Browsing by Subject "Microbiome"

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    Open Access
    The association between childhood environmental exposures and the subsequent development of Crohn's Disease in the Western Cape, South Africa
    (Public Library of Science, 2014) Basson, Abigail; Swart, Rina; Jordaan, Esme; Mazinu, Mikateko; Watermeyer, Gillian
    BACKGROUND: Environmental factors during childhood are thought to play a role in the aetiolgy of Crohn's Disease (CD). However the association between age at time of exposure and the subsequent development of CD in South Africa is unknown. METHODS: A case control study of all consecutive CD patients seen at 2 large inflammatory bowel disease (IBD) referral centers in the Western Cape, South Africa between September 2011 and January 2013 was performed. Numerous environmental exposures during 3 age intervals; 0-5, 6-10 and 11-18 years were extracted using an investigator administered questionnaire. An agreement analysis was performed to determine the reliability of questionnaire data for all the relevant variables. RESULTS: This study included 194 CD patients and 213 controls. On multiple logistic regression analysis, a number of childhood environmental exposures during the 3 age interval were significantly associated with the risk of developing CD. During the age interval 6-10 years, never having had consumed unpasteurized milk (OR = 5.84; 95% CI, 2.73-13.53) and never having a donkey, horse, sheep or cow on the property (OR = 2.48; 95% CI, 1.09-5.98) significantly increased the risk of developing future CD. During the age interval 11-18 years, an independent risk-association was identified for; never having consumed unpasteurized milk (OR = 2.60; 95% CI, 1.17-6.10) and second-hand cigarette smoke exposure (OR = 1.93; 95% CI, 1.13-3.35). CONCLUSION: This study demonstrates that both limited microbial exposures and exposure to second-hand cigarette smoke during childhood is associated with future development of CD.
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    Exploring the gut microbiome: metaproteome analysis of HIV-exposed uninfected infants
    (2025) Miller, Tara; Blackburn, Jonathan
    Background: HAART has decreased mother-to-child transmission, but it has introduced a new generation of HIV infected and unexposed infants (HEU) with unknown health implications. These infants have been observed to be more vulnerable to disease and have weaker immune responses. The gut microbiome plays a pivotal role in human health by aiding in metabolism, nutrient availability and immune development and function. The mucosal immune system and microbiome work in synergy to maintain host immunity and balance for optimal host health. Gut dysbiosis is linked to diseased states, with gut dysbiosis being well documented amongst HIV infected individuals. HEU infants' altered immunity and health could be linked to gut dysbiosis. Looking into the metaproteome of the infant gut to find any perturbations from healthy counterparts could give insight into their weakened states. Aim: To analyse the metaproteome of the infant gut to identify any alterations in a HIV exposed infant's gut, through analysis of the stool microbiome, accounting for their poor health. Design: Analysis of infant stool samples for the 1st week of life from a cohort comprised of HIV infected mothers and HIV uninfected mothers. Using data-independent acquisition mass spectrometry (SWATH) to identify human and microbiome proteins in samples using Evosep40-SPD and TTOF 6600. In-silico library in DIA-NN used for protein identification, followed by data clean up and pre-processing in R studio and excel. Analysis of the proteins carried out in R studio and Metaboanalyst 5.0. Results: Metaproteomic analysis method used allowed for deep metaproteome profiling and gives a greater understanding into the microbiome functioning than genomic analysis. The protein level Random Forest regression model analysis revealed HEU and HU clustering, in which both human and bacterial proteins are contributing. Infant proteins revealed alteration in MUC2 mucin gut barrier and inflammation in HEU infants, differences in immune proteins from breastmilk proteins, and bacterial proteins revealed Ruminococcus gnavus as an HEU associated species. Conclusion: The altered gut barrier paired with gut inflammation is strongly correlated with bacterial dysbiosis seen in HEU guts. The identified differential species, Ruminococcus gnavus, has been implicated in various diseased states in the gut (IBD and Crohn's), involved in autoimmune diseases (lupus) and neurological diseases (Parkinson's). This reveals the focus for future research to identify potential targets for therapeutic treatment to improve the health of these infants.
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    Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research
    (2021-12-15) Allali, Imane; Abotsi, Regina E; Tow, Lemese A; Thabane, Lehana; Zar, Heather J; Mulder, Nicola M; Nicol, Mark P
    Background The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies. Methodology We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction. Results We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168). Conclusions There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract
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    Microbiome associated with Ulva lacinulata and seawater in an integrated abalone (Haliotis midae)–Ulva system with partial recirculation
    (2025) Makhahlela, Nokofa; Coyne, Vernon
    Several commercial abalone farms in South Africa grow Ulva in D-ended raceways to bioremediate farm effluent water, allowing water to be recirculated back to the abalone, while Ulva is often used as a supplementary feed source. Despite Ulva's versatility in integrated multi-trophic aquaculture (IMTA) systems, there are biosecurity concerns with the recirculation of seawater and the use of effluent-grown Ulva as abalone feed, preventing wider adoption of this technology. To better understand the potential disease risks, as well as the benefits of this practise, this study aimed to characterise the bacterial, fungal, and oomycete communities associated with seawater and Ulva in an integrated abalone-Ulva farm with 50% water recirculation. The study was conducted on a commercial abalone farm along the South-Western Cape coast of South Africa. Water (N = 40) and Ulva (N = 20) samples were collected from two different systems. One system consisted of Ulva raceway tanks that received seawater directly from the adjacent coastline, hereafter referred to as the seawater (SW) raceway or non-IMTA system. The other systems comprised raceways receiving abalone effluent water, with 50% recirculation between the abalone and Ulva raceways, referred to as abalone effluent water (AEW) or IMTA systems. Ulva samples were collected from within each raceway, whereas water samples were collected at the inlet (effluent water) and outlet (bioremediated water) of each raceway. One SW raceway (only one exists in the farm) and 4 AEW raceways were sampled in summer, autumn, winter, and spring. The first experimental chapter (Chapter 2) of the study investigated the impact of various DNA extraction kits on the quality and quantity of DNA obtained from environmental samples and compared commonly used bioinformatic pipelines for the 16S rDNA (QIIME2 vs. mothur) and ITS2 (PIPITS vs. QIIME2) genes to evaluate how different bioinformatics pipelines influence taxonomic classification and subsequent diversity analyses. In chapter 3, culture- dependent techniques were used to assess changes in the abundance of specific bacteria on Ulva and in seawater using three selective media types, namely tryptic soy agar (TSA; a general media routinely used for isolation of marine bacteria), thiosulfate-citrate-bile-sucrose (TCBS) agar (Vibrio selective), and Ulvan agar, where the primary carbohydrate of Ulva (Ulvan) was utilised as the main carbohydrate source. A non-culture-based next-generation sequencing (NGS) approach was subsequently used to describe the bacterial microbiome associated with the IMTA and non-IMTA systems, by sequencing the V4 hyper-variable region of the 16S rDNA gene. In Chapter 4, fungi and oomycetes were targeted by sequencing the internal transcriber 2 (ITS2) gene region of nuclear ribosomal DNA. Following NGS using an Illumina MiSeq sequencing platform, sequence data were processed using QIIME2 and reads were mapped against the SILVA 16S rDNA database for the bacterial microbiome and the UNITE database for the mycobiome. The summarised taxonomic abundance was assessed using MicrobiomeAnalyst. The Qiagen QIAamp DNA Micro kit and QIIME2 bioinformatic pipeline exhibited the best overall performance out of the DNA extraction kits and bioinformatic pipelines tested in chapter 2, combining high sensitivity with excellent specificity, and were both used for subsequent analyses. Chapter 3 results showed that culturable bacterial numbers were significantly higher (ANOVA; p < 0.05) in the IMTA raceway systems receiving abalone effluent water than in Ulva raceways receiving seawater directly from the adjacent coastline. Bacterial abundance on all three selective media types was also higher on Ulva blades sampled from AEW systems. However, in both systems, Ulva appeared to have a modulatory effect on the number of culturable bacteria in the water column, as indicated by the general reduction in bacteria recovered from seawater from the inlets to the outlets of both systems (p < 0.001). A greater reduction in marine bacteria between the inlet and outlet of water samples was observed in the effluent water system (IMTA) when compared to the seawater system (non- IMTA), which had lower nutrient levels. A total of 2822 individual bacterial amplicon sequence variants (ASVs) were identified, belonging to 203 family-, 305 genus-, and 320 species-level taxonomic groups. Alpha diversity analyses, based on Chao1, Shannon, and Simpson indices, showed statistically significant differences (ANOVA; p < 0.05) between the respective cohorts, where the greatest amount of diversity was observed in the water cohorts, whereas the Ulva cohorts had the lowest bacterial abundance and diversity relative to the water systems (SW and AEW). The beta diversity analyses (non-metric multidimensional scaling) showed a partial degree of overlap between the water cohorts and Ulva samples from different systems. However, a separation of IMTA and non-IMTA systems was observed. Various genera associated with marine environments were identified, predominantly belonging to Vibrio, Pseudoalteromonas, and Granulosicoccus. Differential abundance analysis (DESeq2) revealed that general marine bacteria such as Roseobacter, Granulosicoccus, and Algitalea were present in high abundance and potentially pathogenic bacteria such as Vibrio exhibited reduced abundance in both system types due to the presence of Ulva. Chapter 4 assessed the fungal communities associated with effluent water and seawater through next-generation sequencing of the ITS2 region and revealed the presence of 169 individual ASVs belonging to 54 family-, 63 genus-, and 71 species. The alpha diversity analyses based on Chao1, Shannon, and Simpson indices displayed a higher degree of fungal diversity (p < 0.001) in the water cohorts (AEW and SW) than in the Ulva cohorts (AEW_Ulva and SW_Ulva), supporting findings from the bacterial microbiome studies. Moreover, the Chao1 richness estimator was significantly (p < 0.001) higher in the AEW (AEW_In and AEW_Out) cohorts than in the SW cohorts. Beta diversity analyses, including principal co-ordinate analysis (PCoA), showed a separation between water samples (AEW and SW), collected from the two system types, which was consistent with the nonmetric multidimensional scaling (NMDS) analysis, demonstrating that sample types tended to have different fungal communities (p < 0.001). Within each cohort, ASVs commonly associated with marine environments were found, predominantly belonging to Ascomycota and Basidiomycota. Collectively, the results of this study indicate that the water cohorts exhibited greater relative abundance and diversity of bacteria and fungi than the Ulva cohorts. Furthermore, the availability of nutrients had a significant impact on the overall diversity of these microbial communities wherein the level of diversity in the IMTA system was notably higher compared to the non-IMTA system. This is because microorganisms tend to proliferate in environments characterised by high nutrient availability. The current study highlights the capability of 16S and ITS2 metabarcoding techniques for assessing microbial diversity within complex environments and has for the first time provided critical in-depth information on the microbiome of an abalone-Ulva IMTA systems and its contribution to system and animal health. Moreover, the observed positive modulatory effect of Ulva on the microbiome of the IMTA system contributes towards a growing body of literature on the benefits of including seaweed(s) in aquaculture systems and aquafeeds. The findings from this study provides critical information on biosecurity of IMTA systems, species health and system health that may promote broader uptake of these more sustainable aquaculture production technologies.
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    The functional role of root-associated microbiome and metabolome of myrothamnus flabellifolia
    (2025) Tebele, Shandry Mmasetshaba; Farrant, Jill Margaret
    Global climate change is predicted to increase the occurrence and severity of drought, particularly in Africa, which will negatively impact crops and food production. Drought is the leading factor that adversely affects agricultural productivity and yield. Over the last four decades, extensive research on resurrection plants has yielded valuable insights into the mechanisms these plants employ to adapt during desiccation. Despite this, the role of the microbiome in desiccation tolerance, particularly in resurrection plants, remains a relatively unexplored area. Myrothamnus flabellifolia, a resurrection plant, stands out for its remarkable ability to endure severe desiccation, making it an ideal model for investigating the contributions of the plant microbiome to desiccation tolerance. Recognising the significance of root-associated microbes in stress tolerance opens up promising opportunities for enhancing drought resilience in crucial crops. However, the intricate dynamics of these interactions under severe water limitations have not been comprehensively investigated. Consequently, a primary objective of this study was to unravel the beneficial root-associated microbiome of M. flabellifolia and delineate their functions in the context of water deficit conditions. The intricate tripartite interplay involving plant roots, soil, and microorganisms remains enigmatic and demands further exploration. This study delved into the microbiome of belowground zones—bulk soil, rhizosphere soil, and endosphere of M. flabellifolia. Metagenomic analysis unveiled prevalent bacterial phyla (Acidobacteriota, Actinobacteriota, Chloroflexota, Planctomycetota, and Pseudomonadota) and dominant fungal phyla (Ascomycota and Basidiomycota) across all zones. While the bulk soil hosted numerous beneficial root-associated microbes, it exhibited lower functional diversity than the rhizosphere, which showcased the highest diversity of bacteria and fungi. Conversely, the endosphere exhibited lower microbial abundance and diversity. These findings suggest that M. flabellifolia may recruits soil microbes from bulk soil to rhizosphere and subsequently to the endosphere. Metatranscriptomic analysis has revealed crucial insights into the dynamics of plant-microbe interactions and the adaptive mechanisms employed by root-associated bacteria during desiccation in M. flabellifolia. The transcriptional activity of bacteria involved both monoderm and diderm lineages, consistent with the bacterial phyla identified in metagenomic analysis. However, the dominance of the Pseudomonadota phyla at the transcriptional activity was observed. Root-associated bacteria showed distinct transcriptional responses during dehydration and rehydration, suggesting dynamic shifts in microbial activity under fluctuating water availability. The expression of differentially expressed genes (DEGs) under dehydration conditions showcased the activation of proteins associated with antioxidant enzymes, molecular chaperones, protein kinases, and biosynthesis of sugars and amino acids. This implies a coordinated response to counteract damage and enhance survival. Intriguingly, the upregulation of genes encoding protein kinases, antioxidant enzymes, and trehalose synthase in root-associated bacteria reflects a common strategy for surviving desiccation stress. This suggests a potential case of convergent evolution in desiccation tolerance within microbiomes. The observed upregulation of genes related to plant growth and enhanced plant-microbe interaction under rehydration conditions suggests a resumption of microbial activity. Exploring the rhizosphere soil metabolome provided insights into the metabolic changes during drought stress in M. flabellifolia. Dehydrated rhizosphere soil exhibited increased levels of sugars (e.g., trehalose), organic acids (malic acid), and phytohormones (indole-3-acetic). Conversely, rehydrated rhizosphere samples showed significantly higher amino acid levels compared to desiccated samples, indicating a shift in biochemical processes in both the plant roots and rhizosphere microbiome. While rhizosphere metabolites are typically attributed to root exudates and microbial activity, this study revealed that many were possibly produced by rhizospheric bacteria. The upregulation of bacterial genes associated with metabolite biosynthesis under dehydration conditions, such as trehalose, further substantiated the the notion that drought serves as a selective pressure driving convergent evolution in species with desiccation tolerance. These findings indicates that the microbiome's adaptability under harsh environmental stress. Furthermore, inoculating maize plants with rhizospheric bacteria from M. flabellifolia's rhizosphere significantly improved drought tolerance, physiological, and morphological traits. The study concludes that root-associated microbiomes play a crucial role in M. flabellifolia's desiccation tolerance and plant growth-promoting microbes have a potential to be used as a biostimulant. This innovative research has implications for enhancing food security, developing resilient agricultural systems, and promoting sustainability.
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    The skin microbiome: impact of modern environments on skin ecology, barrier integrity, and systemic immune programming
    (2017) Prescott, Susan L; Larcombe, Danica-Lea; Logan, Alan C; West, Christina; Burks, Wesley; Caraballo, Luis; Schoeman, Johan; Etten, Eddie Van; Horwitz, Pierre; Kozyrskyj, Anita; Campbell, Dianne E
    Skin barrier structure and function is essential to human health. Hitherto unrecognized functions of epidermal keratinocytes show that the skin plays an important role in adapting whole-body physiology to changing environments, including the capacity to produce a wide variety of hormones, neurotransmitters and cytokine that can potentially influence whole-body states, and quite possibly, even emotions. Skin microbiota play an integral role in the maturation and homeostatic regulation of keratinocytes and host immune networks with systemic implications. As our primary interface with the external environment, the biodiversity of skin habitats is heavily influenced by the biodiversity of the ecosystems in which we reside. Thus, factors which alter the establishment and health of the skin microbiome have the potential to predispose to not only cutaneous disease, but also other inflammatory non-communicable diseases (NCDs). Indeed, disturbances of the stratum corneum have been noted in allergic diseases (eczema and food allergy), psoriasis, rosacea, acne vulgaris and with the skin aging process. The built environment, global biodiversity losses and declining nature relatedness are contributing to erosion of diversity at a micro-ecological level, including our own microbial habitats. This emphasises the importance of ecological perspectives in overcoming the factors that drive dysbiosis and the risk of inflammatory diseases across the life course.