was Actinobacteria during both the dry (56.2–37.2%) and wet (46.3–33.3%) seasons. Unclassified bacterial genera (19.9–27.7%) were the largest inhabitants in the rhizospheres of all five species during the two seasons. The other dominant phyla included Bacteroidetes, Acidobacteria, Proteobacteria and Firmicutes. Mycobacterium and Conexibacter genera were the biggest populations found in the rhizosphere soil of all five test species during both seasons, except for W. obcordata soil sampled during the dry season, which had Dehalogenimonas as the major inhabitant (6.08%). In this study plant species and growth season were the major drivers of microbial community structure, with W. obcordata having the greatest influence on its microbiome than the other test species. The wet season promoted greater microbial diversity than the dry season. [ABSTRACT FROM AUTHOR]

Understanding the role of soil microbes and their associated extracellular enzymes in long-term grassland experiments presents an opportunity for testing relevant ecological questions on grassland nutrient dynamics and functioning. Veld fertilizer trials initiated in 1951 in South Africa were used to assess soil functional microbial diversity and their metabolic activities in the nutrient-poor grassland soils. Phosphorus and liming trials used for this specific study comprised of superphosphate (336 kg ha−1) and dolomitic lime (2250 kg ha−1) (P + L), superphosphate (336 kg ha−1) (+ P) and control trials. These soils were analyzed for their nutrient concentrations, pH, total cations and exchange acidity, microflora and extracellular enzyme activities. The analysed soil characteristics showed significant differences except nitrogen (N) and organic carbon (C) concentrations showing no significant differences. P-solubilizing, N-cycling and N-fixing microbial diversity varied among the different soil treatments. β-glucosaminidase enzyme activity was high in control soils compared to P-fertilized and limed soils. Alkaline phosphatase showed increased activity in P-fertilized soils, whereas acid phosphatase showed increased activity in control soils. Therefore, the application of superphosphate and liming influences the relative abundance of bacterial communities with nutrient cycling and fixing functions which account for nutrient bioavailability in acidic and nutrient stressed grassland ecosystem soils. [ABSTRACT FROM AUTHOR]

Canine microbiome studies are often limited in the geographic and temporal scope of samples studied. This results in a paucity of data on the canine microbiome around the world, especially in contexts where dogs may not be pets or human associated. Here, we present the shotgun sequences of fecal microbiomes of pet dogs from South Africa, shelter and stray dogs from India, and stray village dogs in Laos. We additionally performed a dietary experiment with dogs housed in a veterinary medical school, attempting to replicate the diet of the sampled dogs from Laos. We analyse the taxonomic diversity in these populations and identify the underlying functional redundancy of these microbiomes. Our results show that diet alone is not sufficient to recapitulate the higher diversity seen in the microbiome of dogs from Laos. Comparisons to previous studies and ancient dog fecal microbiomes highlight the need for greater population diversity in studies of canine microbiomes, as modern analogues can provide better comparisons to ancient microbiomes. We identify trends in microbial diversity and industrialization in dogs that mirror results of human studies, suggesting future research can make use of these companion animals as substitutes for humans in studying the effects of industrialization on the microbiome. [ABSTRACT FROM AUTHOR]

Human milk optimizes gut microbial richness and diversity, and is critical for proper immune development. Research has shown differing microbial composition based on geographic location, providing evidence that diverse biospecimen data is needed when studying human bacterial communities. Yet, limited research describes human milk and infant gut microbial communities in Africa. Our study uses breastmilk, stool, and meconium samples from a South African birth cohort to describe the microbial diversity, identify distinct taxonomic units, and determine correlations between bacterial abundance in breastmilk and stool samples. Mother-infant dyads (N = 20) were identified from a longitudinal birth cohort in the Vhembe district of Limpopo Province, South Africa. Breastmilk, meconium, and stool samples were analyzed using 16S ribosomal RNA sequencing of the V4–V5 gene region using the MiSeq platform for identification and relative quantification of bacterial taxa. A non-metric multidimensional scaling using Bray–Curtis distances of sample Z-scores showed that meconium, stool, and breastmilk microbial communities are distinct with varying genus. Breastmilk was mostly comprised of Streptococcus, Staphylococcus, Veillonella, and Corynebacterium. Stool samples showed the highest levels of Bifidobacterium, Faecalibacterium, Bacteroides, and Streptococcus. Alpha diversity measures found that stool samples have the highest Shannon index score compared to breastmilk and meconium. The abundance of Bifidobacterium (r = 0.57), Blautia (r = 0.59), and Haemophilus (r = 0.69) was correlated (p < 0.1) between breastmilk and stool samples. Despite the importance of breastmilk in seeding the infant gut microbiome, we found evidence of distinct bacterial communities between breastmilk and stool samples from South African mother-infant dyads. [ABSTRACT FROM AUTHOR]

Sleep disorders are increasingly being characterized in modern society as contributing to a host of serious medical problems, including obesity and metabolic syndrome. Changes to the microbial community in the human gut have been reportedly associated with many of these cardiometabolic outcomes. In this study, we investigated the impact of sleep length on the gut microbiota in a large cohort of 655 participants of African descent, aged 25–45, from Ghana, South Africa (SA), Jamaica, and the United States (US). The sleep duration was self-reported via a questionnaire. Participants were classified into 3 sleep groups: short (<7hrs), normal (7-<9hrs), and long (≥9hrs). Forty-seven percent of US participants were classified as short sleepers and 88% of SA participants as long sleepers. Gut microbial composition analysis (16S rRNA gene sequencing) revealed that bacterial alpha diversity negatively correlated with sleep length (p<0.05). Furthermore, sleep length significantly contributed to the inter-individual beta diversity dissimilarity in gut microbial composition (p<0.01). Participants with both short and long-sleep durations exhibited significantly higher abundances of several taxonomic features, compared to normal sleep duration participants. The predicted relative proportion of two genes involved in the butyrate synthesis via lysine pathway were enriched in short sleep duration participants. Finally, co-occurrence relationships revealed by network analysis showed unique interactions among the short, normal and long duration sleepers. These results suggest that sleep length in humans may alter gut microbiota by driving population shifts of the whole microbiota and also specific changes in Exact Sequence Variants abundance, which may have implications for chronic inflammation associated diseases. The current findings suggest a possible relationship between disrupted sleep patterns and the composition of the gut microbiota. Prospective investigations in larger and more prolonged sleep researches and causally experimental studies are needed to confirm these findings, investigate the underlying mechanism and determine whether improving microbial homeostasis may buffer against sleep-related health decline in humans. [ABSTRACT FROM AUTHOR]

Oral and fecal microbial biomarkers have previously been associated with cardiometabolic (CM) risk, however, no comprehensive attempt has been made to explore this association in minority populations or across different geographic regions. We characterized gut- and oral-associated microbiota and CM risk in 655 participants of African-origin, aged 25–45, from Ghana, South Africa, Jamaica, and the United States (US). CM risk was classified using the CM risk cut-points for elevated waist circumference, elevated blood pressure and elevated fasted blood glucose, low high-density lipoprotein (HDL), and elevated triglycerides. Gut-associated bacterial alpha diversity negatively correlated with elevated blood pressure and elevated fasted blood glucose. Similarly, gut bacterial beta diversity was also significantly differentiated by waist circumference, blood pressure, triglyceridemia and HDL-cholesterolemia. Notably, differences in inter- and intra-personal gut microbial diversity were geographic-region specific. Participants meeting the cut-points for 3 out of the 5 CM risk factors were significantly more enriched with Lachnospiraceae, and were significantly depleted of Clostridiaceae, Peptostreptococcaceae, and Prevotella. The predicted relative proportions of the genes involved in the pathways for lipopolysaccharides (LPS) and butyrate synthesis were also significantly differentiated by the CM risk phenotype, whereby genes involved in the butyrate synthesis via lysine, glutarate and 4-aminobutyrate/succinate pathways and LPS synthesis pathway were enriched in participants with greater CM risk. Furthermore, inter-individual oral microbiota diversity was also significantly associated with the CM risk factors, and oral-associated Streptococcus, Prevotella, and Veillonella were enriched in participants with 3 out of the 5 CM risk factors. We demonstrate that in a diverse cohort of African-origin adults, CM risk is significantly associated with reduced microbial diversity, and the enrichment of specific bacterial taxa and predicted functional traits in both gut and oral environments. As well as providing new insights into the associations between the gut and oral microbiota and CM risk, this study also highlights the potential for novel therapeutic discoveries which target the oral and gut microbiota in CM risk. [ABSTRACT FROM AUTHOR]

There is a need to profile microorganisms which exist pre-and-post-production of umqombothi, to understand its microbial diversity and the interactions which subsequently influence the final product. Thus, this study sought to determine the relative microbial abundance in umqombothi and predict the functional pathways of bacterial and fungal microbiota present. Full-length bacterial 16S rRNA and internal transcribed spacer (ITS) gene sequencing using PacBio single-molecule, real-time (SMRT) technology was used to assess the microbial compositions. PICRUSt2 was adopted to infer microbial functional differences. A mixture of harmful and beneficial microorganisms was observed in all samples. The microbial diversity differed significantly between the mixed raw ingredients (MRI), customary beer brew (CB), and optimised beer brew (OPB). The highest bacterial species diversity was observed in the MRI, while the highest fungal species diversity was observed in the OPB. The dominant bacterial species in the MRI, CB, and OPB were Kosakonia cowanii, Apilactobacillus pseudoficulneus, and Vibrio alginolyticus, respectively, while the dominant fungal species was Apiotrichum laibachii. The predicted functional annotations revealed significant (p < 0.05) differences in the microbial pathways of the fermented and unfermented samples. The most abundant pathways in the MRI were the branched-chain amino acid biosynthesis super pathway and the pentose phosphate pathway. The CB sample was characterised by folate (vitamin B 9 ) transformations III, and mixed acid fermentation. Biotin (vitamin B 7 ) biosynthesis I and L-valine biosynthesis characterised the OPB sample. These findings can assist in identifying potential starter cultures for the commercial production of umqombothi. Specifically, A. pseudoficulneus can be used for controlled fermentation during the production of umqombothi. Likewise, the use of A. laibachii can allow for better control over the fermentation kinetics such as carbohydrate conversion and end-product characteristics, especially esters and aroma compounds., (© 2023. The Author(s).)

Many studies, mostly in temperate regions of the northern hemisphere, have demonstrated that agricultural practices affect the composition and diversity of soil microbial communities. However, very little is known about the impact of agriculture on the microbial communities in other regions of the world, most particularly on the African continent. In this study, we used MiSeq amplicon sequencing of bacterial 16S rRNA genes and fungal ITS regions to characterise microbial communities in agricultural and natural grassland soils located in the Mpumalanga Province of South Africa. Nine soil chemical parameters were also measured to evaluate the effects of edaphic factors on microbial community diversity. Bacterial and fungal communities were significantly richer and more diverse in natural grassland than in agricultural soils. Microbial taxonomic composition was also significantly different between the two habitat types. The phylum Acidobacteria was significantly more abundant in natural grassland than in agricultural soils, while Actinobacteria and the family Nectriaceae showed the opposite pattern. Soil pH and phosphorus significantly influenced bacterial communities, whereas phosphorus and calcium influenced fungal communities. These findings may be interpreted as a negative impact of land-use change on soil microbial diversity and composition. Significance: * This report is the first of the effect of land-use changes on the diversity of the soil microbial communities in African grassland soils. * Land-use changes influence the diversity and structure of soil microbial communities in the Grassland Biome of South Africa. * This study serves as a baseline for future studies on South African soil microbial diversity. [ABSTRACT FROM AUTHOR]

A 250 t sunflower oil spill in the Con Joubert Bird Sanctuary Wetland, South Africa, was the largest global sunflower oil spill in a freshwater wetland to date. Since there was insufficient historical data for the Con Joubert Bird Sanctuary Wetland prior to the spill, variations in phytoplankton assemblages were used to indicate wetland resilience in relationship with water quality variables. From this study, it was evident that the phytoplankton biodiversity was a more reliable indicator of wetland resilience than vegetable oil concentrations measured in the water column. Vegetable oil concentrations measured in the water column varied both spatially and temporally and can possibly be linked to the passive movement of drifting oil in the water column caused by wind action and temperature changes. While we were unable to pinpoint the exact mechanisms behind the increase in phytoplankton biodiversity, the response was probably driven by the degradation of the oil by natural microbial consortiums in the wetland or a possible increase in phytoplankton grazers. Certain phytoplankton genera were found to be tolerant to the adverse effects of the oil spill. These genera include Oedogonium, Cyclotella, Spirogyra, and Planktothrix. In general, the univariate and multivariate statistical analysis showed a low diversity and richness at sites 1, 2 and 3 during the initial sampling surveys when compared to the remaining sites. However, the phytoplankton diversity and richness subsequently increased at all sampling sites from the second sampling survey, implying that there was a shift in phytoplankton biodiversity to a more stable state. [ABSTRACT FROM AUTHOR]

Highlights: [•] We determined near full-length genomes of six HCV genotype 5a from South Africa. [•] Phylogenetic and evolutionary history of the near full-length were determined. [•] Bayesian analysis of the E1 estimated the time of the most recent common ancestor. [•] The genomes provides insights into South African genotype 5a diversity. [ABSTRACT FROM AUTHOR]

The present study aims firstly at determining the microbial diversity of mine-water collected in Emalahleni, South Africa and secondly isolating and characterizing the most dominant bacterial species found in the mine water in terms of its resistance to both V5+ and Ni2+ in a modified wastewater liquid media. The results revealed a microbial diversity of 17 orders, 27 families and 33 genera were found in the mine-water samples with Marinobacteria (47.02%) and Anabaena (17.66%) being the most abundant genera. Considering their abundance in the mine-water samples, a species of the Marinobacter genera was isolated, identified, and characterised for metal tolerance and removal ability. The MWI-1 isolate (Marinobacter sp. MWI-1 [AB793286]) was found to be closely related to Marinobacter goseongensis at 97% of similarity. The isolate was exposed to various concentrations of Ni2+ and V5+ in wastewater liquid media and its tolerance to metals was also assessed. The MWI-1 isolate could tolerate V5+ and Ni2+ separately at concentrations (in terms of MIC) up to 13.41±0.56 mM and 5.39±0.5 mM at pH 7, whereas at pH 3, the tolerance limit decrease to 11.45±0.57 mM and 2.67±0.1 mM, respectively. The removal of V5+ and Ni2+ in liquid media was noted to gradually decrease with a gradual increase of the test metals. A significant difference (p<0.05) between V5+ and Ni2+ removal was noted. Marinobacter sp. MWI-1 achieved the maximum permissible limit of 0.1 mg-V5+/L prescribed by UN-FAO at 100 mg/L, while at 200 mg/L only V5+ was removed at approximately 95% and Ni2+ at 47%. This study suggests that mine-water indigenous microorganisms are the best solution for the remediation of polluted mine water. [ABSTRACT FROM AUTHOR]

The identification of species within the genus Tetrahymena is known to be difficult due to their essentially identical morphology, the occurrence of cryptic and sibling species and the phenotypic plasticity associated with the polymorphic life cycle of some species. We have combined morphology and molecular biology to describe Tetrahymena aquasubterranea n. sp. from groundwater of Cape Town, Republic of South Africa. The phylogenetic analysis compares the cox1 gene sequence of T. aquasubterranea with the cox1 gene sequences of other Tetrahymena species and uses the interior-branch test to improve the resolution of the evolutionary relationships. This showed a considerable genetic divergence of T. aquasubterranea to its next relative, T. farlyi, of 9.2% (the average cox1 divergence among bona fide species of Tetrahymena is ~ 10%). Moreover, the analysis also suggested a sister relationship between T. aquasubterranea and a big clade comprising T. farleyi, T. tropicalis, T. furgasoni and T. mobilis. The morphological data available for these species show that they share with T. aquasubterranea a pyriformis-like life style and at least two of them, T. farleyi and T. mobilis, a similar type II silverline pattern consisting of primary and secondary meridians. Tetrahymena aquasubterranea exhibits a biphasic life cycle with trophonts and theronts, is amicronucleate, and feeds on bacteria. [ABSTRACT FROM AUTHOR]

Diarrhoea is a hallmark of HIV infections in developing countries, and many diarrhoea-causing agents are often transmitted through water. The objective of the study was to determine the diversity and antibiotic susceptibility profiles of bacterial organisms isolated from samples of household drinking-water consumed by HIV-infected and AIDS patients. In the present study, household water stored for use by HIV-positive patients was tested for microbial quality, and isolated bacterial organisms were analyzed for their susceptibility profiles against 25 different antibiotics. The microbial quality of water was generally poor, and about 58% of water samples (n=270) were contaminated with faecal coliforms, with counts varying from 2 colony-forming unit (CFU)/100 mL to 2.4x104 CFU/100 mL. Values of total coliform counts ranged from 17 CFU/100 mL to 7.9x104 /100 mL. In total, 37 different bacterial species were isolated, and the major isolates included Acinetobacter lwoffii (7.5%), Enterobacter cloacae (7.5%), Shigella spp. (14.2%), Yersinia entero- colitica (6.7%), and Pseudomonas spp. (16.3%). No Vibrio cholerae could be isolated; however, V. fluvialis was isolated from three water samples. The isolated organisms were highly resistant to cefazolin (83.5%), cefoxitin (69.2%), ampicillin (66.4%), and cefuroxime (66.2%). Intermediate resistance was observed against gentamicin (10.6%), cefepime (13.4%), ceftriaxone (27.6%), and cefotaxime (29.9%). Levofloxacin (0.7%), ceftazidime (2.2%), meropenem (3%), and ciprofloxacin (3.7%) were the most active antibiotics against all the microorganisms, with all recording less than 5% resistance. Multiple drug resistance was very common, and 78% of the organisms were resistant to three or more antibiotics. Education on treatment of household water is advised for HIV-positive patients, and measures should be taken to improve point-of-use water treatment as immunosuppressed individuals would be more susceptible to opportunistic infections. [ABSTRACT FROM AUTHOR]

Marine fungi are known to originate from a wide variety of habitats within the marine environment. Marine sediment represents one environmental niche, with most fungi occurring in these sediments being facultative marine fungi with terrestrial origins. It has not been proven whether these fungi merely survive the harsh environmental conditions presented by the ocean sediment, as opposed to playing an active role in this ecological niche. During this study, marine sediment was collected from St. Helena Bay, on the west coast of the Western Cape, South Africa. Using dilution, enrichment, and repetitive culturing techniques, 59 fungal isolates were obtained from marine sediments and identified to at least genus level using morphological and molecular methods. Moreover, a series of tests were performed to characterize the physical and physicochemical attributes of the isolates. Results showed that the isolates not only survived but also had the potential to grow in the natural conditions present in this environment. Extracellular cellulase was produced by the filamentous fungal isolates indicating their probable role in detrital decay processes and therefore the carbon cycle on the ocean bed. Also, denitrification patterns were observed when isolates were grown in liquid media amended with NaNO, NaNO , and (NH)SO, implicating that these fungi have the potential to play an active role in denitrification, co-denitrification, and ammonification phases of nitrogen cycles occurring in the marine sediments. [ABSTRACT FROM AUTHOR]

The diversity of planktonic microorganisms in fluids from a group of flowing subterranean boreholes was monitored from the day they were drilled to as long as three and a half months after drilling as they drained into Evander Au mine. Geochemical analyses of the water, characterization of microbial communities by phospholipids fatty acid (PLFA) and DNA sequence analyses, and calculations of free energy flux indicated that mine-introduced microbial contaminants, dominated by β and γ Proteobacteria, Cenarchaeaceae and Candidatus Nitrososphaera, were flushed from the boreholes and replaced by fracture water derived microbial communities dominated by Firmicutes, Methanosarcinalesand Thermoproteaceaea. The fracture water was a mixture of paleometeoric water and 2.0 Ga old, diagenetically altered, hydrothermal fluid. The C and H isotopic data for C1-4 indicated that the CH4 was primarily abiogenic in origin although ∼35-50% of it might have originated from microbial methanogenesis. Noble gas analyses yielded estimated residence times of some 10 million years for the fracture water, which is estimated to represent a capture cross-section of 0.25-0.50 km2. The 16S rRNA and dsrAB gene sequences indicated that the indigenous bacterial communities were predominantly comprised of sulfate reducers belonging to the genera Desulfotomaculum, Candiditus Desulforudis and Desulfofustis. The sulfur isotopic analyses of sulfate and sulfide yielded fractionation Δ34S values ranging from 16 to 22% consistent with microbial sulfate reduction. Thermodynamic analyses indicate that methanogenic reactions are inhibited by the high partial pressure of abiogenic CH4 and that sulfate-reducing reactions are more favorable, which is consistent with the abundance of 16S rRNA genes belonging to known sulfate reducing bacteria. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the free supplemental files. [ABSTRACT FROM AUTHOR]

Abstract: Ting is a spontaneously fermented sorghum food that is popular for its sour taste and unique flavour. Insight of the microbial diversity and population dynamics during sorghum fermentations is an essential component of the development of starter cultures for commercial production of ting. In this study, bacterial populations associated with spontaneous sorghum fermentations were examined using a culture-independent strategy based on denaturing gradient gel electrophoresis and sequence analysis of V3-16S rRNA gene amplicons, and a culture-dependent strategy using conventional isolation based on culturing followed by 16S rRNA and/or pheS gene sequence analysis. The entire fermentation process was monitored over a 54h period and two phases were observed with respect to pH evolution and microbial succession. The first phase of the process (0–6h) was characterized by relatively high pH conditions and the presence of Enterococcus mundtii, albeit that this species was only detected with the culture-dependent approach. The second phase of the fermentation process (12–54h) was characterized by increased acidity and the predominance of a broader range of lactic acid bacteria, including Lactococcus lactis, Lactobacillus fermentum, Lactobacillus plantarum, Lactobacillus rhamnosus, Weissella cibaria, Enterococcus faecalis, and a close relative of Lactobacillus curvatus, as well as some members of the Enterobacteriaceae family. The Lb. curvatus-like species was only detected with PCR-DGGE, while the majority of the other species was only detected using the culture-dependent approach. These findings highlighted the fact that a combination of both approaches was essential in revealing the microbial diversity and dynamics during spontaneous sorghum fermentations. [Copyright &y& Elsevier]

Abstract: Cores recovered during the Agouron Griqualand Drilling Project contain over 2500m of well-preserved late Archean Transvaal Supergroup sediments, dating from ca. 2.67 to 2.46Ga. Bitumen extracts of these strata were obtained using clean drilling, sampling and analysis protocols that avoided overprinting syngenetic molecular fossil signatures with contaminant hydrocarbons. Comparisons of biomarker contents in stratigraphically correlated intervals from diverse lithofacies in two boreholes separated by 24km, as well as across a ∼2Gyr unconformity, provide compelling support for their syngenetic nature. The suite of molecular fossils identified in the late Archean bitumens includes hopanes attributable to bacteria, potentially including cyanobacteria and methanotrophs, and steranes of eukaryotic origin. This molecular fossil record supports an origin in the Archean Eon of the three Domains of cellular life, as well as of oxygenic photosynthesis and the anabolic use of O2. [Copyright &y& Elsevier]

Variation in tick microbiota may affect pathogen acquisition and transmission but for many vector species, including Amblyomma hebraeum, components and determinants of the microbiome are unidentified. This pilot study aimed to determine baseline microbial community within A. hebraeum nymphs infected- and non-infected with Rickettsia africae from the environment, and within adult ticks infected- and non-infected with R. africae collected from cattle sampled from two locations in the Eastern Cape province of South Africa. Adult A. hebraeum ticks (N = 13) and A. hebraeum nymph (N = 15) preliminary screened for R. africae were randomly selected and subjected to Illumina sequencing targeting the v3–v4 hypervariable regions of the 16S rRNA gene. No significant difference in microbial community composition, as well as rarefied OTU richness and diversity were detected between adults and nymphs. Nymphs showed a higher richness of bacterial taxa indicating blood-feeding could have resulted in loss of microbial diversity during the moulting stage from nymph to adult. Core OTUs that were in at least 50% of nymphs and adults negative and positive for Rickettsia at 1% minimum relative abundance were Rickettsia, Coxiella and Ruminococcaceae UCG-005 with a single genus Arsenophonus occurring only in nymphs negative for Rickettsia. Ehrlichia spp. was present in only four nymphal ticks positive for Rickettsia. Interestingly, Rickettsia aeschlimannii was found in one nymph and one adult, indicating the first ever detection of the species in A. hebraeum. Furthermore, A. hebraeum harboured a Coxiella-like endosymbiont, which should be investigated further as Coxiella may affect the viability and transmission of other organisms. [ABSTRACT FROM AUTHOR]

This study investigated the polycyclic aromatic hydrocarbons (PAHs) occurrence, and their impact on the microbial community and PAH-degrading genera and genes in the Knysna Estuary of South Africa. The results reveal that the estuary exhibits low PAH levels (114.1–356.0 ng g−1). Ignavibacteriae and Deferribacteres, as well as Proteobacteria and Bacteroidetes, are keystone phyla. Among measured environmental factors, total organic carbon (TOC), nutrients such as nitrite and nitrate, metals as Al, Cr, Cu, Ni, Pb and Zn, and environmental properties (pH and salinity) are primary contributors to structuring the bacterial community assemblage. The abundance of alpha subunit genes of the PAH-ring hydroxylating dioxygenases (PAH-RHDα) of Gram-negative bacteria lies in the range of (2.0–4.2) × 105 copies g−1, while that of Gram-positive bacteria ranges from 3.0 × 105 to 1.3 × 107 copies g−1. The PAH-degrading bacteria account for up to 0.1% of the bacterial community and respond mainly to nitrate, TOC and salinity, while PAHs at low concentration are not significant influencing factors. PAH degraders such as Xanthomonadales, Pseudomonas , and Mycobacterium , which play a central role in PAH-metabolization coupled with other biogeochemical processes (e.g. iron cycling), may contribute to maintaining a healthy estuarine ecosystem. These results are important for developing appropriate utilization and protection strategies for pristine estuaries worldwide. Image 1 • The potential of PAH degradation of a temperate estuary was evaluated. • Characteristics of microbial communities of a fairly-polluted estuary were shown. • NO x − are the sharpest shaping factors for the bacterial community structure. • Dominant PAH degraders include Vibrio, Marinobacterium and Pseudoalteromonas. • PAH degraders mainly respond to nitrate, total organic carbon and salinity. Nitrate is the most important driver of PAH-degrading genera in a slightly/fairly polluted estuary with specific microbial community and low PAH-biodegrading potential. [ABSTRACT FROM AUTHOR]

Objective: The objective was to examine the use of a tailor-made DNA microarray containing probes representing the vaginal microbiota to examine bacterial vaginosis. Study Design: One hundred one women attending a health center for HIV testing in South Africa were enrolled. Stained, liquid-based cytology slides were scored for bacterial vaginosis. An inventory of organisms was obtained using microarray technology, probing genera associated with bacterial vaginosis in more detail, namely Gardnerella, Atopobium, Dialister, Leptotrichia, Megasphaera, Mobiluncus, Peptostreptococcus, Prevotella, and Sneathia. Results: Of 101 women, 34 were diagnosed positive for bacterial vaginosis. This condition was associated with an increased microbial diversity. It is no longer useful to base the diagnosis of bacterial vaginosis on Gardnerella alone. Rather, its presence with Leptotrichia and Prevotella species, and especially Atopobium was more indicative of an aberrant state of the vaginal flora. Conclusion: To understand the vaginal microbiota in more detail, microarray-based identification can be used after microscopic scoring. [ABSTRACT FROM AUTHOR]